Negative density-dependent dispersal in the American black bear (Ursus americanus) revealed by noninvasive sampling and genotyping

PubMed Central

Roy, Justin; Yannic, Glenn; Côté, Steeve D; Bernatchez, Louis

2012-01-01

Although the dispersal of animals is influenced by a variety of factors, few studies have used a condition-dependent approach to assess it. The mechanisms underlying dispersal are thus poorly known in many species, especially in large mammals. We used 10 microsatellite loci to examine population density effects on sex-specific dispersal behavior in the American black bear, Ursus americanus. We tested whether dispersal increases with population density in both sexes. Fine-scale genetic structure was investigated in each of four sampling areas using Mantel tests and spatial autocorrelation analyses. Our results revealed male-biased dispersal pattern in low-density areas. As population density increased, females appeared to exhibit philopatry at smaller scales. Fine-scale genetic structure for males at higher densities may indicate reduced dispersal distances and delayed dispersal by subadults. PMID:22822432

Inbreeding Avoidance Drives Consistent Variation of Fine-Scale Genetic Structure Caused by Dispersal in the Seasonal Mating System of Brandt’s Voles

PubMed Central

Liu, Xiao Hui; Yue, Ling Fen; Wang, Da Wei; Li, Ning; Cong, Lin

2013-01-01

Inbreeding depression is a major evolutionary and ecological force influencing population dynamics and the evolution of inbreeding-avoidance traits such as mating systems and dispersal. Mating systems and dispersal are fundamental determinants of population genetic structure. Resolving the relationships among genetic structure, seasonal breeding-related mating systems and dispersal will facilitate our understanding of the evolution of inbreeding avoidance. The goals of this study were as follows: (i) to determine whether females actively avoided mating with relatives in a group-living rodent species, Brandt’s voles (Lasiopodomys brandtii), by combined analysis of their mating system, dispersal and genetic structure; and (ii) to analyze the relationships among the variation in fine-genetic structure, inbreeding avoidance, season-dependent mating strategies and individual dispersal. Using both individual- and population-level analyses, we found that the majority of Brandt’s vole groups consisted of close relatives. However, both group-specific FISs, an inbreeding coefficient that expresses the expected percentage rate of homozygosity arising from a given breeding system, and relatedness of mates showed no sign of inbreeding. Using group pedigrees and paternity analysis, we show that the mating system of Brandt’s voles consists of a type of polygyny for males and extra-group polyandry for females, which may decrease inbreeding by increasing the frequency of mating among distantly-related individuals. The consistent variation in within-group relatedness, among-group relatedness and fine-scale genetic structures was mostly due to dispersal, which primarily occurred during the breeding season. Biologically relevant variation in the fine-scale genetic structure suggests that dispersal during the mating season may be a strategy to avoid inbreeding and drive the polygynous and extra-group polyandrous mating system of this species. PMID:23516435

Reduced fine-scale spatial genetic structure in grazed populations of Dianthus carthusianorum

PubMed Central

Rico, Y; Wagner, H H

2016-01-01

Strong spatial genetic structure in plant populations can increase homozygosity, reducing genetic diversity and adaptive potential. The strength of spatial genetic structure largely depends on rates of seed dispersal and pollen flow. Seeds without dispersal adaptations are likely to be dispersed over short distances within the vicinity of the mother plant, resulting in spatial clustering of related genotypes (fine-scale spatial genetic structure, hereafter spatial genetic structure (SGS)). However, primary seed dispersal by zoochory can promote effective dispersal, increasing the mixing of seeds and influencing SGS within plant populations. In this study, we investigated the effects of seed dispersal by rotational sheep grazing on the strength of SGS and genetic diversity using 11 nuclear microsatellites for 49 populations of the calcareous grassland forb Dianthus carthusianorum. Populations connected by rotational sheep grazing showed significantly weaker SGS and higher genetic diversity than populations in ungrazed grasslands. Independent of grazing treatment, small populations showed significantly stronger SGS and lower genetic diversity than larger populations, likely due to genetic drift. A lack of significant differences in the strength of SGS and genetic diversity between populations that were recently colonized and pre-existing populations suggested that populations colonized after the reintroduction of rotational sheep grazing were likely founded by colonists from diverse source populations. We conclude that dispersal by rotational sheep grazing has the potential to considerably reduce SGS within D. carthusianorum populations. Our study highlights the effectiveness of landscape management by rotational sheep grazing to importantly reduce genetic structure at local scales within restored plant populations. PMID:27381322

Reduced fine-scale spatial genetic structure in grazed populations of Dianthus carthusianorum.

PubMed

Rico, Y; Wagner, H H

2016-11-01

Strong spatial genetic structure in plant populations can increase homozygosity, reducing genetic diversity and adaptive potential. The strength of spatial genetic structure largely depends on rates of seed dispersal and pollen flow. Seeds without dispersal adaptations are likely to be dispersed over short distances within the vicinity of the mother plant, resulting in spatial clustering of related genotypes (fine-scale spatial genetic structure, hereafter spatial genetic structure (SGS)). However, primary seed dispersal by zoochory can promote effective dispersal, increasing the mixing of seeds and influencing SGS within plant populations. In this study, we investigated the effects of seed dispersal by rotational sheep grazing on the strength of SGS and genetic diversity using 11 nuclear microsatellites for 49 populations of the calcareous grassland forb Dianthus carthusianorum. Populations connected by rotational sheep grazing showed significantly weaker SGS and higher genetic diversity than populations in ungrazed grasslands. Independent of grazing treatment, small populations showed significantly stronger SGS and lower genetic diversity than larger populations, likely due to genetic drift. A lack of significant differences in the strength of SGS and genetic diversity between populations that were recently colonized and pre-existing populations suggested that populations colonized after the reintroduction of rotational sheep grazing were likely founded by colonists from diverse source populations. We conclude that dispersal by rotational sheep grazing has the potential to considerably reduce SGS within D. carthusianorum populations. Our study highlights the effectiveness of landscape management by rotational sheep grazing to importantly reduce genetic structure at local scales within restored plant populations.

Strontium isotopes delineate fine-scale natal origins and migration histories of Pacific salmon

USGS Publications Warehouse

Brennan, Sean R.; Zimmerman, Christian E.; Fernandez, Diego P.; Cerling, Thure E.; McPhee, Megan V.; Wooller, Matthew J.

2015-01-01

Highly migratory organisms present major challenges to conservation efforts. This is especially true for exploited anadromous fish species, which exhibit long-range dispersals from natal sites, complex population structures, and extensive mixing of distinct populations during exploitation. By tracing the migratory histories of individual Chinook salmon caught in fisheries using strontium isotopes, we determined the relative production of natal habitats at fine spatial scales and different life histories. Although strontium isotopes have been widely used in provenance research, we present a new robust framework to simultaneously assess natal sources and migrations of individuals within fishery harvests through time. Our results pave the way for investigating how fine-scale habitat production and life histories of salmon respond to perturbations—providing crucial insights for conservation.

Fine-scale genetic response to landscape change in a gliding mammal.

PubMed

Goldingay, Ross L; Harrisson, Katherine A; Taylor, Andrea C; Ball, Tina M; Sharpe, David J; Taylor, Brendan D

2013-01-01

Understanding how populations respond to habitat loss is central to conserving biodiversity. Population genetic approaches enable the identification of the symptoms of population disruption in advance of population collapse. However, the spatio-temporal scales at which population disruption occurs are still too poorly known to effectively conserve biodiversity in the face of human-induced landscape change. We employed microsatellite analysis to examine genetic structure and diversity over small spatial (mostly 1-50 km) and temporal scales (20-50 years) in the squirrel glider (Petaurus norfolcensis), a gliding mammal that is commonly subjected to a loss of habitat connectivity. We identified genetically differentiated local populations over distances as little as 3 km and within 30 years of landscape change. Genetically isolated local populations experienced the loss of genetic diversity, and significantly increased mean relatedness, which suggests increased inbreeding. Where tree cover remained, genetic differentiation was less evident. This pattern was repeated in two landscapes located 750 km apart. These results lend support to other recent studies that suggest the loss of habitat connectivity can produce fine-scale population genetic change in a range of taxa. This gives rise to the prediction that many other vertebrates will experience similar genetic changes. Our results suggest the future collapse of local populations of this gliding mammal is likely unless habitat connectivity is maintained or restored. Landscape management must occur on a fine-scale to avert the erosion of biodiversity.

FINE-SCALE GENETIC DIFFERENTIATION BETWEEN CONTAMINANT-TOLERANT AND CONTAMINANT SENSITIVE FISH POPULATIONS

EPA Science Inventory

Studies have suggested that environmental contaminants can act as selective forces on exposed populations of wildlife species. Chronically exposed populations have shown reduced genetic diversity and/or demonstrated other genetic changes. We evaluated the genetic structure of pop...

Evidence of segregated spawning in a single marine fish stock: Sympatric divergence of ecotypes in icelandic cod?

USGS Publications Warehouse

Grabowski, T.B.; Thorsteinsson, Vilhjalmur; McAdam, B.J.; Marteinsdottir, G.

2011-01-01

There is increasing recognition of intraspecific diversity and population structure within marine fish species, yet there is little direct evidence of the isolating mechanisms that maintain it or documentation of its ecological extent. We analyzed depth and temperature histories collected by electronic data storage tags retrieved from 104 Atlantic cod at liberty ???1 year to evaluate a possible isolating mechanisms maintaining population structure within the Icelandic cod stock. This stock consists of two distinct behavioral types, resident coastal cod and migratory frontal cod, each occurring within two geographically distinct populations. Despite being captured together on the same spawning grounds, we show the behavioral types seem reproductively isolated by fine-scale differences in spawning habitat selection, primarily depth. Additionally, the different groups occupied distinct seasonal thermal and bathymetric niches that generally demonstrated low levels of overlap throughout the year. Our results indicate that isolating mechanisms, such as differential habitat selection during spawning, might contribute to maintaining diversity and fine-scale population structure in broadcast-spawning marine fishes.

Relative information content of polymorphic microsatellites and mitochondrial DNA for inferring dispersal and population genetic structure in the olive sea snake, Aipysurus laevis.

PubMed

Lukoschek, V; Waycott, M; Keogh, J S

2008-07-01

Polymorphic microsatellites are widely considered more powerful for resolving population structure than mitochondrial DNA (mtDNA) markers, particularly for recently diverged lineages or geographically proximate populations. Weaker population subdivision for biparentally inherited nuclear markers than maternally inherited mtDNA may signal male-biased dispersal but can also be attributed to marker-specific evolutionary characteristics and sampling properties. We discriminated between these competing explanations with a population genetic study on olive sea snakes, Aipysurus laevis. A previous mtDNA study revealed strong regional population structure for A. laevis around northern Australia, where Pleistocene sea-level fluctuations have influenced the genetic signatures of shallow-water marine species. Divergences among phylogroups dated to the Late Pleistocene, suggesting recent range expansions by previously isolated matrilines. Fine-scale population structure within regions was, however, poorly resolved for mtDNA. In order to improve estimates of fine-scale genetic divergence and to compare population structure between nuclear and mtDNA, 354 olive sea snakes (previously sequenced for mtDNA) were genotyped for five microsatellite loci. F statistics and Bayesian multilocus genotype clustering analyses found similar regional population structure as mtDNA and, after standardizing microsatellite F statistics for high heterozygosities, regional divergence estimates were quantitatively congruent between marker classes. Over small spatial scales, however, microsatellites recovered almost no genetic structure and standardized F statistics were orders of magnitude smaller than for mtDNA. Three tests for male-biased dispersal were not significant, suggesting that recent demographic expansions to the typically large population sizes of A. laevis have prevented microsatellites from reaching mutation-drift equilibrium and local populations may still be diverging.

Fine-Scale Genetic Response to Landscape Change in a Gliding Mammal

PubMed Central

Goldingay, Ross L.; Harrisson, Katherine A.; Taylor, Andrea C.; Ball, Tina M.; Sharpe, David J.; Taylor, Brendan D.

2013-01-01

Understanding how populations respond to habitat loss is central to conserving biodiversity. Population genetic approaches enable the identification of the symptoms of population disruption in advance of population collapse. However, the spatio-temporal scales at which population disruption occurs are still too poorly known to effectively conserve biodiversity in the face of human-induced landscape change. We employed microsatellite analysis to examine genetic structure and diversity over small spatial (mostly 1-50 km) and temporal scales (20-50 years) in the squirrel glider (Petaurus norfolcensis), a gliding mammal that is commonly subjected to a loss of habitat connectivity. We identified genetically differentiated local populations over distances as little as 3 km and within 30 years of landscape change. Genetically isolated local populations experienced the loss of genetic diversity, and significantly increased mean relatedness, which suggests increased inbreeding. Where tree cover remained, genetic differentiation was less evident. This pattern was repeated in two landscapes located 750 km apart. These results lend support to other recent studies that suggest the loss of habitat connectivity can produce fine-scale population genetic change in a range of taxa. This gives rise to the prediction that many other vertebrates will experience similar genetic changes. Our results suggest the future collapse of local populations of this gliding mammal is likely unless habitat connectivity is maintained or restored. Landscape management must occur on a fine-scale to avert the erosion of biodiversity. PMID:24386079

Fine-scale population structure and riverscape genetics of brook trout (Salvelinus fontinalis) distributed continuously along headwater channel networks

USGS Publications Warehouse

Kanno, Yoichiro; Vokoun, Jason C.; Letcher, Benjamin H.

2011-01-01

Linear and heterogeneous habitat makes headwater stream networks an ideal ecosystem in which to test the influence of environmental factors on spatial genetic patterns of obligatory aquatic species. We investigated fine-scale population structure and influence of stream habitat on individual-level genetic differentiation in brook trout (Salvelinus fontinalis) by genotyping eight microsatellite loci in 740 individuals in two headwater channel networks (7.7 and 4.4 km) in Connecticut, USA. A weak but statistically significant isolation-by-distance pattern was common in both sites. In the field, many tagged individuals were recaptured in the same 50-m reaches within a single field season (summer to fall). One study site was characterized with a hierarchical population structure, where seasonal barriers (natural falls of 1.5–2.5 m in height during summer base-flow condition) greatly reduced gene flow and perceptible spatial patterns emerged because of the presence of tributaries, each with a group of genetically distinguishable individuals. Genetic differentiation increased when pairs of individuals were separated by high stream gradient (steep channel slope) or warm stream temperature in this site, although the evidence of their influence was equivocal. In a second site, evidence for genetic clusters was weak at best, but genetic differentiation between individuals was positively correlated with number of tributary confluences. We concluded that the population-level movement of brook trout was limited in the study headwater stream networks, resulting in the fine-scale population structure (genetic clusters and clines) even at distances of a few kilometres, and gene flow was mitigated by ‘riverscape’ variables, particularly by physical barriers, waterway distance (i.e. isolation-by-distance) and the presence of tributaries.

Genetic Population Structure of Tectura paleacea: Implications for the Mechanisms Regulating Population Structure in Patchy Coastal Habitats

PubMed Central

Begovic, Emina; Lindberg, David R.

2011-01-01

The seagrass limpet Tectura paleacea (Gastropoda; Patellogastropoda) belongs to a seagrass obligate lineage that has shifted from the Caribbean in the late Miocene, across the Isthmus of Panama prior to the closing of the Panamanian seaway, and then northward to its modern Baja California – Oregon distribution. To address whether larval entrainment by seagrass beds contributes to population structuring, populations were sampled at six California/Oregon localities approximately 2 degrees latitude apart during two post-settlement periods in July 2002 and June 2003. Partial cytochrome oxidase b (Cytb) sequences were obtained from 20 individuals (10 per year) from each population in order to determine the levels of population subdivision/connectivity. From the 120 individuals sequenced, there were eighty-one unique haplotypes, with the greatest haplotype diversity occurring in southern populations. The only significant genetic break detected was consistent with a peri-Point Conception (PPC) biogeographic boundary while populations north and south of Point Conception were each panmictic. The data further indicate that populations found south of the PPC biogeographic boundary originated from northern populations. This pattern of population structure suggests that seagrass patches are not entraining the larvae of T. paleacea by altering flow regimes within their environment; a process hypothesized to produce extensive genetic subdivision on fine geographic scales. In contrast to the haplotype data, morphological patterns vary significantly over very fine geographic scales that are inconsistent with the observed patterns of genetic population structure, indicating that morphological variation in T. paleacea might be attributed to differential ecophenotypic expression in response to local habitat variability throughout its distribution. These results suggest that highly localized conservation efforts may not be as effective as large-scale conservation efforts in near shore marine environments. PMID:21490969

Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata

PubMed Central

2017-01-01

The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, we use genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata, to reveal fine-scale population structure and infer the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 11 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 13 candidate loci under positive selection, however there was no correlation between available environmental parameters and genetic distance. Together, these results suggest that reef restoration efforts should use local sources and utilize existing functional variation among geographic regions in ex situ crossing experiments to improve stress resistance of this species. PMID:29181279

The impact of mating systems and dispersal on fine-scale genetic structure at maternally, paternally and biparentally inherited markers.

PubMed

Shaw, Robyn E; Banks, Sam C; Peakall, Rod

2018-01-01

For decades, studies have focused on how dispersal and mating systems influence genetic structure across populations or social groups. However, we still lack a thorough understanding of how these processes and their interaction shape spatial genetic patterns over a finer scale (tens-hundreds of metres). Using uniparentally inherited markers may help answer these questions, yet their potential has not been fully explored. Here, we use individual-level simulations to investigate the effects of dispersal and mating system on fine-scale genetic structure at autosomal, mitochondrial and Y chromosome markers. Using genetic spatial autocorrelation analysis, we found that dispersal was the major driver of fine-scale genetic structure across maternally, paternally and biparentally inherited markers. However, when dispersal was restricted (mean distance = 100 m), variation in mating behaviour created strong differences in the comparative level of structure detected at maternally and paternally inherited markers. Promiscuity reduced spatial genetic structure at Y chromosome loci (relative to monogamy), whereas structure increased under polygyny. In contrast, mitochondrial and autosomal markers were robust to differences in the specific mating system, although genetic structure increased across all markers when reproductive success was skewed towards fewer individuals. Comparing males and females at Y chromosome vs. mitochondrial markers, respectively, revealed that some mating systems can generate similar patterns to those expected under sex-biased dispersal. This demonstrates the need for caution when inferring ecological and behavioural processes from genetic results. Comparing patterns between the sexes, across a range of marker types, may help us tease apart the processes shaping fine-scale genetic structure. © 2017 John Wiley & Sons Ltd.

Dissecting the multi-scale spatial relationship of earthworm assemblages with soil environmental variability.

PubMed

Jiménez, Juan J; Decaëns, Thibaud; Lavelle, Patrick; Rossi, Jean-Pierre

2014-12-05

Studying the drivers and determinants of species, population and community spatial patterns is central to ecology. The observed structure of community assemblages is the result of deterministic abiotic (environmental constraints) and biotic factors (positive and negative species interactions), as well as stochastic colonization events (historical contingency). We analyzed the role of multi-scale spatial component of soil environmental variability in structuring earthworm assemblages in a gallery forest from the Colombian "Llanos". We aimed to disentangle the spatial scales at which species assemblages are structured and determine whether these scales matched those expressed by soil environmental variables. We also tested the hypothesis of the "single tree effect" by exploring the spatial relationships between root-related variables and soil nutrient and physical variables in structuring earthworm assemblages. Multivariate ordination techniques and spatially explicit tools were used, namely cross-correlograms, Principal Coordinates of Neighbor Matrices (PCNM) and variation partitioning analyses. The relationship between the spatial organization of earthworm assemblages and soil environmental parameters revealed explicitly multi-scale responses. The soil environmental variables that explained nested population structures across the multi-spatial scale gradient differed for earthworms and assemblages at the very-fine- (<10 m) to medium-scale (10-20 m). The root traits were correlated with areas of high soil nutrient contents at a depth of 0-5 cm. Information on the scales of PCNM variables was obtained using variogram modeling. Based on the size of the plot, the PCNM variables were arbitrarily allocated to medium (>30 m), fine (10-20 m) and very fine scales (<10 m). Variation partitioning analysis revealed that the soil environmental variability explained from less than 1% to as much as 48% of the observed earthworm spatial variation. A large proportion of the spatial variation did not depend on the soil environmental variability for certain species. This finding could indicate the influence of contagious biotic interactions, stochastic factors, or unmeasured relevant soil environmental variables.

Fine-Scale Ecological and Genetic Population Structure of Two Whitefish (Coregoninae) Species in the Vicinity of Industrial Thermal Emissions.

PubMed

Graham, Carly F; Eberts, Rebecca L; Morgan, Thomas D; Boreham, Douglas R; Lance, Stacey L; Manzon, Richard G; Martino, Jessica A; Rogers, Sean M; Wilson, Joanna Y; Somers, Christopher M

2016-01-01

Thermal pollution from industrial processes can have negative impacts on the spawning and development of cold-water fish. Point sources of thermal effluent may need to be managed to avoid affecting discrete populations. Correspondingly, we examined fine-scale ecological and genetic population structure of two whitefish species (Coregonus clupeaformis and Prosopium cylindraceum) on Lake Huron, Canada, in the immediate vicinity of thermal effluent from nuclear power generation. Niche metrics using δ13C and δ15N stable isotopes showed high levels of overlap (48.6 to 94.5%) in resource use by adult fish captured in areas affected by thermal effluent compared to nearby reference locations. Isotopic niche size, a metric of resource use diversity, was 1.3- to 2.8-fold higher than reference values in some thermally affected areas, indicative of fish mixing. Microsatellite analyses of genetic population structure (Fst, STRUCTURE and DAPC) indicated that fish captured at all locations in the vicinity of the power plant were part of a larger population extending beyond the study area. In concert, ecological and genetic markers do not support the presence of an evolutionarily significant unit in the vicinity of the power plant. Thus, future research should focus on the potential impacts of thermal emissions on development and recruitment.

Fine-Scale Ecological and Genetic Population Structure of Two Whitefish (Coregoninae) Species in the Vicinity of Industrial Thermal Emissions

PubMed Central

Graham, Carly F.; Eberts, Rebecca L.; Morgan, Thomas D.; Boreham, Douglas R.; Lance, Stacey L.; Manzon, Richard G.; Martino, Jessica A.; Rogers, Sean M.; Wilson, Joanna Y.; Somers, Christopher M.

2016-01-01

Thermal pollution from industrial processes can have negative impacts on the spawning and development of cold-water fish. Point sources of thermal effluent may need to be managed to avoid affecting discrete populations. Correspondingly, we examined fine-scale ecological and genetic population structure of two whitefish species (Coregonus clupeaformis and Prosopium cylindraceum) on Lake Huron, Canada, in the immediate vicinity of thermal effluent from nuclear power generation. Niche metrics using δ13C and δ15N stable isotopes showed high levels of overlap (48.6 to 94.5%) in resource use by adult fish captured in areas affected by thermal effluent compared to nearby reference locations. Isotopic niche size, a metric of resource use diversity, was 1.3- to 2.8-fold higher than reference values in some thermally affected areas, indicative of fish mixing. Microsatellite analyses of genetic population structure (Fst, STRUCTURE and DAPC) indicated that fish captured at all locations in the vicinity of the power plant were part of a larger population extending beyond the study area. In concert, ecological and genetic markers do not support the presence of an evolutionarily significant unit in the vicinity of the power plant. Thus, future research should focus on the potential impacts of thermal emissions on development and recruitment. PMID:26807722

Fine-Scale Analysis Reveals Cryptic Landscape Genetic Structure in Desert Tortoises

PubMed Central

Latch, Emily K.; Boarman, William I.; Walde, Andrew; Fleischer, Robert C.

2011-01-01

Characterizing the effects of landscape features on genetic variation is essential for understanding how landscapes shape patterns of gene flow and spatial genetic structure of populations. Most landscape genetics studies have focused on patterns of gene flow at a regional scale. However, the genetic structure of populations at a local scale may be influenced by a unique suite of landscape variables that have little bearing on connectivity patterns observed at broader spatial scales. We investigated fine-scale spatial patterns of genetic variation and gene flow in relation to features of the landscape in desert tortoise (Gopherus agassizii), using 859 tortoises genotyped at 16 microsatellite loci with associated data on geographic location, sex, elevation, slope, and soil type, and spatial relationship to putative barriers (power lines, roads). We used spatially explicit and non-explicit Bayesian clustering algorithms to partition the sample into discrete clusters, and characterize the relationships between genetic distance and ecological variables to identify factors with the greatest influence on gene flow at a local scale. Desert tortoises exhibit weak genetic structure at a local scale, and we identified two subpopulations across the study area. Although genetic differentiation between the subpopulations was low, our landscape genetic analysis identified both natural (slope) and anthropogenic (roads) landscape variables that have significantly influenced gene flow within this local population. We show that desert tortoise movements at a local scale are influenced by features of the landscape, and that these features are different than those that influence gene flow at larger scales. Our findings are important for desert tortoise conservation and management, particularly in light of recent translocation efforts in the region. More generally, our results indicate that recent landscape changes can affect gene flow at a local scale and that their effects can be detected almost immediately. PMID:22132143

Fine-scale analysis reveals cryptic landscape genetic structure in desert tortoises.

PubMed

Latch, Emily K; Boarman, William I; Walde, Andrew; Fleischer, Robert C

2011-01-01

Characterizing the effects of landscape features on genetic variation is essential for understanding how landscapes shape patterns of gene flow and spatial genetic structure of populations. Most landscape genetics studies have focused on patterns of gene flow at a regional scale. However, the genetic structure of populations at a local scale may be influenced by a unique suite of landscape variables that have little bearing on connectivity patterns observed at broader spatial scales. We investigated fine-scale spatial patterns of genetic variation and gene flow in relation to features of the landscape in desert tortoise (Gopherus agassizii), using 859 tortoises genotyped at 16 microsatellite loci with associated data on geographic location, sex, elevation, slope, and soil type, and spatial relationship to putative barriers (power lines, roads). We used spatially explicit and non-explicit Bayesian clustering algorithms to partition the sample into discrete clusters, and characterize the relationships between genetic distance and ecological variables to identify factors with the greatest influence on gene flow at a local scale. Desert tortoises exhibit weak genetic structure at a local scale, and we identified two subpopulations across the study area. Although genetic differentiation between the subpopulations was low, our landscape genetic analysis identified both natural (slope) and anthropogenic (roads) landscape variables that have significantly influenced gene flow within this local population. We show that desert tortoise movements at a local scale are influenced by features of the landscape, and that these features are different than those that influence gene flow at larger scales. Our findings are important for desert tortoise conservation and management, particularly in light of recent translocation efforts in the region. More generally, our results indicate that recent landscape changes can affect gene flow at a local scale and that their effects can be detected almost immediately.

Genome-wide SNPs reveal fine-scale differentiation among wingless alpine stonefly populations and introgression between winged and wingless forms.

PubMed

Dussex, Nicolas; Chuah, Aaron; Waters, Jonathan M

2016-01-01

Insect flight loss is a repeated phenomenon in alpine habitats, where wing reduction is thought to enhance local recruitment and increase fecundity. One predicted consequence of flight loss is reduced dispersal ability, which should lead to population genetic differentiation and perhaps ultimately to speciation. Using a dataset of 15,123 SNP loci, we present comparative analyses of fine-scale population structure in codistributed Zelandoperla stonefly species, across three parallel altitudinal transects in New Zealand's Rock and Pillar mountain range. We find that winged populations (altitude 200-500 m; Zelandoperla decorata) show no genetic structuring within or among streams, suggesting substantial dispersal mediated by flight. By contrast, wingless populations (Zelandoperla fenestrata; altitude 200-1100 m) exhibit distinct genetic clusters associated with each stream, and additional evidence of isolation by distance within streams. Our data support the hypothesis that wing-loss can initiate diversification in alpine insect populations over small spatial scales. The often deep phylogenetic placement of lowland Z. fenestrata within their stream-specific clades suggests the possibility of independent alpine colonization events for each stream. Additionally, the detection of winged, interspecific hybrid individuals raises the intriguing possibility that a previously flightless lineage could reacquire flight via introgression. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Effects of seed bank disturbance on the fine-scale genetic structure of populations of the rare shrub Grevillea macleayana.

PubMed

England, P R; Whelan, R J; Ayre, D J

2003-11-01

Dispersal in most plants is mediated by the movement of seeds and pollen, which move genes across the landscape differently. Grevillea macleayana is a rare, fire-dependent Australian shrub with large seeds lacking adaptations for dispersal; yet it produces inflorescences adapted to pollination by highly mobile vertebrates (eg birds). Interpreting fine-scale genetic structure in the light of these two processes is confounded by the recent imposition of anthropogenic disturbances with potentially contrasting genetic consequences: (1) the unusual foraging behaviour of exotic honeybees and 2. widespread disturbance of the soil-stored seedbank by road building and quarrying. To test for evidence of fine-scale genetic structure within G. macleayana populations and to test the prediction that such structure might be masked by disturbance of the seed bank, we sampled two sites in undisturbed habitat and compared their genetic structure with two sites that had been strongly affected by road building using a test for spatial autocorrelation of genotypes. High selfing levels inferred from genotypes at all four sites implies that pollen dispersal is limited. Consistent with this, we observed substantial spatial clustering of genes at 10 m or less in the two undisturbed populations and argue that this reflects the predicted effects of both high selfing levels and limited seed dispersal. In contrast, at the two sites disturbed by road building, spatial autocorrelation was weak. This suggests there has been mixing of the seed bank, counteracting the naturally low dispersal and elevated selfing due to honeybees. Pollination between near neighbours with reduced relatedness potentially has fitness consequences for G. macleayana in disturbed sites.

Fine-Scale Human Population Structure in Southern Africa Reflects Ecogeographic Boundaries

PubMed Central

Uren, Caitlin; Kim, Minju; Martin, Alicia R.; Bobo, Dean; Gignoux, Christopher R.; van Helden, Paul D.; Möller, Marlo; Hoal, Eileen G.; Henn, Brenna M.

2016-01-01

Recent genetic studies have established that the KhoeSan populations of southern Africa are distinct from all other African populations and have remained largely isolated during human prehistory until ∼2000 years ago. Dozens of different KhoeSan groups exist, belonging to three different language families, but very little is known about their population history. We examine new genome-wide polymorphism data and whole mitochondrial genomes for >100 South Africans from the ≠Khomani San and Nama populations of the Northern Cape, analyzed in conjunction with 19 additional southern African populations. Our analyses reveal fine-scale population structure in and around the Kalahari Desert. Surprisingly, this structure does not always correspond to linguistic or subsistence categories as previously suggested, but rather reflects the role of geographic barriers and the ecology of the greater Kalahari Basin. Regardless of subsistence strategy, the indigenous Khoe-speaking Nama pastoralists and the N|u-speaking ≠Khomani (formerly hunter-gatherers) share ancestry with other Khoe-speaking forager populations that form a rim around the Kalahari Desert. We reconstruct earlier migration patterns and estimate that the southern Kalahari populations were among the last to experience gene flow from Bantu speakers, ∼14 generations ago. We conclude that local adoption of pastoralism, at least by the Nama, appears to have been primarily a cultural process with limited genetic impact from eastern Africa. PMID:27474727

Fine-Scale Population Estimation by 3D Reconstruction of Urban Residential Buildings

PubMed Central

Wang, Shixin; Tian, Ye; Zhou, Yi; Liu, Wenliang; Lin, Chenxi

2016-01-01

Fine-scale population estimation is essential in emergency response and epidemiological applications as well as urban planning and management. However, representing populations in heterogeneous urban regions with a finer resolution is a challenge. This study aims to obtain fine-scale population distribution based on 3D reconstruction of urban residential buildings with morphological operations using optical high-resolution (HR) images from the Chinese No. 3 Resources Satellite (ZY-3). Specifically, the research area was first divided into three categories when dasymetric mapping was taken into consideration. The results demonstrate that the morphological building index (MBI) yielded better results than built-up presence index (PanTex) in building detection, and the morphological shadow index (MSI) outperformed color invariant indices (CIIT) in shadow extraction and height retrieval. Building extraction and height retrieval were then combined to reconstruct 3D models and to estimate population. Final results show that this approach is effective in fine-scale population estimation, with a mean relative error of 16.46% and an overall Relative Total Absolute Error (RATE) of 0.158. This study gives significant insights into fine-scale population estimation in complicated urban landscapes, when detailed 3D information of buildings is unavailable. PMID:27775670

The influence of fine-scale habitat features on regional variation in population performance of alpine White-tailed Ptarmigan

USGS Publications Warehouse

Fedy, B.; Martin, K.

2011-01-01

It is often assumed (explicitly or implicitly) that animals select habitat features to maximize fitness. However, there is often a mismatch between preferred habitats and indices of individual and population measures of performance. We examined the influence of fine-scale habitat selection on the overall population performance of the White-tailed Ptarmigan (Lagopus leucura), an alpine specialist, in two subdivided populations whose habitat patches are configured differently. The central region of Vancouver Island, Canada, has more continuous and larger habitat patches than the southern region. In 2003 and 2004, using paired logistic regression between used (n = 176) and available (n = 324) sites, we identified food availability, distance to standing water, and predator cover as preferred habitat components . We then quantified variation in population performance in the two regions in terms of sex ratio, age structure (n = 182 adults and yearlings), and reproductive success (n = 98 females) on the basis of 8 years of data (1995-1999, 2002-2004). Region strongly influenced females' breeding success, which, unsuccessful hens included, was consistently higher in the central region (n = 77 females) of the island than in the south (n = 21 females, P = 0.01). The central region also had a much higher proportion of successful hens (87%) than did the south (55%, P < 0.001). In light of our findings, we suggest that population performance is influenced by a combination of fine-scale habitat features and coarse-scale habitat configuration. ?? The Cooper Ornithological Society 2011.

Restricted gene flow and fine-scale population structuring in tool using New Caledonian crows

NASA Astrophysics Data System (ADS)

Rutz, C.; Ryder, T. B.; Fleischer, R. C.

2012-04-01

New Caledonian crows Corvus moneduloides are the most prolific avian tool users. It has been suggested that some aspects of their complex tool use behaviour are under the influence of cultural processes, involving the social transmission—and perhaps even progressive refinement—of tool designs. Using microsatellite and mt-haplotype profiling of crows from three distinct habitats (dry forest, farmland and beachside habitat), we show that New Caledonian crow populations can exhibit significant fine-scale genetic structuring. Our finding that some sites of <10 km apart were highly differentiated demonstrates considerable potential for genetic and/or cultural isolation of crow groups. Restricted movement of birds between local populations at such small spatial scales, especially across habitat boundaries, illustrates how specific tool designs could be preserved over time, and how tool technologies of different crow groups could diverge due to drift and local selection pressures. Young New Caledonian crows have an unusually long juvenile dependency period, during which they acquire complex tool-related foraging skills. We suggest that the resulting delayed natal dispersal drives population-divergence patterns in this species. Our work provides essential context for future studies that examine the genetic makeup of crow populations across larger geographic areas, including localities with suspected cultural differences in crow tool technologies.

PRELIMINARY ANALYSIS OF COMMON LOON GENETIC STRUCTURE IN NORTH AMERICA BASED ON FIVE MICROSATELLITE LOCI

EPA Science Inventory

This study seeks to determine fine-scale genetic structure of Common Loon breeding populations in order to link wintering birds with their breeding regions. Common Loons are large piscivorous birds that breed in lakes of northern North America and Iceland. Loons are highly phil...

Inference of Population Structure using Dense Haplotype Data

PubMed Central

Lawson, Daniel John; Hellenthal, Garrett

2012-01-01

The advent of genome-wide dense variation data provides an opportunity to investigate ancestry in unprecedented detail, but presents new statistical challenges. We propose a novel inference framework that aims to efficiently capture information on population structure provided by patterns of haplotype similarity. Each individual in a sample is considered in turn as a recipient, whose chromosomes are reconstructed using chunks of DNA donated by the other individuals. Results of this “chromosome painting” can be summarized as a “coancestry matrix,” which directly reveals key information about ancestral relationships among individuals. If markers are viewed as independent, we show that this matrix almost completely captures the information used by both standard Principal Components Analysis (PCA) and model-based approaches such as STRUCTURE in a unified manner. Furthermore, when markers are in linkage disequilibrium, the matrix combines information across successive markers to increase the ability to discern fine-scale population structure using PCA. In parallel, we have developed an efficient model-based approach to identify discrete populations using this matrix, which offers advantages over PCA in terms of interpretability and over existing clustering algorithms in terms of speed, number of separable populations, and sensitivity to subtle population structure. We analyse Human Genome Diversity Panel data for 938 individuals and 641,000 markers, and we identify 226 populations reflecting differences on continental, regional, local, and family scales. We present multiple lines of evidence that, while many methods capture similar information among strongly differentiated groups, more subtle population structure in human populations is consistently present at a much finer level than currently available geographic labels and is only captured by the haplotype-based approach. The software used for this article, ChromoPainter and fineSTRUCTURE, is available from http://www.paintmychromosomes.com/. PMID:22291602

Modulation of Temporal Precision in Thalamic Population Responses to Natural Visual Stimuli

PubMed Central

Desbordes, Gaëlle; Jin, Jianzhong; Alonso, Jose-Manuel; Stanley, Garrett B.

2010-01-01

Natural visual stimuli have highly structured spatial and temporal properties which influence the way visual information is encoded in the visual pathway. In response to natural scene stimuli, neurons in the lateral geniculate nucleus (LGN) are temporally precise – on a time scale of 10–25 ms – both within single cells and across cells within a population. This time scale, established by non stimulus-driven elements of neuronal firing, is significantly shorter than that of natural scenes, yet is critical for the neural representation of the spatial and temporal structure of the scene. Here, a generalized linear model (GLM) that combines stimulus-driven elements with spike-history dependence associated with intrinsic cellular dynamics is shown to predict the fine timing precision of LGN responses to natural scene stimuli, the corresponding correlation structure across nearby neurons in the population, and the continuous modulation of spike timing precision and latency across neurons. A single model captured the experimentally observed neural response, across different levels of contrasts and different classes of visual stimuli, through interactions between the stimulus correlation structure and the nonlinearity in spike generation and spike history dependence. Given the sensitivity of the thalamocortical synapse to closely timed spikes and the importance of fine timing precision for the faithful representation of natural scenes, the modulation of thalamic population timing over these time scales is likely important for cortical representations of the dynamic natural visual environment. PMID:21151356

Fine-scale ecological and genetic population structure of two whitefish (Coregoninae) species in the vicinity of industrial thermal emissions

DOE PAGES

Graham, Carly F.; Eberts, Rebecca L.; Morgan, Thomas D.; ...

2016-01-25

Thermal pollution from industrial processes can have negative impacts on the spawning and development of cold-water fish. Point sources of thermal effluent may need to be managed to avoid affecting discrete populations. Correspondingly, we examined fine-scale ecological and genetic population structure of two whitefish species ( Coregonus clupeaformis and Prosopium cylindraceum) on Lake Huron, Canada, in the immediate vicinity of thermal effluent from nuclear power generation. Niche metrics using δ 13C and δ 15N stable isotopes showed high levels of overlap (48.6 to 94.5%) in resource use by adult fish captured in areas affected by thermal effluent compared to nearbymore » reference locations. Isotopic niche size, a metric of resource use diversity, was 1.3- to 2.8-fold higher than reference values in some thermally affected areas, indicative of fish mixing. Microsatellite analyses of genetic population structure (F st, STRUCTURE and DAPC) indicated that fish captured at all locations in the vicinity of the power plant were part of a larger population extending beyond the study area. In concert, ecological and genetic markers do not support the presence of an evolutionarily significant unit in the vicinity of the power plant. Furthermore, future research should focus on the potential impacts of thermal emissions on development and recruitment.« less

Fine-scale ecological and genetic population structure of two whitefish (Coregoninae) species in the vicinity of industrial thermal emissions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graham, Carly F.; Eberts, Rebecca L.; Morgan, Thomas D.

Thermal pollution from industrial processes can have negative impacts on the spawning and development of cold-water fish. Point sources of thermal effluent may need to be managed to avoid affecting discrete populations. Correspondingly, we examined fine-scale ecological and genetic population structure of two whitefish species ( Coregonus clupeaformis and Prosopium cylindraceum) on Lake Huron, Canada, in the immediate vicinity of thermal effluent from nuclear power generation. Niche metrics using δ 13C and δ 15N stable isotopes showed high levels of overlap (48.6 to 94.5%) in resource use by adult fish captured in areas affected by thermal effluent compared to nearbymore » reference locations. Isotopic niche size, a metric of resource use diversity, was 1.3- to 2.8-fold higher than reference values in some thermally affected areas, indicative of fish mixing. Microsatellite analyses of genetic population structure (F st, STRUCTURE and DAPC) indicated that fish captured at all locations in the vicinity of the power plant were part of a larger population extending beyond the study area. In concert, ecological and genetic markers do not support the presence of an evolutionarily significant unit in the vicinity of the power plant. Furthermore, future research should focus on the potential impacts of thermal emissions on development and recruitment.« less

Mating system and gene flow in the red seaweed Gracilaria gracilis: effect of haploid-diploid life history and intertidal rocky shore landscape on fine-scale genetic structure.

PubMed

Engel, C R; Destombe, C; Valero, M

2004-04-01

The impact of haploid-diploidy and the intertidal landscape on a fine-scale genetic structure was explored in a red seaweed Gracilaria gracilis. The pattern of genetic structure was compared in haploid and diploid stages at a microgeographic scale (< 5 km): a total of 280 haploid and 296 diploid individuals located in six discrete, scattered rock pools were genotyped using seven microsatellite loci. Contrary to the theoretical expectation of predominantly endogamous mating systems in haploid-diploid organisms, G. gracilis showed a clearly allogamous mating system. Although within-population allele frequencies were similar between haploids and diploids, genetic differentiation among haploids was more than twice that of diploids, suggesting that there may be a lag between migration and (local) breeding due to the long generation times in G. gracilis. Weak, but significant, population differentiation was detected in both haploids and diploids and varied with landscape features, and not with geographic distance. Using an assignment test, we establish that effective migration rates varied according to height on the shore. In this intertidal species, biased spore dispersal may occur during the transport of spores and gametes at low tide when small streams flow from high- to lower-shore pools. The longevity of both haploid and diploid free-living stages and the long generation times typical of G. gracilis populations may promote the observed pattern of high genetic diversity within populations relative to that among populations.

The fine-scale genetic structure and evolution of the Japanese population.

PubMed

Takeuchi, Fumihiko; Katsuya, Tomohiro; Kimura, Ryosuke; Nabika, Toru; Isomura, Minoru; Ohkubo, Takayoshi; Tabara, Yasuharu; Yamamoto, Ken; Yokota, Mitsuhiro; Liu, Xuanyao; Saw, Woei-Yuh; Mamatyusupu, Dolikun; Yang, Wenjun; Xu, Shuhua; Teo, Yik-Ying; Kato, Norihiro

2017-01-01

The contemporary Japanese populations largely consist of three genetically distinct groups-Hondo, Ryukyu and Ainu. By principal-component analysis, while the three groups can be clearly separated, the Hondo people, comprising 99% of the Japanese, form one almost indistinguishable cluster. To understand fine-scale genetic structure, we applied powerful haplotype-based statistical methods to genome-wide single nucleotide polymorphism data from 1600 Japanese individuals, sampled from eight distinct regions in Japan. We then combined the Japanese data with 26 other Asian populations data to analyze the shared ancestry and genetic differentiation. We found that the Japanese could be separated into nine genetic clusters in our dataset, showing a marked concordance with geography; and that major components of ancestry profile of Japanese were from the Korean and Han Chinese clusters. We also detected and dated admixture in the Japanese. While genetic differentiation between Ryukyu and Hondo was suggested to be caused in part by positive selection, genetic differentiation among the Hondo clusters appeared to result principally from genetic drift. Notably, in Asians, we found the possibility that positive selection accentuated genetic differentiation among distant populations but attenuated genetic differentiation among close populations. These findings are significant for studies of human evolution and medical genetics.

Global Impacts of Long-Term Land Cover Changes Within China's Densely Populated Rural Regions

NASA Astrophysics Data System (ADS)

Ellis, E. C.

2006-12-01

Long-term changes in land cover are usually investigated in terms of large-scale change processes such as urban expansion, deforestation and land conversion to agriculture. Yet China's densely populated agricultural regions, which cover more than 2 million square kilometers of Monsoon Asia, have been transformed profoundly over the past fifty years by fine-scale changes in land cover caused by unprecedented changes in population, technology and social conditions. Using a regional sampling and upscaling design coupled with high-resolution landscape change measurements at five field sites, we investigated long-term changes in land cover and ecological processes, circa 1945 to 2002, within and across China's densely populated agricultural regions. As expected, the construction of buildings and roads increased impervious surface area over time, but the total net increase was surprising, being similar in magnitude to the total current extent of China's cities. Agricultural land area declined over the same period, while tree cover increased, by about 10%, driven by tree planting and regrowth around new buildings, the introduction of perennial agriculture, improved forestry, and declines in annual crop cultivation. Though changes in impervious surface areas were closely related to changes in population density, long-term changes in agricultural land and tree cover were unrelated to populated density and required explanation by more complex models with strong regional and biophysical components. Moreover, most of these changes occurred primarily at fine spatial scales (< 30 m), under the threshold for conventional global and regional land cover change measurements. Given that these changes in built structures and vegetation cover have the potential to contribute substantially to regional and global changes in biogeochemistry, hydrology, and land-atmosphere interactions, future investigations of these changes and their impacts across Monsoon Asia would benefit from models that incorporate fine-scale landscape structure and its changes over time.

Microsatellite variation suggests a recent fine-scale population structure of Drosophila sechellia, a species endemic of the Seychelles archipelago.

PubMed

Legrand, Delphine; Vautrin, Dominique; Lachaise, Daniel; Cariou, Marie-Louise

2011-07-01

Drosophila sechellia is closely related to the cosmopolitan and widespread model species, D. simulans. This species, endemic to the Seychelles archipelago, is specialized on the fruits of Morinda citrifolia, and harbours the lowest overall genetic diversity compared to other species of Drosophila. This low diversity is associated with a small population size. In addition, no obvious population structure has been evidenced so far across islands of the Seychelles archipelago. Here, a microsatellite panel of 17 loci in ten populations from nine islands of the Seychelles was used to assess the effect of the D. sechellia's fragmented distribution on the fine-scale population genetic structure, the migration pattern, as well as on the demography of the species. Contrary to previous results, also based on microsatellites, no evidence for population contraction in D. sechellia was found. The results confirm previous studies based on gene sequence polymorphism that showed a long-term stable population size for this species. Interestingly, a pattern of Isolation By Distance which had not been described yet in D. sechellia was found, with evidence of first-generation migrants between some neighbouring islands. Bayesian structuring algorithm results were consistent with a split of D. sechellia into two main groups of populations: Silhouette/Mahé versus all the other islands. Thus, microsatellites suggest that variability in D. sechellia is most likely explained by local genetic exchanges between neighbouring islands that have recently resulted in slight differentiation of the two largest island populations from all the others.

Genome-Wide Fine-Scale Recombination Rate Variation in Drosophila melanogaster

PubMed Central

Song, Yun S.

2012-01-01

Estimating fine-scale recombination maps of Drosophila from population genomic data is a challenging problem, in particular because of the high background recombination rate. In this paper, a new computational method is developed to address this challenge. Through an extensive simulation study, it is demonstrated that the method allows more accurate inference, and exhibits greater robustness to the effects of natural selection and noise, compared to a well-used previous method developed for studying fine-scale recombination rate variation in the human genome. As an application, a genome-wide analysis of genetic variation data is performed for two Drosophila melanogaster populations, one from North America (Raleigh, USA) and the other from Africa (Gikongoro, Rwanda). It is shown that fine-scale recombination rate variation is widespread throughout the D. melanogaster genome, across all chromosomes and in both populations. At the fine-scale, a conservative, systematic search for evidence of recombination hotspots suggests the existence of a handful of putative hotspots each with at least a tenfold increase in intensity over the background rate. A wavelet analysis is carried out to compare the estimated recombination maps in the two populations and to quantify the extent to which recombination rates are conserved. In general, similarity is observed at very broad scales, but substantial differences are seen at fine scales. The average recombination rate of the X chromosome appears to be higher than that of the autosomes in both populations, and this pattern is much more pronounced in the African population than the North American population. The correlation between various genomic features—including recombination rates, diversity, divergence, GC content, gene content, and sequence quality—is examined using the wavelet analysis, and it is shown that the most notable difference between D. melanogaster and humans is in the correlation between recombination and diversity. PMID:23284288

Fine-scale structure in the far-infrared Milky-Way

NASA Technical Reports Server (NTRS)

Waller, William H.; Wall, William F.; Reach, William T.; Varosi, Frank; Ebert, Rick; Laughlin, Gaylin; Boulanger, Francois

1995-01-01

This final report summarizes the work performed and which falls into five broad categories: (1) generation of a new data product (mosaics of the far-infrared emission in the Milky Way); (2) acquisition of associated data products at other wavelengths; (3) spatial filtering of the far-infrared mosaics and resulting images of the FIR fine-scale structure; (4) evaluation of the spatially filtered data; (5) characterization of the FIR fine-scale structure in terms of its spatial statistics; and (6) identification of interstellar counterparts to the FIR fine-scale structure.

Fine-scale patterns of population stratification confound rare variant association tests.

PubMed

O'Connor, Timothy D; Kiezun, Adam; Bamshad, Michael; Rich, Stephen S; Smith, Joshua D; Turner, Emily; Leal, Suzanne M; Akey, Joshua M

2013-01-01

Advances in next-generation sequencing technology have enabled systematic exploration of the contribution of rare variation to Mendelian and complex diseases. Although it is well known that population stratification can generate spurious associations with common alleles, its impact on rare variant association methods remains poorly understood. Here, we performed exhaustive coalescent simulations with demographic parameters calibrated from exome sequence data to evaluate the performance of nine rare variant association methods in the presence of fine-scale population structure. We find that all methods have an inflated spurious association rate for parameter values that are consistent with levels of differentiation typical of European populations. For example, at a nominal significance level of 5%, some test statistics have a spurious association rate as high as 40%. Finally, we empirically assess the impact of population stratification in a large data set of 4,298 European American exomes. Our results have important implications for the design, analysis, and interpretation of rare variant genome-wide association studies.

Genetic variation among interconnected populations of Catostomus occidentalis: Implications for distinguishing impacts of contaminants from biogeographical structuring

USGS Publications Warehouse

Whitehead, A.; Anderson, S.L.; Kuivila, K.M.; Roach, J.L.; May, B.

2003-01-01

Exposure to contaminants can affect survivorship, recruitment, reproductive success, mutation rates and migration, and may play a significant role in the partitioning of genetic variation among exposed and nonexposed populations. However, the application of molecular population genetic data to evaluate such influences has been uncommon and often flawed. We tested whether patterns of genetic variation among native fish populations (Sacramento sucker, Catostomus occidentalis) in the Central Valley of California were consistent with long-term pesticide exposure history, or primarily with expectations based on biogeography. Field sampling was designed to rigorously test for both geographical and contamination influences. Fine-scale structure of these interconnected populations was detected with both amplified fragment length polymorphisms (AFLP) and microsatellite markers, and patterns of variation elucidated by the two marker systems were highly concordant. Analyses indicated that biogeographical hypotheses described the data set better than hypotheses relating to common historical pesticide exposure. Downstream populations had higher genetic diversity than upstream populations, regardless of exposure history, and genetic distances showed that populations from the same river system tended to cluster together. Relatedness among populations reflected primarily directions of gene flow, rather than convergence among contaminant-exposed populations. Watershed geography accounted for significant partitioning of genetic variation among populations, whereas contaminant exposure history did not. Genetic patterns indicating contaminant-induced selection, increased mutation rates or recent bottlenecks were weak or absent. We stress the importance of testing contaminant-induced genetic change hypotheses within a biogeographical context. Strategic application of molecular markers for analysis of fine-scale structure, and for evaluating contaminant impacts on gene pools, is discussed.

Genomic Footprints of Selective Sweeps from Metabolic Resistance to Pyrethroids in African Malaria Vectors Are Driven by Scale up of Insecticide-Based Vector Control.

PubMed

Barnes, Kayla G; Weedall, Gareth D; Ndula, Miranda; Irving, Helen; Mzihalowa, Themba; Hemingway, Janet; Wondji, Charles S

2017-02-01

Insecticide resistance in mosquito populations threatens recent successes in malaria prevention. Elucidating patterns of genetic structure in malaria vectors to predict the speed and direction of the spread of resistance is essential to get ahead of the 'resistance curve' and to avert a public health catastrophe. Here, applying a combination of microsatellite analysis, whole genome sequencing and targeted sequencing of a resistance locus, we elucidated the continent-wide population structure of a major African malaria vector, Anopheles funestus. We identified a major selective sweep in a genomic region controlling cytochrome P450-based metabolic resistance conferring high resistance to pyrethroids. This selective sweep occurred since 2002, likely as a direct consequence of scaled up vector control as revealed by whole genome and fine-scale sequencing of pre- and post-intervention populations. Fine-scaled analysis of the pyrethroid resistance locus revealed that a resistance-associated allele of the cytochrome P450 monooxygenase CYP6P9a has swept through southern Africa to near fixation, in contrast to high polymorphism levels before interventions, conferring high levels of pyrethroid resistance linked to control failure. Population structure analysis revealed a barrier to gene flow between southern Africa and other areas, which may prevent or slow the spread of the southern mechanism of pyrethroid resistance to other regions. By identifying a genetic signature of pyrethroid-based interventions, we have demonstrated the intense selective pressure that control interventions exert on mosquito populations. If this level of selection and spread of resistance continues unabated, our ability to control malaria with current interventions will be compromised.

Fine-scale genetic structure of bull trout at the southern limit of their distribution

Treesearch

A. Whiteley; P. Spruell; B. Rieman; F. Allendorf

2006-01-01

We used six polymorphic microsatellite loci to analyze the population genetic structure of bull trout Salvelinus confluentus in the Boise River, Idaho, and we compared our results with previous data from similarly sized river systems in western North America. Within the Boise River, we found low genetic variation within and significant...

Genetic differentiation over a small spatial scale of the sand fly Lutzomyia vexator (Diptera: Psychodidae).

PubMed

Neal, Allison T; Ross, Max S; Schall, Jos J; Vardo-Zalik, Anne M

2016-10-18

The geographic scale and degree of genetic differentiation for arthropod vectors that transmit parasites play an important role in the distribution, prevalence and coevolution of pathogens of human and wildlife significance. We determined the genetic diversity and population structure of the sand fly Lutzomyia vexator over spatial scales from 0.56 to 3.79 km at a study region in northern California. The study was provoked by observations of differentiation at fine spatial scales of a lizard malaria parasite vectored by Lu. vexator. A microsatellite enrichment/next-generation sequencing protocol was used to identify variable microsatellite loci within the genome of Lu. vexator. Alleles present at these loci were examined in four populations of Lu. vexator in Hopland, CA. Population differentiation was assessed using Fst and D (of Cavalli-Sforza and Edwards), and the program Structure was used to determine the degree of subdivision present. The effective population size for the sand fly populations was also calculated. Eight microsatellite markers were characterized and revealed high genetic diversity (uHe = 0.79-0.92, Na = 12-24) and slight but significant differentiation across the fine spatial scale examined (average pairwise D = 0.327; F ST  = 0.0185 (95 % bootstrapped CI: 0.0102-0.0264). Even though the insects are difficult to capture using standard methods, the estimated population size was thousands per local site. The results argue that Lu. vexator at the study sites are abundant and not highly mobile, which may influence the overall transmission dynamics of the lizard malaria parasite, Plasmodium mexicanum, and other parasites transmitted by this species.

The fine-scale genetic structure and evolution of the Japanese population

PubMed Central

Katsuya, Tomohiro; Kimura, Ryosuke; Nabika, Toru; Isomura, Minoru; Ohkubo, Takayoshi; Tabara, Yasuharu; Yamamoto, Ken; Yokota, Mitsuhiro; Liu, Xuanyao; Saw, Woei-Yuh; Mamatyusupu, Dolikun; Yang, Wenjun; Xu, Shuhua

2017-01-01

The contemporary Japanese populations largely consist of three genetically distinct groups—Hondo, Ryukyu and Ainu. By principal-component analysis, while the three groups can be clearly separated, the Hondo people, comprising 99% of the Japanese, form one almost indistinguishable cluster. To understand fine-scale genetic structure, we applied powerful haplotype-based statistical methods to genome-wide single nucleotide polymorphism data from 1600 Japanese individuals, sampled from eight distinct regions in Japan. We then combined the Japanese data with 26 other Asian populations data to analyze the shared ancestry and genetic differentiation. We found that the Japanese could be separated into nine genetic clusters in our dataset, showing a marked concordance with geography; and that major components of ancestry profile of Japanese were from the Korean and Han Chinese clusters. We also detected and dated admixture in the Japanese. While genetic differentiation between Ryukyu and Hondo was suggested to be caused in part by positive selection, genetic differentiation among the Hondo clusters appeared to result principally from genetic drift. Notably, in Asians, we found the possibility that positive selection accentuated genetic differentiation among distant populations but attenuated genetic differentiation among close populations. These findings are significant for studies of human evolution and medical genetics. PMID:29091727

The roles of competition and habitat in the dynamics of populations and species distributions Ecology

Treesearch

Charles B. Yackulic; Janice Reid; James D. Nichols; James E. Hines; Raymond Davis; Eric Forsman

2014-01-01

The role of competition in structuring biotic communities at fine spatial scales is well known from detailed process-based studies. Our understanding of competition’s importance at broader scales is less resolved and mainly based on static species distribution maps. Here, we bridge this gap by examining the joint occupancy dynamics of an invading species (Barred Owl,...

Fine-scale genetic structure and cryptic associations reveal evidence of kin-based sociality in the African forest elephant.

PubMed

Schuttler, Stephanie G; Philbrick, Jessica A; Jeffery, Kathryn J; Eggert, Lori S

2014-01-01

Spatial patterns of relatedness within animal populations are important in the evolution of mating and social systems, and have the potential to reveal information on species that are difficult to observe in the wild. This study examines the fine-scale genetic structure and connectivity of groups within African forest elephants, Loxodonta cyclotis, which are often difficult to observe due to forest habitat. We tested the hypothesis that genetic similarity will decline with increasing geographic distance, as we expect kin to be in closer proximity, using spatial autocorrelation analyses and Tau K(r) tests. Associations between individuals were investigated through a non-invasive genetic capture-recapture approach using network models, and were predicted to be more extensive than the small groups found in observational studies, similar to fission-fusion sociality found in African savanna (Loxodonta africana) and Asian (Elephas maximus) species. Dung samples were collected in Lopé National Park, Gabon in 2008 and 2010 and genotyped at 10 microsatellite loci, genetically sexed, and sequenced at the mitochondrial DNA control region. We conducted analyses on samples collected at three different temporal scales: a day, within six-day sampling sessions, and within each year. Spatial autocorrelation and Tau K(r) tests revealed genetic structure, but results were weak and inconsistent between sampling sessions. Positive spatial autocorrelation was found in distance classes of 0-5 km, and was strongest for the single day session. Despite weak genetic structure, individuals within groups were significantly more related to each other than to individuals between groups. Social networks revealed some components to have large, extensive groups of up to 22 individuals, and most groups were composed of individuals of the same matriline. Although fine-scale population genetic structure was weak, forest elephants are typically found in groups consisting of kin and based on matrilines, with some individuals having more associates than observed from group sizes alone.

Sample-based synthesis of two-scale structures with anisotropy

DOE PAGES

Liu, Xingchen; Shapiro, Vadim

2017-05-19

A vast majority of natural or synthetic materials are characterized by their anisotropic properties, such as stiffness. Such anisotropy is effected by the spatial distribution of the fine-scale structure and/or anisotropy of the constituent phases at a finer scale. In design, proper control of the anisotropy may greatly enhance the efficiency and performance of synthesized structures. In this paper, we propose a sample-based two-scale structure synthesis approach that explicitly controls anisotropic effective material properties of the structure on the coarse scale by orienting sampled material neighborhoods at the fine scale. We first characterize the non-uniform orientations distribution of the samplemore » structure by showing that the principal axes of an orthotropic material may be determined by the eigenvalue decomposition of its effective stiffness tensor. Such effective stiffness tensors can be efficiently estimated based on the two-point correlation functions of the fine-scale structures. Then we synthesize the two-scale structure by rotating fine-scale structures from the sample to follow a given target orientation field. Finally, the effectiveness of the proposed approach is demonstrated through examples in both 2D and 3D.« less

Sample-based synthesis of two-scale structures with anisotropy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Xingchen; Shapiro, Vadim

A vast majority of natural or synthetic materials are characterized by their anisotropic properties, such as stiffness. Such anisotropy is effected by the spatial distribution of the fine-scale structure and/or anisotropy of the constituent phases at a finer scale. In design, proper control of the anisotropy may greatly enhance the efficiency and performance of synthesized structures. In this paper, we propose a sample-based two-scale structure synthesis approach that explicitly controls anisotropic effective material properties of the structure on the coarse scale by orienting sampled material neighborhoods at the fine scale. We first characterize the non-uniform orientations distribution of the samplemore » structure by showing that the principal axes of an orthotropic material may be determined by the eigenvalue decomposition of its effective stiffness tensor. Such effective stiffness tensors can be efficiently estimated based on the two-point correlation functions of the fine-scale structures. Then we synthesize the two-scale structure by rotating fine-scale structures from the sample to follow a given target orientation field. Finally, the effectiveness of the proposed approach is demonstrated through examples in both 2D and 3D.« less

A fine-scale assessment of using barriers to conserve native stream salmonids: a case study in Akokala Creek, Glacier National Park, USA

USGS Publications Warehouse

Muhlfeld, Clint C.; D'Angelo, Vincent S.; S. T. Kalinowski,; Landguth, Erin L.; C. C. Downs,; J. Tohtz,; Kershner, Jeffrey L.

2012-01-01

Biologists are often faced with the difficult decision in managing native salmonids of where and when to install barriers as a conservation action to prevent upstream invasion of nonnative fishes. However, fine-scale approaches to assess long-term persistence of populations within streams and watersheds chosen for isolation management are often lacking. We employed a spatially-explicit approach to evaluate stream habitat conditions, relative abundance, and genetic diversity of native westslope cutthroat trout (Oncorhynchus clarkii lewisi) within the Akokala Creek watershed in Glacier National Park- a population threatened by introgressive hybridization with nonnative rainbow trout (O. mykiss) from nearby sources. The systematic survey of 24 stream reaches showed broad overlap in fish population and suitable habitat characteristics among reaches and no natural barriers to fish migration were found. Analysis of population structure using 16 microsatellite loci showed modest amounts of genetic diversity among reaches, and that fish from Long Bow Creek were the only moderately distinct genetic group. We then used this information to assess the potential impacts of three barrier placement scenarios on long-term population persistence and genetic diversity. The two barrier placement scenarios in headwater areas generally failed to meet general persistence criteria for minimum population size (2,500 individuals, Ne = 500), maintenance of long-term genetic diversity (He), and no population subdivision. Conversely, placing a barrier near the stream mouth and selectively passing non-hybridized, migratory spawners entering Akokala Creek met all persistence criteria and may offer the best option to conserve native trout populations and life history diversity. Systematic, fine-scale stream habitat, fish distribution, and genetic assessments in streams chosen for barrier installation are needed in conjunction with broader scale assessments to understand the potential impacts of using barriers for conservation of native salmonid populations threatened by nonnative fish invasions.

Polygamy and an absence of fine-scale structure in Dendroctonus ponderosae (Hopk.) (Coleoptera: Curcilionidae) confirmed using molecular markers

PubMed Central

Janes, J K; Roe, A D; Rice, A V; Gorrell, J C; Coltman, D W; Langor, D W; Sperling, F A H

2016-01-01

An understanding of mating systems and fine-scale spatial genetic structure is required to effectively manage forest pest species such as Dendroctonus ponderosae (mountain pine beetle). Here we used genome-wide single-nucleotide polymorphisms to assess the fine-scale genetic structure and mating system of D. ponderosae collected from a single stand in Alberta, Canada. Fine-scale spatial genetic structure was absent within the stand and the majority of genetic variation was best explained at the individual level. Relatedness estimates support previous reports of pre-emergence mating. Parentage assignment tests indicate that a polygamous mating system better explains the relationships among individuals within a gallery than the previously reported female monogamous/male polygynous system. Furthermore, there is some evidence to suggest that females may exploit the galleries of other females, at least under epidemic conditions. Our results suggest that current management models are likely to be effective across large geographic areas based on the absence of fine-scale genetic structure. PMID:26286666

Genetic structuring of northern myotis (Myotis septentrionalis) at multiple spatial scales

USGS Publications Warehouse

Johnson, Joshua B.; Roberts, James H.; King, Timothy L.; Edwards, John W.; Ford, W. Mark; Ray, David A.

2014-01-01

Although groups of bats may be genetically distinguishable at large spatial scales, the effects of forest disturbances, particularly permanent land use conversions on fine-scale population structure and gene flow of summer aggregations of philopatric bat species are less clear. We genotyped and analyzed variation at 10 nuclear DNA microsatellite markers in 182 individuals of the forest-dwelling northern myotis (Myotis septentrionalis) at multiple spatial scales, from within first-order watersheds scaling up to larger regional areas in West Virginia and New York. Our results indicate that groups of northern myotis were genetically indistinguishable at any spatial scale we considered, and the collective population maintained high genetic diversity. It is likely that the ability to migrate, exploit small forest patches, and use networks of mating sites located throughout the Appalachian Mountains, Interior Highlands, and elsewhere in the hibernation range have allowed northern myotis to maintain high genetic diversity and gene flow regardless of forest disturbances at local and regional spatial scales. A consequence of maintaining high gene flow might be the potential to minimize genetic founder effects following population declines caused currently by the enzootic White-nose Syndrome.

Elevated genetic structure in the coastal tailed frog (Ascaphus truei) in managed redwood forests.

PubMed

Aguilar, Andres; Douglas, Robert B; Gordon, Eric; Baumsteiger, Jason; Goldsworthy, Matthew O

2013-03-01

Landscape alterations have dramatic impacts on the distribution of genetic variation within and among populations and understanding these effects can guide contemporary and future conservation strategies. We initiated a landscape-scale genetic study of the coastal tailed frog (Ascaphus truei) on commercial timberlands within the southern range of the species in Mendocino County (CA, USA). In total, 294 individuals from 13 populations were analyzed at 9 microsatellite loci. None of the sampled populations departed from mutation-drift equilibrium, indicating recent population bottlenecks were not detected in contemporary samples. Fine-scale analysis indicated sampled populations were structured at the watershed level (mean F (ST) = 0.077 and mean G'(ST) = 0.425). Landscape analyses suggested wet and moist areas may serve as significant corridors for gene flow within watersheds in this region (r (2) = 0.32-0.54 for moisture-related features). Results indicate populations of frogs may have persisted at this scale through intense periods of timber harvest, making southern range edge populations of coastal tailed frogs resilient to past land use practices.

Fine-scale natal homing and localized movement as shaped by sex and spawning habitat in Chinook salmon: Insights from spatial autocorrelation analysis of individual genotypes

Treesearch

H. M. Neville; D. J. Isaak; J. B. Dunham; R. F. Thurow; B. E. Rieman

2006-01-01

Natal homing is a hallmark of the life history of salmonid fishes, but the spatial scale of homing within local, naturally reproducing salmon populations is still poorly understood. Accurate homing (paired with restricted movement) should lead to the existence of finescale genetic structuring due to the spatial clustering of related individuals on spawning grounds....

Fine resolution mapping of population age-structures for health and development applications.

PubMed

Alegana, V A; Atkinson, P M; Pezzulo, C; Sorichetta, A; Weiss, D; Bird, T; Erbach-Schoenberg, E; Tatem, A J

2015-04-06

The age-group composition of populations varies considerably across the world, and obtaining accurate, spatially detailed estimates of numbers of children under 5 years is important in designing vaccination strategies, educational planning or maternal healthcare delivery. Traditionally, such estimates are derived from population censuses, but these can often be unreliable, outdated and of coarse resolution for resource-poor settings. Focusing on Nigeria, we use nationally representative household surveys and their cluster locations to predict the proportion of the under-five population in 1 × 1 km using a Bayesian hierarchical spatio-temporal model. Results showed that land cover, travel time to major settlements, night-time lights and vegetation index were good predictors and that accounting for fine-scale variation, rather than assuming a uniform proportion of under 5 year olds can result in significant differences in health metrics. The largest gaps in estimated bednet and vaccination coverage were in Kano, Katsina and Jigawa. Geolocated household surveys are a valuable resource for providing detailed, contemporary and regularly updated population age-structure data in the absence of recent census data. By combining these with covariate layers, age-structure maps of unprecedented detail can be produced to guide the targeting of interventions in resource-poor settings.

The fine scale genetic structure of the British population

PubMed Central

Davison, Dan; Boumertit, Abdelhamid; Day, Tammy; Hutnik, Katarzyna; Royrvik, Ellen C; Cunliffe, Barry; Lawson, Daniel J; Falush, Daniel; Freeman, Colin; Pirinen, Matti; Myers, Simon; Robinson, Mark; Donnelly, Peter; Bodmer, Walter

2015-01-01

Summary Fine-scale genetic variation between human populations is interesting as a signature of historical demographic events and because of its potential for confounding disease studies. We use haplotype-based statistical methods to analyse genome-wide SNP data from a carefully chosen geographically diverse sample of 2,039 individuals from the United Kingdom (UK). This reveals a rich and detailed pattern of genetic differentiation with remarkable concordance between genetic clusters and geography. The regional genetic differentiation and differing patterns of shared ancestry with 6,209 individuals from across Europe carry clear signals of historical demographic events. We estimate the genetic contribution to SE England from Anglo-Saxon migrations to be under half, identify the regions not carrying genetic material from these migrations, suggest significant pre-Roman but post-Mesolithic movement into SE England from the Continent, and show that in non-Saxon parts of the UK there exist genetically differentiated subgroups rather than a general “Celtic” population. PMID:25788095

Spatial structure of morphological and neutral genetic variation in Brook Trout

USGS Publications Warehouse

Kazyak, David C.; Hilderbrand, Robert H.; Keller, Stephen R.; Colaw, Mark C.; Holloway, Amanda E.; Morgan, Raymond P.; King, Timothy L.

2015-01-01

Brook Trout Salvelinus fontinalis exhibit exceptional levels of life history variation, remarkable genetic variability, and fine-scale population structure. In many cases, neighboring populations may be highly differentiated from one another to an extent that is comparable with species-level distinctions in other taxa. Although genetic samples have been collected from hundreds of populations and tens of thousands of individuals, little is known about whether differentiation at neutral markers reflects phenotypic differences among Brook Trout populations. We compared differentiation in morphology and neutral molecular markers among populations from four geographically proximate locations (all within 24 km) to examine how genetic diversity covaries with morphology. We found significant differences among and/or within streams for all three morphological axes examined and identified the source stream of many individuals based on morphology (52.3% classification efficiency). Although molecular and morphological differentiation among streams ranged considerably (mean pairwise FST: 0.023–0.264; pairwise PST: 0.000–0.339), the two measures were not significantly correlated. While in some cases morphological characters appear to have diverged to a greater extent than expected by neutral genetic drift, many traits were conserved to a greater extent than were neutral genetic markers. Thus, while Brook Trout exhibit fine-scale spatial patterns in both morphology and neutral genetic diversity, these types of biological variabilities are being structured by different ecological and evolutionary processes. The relative influences of genetic drift versus selection and phenotypic plasticity in shaping morphology appear to vary among populations occupying nearby streams.

Forest structure within barred owl (Strix varia) home ranges in the eastern cascade range, Washington

Treesearch

Peter H. Singleton

2015-01-01

Competitive interactions with Barred Owls (Strix varia) are an important factor contributing to the decline of the Northern Spotted Owl (Strix occidentalis caurina) population. Understanding the degree of similarity in fine-scale habitat associations for Spotted Owls and Barred Owls will help land managers evaluate whether...

Comparative population genetic structure and diversity of Yellow Perch and Walleye: Broad- and fine-scale patterns across North America

USDA-ARS?s Scientific Manuscript database

The yellow perch Perca flavescens and the walleye Sander vitreus are native North American percid fishes, which have considerable fishery and ecological importance across their wide geographic ranges. Over the past century, they were stocked into new habitats, often with relative disregard for conse...

Altitudinal gradients, biogeographic history and microhabitat adaptation affect fine-scale spatial genetic structure in African and Neotropical populations of an ancient tropical tree species.

PubMed

Torroba-Balmori, Paloma; Budde, Katharina B; Heer, Katrin; González-Martínez, Santiago C; Olsson, Sanna; Scotti-Saintagne, Caroline; Casalis, Maxime; Sonké, Bonaventure; Dick, Christopher W; Heuertz, Myriam

2017-01-01

The analysis of fine-scale spatial genetic structure (FSGS) within populations can provide insights into eco-evolutionary processes. Restricted dispersal and locally occurring genetic drift are the primary causes for FSGS at equilibrium, as described in the isolation by distance (IBD) model. Beyond IBD expectations, spatial, environmental or historical factors can affect FSGS. We examined FSGS in seven African and Neotropical populations of the late-successional rain forest tree Symphonia globulifera L. f. (Clusiaceae) to discriminate the influence of drift-dispersal vs. landscape/ecological features and historical processes on FSGS. We used spatial principal component analysis and Bayesian clustering to assess spatial genetic heterogeneity at SSRs and examined its association with plastid DNA and habitat features. African populations (from Cameroon and São Tomé) displayed a stronger FSGS than Neotropical populations at both marker types (mean Sp = 0.025 vs. Sp = 0.008 at SSRs) and had a stronger spatial genetic heterogeneity. All three African populations occurred in pronounced altitudinal gradients, possibly restricting animal-mediated seed dispersal. Cyto-nuclear disequilibria in Cameroonian populations also suggested a legacy of biogeographic history to explain these genetic patterns. Conversely, Neotropical populations exhibited a weaker FSGS, which may reflect more efficient wide-ranging seed dispersal by Neotropical bats and other dispersers. The population from French Guiana displayed an association of plastid haplotypes with two morphotypes characterized by differential habitat preferences. Our results highlight the importance of the microenvironment for eco-evolutionary processes within persistent tropical tree populations.

Altitudinal gradients, biogeographic history and microhabitat adaptation affect fine-scale spatial genetic structure in African and Neotropical populations of an ancient tropical tree species

PubMed Central

Torroba-Balmori, Paloma; Budde, Katharina B.; Heer, Katrin; González-Martínez, Santiago C.; Olsson, Sanna; Scotti-Saintagne, Caroline; Sonké, Bonaventure; Dick, Christopher W.

2017-01-01

The analysis of fine-scale spatial genetic structure (FSGS) within populations can provide insights into eco-evolutionary processes. Restricted dispersal and locally occurring genetic drift are the primary causes for FSGS at equilibrium, as described in the isolation by distance (IBD) model. Beyond IBD expectations, spatial, environmental or historical factors can affect FSGS. We examined FSGS in seven African and Neotropical populations of the late-successional rain forest tree Symphonia globulifera L. f. (Clusiaceae) to discriminate the influence of drift-dispersal vs. landscape/ecological features and historical processes on FSGS. We used spatial principal component analysis and Bayesian clustering to assess spatial genetic heterogeneity at SSRs and examined its association with plastid DNA and habitat features. African populations (from Cameroon and São Tomé) displayed a stronger FSGS than Neotropical populations at both marker types (mean Sp = 0.025 vs. Sp = 0.008 at SSRs) and had a stronger spatial genetic heterogeneity. All three African populations occurred in pronounced altitudinal gradients, possibly restricting animal-mediated seed dispersal. Cyto-nuclear disequilibria in Cameroonian populations also suggested a legacy of biogeographic history to explain these genetic patterns. Conversely, Neotropical populations exhibited a weaker FSGS, which may reflect more efficient wide-ranging seed dispersal by Neotropical bats and other dispersers. The population from French Guiana displayed an association of plastid haplotypes with two morphotypes characterized by differential habitat preferences. Our results highlight the importance of the microenvironment for eco-evolutionary processes within persistent tropical tree populations. PMID:28771629

Unravelling the hidden ancestry of American admixed populations.

PubMed

Montinaro, Francesco; Busby, George B J; Pascali, Vincenzo L; Myers, Simon; Hellenthal, Garrett; Capelli, Cristian

2015-03-24

The movement of people into the Americas has brought different populations into contact, and contemporary American genomes are the product of a range of complex admixture events. Here we apply a haplotype-based ancestry identification approach to a large set of genome-wide SNP data from a variety of American, European and African populations to determine the contributions of different ancestral populations to the Americas. Our results provide a fine-scale characterization of the source populations, identify a series of novel, previously unreported contributions from Africa and Europe and highlight geohistorical structure in the ancestry of American admixed populations.

Sexual networks: measuring sexual selection in structured, polyandrous populations.

PubMed

McDonald, Grant C; James, Richard; Krause, Jens; Pizzari, Tommaso

2013-03-05

Sexual selection is traditionally measured at the population level, assuming that populations lack structure. However, increasing evidence undermines this approach, indicating that intrasexual competition in natural populations often displays complex patterns of spatial and temporal structure. This complexity is due in part to the degree and mechanisms of polyandry within a population, which can influence the intensity and scale of both pre- and post-copulatory sexual competition. Attempts to measure selection at the local and global scale have been made through multi-level selection approaches. However, definitions of local scale are often based on physical proximity, providing a rather coarse measure of local competition, particularly in polyandrous populations where the local scale of pre- and post-copulatory competition may differ drastically from each other. These limitations can be solved by social network analysis, which allows us to define a unique sexual environment for each member of a population: 'local scale' competition, therefore, becomes an emergent property of a sexual network. Here, we first propose a novel quantitative approach to measure pre- and post-copulatory sexual selection, which integrates multi-level selection with information on local scale competition derived as an emergent property of networks of sexual interactions. We then use simple simulations to illustrate the ways in which polyandry can impact estimates of sexual selection. We show that for intermediate levels of polyandry, the proposed network-based approach provides substantially more accurate measures of sexual selection than the more traditional population-level approach. We argue that the increasing availability of fine-grained behavioural datasets provides exciting new opportunities to develop network approaches to study sexual selection in complex societies.

Genome-wide SNPs lead to strong signals of geographic structure and relatedness patterns in the major arbovirus vector, Aedes aegypti.

PubMed

Rašić, Gordana; Filipović, Igor; Weeks, Andrew R; Hoffmann, Ary A

2014-04-11

Genetic markers are widely used to understand the biology and population dynamics of disease vectors, but often markers are limited in the resolution they provide. In particular, the delineation of population structure, fine scale movement and patterns of relatedness are often obscured unless numerous markers are available. To address this issue in the major arbovirus vector, the yellow fever mosquito (Aedes aegypti), we used double digest Restriction-site Associated DNA (ddRAD) sequencing for the discovery of genome-wide single nucleotide polymorphisms (SNPs). We aimed to characterize the new SNP set and to test the resolution against previously described microsatellite markers in detecting broad and fine-scale genetic patterns in Ae. aegypti. We developed bioinformatics tools that support the customization of restriction enzyme-based protocols for SNP discovery. We showed that our approach for RAD library construction achieves unbiased genome representation that reflects true evolutionary processes. In Ae. aegypti samples from three continents we identified more than 18,000 putative SNPs. They were widely distributed across the three Ae. aegypti chromosomes, with 47.9% found in intergenic regions and 17.8% in exons of over 2,300 genes. Pattern of their imputed effects in ORFs and UTRs were consistent with those found in a recent transcriptome study. We demonstrated that individual mosquitoes from Indonesia, Australia, Vietnam and Brazil can be assigned with a very high degree of confidence to their region of origin using a large SNP panel. We also showed that familial relatedness of samples from a 0.4 km2 area could be confidently established with a subset of SNPs. Using a cost-effective customized RAD sequencing approach supported by our bioinformatics tools, we characterized over 18,000 SNPs in field samples of the dengue fever mosquito Ae. aegypti. The variants were annotated and positioned onto the three Ae. aegypti chromosomes. The new SNP set provided much greater resolution in detecting population structure and estimating fine-scale relatedness than a set of polymorphic microsatellites. RAD-based markers demonstrate great potential to advance our understanding of mosquito population processes, critical for implementing new control measures against this major disease vector.

Genetics of Central Valley O. mykiss populations: drainage and watershed scale analyses

USGS Publications Warehouse

Nielsen, Jennifer L.; Pavey, Scott A.; Wiacek, Talia; Williams, Ian S.

2005-01-01

Genetic variation at 11 microsatellite loci described population genetic structure for Oncorhynchus mykiss in the Central Valley, California. Spatial and temporal variation was examined as well as relationships between hatchery and putative natural spawning anadromous stocks. Genetic diversity was analyzed at two distinct spatial scales: fine-scale within drainage for five populations on Clear Creek; between and among drainage diversity for 23 populations. Significant regional spatial structure was apparent, both within Clear Creek and among rainbow trout populations throughout the Central Valley. Significant differences in allelic frequencies were found among most river or drainage systems. Less than 1% of the molecular variance could be attributed to differences found between drainages. Hatchery populations were shown to carry similar genetic diversity to geographically proximate wild populations. Central Valley M = 0.626 (below the M < 0.68 threshold) supported recent population reductions within the Central Valley. However, average estimated effective population size was relatively high (Ne = 5066). Significant allelic differences were found in rainbow trout collected above and below impassable dams on the American, Yuba, Stanislaus and Tuolumne rivers. Rainbow trout sampled in Spring Creek were extremely bottlenecked with allelic variation at only two loci and an estimated effective population size of 62, suggesting some local freshwater O. mykiss stocks may be declining rapidly. These data support significant genetic population structure for steelhead and rainbow trout populations within the Central Valley across multiple scales. Careful consideration of this genetic diversity and its distribution across the landscape should be part of future conservation and restoration efforts. 

Fine resolution mapping of population age-structures for health and development applications

PubMed Central

Alegana, V. A.; Atkinson, P. M.; Pezzulo, C.; Sorichetta, A.; Weiss, D.; Bird, T.; Erbach-Schoenberg, E.; Tatem, A. J.

2015-01-01

The age-group composition of populations varies considerably across the world, and obtaining accurate, spatially detailed estimates of numbers of children under 5 years is important in designing vaccination strategies, educational planning or maternal healthcare delivery. Traditionally, such estimates are derived from population censuses, but these can often be unreliable, outdated and of coarse resolution for resource-poor settings. Focusing on Nigeria, we use nationally representative household surveys and their cluster locations to predict the proportion of the under-five population in 1 × 1 km using a Bayesian hierarchical spatio-temporal model. Results showed that land cover, travel time to major settlements, night-time lights and vegetation index were good predictors and that accounting for fine-scale variation, rather than assuming a uniform proportion of under 5 year olds can result in significant differences in health metrics. The largest gaps in estimated bednet and vaccination coverage were in Kano, Katsina and Jigawa. Geolocated household surveys are a valuable resource for providing detailed, contemporary and regularly updated population age-structure data in the absence of recent census data. By combining these with covariate layers, age-structure maps of unprecedented detail can be produced to guide the targeting of interventions in resource-poor settings. PMID:25788540

Multi-scale temporal and spatial variation in genotypic composition of Cladophora-borne Escherichia coli populations in Lake Michigan.

PubMed

Badgley, Brian D; Ferguson, John; Vanden Heuvel, Amy; Kleinheinz, Gregory T; McDermott, Colleen M; Sandrin, Todd R; Kinzelman, Julie; Junion, Emily A; Byappanahalli, Muruleedhara N; Whitman, Richard L; Sadowsky, Michael J

2011-01-01

High concentrations of Escherichia coli in mats of Cladophora in the Great Lakes have raised concern over the continued use of this bacterium as an indicator of microbial water quality. Determining the impacts of these environmentally abundant E. coli, however, necessitates a better understanding of their ecology. In this study, the population structure of 4285 Cladophora-borne E. coli isolates, obtained over multiple three day periods from Lake Michigan Cladophora mats in 2007-2009, was examined by using DNA fingerprint analyses. In contrast to previous studies that have been done using isolates from attached Cladophora obtained over large time scales and distances, the extensive sampling done here on free-floating mats over successive days at multiple sites provided a large dataset that allowed for a detailed examination of changes in population structure over a wide range of spatial and temporal scales. While Cladophora-borne E. coli populations were highly diverse and consisted of many unique isolates, multiple clonal groups were also present and accounted for approximately 33% of all isolates examined. Patterns in population structure were also evident. At the broadest scales, E. coli populations showed some temporal clustering when examined by year, but did not show good spatial distinction among sites. E. coli population structure also showed significant patterns at much finer temporal scales. Populations were distinct on an individual mat basis at a given site, and on individual days within a single mat. Results of these studies indicate that Cladophora-borne E. coli populations consist of a mixture of stable, and possibly naturalized, strains that persist during the life of the mat, and more unique, transient strains that can change over rapid time scales. It is clear that further study of microbial processes at fine spatial and temporal scales is needed, and that caution must be taken when interpolating short term microbial dynamics from results obtained from weekly or monthly samples. Copyright © 2010 Elsevier Ltd. All rights reserved.

Multi-scale temporal and spatial variation in genotypic composition of Cladophora-borne Escherichia coli populations in Lake Michigan

USGS Publications Warehouse

Badgley, B.D.; Ferguson, J.; Heuvel, A.V.; Kleinheinz, G.T.; McDermott, C.M.; Sandrin, T.R.; Kinzelman, J.; Junion, E.A.; Byappanahalli, M.N.; Whitman, R.L.; Sadowsky, M.J.

2011-01-01

High concentrations of Escherichia coli in mats of Cladophora in the Great Lakes have raised concern over the continued use of this bacterium as an indicator of microbial water quality. Determining the impacts of these environmentally abundant E. coli, however, necessitates a better understanding of their ecology. In this study, the population structure of 4285 Cladophora-borne E. coli isolates, obtained over multiple three day periods from Lake Michigan Cladophora mats in 2007-2009, was examined by using DNA fingerprint analyses. In contrast to previous studies that have been done using isolates from attached Cladophora obtained over large time scales and distances, the extensive sampling done here on free-floating mats over successive days at multiple sites provided a large dataset that allowed for a detailed examination of changes in population structure over a wide range of spatial and temporal scales. While Cladophora-borne E. coli populations were highly diverse and consisted of many unique isolates, multiple clonal groups were also present and accounted for approximately 33% of all isolates examined. Patterns in population structure were also evident. At the broadest scales, E. coli populations showed some temporal clustering when examined by year, but did not show good spatial distinction among sites. E. coli population structure also showed significant patterns at much finer temporal scales. Populations were distinct on an individual mat basis at a given site, and on individual days within a single mat. Results of these studies indicate that Cladophora-borne E. coli populations consist of a mixture of stable, and possibly naturalized, strains that persist during the life of the mat, and more unique, transient strains that can change over rapid time scales. It is clear that further study of microbial processes at fine spatial and temporal scales is needed, and that caution must be taken when interpolating short term microbial dynamics from results obtained from weekly or monthly samples.

Highly asymmetric fine-scale genetic structure between sexes of African striped mice and indication for condition dependent alternative male dispersal tactics.

PubMed

Solmsen, N; Johannesen, J; Schradin, C

2011-04-01

Sex-biased dispersal is observed in many taxa, but few studies have compared sex-biased dispersal among and within populations. We addressed the magnitude and habitat dependency of sex-biased dispersal in social African striped mice by separating group-related from population-related genetic variance to understand the contribution of each sex to deme structure. As dispersal over unoccupied habitat is likely to be more costly than dispersal within a population, we predicted that individuals leaving the natal population have a lower body condition, being inferior to heavier territorial individuals. Fine-scale genetic structure was detected in both sexes. Female relatedness decreased continuously from R = 0.21 at 25 m to zero at 500 m. Maximum male relatedness R = 0.05 was constant at distances between 25 and 75 m, becoming zero at 100 m. Genetic variance (F(ST) ) among seven locations was significantly higher in females than in males, while inbreeding estimates (F(IS) ) were significantly higher in males than in females. Assignment tests estimated significantly more migrants among males, while Bayesian clustering estimated only a single genetic unit cluster for males among the seven locations. The mean body mass of migrant males (44 g) was significantly lower than for males that remained resident and thus dispersed within their sub-population (48 g). Combined, the results showed habitat-independent male-biased dispersal and high female philopatry, and suggested that body condition was more important than kinship in male dispersal decisions. We suggest that locally inferior males are important for gene flow between sub-populations. Thus, males might follow alternative dispersal tactics. © 2011 Blackwell Publishing Ltd.

Patterns of genetic variability and habitat occupancy in Crepis triasii (Asteraceae) at different spatial scales: insights on evolutionary processes leading to diversification in continental islands.

PubMed

Mayol, Maria; Palau, Carles; Rosselló, Josep A; González-Martínez, Santiago C; Molins, Arántzazu; Riba, Miquel

2012-02-01

Archipelagos are unique systems for studying evolutionary processes promoting diversification and speciation. The islands of the Mediterranean basin are major areas of plant richness, including a high proportion of narrow endemics. Many endemic plants are currently found in rocky habitats, showing varying patterns of habitat occupancy at different spatial scales throughout their range. The aim of the present study was to understand the impact of varying patterns of population distribution on genetic diversity and structure to shed light on demographic and evolutionary processes leading to population diversification in Crepis triasii, an endemic plant from the eastern Balearic Islands. Using allozyme and chloroplast markers, we related patterns of genetic structure and diversity to those of habitat occupancy at a regional (between islands and among populations within islands) and landscape (population size and connectivity) scale. Genetic diversity was highly structured both at the regional and at the landscape level, and was positively correlated with population connectivity in the landscape. Populations located in small isolated mountains and coastal areas, with restricted patterns of regional occupancy, were genetically less diverse and much more differentiated. In addition, more isolated populations had stronger fine-scale genetic structure than well-connected ones. Changes in habitat availability and quality arising from marine transgressions during the Quaternary, as well as progressive fragmentation associated with the aridification of the climate since the last glaciation, are the most plausible factors leading to the observed patterns of genetic diversity and structure. Our results emphasize the importance of gene flow in preventing genetic erosion and maintaining the evolutionary potential of populations. They also agree with recent studies highlighting the importance of restricted gene flow and genetic drift as drivers of plant evolution in Mediterranean continental islands.

Fine-scale population genetic structure of the Bengal tiger (Panthera tigris tigris) in a human-dominated western Terai Arc Landscape, India

PubMed Central

Singh, Sujeet Kumar; Aspi, Jouni; Kvist, Laura; Sharma, Reeta; Pandey, Puneet; Mishra, Sudhanshu; Singh, Randeep; Agrawal, Manoj; Goyal, Surendra Prakash

2017-01-01

Despite massive global conservation strategies, tiger populations continued to decline until recently, mainly due to habitat loss, human-animal conflicts, and poaching. These factors are known to affect the genetic characteristics of tiger populations and decrease local effective population sizes. The Terai Arc Landscape (TAL) at the foothills of the Himalaya is one of the 42 source sites of tigers around the globe. Therefore, information on how landscape features and anthropogenic factors affect the fine-scale spatial genetic structure and variation of tigers in TAL is needed to develop proper management strategies for achieving long-term conservation goals. We document, for the first time, the genetic characteristics of this tiger population by genotyping 71 tiger samples using 13 microsatellite markers from the western region of TAL (WTAL) of 1800 km2. Specifically, we aimed to estimate the genetic variability, population structure, and gene flow. The microsatellite markers indicated that the levels of allelic diversity (MNA = 6.6) and genetic variation (Ho = 0.50, HE = 0.64) were slightly lower than those reported previously in other Bengal tiger populations. We observed moderate gene flow and significant genetic differentiation (FST= 0.060) and identified the presence of cryptic genetic structure using Bayesian and non-Bayesian approaches. There was low and significantly asymmetric migration between the two main subpopulations of the Rajaji Tiger Reserve and the Corbett Tiger Reserve in WTAL. Sibship relationships indicated that the functionality of the corridor between these subpopulations may be retained if the quality of the habitat does not deteriorate. However, we found that gene flow is not adequate in view of changing land use matrices. We discuss the need to maintain connectivity by implementing the measures that have been suggested previously to minimize the level of human disturbance, including relocation of villages and industries, prevention of encroachment, and banning sand and boulder mining in the corridors. PMID:28445499

Fine-scale population genetic structure of the Bengal tiger (Panthera tigris tigris) in a human-dominated western Terai Arc Landscape, India.

PubMed

Singh, Sujeet Kumar; Aspi, Jouni; Kvist, Laura; Sharma, Reeta; Pandey, Puneet; Mishra, Sudhanshu; Singh, Randeep; Agrawal, Manoj; Goyal, Surendra Prakash

2017-01-01

Despite massive global conservation strategies, tiger populations continued to decline until recently, mainly due to habitat loss, human-animal conflicts, and poaching. These factors are known to affect the genetic characteristics of tiger populations and decrease local effective population sizes. The Terai Arc Landscape (TAL) at the foothills of the Himalaya is one of the 42 source sites of tigers around the globe. Therefore, information on how landscape features and anthropogenic factors affect the fine-scale spatial genetic structure and variation of tigers in TAL is needed to develop proper management strategies for achieving long-term conservation goals. We document, for the first time, the genetic characteristics of this tiger population by genotyping 71 tiger samples using 13 microsatellite markers from the western region of TAL (WTAL) of 1800 km2. Specifically, we aimed to estimate the genetic variability, population structure, and gene flow. The microsatellite markers indicated that the levels of allelic diversity (MNA = 6.6) and genetic variation (Ho = 0.50, HE = 0.64) were slightly lower than those reported previously in other Bengal tiger populations. We observed moderate gene flow and significant genetic differentiation (FST= 0.060) and identified the presence of cryptic genetic structure using Bayesian and non-Bayesian approaches. There was low and significantly asymmetric migration between the two main subpopulations of the Rajaji Tiger Reserve and the Corbett Tiger Reserve in WTAL. Sibship relationships indicated that the functionality of the corridor between these subpopulations may be retained if the quality of the habitat does not deteriorate. However, we found that gene flow is not adequate in view of changing land use matrices. We discuss the need to maintain connectivity by implementing the measures that have been suggested previously to minimize the level of human disturbance, including relocation of villages and industries, prevention of encroachment, and banning sand and boulder mining in the corridors.

Nest suitability, fine-scale population structure and male-mediated dispersal of a solitary ground nesting bee in an urban landscape.

PubMed

López-Uribe, Margarita M; Morreale, Stephen J; Santiago, Christine K; Danforth, Bryan N

2015-01-01

Bees are the primary pollinators of flowering plants in almost all ecosystems. Worldwide declines in bee populations have raised awareness about the importance of their ecological role in maintaining ecosystem functioning. The naturally strong philopatric behavior that some bee species show can be detrimental to population viability through increased probability of inbreeding. Furthermore, bee populations found in human-altered landscapes, such as urban areas, can experience lower levels of gene flow and effective population sizes, increasing potential for inbreeding depression in wild bee populations. In this study, we investigated the fine-scale population structure of the solitary bee Colletes inaequalis in an urbanized landscape. First, we developed a predictive spatial model to detect suitable nesting habitat for this ground nesting bee and to inform our field search for nests. We genotyped 18 microsatellites in 548 female individuals collected from nest aggregations throughout the study area. Genetic relatedness estimates revealed that genetic similarity among individuals was slightly greater within nest aggregations than among randomly chosen individuals. However, genetic structure among nest aggregations was low (Nei's GST = 0.011). Reconstruction of parental genotypes revealed greater genetic relatedness among females than among males within nest aggregations, suggesting male-mediated dispersal as a potentially important mechanism of population connectivity and inbreeding avoidance. Size of nesting patch was positively correlated with effective population size, but not with other estimators of genetic diversity. We detected a positive trend between geographic distance and genetic differentiation between nest aggregations. Our landscape genetic models suggest that increased urbanization is likely associated with higher levels of inbreeding. Overall, these findings emphasize the importance of density and distribution of suitable nesting patches for enhancing bee population abundance and connectivity in human dominated habitats and highlights the critical contribution of landscape genetic studies for enhanced conservation and management of native pollinators.

Nest Suitability, Fine-Scale Population Structure and Male-Mediated Dispersal of a Solitary Ground Nesting Bee in an Urban Landscape

PubMed Central

López-Uribe, Margarita M.; Morreale, Stephen J.; Santiago, Christine K.; Danforth, Bryan N.

2015-01-01

Bees are the primary pollinators of flowering plants in almost all ecosystems. Worldwide declines in bee populations have raised awareness about the importance of their ecological role in maintaining ecosystem functioning. The naturally strong philopatric behavior that some bee species show can be detrimental to population viability through increased probability of inbreeding. Furthermore, bee populations found in human-altered landscapes, such as urban areas, can experience lower levels of gene flow and effective population sizes, increasing potential for inbreeding depression in wild bee populations. In this study, we investigated the fine-scale population structure of the solitary bee Colletes inaequalis in an urbanized landscape. First, we developed a predictive spatial model to detect suitable nesting habitat for this ground nesting bee and to inform our field search for nests. We genotyped 18 microsatellites in 548 female individuals collected from nest aggregations throughout the study area. Genetic relatedness estimates revealed that genetic similarity among individuals was slightly greater within nest aggregations than among randomly chosen individuals. However, genetic structure among nest aggregations was low (Nei’s GST = 0.011). Reconstruction of parental genotypes revealed greater genetic relatedness among females than among males within nest aggregations, suggesting male-mediated dispersal as a potentially important mechanism of population connectivity and inbreeding avoidance. Size of nesting patch was positively correlated with effective population size, but not with other estimators of genetic diversity. We detected a positive trend between geographic distance and genetic differentiation between nest aggregations. Our landscape genetic models suggest that increased urbanization is likely associated with higher levels of inbreeding. Overall, these findings emphasize the importance of density and distribution of suitable nesting patches for enhancing bee population abundance and connectivity in human dominated habitats and highlights the critical contribution of landscape genetic studies for enhanced conservation and management of native pollinators. PMID:25950429

Spatial Heterogeneity as a Genetic Mixing Mechanism in Highly Philopatric Colonial Seabirds

PubMed Central

Cristofari, Robin; Trucchi, Emiliano; Whittington, Jason D.; Vigetta, Stéphanie; Gachot-Neveu, Hélène; Stenseth, Nils Christian; Le Maho, Yvon; Le Bohec, Céline

2015-01-01

How genetic diversity is maintained in philopatric colonial systems remains unclear, and understanding the dynamic balance of philopatry and dispersal at all spatial scales is essential to the study of the evolution of coloniality. In the King penguin, Aptenodytes patagonicus, return rates of post-fledging chicks to their natal sub-colony are remarkably high. Empirical studies have shown that adults return year after year to their previous breeding territories within a radius of a few meters. Yet, little reliable data are available on intra- and inter-colonial dispersal in this species. Here, we present the first fine-scale study of the genetic structure in a king penguin colony in the Crozet Archipelago. Samples were collected from individual chicks and analysed at 8 microsatellite loci. Precise geolocation data of hatching sites and selective pressures associated with habitat features were recorded for all sampling locations. We found that despite strong natal and breeding site fidelity, king penguins retain a high degree of panmixia and genetic diversity. Yet, genetic structure appears markedly heterogeneous across the colony, with higher-than-expected inbreeding levels, and local inbreeding and relatedness hotspots that overlap predicted higher-quality nesting locations. This points towards heterogeneous population structure at the sub-colony level, in which fine-scale environmental features drive local philopatric behaviour, while lower-quality patches may act as genetic mixing mechanisms at the colony level. These findings show how a lack of global genetic structuring can emerge from small-scale heterogeneity in ecological parameters, as opposed to the classical model of homogeneous dispersal. Our results also emphasize the importance of sampling design for estimation of population parameters in colonial seabirds, as at high spatial resolution, basic genetic features are shown to be location-dependent. Finally, this study stresses the importance of understanding intra-colonial dispersal and genetic mixing mechanisms in order to better estimate species-wide gene flows and population dynamics. PMID:25680103

Spatial heterogeneity as a genetic mixing mechanism in highly philopatric colonial seabirds.

PubMed

Cristofari, Robin; Trucchi, Emiliano; Whittington, Jason D; Vigetta, Stéphanie; Gachot-Neveu, Hélène; Stenseth, Nils Christian; Le Maho, Yvon; Le Bohec, Céline

2015-01-01

How genetic diversity is maintained in philopatric colonial systems remains unclear, and understanding the dynamic balance of philopatry and dispersal at all spatial scales is essential to the study of the evolution of coloniality. In the King penguin, Aptenodytes patagonicus, return rates of post-fledging chicks to their natal sub-colony are remarkably high. Empirical studies have shown that adults return year after year to their previous breeding territories within a radius of a few meters. Yet, little reliable data are available on intra- and inter-colonial dispersal in this species. Here, we present the first fine-scale study of the genetic structure in a king penguin colony in the Crozet Archipelago. Samples were collected from individual chicks and analysed at 8 microsatellite loci. Precise geolocation data of hatching sites and selective pressures associated with habitat features were recorded for all sampling locations. We found that despite strong natal and breeding site fidelity, king penguins retain a high degree of panmixia and genetic diversity. Yet, genetic structure appears markedly heterogeneous across the colony, with higher-than-expected inbreeding levels, and local inbreeding and relatedness hotspots that overlap predicted higher-quality nesting locations. This points towards heterogeneous population structure at the sub-colony level, in which fine-scale environmental features drive local philopatric behaviour, while lower-quality patches may act as genetic mixing mechanisms at the colony level. These findings show how a lack of global genetic structuring can emerge from small-scale heterogeneity in ecological parameters, as opposed to the classical model of homogeneous dispersal. Our results also emphasize the importance of sampling design for estimation of population parameters in colonial seabirds, as at high spatial resolution, basic genetic features are shown to be location-dependent. Finally, this study stresses the importance of understanding intra-colonial dispersal and genetic mixing mechanisms in order to better estimate species-wide gene flows and population dynamics.

Fine-scale habitat characteristics related to occupancy of the Yosemite Toad, Anaxyrus canorus

Treesearch

Christina T. Liang; Robert L. Grasso; Julie J. Nelson-Paul; Kim E. Vincent; Amy J. Lind

2017-01-01

Fine-scale habitat information can provide insight into species occupancy and persistence that is not apparent at the landscape-scale. Such information is particularly important for rare species that are experiencing population declines, such as the threatened Yosemite Toad (Anaxyrus canorus). Our study examined differences in physical...

Genetic structure in the Sherpa and neighboring Nepalese populations.

PubMed

Cole, Amy M; Cox, Sean; Jeong, Choongwon; Petousi, Nayia; Aryal, Dhana R; Droma, Yunden; Hanaoka, Masayuki; Ota, Masao; Kobayashi, Nobumitsu; Gasparini, Paolo; Montgomery, Hugh; Robbins, Peter; Di Rienzo, Anna; Cavalleri, Gianpiero L

2017-01-19

We set out to describe the fine-scale population structure across the Eastern region of Nepal. To date there is relatively little known about the genetic structure of the Sherpa residing in Nepal and their genetic relationship with the Nepalese. We assembled dense genotype data from a total of 1245 individuals representing Nepal and a variety of different populations resident across the greater Himalayan region including Tibet, China, India, Pakistan, Kazakhstan, Uzbekistan, Tajikistan and Kirghizstan. We performed analysis of principal components, admixture and homozygosity. We identified clear substructure across populations resident in the Himalayan arc, with genetic structure broadly mirroring geographical features of the region. Ethnic subgroups within Nepal show distinct genetic structure, on both admixture and principal component analysis. We detected differential proportions of ancestry from northern Himalayan populations across Nepalese subgroups, with the Nepalese Rai, Magar and Tamang carrying the greatest proportions of Tibetan ancestry. We show that populations dwelling on the Himalayan plateau have had a clear impact on the Northern Indian gene pool. We illustrate how the Sherpa are a remarkably isolated population, with little gene flow from surrounding Nepalese populations.

Development and validation of a fine-motor assessment tool for use with young children in a Chinese population.

PubMed

Siu, Andrew M H; Lai, Cynthia Y Y; Chiu, Amy S M; Yip, Calvin C K

2011-01-01

Most of the fine-motor assessment tools used in Hong Kong have been designed in Western countries, so there is a need to develop a standardized assessment which is relevant to the culture and daily living tasks of the local (that is, Chinese) population. This study aimed to (1) develop a fine-motor assessment tool (the Hong Kong Preschool Fine-Motor Developmental Assessment [HK-PFMDA]) for use with young children in a Chinese population and (2) examine the HK-PFMDA's psychometric properties. The HK-PFMDA was developed by a group of occupational therapists specializing in the area of developmental disabilities in Hong Kong. A panel of 21 experts reviewed the content validity of the instrument. Rasch item analysis was used to examine the model fit of items against the rating scale model, and to explore the dimensionality of the test. Intra- and interrater reliability, convergent validity, and criterion-related validity were examined. The participants included 783 children without disabilities, 45 with autistic spectrum disorder, and 35 with developmental delay. The Rasch analysis suggested that the 87-item HK-PFMDA had a unidimensional structure, as the items explained most (91.6%) of the variance. The HK-PFMDA demonstrated excellent intra- (ICC = .99) and interrater reliability (ICC = .99), and internal consistency (α ranging from .83 to .92). In terms of validity, the HK-PFMDA had significant positive correlations with both age and the convergent measures of the Peabody Developmental Motor Scales (PDMS-2). A set of normative data for local children aged from birth to 6 years was established. The HK-PFMDA has shown excellent psychometric properties and is suitable for clinical application by occupational therapists in the assessment of fine-motor skills development of young children in Chinese populations. Copyright © 2010 Elsevier Ltd. All rights reserved.

Fine-scale natal homing and localized movement as shaped by sex and spawning habitat in chinook salmon

USGS Publications Warehouse

Neville, Helen; Isaak, Daniel; Dunham, J.B.; Thurow, Russel; Rieman, B.

2006-01-01

Natal homing is a hallmark of the life history of salmonid fishes, but the spatial scale of homing within local, naturally reproducing salmon populations is still poorly understood. Accurate homing (paired with restricted movement) should lead to the existence of fine-scale genetic structuring due to the spatial clustering of related individuals on spawning grounds. Thus, we explored the spatial resolution of natal homing using genetic associations among individual Chinook salmon (Oncorhynchus tshawytscha) in an interconnected stream network. We also investigated the relationship between genetic patterns and two factors hypothesized to influence natal homing and localized movements at finer scales in this species, localized patterns in the distribution of spawning gravels and sex. Spatial autocorrelation analyses showed that spawning locations in both sub-basins of our study site were spatially clumped, but the upper sub-basin generally had a larger spatial extent and continuity of redd locations than the lower sub-basin, where the distribution of redds and associated habitat conditions were more patchy. Male genotypes were not autocorrelated at any spatial scale in either sub-basin. Female genotypes showed significant spatial autocorrelation and genetic patterns for females varied in the direction predicted between the two sub-basins, with much stronger autocorrelation in the sub-basin with less continuity in spawning gravels. The patterns observed here support predictions about differential constraints and breeding tactics between the two sexes and the potential for fine-scale habitat structure to influence the precision of natal homing and localized movements of individual Chinook salmon on their breeding grounds.

The empirical Bayes estimators of fine-scale population structure in high gene flow species.

PubMed

Kitada, Shuichi; Nakamichi, Reiichiro; Kishino, Hirohisa

2017-11-01

An empirical Bayes (EB) pairwise F ST estimator was previously introduced and evaluated for its performance by numerical simulation. In this study, we conducted coalescent simulations and generated genetic population structure mechanistically, and compared the performance of the EBF ST with Nei's G ST , Nei and Chesser's bias-corrected G ST (G ST_NC ), Weir and Cockerham's θ (θ WC ) and θ with finite sample correction (θ WC_F ). We also introduced EB estimators for Hedrick' G' ST and Jost' D. We applied these estimators to publicly available SNP genotypes of Atlantic herring. We also examined the power to detect the environmental factors causing the population structure. Our coalescent simulations revealed that the finite sample correction of θ WC is necessary to assess population structure using pairwise F ST values. For microsatellite markers, EBF ST performed the best among the present estimators regarding both bias and precision under high gene flow scenarios (FST≤0.032). For 300 SNPs, EBF ST had the highest precision in all cases, but the bias was negative and greater than those for G ST_NC and θ WC_F in all cases. G ST_NC and θ WC_F performed very similarly at all levels of F ST . As the number of loci increased up to 10 000, the precision of G ST_NC and θ WC_F became slightly better than for EBF ST for cases with FST≥0.004, even though the size of the bias remained constant. The EB estimators described the fine-scale population structure of the herring and revealed that ~56% of the genetic differentiation was caused by sea surface temperature and salinity. The R package finepop for implementing all estimators used here is available on CRAN. © 2017 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

Fine-scale population genetic structure of a wildlife disease vector: The southern house mosquito on the island of Hawaii

USGS Publications Warehouse

Keyghobadi, N.; LaPointe, D.; Fleischer, R.C.; Fonseca, D.M.

2006-01-01

The southern house mosquito, Culex quinquefasciatus, is a widespread tropical and subtropical disease vector. In the Hawaiian Islands, where it was introduced accidentally almost two centuries ago, it is considered the primary vector of avian malaria and pox. Avian malaria in particular has contributed to the extinction and endangerment of Hawaii's native avifauna, and has altered the altitudinal distribution of native bird populations. We examined the population genetic structure of Cx. quinquefasciatus on the island of Hawaii at a smaller spatial scale than has previously been attempted, with particular emphasis on the effects of elevation on population genetic structure. We found significant genetic differentiation among populations and patterns of isolation by distance within the island. Elevation per se did not have a limiting effect on gene flow; however, there was significantly lower genetic diversity among populations at mid elevations compared to those at low elevations. A recent sample taken from just above the predicted upper altitudinal distribution of Cx. quinquefasciatus on the island of Hawaii was confirmed as being a temporary summer population and appeared to consist of individuals from more than one source population. Our results indicate effects of elevation gradients on genetic structure that are consistent with known effects of elevation on population dynamics of this disease vector. ?? 2006 The Authors.

Estimation of fine-scale recombination intensity variation in the white-echinus interval of D. melanogaster

PubMed Central

Singh, Nadia D.; Aquadro, Charles F.; Clark, Andrew G.

2009-01-01

Accurate assessment of local recombination rate variation is crucial for understanding the recombination process and for determining the impact of natural selection on linked sites. In Drosophila, local recombination intensity has been estimated primarily by statistical approaches, estimating the local slope of the relationship between the physical and genetic maps. However, these estimates are limited in resolution, and as a result, the physical scale at which recombination intensity varies in Drosophila is largely unknown. While there is some evidence suggesting as much as a 40-fold variation in crossover rate at a local scale in D. pseudoobscura, little is known about the fine-scale structure of recombination rate variation in D. melanogaster. Here, we experimentally examine the fine-scale distribution of crossover events in a 1.2 Mb region on the D. melanogaster X chromosome using a classic genetic mapping approach. Our results show that crossover frequency is significantly heterogeneous within this region, varying ~ 3.5 fold. Simulations suggest that this degree of heterogeneity is sufficient to affect levels of standing nucleotide diversity, although the magnitude of this effect is small. We recover no statistical association between empirical estimates of nucleotide diversity and recombination intensity, which is likely due to the limited number of loci sampled in our population genetic dataset. However, codon bias is significantly negatively correlated with fine-scale recombination intensity estimates, as expected. Our results shed light on the relevant physical scale to consider in evolutionary analyses relating to recombination rate, and highlight the motivations to increase the resolution of the recombination map in Drosophila. PMID:19504037

High Resolutions Studies of the Structure of the Solar Atmosphere

DTIC Science & Technology

1992-06-30

Pairs in the Solar Wind", submitted to J. Geophys. Res., July 20, 1992. M. Karovska , F. Blundell and S. R. Habbal, "Fine Scale Structure of Active...Regions", manuscript in preparation. M. Karovska , F. Blundell and S. R. Habbal, "Fine Scale Structure of the Solar Limb in a Coronal Hole", manuscript in

Fine-scale genetic structure of whitebark pine (Pinus albicaulis) associations with watershed and growth form

Treesearch

Deborah L. Rogers; Constance I. Millar; Robert D. Westfall

1999-01-01

The fine-scale genetic structure of a subalpine conifer, whitebark pine (Pinus albicaulis Engelm.), was studied at nested geographic levels from watershed to adjacent stems in the eastern Sierra Nevada Range of California. A combination of several characteristics contributed to unpredicted genetic structure in this species. This includes being one of...

Fear of predation drives stable and differentiated social relationships in guppies

PubMed Central

Heathcote, Robert J. P.; Darden, Safi K.; Franks, Daniel W.; Ramnarine, Indar W.; Croft, Darren P.

2017-01-01

Social relationships can have important consequences for fitness in animals. Whilst numerous studies have shown that individuals often join larger groups in response to perceived predation risk (i.e. fear of predation), the importance of predation risk in driving the formation and stability of social relationships within groups has been relatively ignored. We experimentally tested how predation threat influenced fine-scale social network structure using Trinidadian guppies (Poecilia reticulata). When perceived predation risk was high, individuals developed stable and more differentiated social ties compared to when perceived risk was low. Intriguingly, social differentiation coincided with shoals being somewhat smaller under high-perceived risk, suggesting a possible conflict between forming stable social relationships and larger social groups. Individuals most at risk of predation (large and bold individuals) showed the most exaggerated responses in several social measures. Taken together, we provide the first experimental evidence that proximate risk of predation can increase the intensity of social relationships and fine-scale social structure in animal populations. PMID:28150706

Fear of predation drives stable and differentiated social relationships in guppies.

PubMed

Heathcote, Robert J P; Darden, Safi K; Franks, Daniel W; Ramnarine, Indar W; Croft, Darren P

2017-02-02

Social relationships can have important consequences for fitness in animals. Whilst numerous studies have shown that individuals often join larger groups in response to perceived predation risk (i.e. fear of predation), the importance of predation risk in driving the formation and stability of social relationships within groups has been relatively ignored. We experimentally tested how predation threat influenced fine-scale social network structure using Trinidadian guppies (Poecilia reticulata). When perceived predation risk was high, individuals developed stable and more differentiated social ties compared to when perceived risk was low. Intriguingly, social differentiation coincided with shoals being somewhat smaller under high-perceived risk, suggesting a possible conflict between forming stable social relationships and larger social groups. Individuals most at risk of predation (large and bold individuals) showed the most exaggerated responses in several social measures. Taken together, we provide the first experimental evidence that proximate risk of predation can increase the intensity of social relationships and fine-scale social structure in animal populations.

Climate and Human Pressure Constraints Co-Explain Regional Plant Invasion at Different Spatial Scales

PubMed Central

García-Baquero, Gonzalo; Caño, Lidia; Biurrun, Idoia; García-Mijangos, Itziar; Loidi, Javier; Herrera, Mercedes

2016-01-01

Alien species invasion represents a global threat to biodiversity and ecosystems. Explaining invasion patterns in terms of environmental constraints will help us to assess invasion risks and plan control strategies. We aim to identify plant invasion patterns in the Basque Country (Spain), and to determine the effects of climate and human pressure on that pattern. We modeled the regional distribution of 89 invasive plant species using two approaches. First, distance-based Moran’s eigenvector maps were used to partition variation in the invasive species richness, S, into spatial components at broad and fine scales; redundancy analysis was then used to explain those components on the basis of climate and human pressure descriptors. Second, we used generalized additive mixed modeling to fit species-specific responses to the same descriptors. Climate and human pressure descriptors have different effects on S at different spatial scales. Broad-scale spatially structured temperature and precipitation, and fine-scale spatially structured human population density and percentage of natural and semi-natural areas, explained altogether 38.7% of the total variance. The distribution of 84% of the individually tested species was related to either temperature, precipitation or both, and 68% was related to either population density or natural and semi-natural areas, displaying similar responses. The spatial pattern of the invasive species richness is strongly environmentally forced, mainly by climate factors. Since individual species responses were proved to be both similarly constrained in shape and explained variance by the same environmental factors, we conclude that the pattern of invasive species richness results from individual species’ environmental preferences. PMID:27741276

Pollen-mediated gene flow and fine-scale spatial genetic structure in Olea europaea subsp. europaea var. sylvestris

PubMed Central

Piotti, A.; Satovic, Z.; de la Rosa, R.; Belaj, A.

2017-01-01

Abstract Background and Aims Wild olive (Olea europaea subsp. europaea var. sylvestris) is important from an economic and ecological point of view. The effects of anthropogenic activities may lead to the genetic erosion of its genetic patrimony, which has high value for breeding programmes. In particular, the consequences of the introgression from cultivated stands are strongly dependent on the extent of gene flow and therefore this work aims at quantitatively describing contemporary gene flow patterns in wild olive natural populations. Methods The studied wild population is located in an undisturbed forest, in southern Spain, considered one of the few extant hotspots of true oleaster diversity. A total of 225 potential father trees and seeds issued from five mother trees were genotyped by eight microsatellite markers. Levels of contemporary pollen flow, in terms of both pollen immigration rates and within-population dynamics, were measured through paternity analyses. Moreover, the extent of fine-scale spatial genetic structure (SGS) was studied to assess the relative importance of seed and pollen dispersal in shaping the spatial distribution of genetic variation. Key Results The results showed that the population under study is characterized by a high genetic diversity, a relatively high pollen immigration rate (0·57), an average within-population pollen dispersal of about 107 m and weak but significant SGS up to 40 m. The population is a mosaic of several intermingled genetic clusters that is likely to be generated by spatially restricted seed dispersal. Moreover, wild oleasters were found to be self-incompatible and preferential mating between some genotypes was revealed. Conclusions Knowledge of the within-population genetic structure and gene flow dynamics will lead to identifying possible strategies aimed at limiting the effect of anthropogenic activities and improving breeding programmes for the conservation of olive tree forest genetic resources. PMID:28028015

Pollen-mediated gene flow and fine-scale spatial genetic structure in Olea europaea subsp. europaea var. sylvestris.

PubMed

Beghè, D; Piotti, A; Satovic, Z; de la Rosa, R; Belaj, A

2017-03-01

Wild olive ( Olea europaea subsp. europaea var. sylvestris ) is important from an economic and ecological point of view. The effects of anthropogenic activities may lead to the genetic erosion of its genetic patrimony, which has high value for breeding programmes. In particular, the consequences of the introgression from cultivated stands are strongly dependent on the extent of gene flow and therefore this work aims at quantitatively describing contemporary gene flow patterns in wild olive natural populations. The studied wild population is located in an undisturbed forest, in southern Spain, considered one of the few extant hotspots of true oleaster diversity. A total of 225 potential father trees and seeds issued from five mother trees were genotyped by eight microsatellite markers. Levels of contemporary pollen flow, in terms of both pollen immigration rates and within-population dynamics, were measured through paternity analyses. Moreover, the extent of fine-scale spatial genetic structure (SGS) was studied to assess the relative importance of seed and pollen dispersal in shaping the spatial distribution of genetic variation. The results showed that the population under study is characterized by a high genetic diversity, a relatively high pollen immigration rate (0·57), an average within-population pollen dispersal of about 107 m and weak but significant SGS up to 40 m. The population is a mosaic of several intermingled genetic clusters that is likely to be generated by spatially restricted seed dispersal. Moreover, wild oleasters were found to be self-incompatible and preferential mating between some genotypes was revealed. Knowledge of the within-population genetic structure and gene flow dynamics will lead to identifying possible strategies aimed at limiting the effect of anthropogenic activities and improving breeding programmes for the conservation of olive tree forest genetic resources. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Combining microsatellite, otolith shape and parasites community analyses as a holistic approach to assess population structure of Dentex dentex

NASA Astrophysics Data System (ADS)

Marengo, M.; Baudouin, M.; Viret, A.; Laporte, M.; Berrebi, P.; Vignon, M.; Marchand, B.; Durieux, E. D. H.

2017-10-01

The common dentex, Dentex dentex, is an iconic marine coastal fish of the Mediterranean Sea. Despite its economic and ecological importance, data on the population structure of this species are still very limited. The aim of this study was to identify the stock structure of the common dentex at relatively fine spatial scale around Corsica Island, using a combination of markers that have different spatial and temporal scales of integration: microsatellite DNA markers, otolith shape analysis and parasites communities. Microsatellite analysis indicated that there was no significant genetic differentiation in D. dentex between the four sampling sites around Corsica. Otolith shape analysis suggests one potential distinct population unit of D. dentex centered in one site (Cap Corse) varying in their degree of differentiation from those in the other zones. Multivariate analysis on parasite abundance data highlights to a lower extent two sites (Bonifacio and Galeria) with some connectivity between adjacent zones. The combination of these three markers together highlights the resulting three sites while giving complementary insights and an opportunity to compare their utility and potential to understand population interactions. A complex population structure around Corsican coasts is then proposed, providing a new perspective on common dentex fishery stock conservation and management strategies.

Patterns of gene flow in Encholirium horridum L.B.Sm., a monocarpic species of Bromeliaceae from Brazil.

PubMed

Hmeljevski, Karina Vanessa; dos Reis, Maurício Sedrez; Forzza, Rafaela Campostrini

2015-01-01

Encholirium horridum is a bromeliad that occurs exclusively on inselbergs in the Atlantic Forest biome of Brazil. These rock outcrops form natural islands that isolate populations from each other. We investigated gene flow by pollen through paternity analyses of a bromeliad population in an area of approximately 2 ha in Espírito Santo State, Brazil. To that end, seed rosettes and seedlings were genotyped using nuclear microsatellite loci. A plot was also established from the same population and specimens were genotyped to evaluate their fine-scale spatial genetic structure (SGS) through analyses of spatial autocorrelation and clonal growth. Paternity analysis indicated that 80% of the attributed progenitors of the genotyped seedlings were from inside the study area. The pollen dispersal distances within the area were restricted (mean distance of 45.5 m, varying from 3 to 156 m) and fine-scale SGS was weak (F(ij) = 0.0122, P < 0.001; Sp = 0.009). Clonal growth was found to be a rare event, supporting the monocarpy of this species. © The American Genetic Association 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Genetic analysis reveals efficient sexual spore dispersal at a fine spatial scale in Armillaria ostoyae, the causal agent of root-rot disease in conifers.

PubMed

Dutech, Cyril; Labbé, Frédéric; Capdevielle, Xavier; Lung-Escarmant, Brigitte

Armillaria ostoyae (sometimes named Armillaria solidipes) is a fungal species causing root diseases in numerous coniferous forests of the northern hemisphere. The importance of sexual spores for the establishment of new disease centres remains unclear, particularly in the large maritime pine plantations of southwestern France. An analysis of the genetic diversity of a local fungal population distributed over 500 ha in this French forest showed genetic recombination between genotypes to be frequent, consistent with regular sexual reproduction within the population. The estimated spatial genetic structure displayed a significant pattern of isolation by distance, consistent with the dispersal of sexual spores mostly at the spatial scale studied. Using these genetic data, we inferred an effective density of reproductive individuals of 0.1-0.3 individuals/ha, and a second moment of parent-progeny dispersal distance of 130-800 m, compatible with the main models of fungal spore dispersal. These results contrast with those obtained for studies of A. ostoyae over larger spatial scales, suggesting that inferences about mean spore dispersal may be best performed at fine spatial scales (i.e. a few kilometres) for most fungal species. Copyright © 2017 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Using ancestry-informative markers to identify fine structure across 15 populations of European origin.

PubMed

Huckins, Laura M; Boraska, Vesna; Franklin, Christopher S; Floyd, James A B; Southam, Lorraine; Sullivan, Patrick F; Bulik, Cynthia M; Collier, David A; Tyler-Smith, Chris; Zeggini, Eleftheria; Tachmazidou, Ioanna

2014-10-01

The Wellcome Trust Case Control Consortium 3 anorexia nervosa genome-wide association scan includes 2907 cases from 15 different populations of European origin genotyped on the Illumina 670K chip. We compared methods for identifying population stratification, and suggest list of markers that may help to counter this problem. It is usual to identify population structure in such studies using only common variants with minor allele frequency (MAF) >5%; we find that this may result in highly informative SNPs being discarded, and suggest that instead all SNPs with MAF >1% may be used. We established informative axes of variation identified via principal component analysis and highlight important features of the genetic structure of diverse European-descent populations, some studied for the first time at this scale. Finally, we investigated the substructure within each of these 15 populations and identified SNPs that help capture hidden stratification. This work can provide information regarding the designing and interpretation of association results in the International Consortia.

Demonstrating the Uneven Importance of Fine-Scale Forest Structure on Snow Distributions using High Resolution Modeling

NASA Astrophysics Data System (ADS)

Broxton, P. D.; Harpold, A. A.; van Leeuwen, W.; Biederman, J. A.

2016-12-01

Quantifying the amount of snow in forested mountainous environments, as well as how it may change due to warming and forest disturbance, is critical given its importance for water supply and ecosystem health. Forest canopies affect snow accumulation and ablation in ways that are difficult to observe and model. Furthermore, fine-scale forest structure can accentuate or diminish the effects of forest-snow interactions. Despite decades of research demonstrating the importance of fine-scale forest structure (e.g. canopy edges and gaps) on snow, we still lack a comprehensive understanding of where and when forest structure has the largest impact on snowpack mass and energy budgets. Here, we use a hyper-resolution (1 meter spatial resolution) mass and energy balance snow model called the Snow Physics and Laser Mapping (SnowPALM) model along with LIDAR-derived forest structure to determine where spatial variability of fine-scale forest structure has the largest influence on large scale mass and energy budgets. SnowPALM was set up and calibrated at sites representing diverse climates in New Mexico, Arizona, and California. Then, we compared simulations at different model resolutions (i.e. 1, 10, and 100 m) to elucidate the effects of including versus not including information about fine scale canopy structure. These experiments were repeated for different prescribed topographies (i.e. flat, 30% slope north, and south-facing) at each site. Higher resolution simulations had more snow at lower canopy cover, with the opposite being true at high canopy cover. Furthermore, there is considerable scatter, indicating that different canopy arrangements can lead to different amounts of snow, even when the overall canopy coverage is the same. This modeling is contributing to the development of a high resolution machine learning algorithm called the Snow Water Artificial Network (SWANN) model to generate predictions of snow distributions over much larger domains, which has implications for improving land surface models that do not currently resolve or parameterize fine-scale canopy structure. In addition, these findings have implications for understanding the potential of different forest management strategies (i.e. thinning) based on local topography and climate to maximize the amount and retention of snow.

Pollen limitation and reduced reproductive success are associated with local genetic effects in Prunus virginiana, a widely distributed self-incompatible shrub.

PubMed

Suarez-Gonzalez, Adriana; Good, Sara V

2014-03-01

A vast quantity of empirical evidence suggests that insufficient quantity or quality of pollen may lead to a reduction in fruit set, in particular for self-incompatible species. This study uses an integrative approach that combines field research with marker gene analysis to understand the factors affecting reproductive success in a widely distributed self-incompatible species, Prunus virginiana (Rosaceae). Twelve patches of P. virginiana distributed within three populations that differed in degree of disturbance were examined. Two of the sites were small (7-35 km(2)) remnants of forest in an intensively used agricultural landscape, while the third was continuous (350 km(2)) and less disturbed. Field studies (natural and hand cross-pollinations) were combined with marker gene analyses (microsatellites and S-locus) in order to explore potential factors affecting pollen delivery and consequently reproductive success at landscape (between populations) and fine scales (within populations). Reductions in reproductive output were found in the two fragments compared with the continuous population, and suggest that pollen is an important factor limiting fruit production. Genetic analyses carried out in one of the fragments and in the continuous site suggest that even though S-allele diversity is high in both populations, the fragment exhibits an increase in biparental inbreeding and correlated paternity. The increase in biparental inbreeding in the fragment is potentially attributable to variation in the density of individuals and/or the spatial distribution of genotypes among populations, both of which could alter mating dynamics. By using a novel integrative approach, this study shows that even though P. virginiana is a widespread species, fragmented populations can experience significant reductions in fruit set and pollen limitation in the field. Deatiled examination of one fragmented population suggests that these linitations may be explained by an increase in biparental inbreeding, correlated paternity and fine-scale genetic structure. The consistency of the field and fine-scale genetic analyses, and the consistency of the results within patches and across years, suggest that these are important processes driving pollen limitation in the fragment.

Pollen limitation and reduced reproductive success are associated with local genetic effects in Prunus virginiana, a widely distributed self-incompatible shrub

PubMed Central

Suarez-Gonzalez, Adriana; Good, Sara V.

2014-01-01

Background and Aims A vast quantity of empirical evidence suggests that insufficient quantity or quality of pollen may lead to a reduction in fruit set, in particular for self-incompatible species. This study uses an integrative approach that combines field research with marker gene analysis to understand the factors affecting reproductive success in a widely distributed self-incompatible species, Prunus virginiana (Rosaceae). Methods Twelve patches of P. virginiana distributed within three populations that differed in degree of disturbance were examined. Two of the sites were small (7–35 km2) remnants of forest in an intensively used agricultural landscape, while the third was continuous (350 km2) and less disturbed. Field studies (natural and hand cross-pollinations) were combined with marker gene analyses (microsatellites and S-locus) in order to explore potential factors affecting pollen delivery and consequently reproductive success at landscape (between populations) and fine scales (within populations). Key Results Reductions in reproductive output were found in the two fragments compared with the continuous population, and suggest that pollen is an important factor limiting fruit production. Genetic analyses carried out in one of the fragments and in the continuous site suggest that even though S-allele diversity is high in both populations, the fragment exhibits an increase in biparental inbreeding and correlated paternity. The increase in biparental inbreeding in the fragment is potentially attributable to variation in the density of individuals and/or the spatial distribution of genotypes among populations, both of which could alter mating dynamics. Conclusions By using a novel integrative approach, this study shows that even though P. virginiana is a widespread species, fragmented populations can experience significant reductions in fruit set and pollen limitation in the field. Deatiled examination of one fragmented population suggests that these linitations may be explained by an increase in biparental inbreeding, correlated paternity and fine-scale genetic structure. The consistency of the field and fine-scale genetic analyses, and the consistency of the results within patches and across years, suggest that these are important processes driving pollen limitation in the fragment. PMID:24327534

Fine-scale thermal adaptation in a green turtle nesting population

PubMed Central

Weber, Sam B.; Broderick, Annette C.; Groothuis, Ton G. G.; Ellick, Jacqui; Godley, Brendan J.; Blount, Jonathan D.

2012-01-01

The effect of climate warming on the reproductive success of ectothermic animals is currently a subject of major conservation concern. However, for many threatened species, we still know surprisingly little about the extent of naturally occurring adaptive variation in heat-tolerance. Here, we show that the thermal tolerances of green turtle (Chelonia mydas) embryos in a single, island-breeding population have diverged in response to the contrasting incubation temperatures of nesting beaches just a few kilometres apart. In natural nests and in a common-garden rearing experiment, the offspring of females nesting on a naturally hot (black sand) beach survived better and grew larger at hot incubation temperatures compared with the offspring of females nesting on a cooler (pale sand) beach nearby. These differences were owing to shallower thermal reaction norms in the hot beach population, rather than shifts in thermal optima, and could not be explained by egg-mediated maternal effects. Our results suggest that marine turtle nesting behaviour can drive adaptive differentiation at remarkably fine spatial scales, and have important implications for how we define conservation units for protection. In particular, previous studies may have underestimated the extent of adaptive structuring in marine turtle populations that may significantly affect their capacity to respond to environmental change. PMID:21937495

Testing the effect of the Himalayan mountains as a physical barrier to gene flow in Hippophae tibetana Schlect. (Elaeagnaceae)

PubMed Central

Qiong, La; Zhang, Wenju; Wang, Hao; Zeng, Liyan; Birks, H. John B.; Zhong, Yang

2017-01-01

Hippophae tibetana is a small, dioecious wind-pollinated shrub endemic to the Tibetan-Qinghai Plateau. It is one of the shrubs that occur at very high elevations (5250 m a.s.l.). The Himalayan mountains provides a significant geographical barrier to the Qinghai-Tibetan Plateau, dividing the Himalayan area into two regions with Nepal to the south and Tibet to the north. There is no information on how the Himalayan mountains influence gene flow and population differentiation of alpine plants. In this study, we analyzed eight nuclear microsatellite markers and cpDNA trnT-trnF regions to test the role of the Himalayan mountains as a barrier to gene flow between populations of H. tibetana. We also examined the fine-scale genetic structure within a population of H. tibetana on the north slope of Mount (Mt.) Everest. For microsatellite analyses, a total of 241 individuals were sampled from seven populations in our study area (4 from Nepal, 3 from Tibet), including 121 individuals that were spatially mapped within a 100 m × 100 m plot. To test for seed flow, the cpDNA trnT-trnF regions of 100 individuals from 6 populations (4 from Nepal, 2 from Tibet) were also sequenced. Significant genetic differentiation was detected between the two regions by both microsatellite and cpDNA data analyses. These two datasets agree about southern and northern population differentiation, indicating that the Himalayan mountains represent a barrier to H. tibetana limiting gene flow between these two areas. At a fine scale, spatial autocorrelation analysis suggests significant genetic structure within a distance of less than 45 m, which may be attributed mainly to vegetative reproduction and habitat fragmentation, as well as limited gene flow. PMID:28489850

Testing the effect of the Himalayan mountains as a physical barrier to gene flow in Hippophae tibetana Schlect. (Elaeagnaceae).

PubMed

Qiong, La; Zhang, Wenju; Wang, Hao; Zeng, Liyan; Birks, H John B; Zhong, Yang

2017-01-01

Hippophae tibetana is a small, dioecious wind-pollinated shrub endemic to the Tibetan-Qinghai Plateau. It is one of the shrubs that occur at very high elevations (5250 m a.s.l.). The Himalayan mountains provides a significant geographical barrier to the Qinghai-Tibetan Plateau, dividing the Himalayan area into two regions with Nepal to the south and Tibet to the north. There is no information on how the Himalayan mountains influence gene flow and population differentiation of alpine plants. In this study, we analyzed eight nuclear microsatellite markers and cpDNA trnT-trnF regions to test the role of the Himalayan mountains as a barrier to gene flow between populations of H. tibetana. We also examined the fine-scale genetic structure within a population of H. tibetana on the north slope of Mount (Mt.) Everest. For microsatellite analyses, a total of 241 individuals were sampled from seven populations in our study area (4 from Nepal, 3 from Tibet), including 121 individuals that were spatially mapped within a 100 m × 100 m plot. To test for seed flow, the cpDNA trnT-trnF regions of 100 individuals from 6 populations (4 from Nepal, 2 from Tibet) were also sequenced. Significant genetic differentiation was detected between the two regions by both microsatellite and cpDNA data analyses. These two datasets agree about southern and northern population differentiation, indicating that the Himalayan mountains represent a barrier to H. tibetana limiting gene flow between these two areas. At a fine scale, spatial autocorrelation analysis suggests significant genetic structure within a distance of less than 45 m, which may be attributed mainly to vegetative reproduction and habitat fragmentation, as well as limited gene flow.

Patterns of genetic variability and habitat occupancy in Crepis triasii (Asteraceae) at different spatial scales: insights on evolutionary processes leading to diversification in continental islands

PubMed Central

Mayol, Maria; Palau, Carles; Rosselló, Josep A.; González-Martínez, Santiago C.; Molins, Arántzazu; Riba, Miquel

2012-01-01

Background and Aims Archipelagos are unique systems for studying evolutionary processes promoting diversification and speciation. The islands of the Mediterranean basin are major areas of plant richness, including a high proportion of narrow endemics. Many endemic plants are currently found in rocky habitats, showing varying patterns of habitat occupancy at different spatial scales throughout their range. The aim of the present study was to understand the impact of varying patterns of population distribution on genetic diversity and structure to shed light on demographic and evolutionary processes leading to population diversification in Crepis triasii, an endemic plant from the eastern Balearic Islands. Methods Using allozyme and chloroplast markers, we related patterns of genetic structure and diversity to those of habitat occupancy at a regional (between islands and among populations within islands) and landscape (population size and connectivity) scale. Key Results Genetic diversity was highly structured both at the regional and at the landscape level, and was positively correlated with population connectivity in the landscape. Populations located in small isolated mountains and coastal areas, with restricted patterns of regional occupancy, were genetically less diverse and much more differentiated. In addition, more isolated populations had stronger fine-scale genetic structure than well-connected ones. Changes in habitat availability and quality arising from marine transgressions during the Quaternary, as well as progressive fragmentation associated with the aridification of the climate since the last glaciation, are the most plausible factors leading to the observed patterns of genetic diversity and structure. Conclusions Our results emphasize the importance of gene flow in preventing genetic erosion and maintaining the evolutionary potential of populations. They also agree with recent studies highlighting the importance of restricted gene flow and genetic drift as drivers of plant evolution in Mediterranean continental islands. PMID:22167790

Fine Structure of Anomalously Intense Pulses of PSR J0814+7429 Radio Emission in the Decameter Range

NASA Astrophysics Data System (ADS)

Skoryk, A. O.; Ulyanov, O. M.; Zakharenko, V. V.; Shevtsova, A. I.; Vasylieva, I. Y.; Plakhov, M. S.; Kravtsov, I. M.

2017-06-01

Purpose: The fine structure of the anomalously intense pulses of PSR J0814+7429 (B0809+74) has been studied. The pulsar radio emission fine structure is investigated to determine its parameters in the lowest part of spectrum available for groundbased observations. Design/methodology/approach: The scattering measure in the interstellar plasma have been estimated using the spectral and correlation analyses of pulsar data recorded by the UTR-2 radio telescope. Results: Two characteristic time scales of the anomalously intense pulses fine structure of the PSR J0814+7429 radio emission have been found. The strongest pulses of this pulsar in the decameter range can have a duration of about t 2÷3 ms. These pulses are emitted in short series. In some cases, they are emitted over the low-intensity plateau consisting of the “long” subpulse component. Conclusions: The narrowest correlation scale of pulsar J0814+7429 radio emission corresponds to the doubled scattering time constant of the interstellar medium impulse response. Broader scale of the fine structure of its radio emission can be explained by the radiation of a short series of narrow pulses or relatively broad pulses inside this pulsar magnetosphere.

Landscape genetics of Schistocephalus solidus parasites in threespine stickleback (Gasterosteus aculeatus) from Alaska.

PubMed

Sprehn, C Grace; Blum, Michael J; Quinn, Thomas P; Heins, David C

2015-01-01

The nature of gene flow in parasites with complex life cycles is poorly understood, particularly when intermediate and definitive hosts have contrasting movement potential. We examined whether the fine-scale population genetic structure of the diphyllobothriidean cestode Schistocephalus solidus reflects the habits of intermediate threespine stickleback hosts or those of its definitive hosts, semi-aquatic piscivorous birds, to better understand complex host-parasite interactions. Seventeen lakes in the Cook Inlet region of south-central Alaska were sampled, including ten in the Matanuska-Susitna Valley, five on the Kenai Peninsula, and two in the Bristol Bay drainage. We analyzed sequence variation across a 759 bp region of the mitochondrial DNA (mtDNA) cytochrome oxidase I region for 1,026 S. solidus individuals sampled from 2009-2012. We also analyzed allelic variation at 8 microsatellite loci for 1,243 individuals. Analysis of mtDNA haplotype and microsatellite genotype variation recovered evidence of significant population genetic structure within S. solidus. Host, location, and year were factors in structuring observed genetic variation. Pairwise measures revealed significant differentiation among lakes, including a pattern of isolation-by-distance. Bayesian analysis identified three distinct genotypic clusters in the study region, little admixture within hosts and lakes, and a shift in genotype frequencies over time. Evidence of fine-scale population structure in S. solidus indicates that movement of its vagile, definitive avian hosts has less influence on gene flow than expected based solely on movement potential. Observed patterns of genetic variation may reflect genetic drift, behaviors of definitive hosts that constrain dispersal, life history of intermediate hosts, and adaptive specificity of S. solidus to intermediate host genotype.

Structural Variation Shapes the Landscape of Recombination in Mouse

PubMed Central

Morgan, Andrew P.; Gatti, Daniel M.; Najarian, Maya L.; Keane, Thomas M.; Galante, Raymond J.; Pack, Allan I.; Mott, Richard; Churchill, Gary A.; de Villena, Fernando Pardo-Manuel

2017-01-01

Meiotic recombination is an essential feature of sexual reproduction that ensures faithful segregation of chromosomes and redistributes genetic variants in populations. Multiparent populations such as the Diversity Outbred (DO) mouse stock accumulate large numbers of crossover (CO) events between founder haplotypes, and thus present a unique opportunity to study the role of genetic variation in shaping the recombination landscape. We obtained high-density genotype data from 6886 DO mice, and localized 2.2 million CO events to intervals with a median size of 28 kb. The resulting sex-averaged genetic map of the DO population is highly concordant with large-scale (order 10 Mb) features of previously reported genetic maps for mouse. To examine fine-scale (order 10 kb) patterns of recombination in the DO, we overlaid putative recombination hotspots onto our CO intervals. We found that CO intervals are enriched in hotspots compared to the genomic background. However, as many as 26% of CO intervals do not overlap any putative hotspots, suggesting that our understanding of hotspots is incomplete. We also identified coldspots encompassing 329 Mb, or 12% of observable genome, in which there is little or no recombination. In contrast to hotspots, which are a few kilobases in size, and widely scattered throughout the genome, coldspots have a median size of 2.1 Mb and are spatially clustered. Coldspots are strongly associated with copy-number variant (CNV) regions, especially multi-allelic clusters, identified from whole-genome sequencing of 228 DO mice. Genes in these regions have reduced expression, and epigenetic features of closed chromatin in male germ cells, which suggests that CNVs may repress recombination by altering chromatin structure in meiosis. Our findings demonstrate how multiparent populations, by bridging the gap between large-scale and fine-scale genetic mapping, can reveal new features of the recombination landscape. PMID:28592499

Structural Variation Shapes the Landscape of Recombination in Mouse.

PubMed

Morgan, Andrew P; Gatti, Daniel M; Najarian, Maya L; Keane, Thomas M; Galante, Raymond J; Pack, Allan I; Mott, Richard; Churchill, Gary A; de Villena, Fernando Pardo-Manuel

2017-06-01

Meiotic recombination is an essential feature of sexual reproduction that ensures faithful segregation of chromosomes and redistributes genetic variants in populations. Multiparent populations such as the Diversity Outbred (DO) mouse stock accumulate large numbers of crossover (CO) events between founder haplotypes, and thus present a unique opportunity to study the role of genetic variation in shaping the recombination landscape. We obtained high-density genotype data from [Formula: see text] DO mice, and localized 2.2 million CO events to intervals with a median size of 28 kb. The resulting sex-averaged genetic map of the DO population is highly concordant with large-scale (order 10 Mb) features of previously reported genetic maps for mouse. To examine fine-scale (order 10 kb) patterns of recombination in the DO, we overlaid putative recombination hotspots onto our CO intervals. We found that CO intervals are enriched in hotspots compared to the genomic background. However, as many as [Formula: see text] of CO intervals do not overlap any putative hotspots, suggesting that our understanding of hotspots is incomplete. We also identified coldspots encompassing 329 Mb, or [Formula: see text] of observable genome, in which there is little or no recombination. In contrast to hotspots, which are a few kilobases in size, and widely scattered throughout the genome, coldspots have a median size of 2.1 Mb and are spatially clustered. Coldspots are strongly associated with copy-number variant (CNV) regions, especially multi-allelic clusters, identified from whole-genome sequencing of 228 DO mice. Genes in these regions have reduced expression, and epigenetic features of closed chromatin in male germ cells, which suggests that CNVs may repress recombination by altering chromatin structure in meiosis. Our findings demonstrate how multiparent populations, by bridging the gap between large-scale and fine-scale genetic mapping, can reveal new features of the recombination landscape. Copyright © 2017 by the Genetics Society of America.

The walk is never random: subtle landscape effects shape gene flow in a continuous white-tailed deer population in the Midwestern United States

USGS Publications Warehouse

Robinson, Stacie J.; Samuel, Michael D.; Lopez, Davin L.; Shelton, Paul

2012-01-01

One of the pervasive challenges in landscape genetics is detecting gene flow patterns within continuous populations of highly mobile wildlife. Understanding population genetic structure within a continuous population can give insights into social structure, movement across the landscape and contact between populations, which influence ecological interactions, reproductive dynamics or pathogen transmission. We investigated the genetic structure of a large population of deer spanning the area of Wisconsin and Illinois, USA, affected by chronic wasting disease. We combined multiscale investigation, landscape genetic techniques and spatial statistical modelling to address the complex questions of landscape factors influencing population structure. We sampled over 2000 deer and used spatial autocorrelation and a spatial principal components analysis to describe the population genetic structure. We evaluated landscape effects on this pattern using a spatial autoregressive model within a model selection framework to test alternative hypotheses about gene flow. We found high levels of genetic connectivity, with gradients of variation across the large continuous population of white-tailed deer. At the fine scale, spatial clustering of related animals was correlated with the amount and arrangement of forested habitat. At the broader scale, impediments to dispersal were important to shaping genetic connectivity within the population. We found significant barrier effects of individual state and interstate highways and rivers. Our results offer an important understanding of deer biology and movement that will help inform the management of this species in an area where overabundance and disease spread are primary concerns.

Ancestry estimation and control of population stratification for sequence-based association studies.

PubMed

Wang, Chaolong; Zhan, Xiaowei; Bragg-Gresham, Jennifer; Kang, Hyun Min; Stambolian, Dwight; Chew, Emily Y; Branham, Kari E; Heckenlively, John; Fulton, Robert; Wilson, Richard K; Mardis, Elaine R; Lin, Xihong; Swaroop, Anand; Zöllner, Sebastian; Abecasis, Gonçalo R

2014-04-01

Estimating individual ancestry is important in genetic association studies where population structure leads to false positive signals, although assigning ancestry remains challenging with targeted sequence data. We propose a new method for the accurate estimation of individual genetic ancestry, based on direct analysis of off-target sequence reads, and implement our method in the publicly available LASER software. We validate the method using simulated and empirical data and show that the method can accurately infer worldwide continental ancestry when used with sequencing data sets with whole-genome shotgun coverage as low as 0.001×. For estimates of fine-scale ancestry within Europe, the method performs well with coverage of 0.1×. On an even finer scale, the method improves discrimination between exome-sequenced study participants originating from different provinces within Finland. Finally, we show that our method can be used to improve case-control matching in genetic association studies and to reduce the risk of spurious findings due to population structure.

Assessment of fine-scale resource selection and spatially explicit habitat suitability modelling for a re-introduced tiger (Panthera tigris) population in central India

PubMed Central

Sarkar, Mriganka Shekhar; Johnson, Jeyaraj A.; Sen, Subharanjan

2017-01-01

Background Large carnivores influence ecosystem functions at various scales. Thus, their local extinction is not only a species-specific conservation concern, but also reflects on the overall habitat quality and ecosystem value. Species-habitat relationships at fine scale reflect the individuals’ ability to procure resources and negotiate intraspecific competition. Such fine scale habitat choices are more pronounced in large carnivores such as tiger (Panthera tigris), which exhibits competitive exclusion in habitat and mate selection strategies. Although landscape level policies and conservation strategies are increasingly promoted for tiger conservation, specific management interventions require knowledge of the habitat correlates at fine scale. Methods We studied nine radio-collared individuals of a successfully reintroduced tiger population in Panna Tiger Reserve, central India, focussing on the species-habitat relationship at fine scales. With 16 eco-geographical variables, we performed Manly’s selection ratio and K-select analyses to define population-level and individual-level variation in resource selection, respectively. We analysed the data obtained during the exploratory period of six tigers and during the settled period of eight tigers separately, and compared the consequent results. We further used the settled period characteristics to model and map habitat suitability based on the Mahalanobis D2 method and the Boyce index. Results There was a clear difference in habitat selection by tigers between the exploratory and the settled period. During the exploratory period, tigers selected dense canopy and bamboo forests, but also spent time near villages and relocated village sites. However, settled tigers predominantly selected bamboo forests in complex terrain, riverine forests and teak-mixed forest, and totally avoided human settlements and agriculture areas. There were individual variations in habitat selection between exploratory and settled periods. Based on threshold limits of habitat selection by the Boyce Index, we established that 83% of core and 47% of buffer areas are now suitable habitats for tiger in this reserve. Discussion Tiger management often focuses on large-scale measures, but this study for the first time highlights the behaviour and fine-scale individual-specific habitat selection strategies. Such knowledge is vital for management of critical tiger habitats and specifically for the success of reintroduction programs. Our spatially explicit habitat suitability map provides a baseline for conservation planning and optimizing carrying capacity of the tiger population in this reserve. PMID:29114438

Assessment of fine-scale resource selection and spatially explicit habitat suitability modelling for a re-introduced tiger (Panthera tigris) population in central India.

PubMed

Sarkar, Mriganka Shekhar; Krishnamurthy, Ramesh; Johnson, Jeyaraj A; Sen, Subharanjan; Saha, Goutam Kumar

2017-01-01

Large carnivores influence ecosystem functions at various scales. Thus, their local extinction is not only a species-specific conservation concern, but also reflects on the overall habitat quality and ecosystem value. Species-habitat relationships at fine scale reflect the individuals' ability to procure resources and negotiate intraspecific competition. Such fine scale habitat choices are more pronounced in large carnivores such as tiger ( Panthera tigris ), which exhibits competitive exclusion in habitat and mate selection strategies. Although landscape level policies and conservation strategies are increasingly promoted for tiger conservation, specific management interventions require knowledge of the habitat correlates at fine scale. We studied nine radio-collared individuals of a successfully reintroduced tiger population in Panna Tiger Reserve, central India, focussing on the species-habitat relationship at fine scales. With 16 eco-geographical variables, we performed Manly's selection ratio and K-select analyses to define population-level and individual-level variation in resource selection, respectively. We analysed the data obtained during the exploratory period of six tigers and during the settled period of eight tigers separately, and compared the consequent results. We further used the settled period characteristics to model and map habitat suitability based on the Mahalanobis D 2 method and the Boyce index. There was a clear difference in habitat selection by tigers between the exploratory and the settled period. During the exploratory period, tigers selected dense canopy and bamboo forests, but also spent time near villages and relocated village sites. However, settled tigers predominantly selected bamboo forests in complex terrain, riverine forests and teak-mixed forest, and totally avoided human settlements and agriculture areas. There were individual variations in habitat selection between exploratory and settled periods. Based on threshold limits of habitat selection by the Boyce Index, we established that 83% of core and 47% of buffer areas are now suitable habitats for tiger in this reserve. Tiger management often focuses on large-scale measures, but this study for the first time highlights the behaviour and fine-scale individual-specific habitat selection strategies. Such knowledge is vital for management of critical tiger habitats and specifically for the success of reintroduction programs. Our spatially explicit habitat suitability map provides a baseline for conservation planning and optimizing carrying capacity of the tiger population in this reserve.

Fine-scale spatial genetic dynamics over the life cycle of the tropical tree Prunus africana.

PubMed

Berens, D G; Braun, C; González-Martínez, S C; Griebeler, E M; Nathan, R; Böhning-Gaese, K

2014-11-01

Studying fine-scale spatial genetic patterns across life stages is a powerful approach to identify ecological processes acting within tree populations. We investigated spatial genetic dynamics across five life stages in the insect-pollinated and vertebrate-dispersed tropical tree Prunus africana in Kakamega Forest, Kenya. Using six highly polymorphic microsatellite loci, we assessed genetic diversity and spatial genetic structure (SGS) from seed rain and seedlings, and different sapling stages to adult trees. We found significant SGS in all stages, potentially caused by limited seed dispersal and high recruitment rates in areas with high light availability. SGS decreased from seed and early seedling stages to older juvenile stages. Interestingly, SGS was stronger in adults than in late juveniles. The initial decrease in SGS was probably driven by both random and non-random thinning of offspring clusters during recruitment. Intergenerational variation in SGS could have been driven by variation in gene flow processes, overlapping generations in the adult stage or local selection. Our study shows that complex sequential processes during recruitment contribute to SGS of tree populations.

Dispersal and population structure at different spatial scales in the subterranean rodent Ctenomys australis

PubMed Central

2010-01-01

Background The population genetic structure of subterranean rodent species is strongly affected by demographic (e.g. rates of dispersal and social structure) and stochastic factors (e.g. random genetic drift among subpopulations and habitat fragmentation). In particular, gene flow estimates at different spatial scales are essential to understand genetic differentiation among populations of a species living in a highly fragmented landscape. Ctenomys australis (the sand dune tuco-tuco) is a territorial subterranean rodent that inhabits a relatively secure, permanently sealed burrow system, occurring in sand dune habitats on the coastal landscape in the south-east of Buenos Aires province, Argentina. Currently, this habitat is threatened by urban development and forestry and, therefore, the survival of this endemic species is at risk. Here, we assess population genetic structure and patterns of dispersal among individuals of this species at different spatial scales using 8 polymorphic microsatellite loci. Furthermore, we evaluate the relative importance of sex and habitat configuration in modulating the dispersal patterns at these geographical scales. Results Our results show that dispersal in C. australis is not restricted at regional spatial scales (~ 4 km). Assignment tests revealed significant population substructure within the study area, providing support for the presence of two subpopulations from three original sampling sites. Finally, male-biased dispersal was found in the Western side of our study area, but in the Eastern side no apparent philopatric pattern was found, suggesting that in a more continuous habitat males might move longer distances than females. Conclusions Overall, the assignment-based approaches were able to detect population substructure at fine geographical scales. Additionally, the maintenance of a significant genetic structure at regional (~ 4 km) and small (less than 1 km) spatial scales despite apparently moderate to high levels of gene flow between local sampling sites could not be explained simply by the linear distance among them. On the whole, our results support the hypothesis that males disperse more frequently than females; however they do not provide support for strict philopatry within females. PMID:20109219

Regulation of the demographic structure in isomorphic biphasic life cycles at the spatial fine scale.

PubMed

Vieira, Vasco Manuel Nobre de Carvalho da Silva; Mateus, Marcos Duarte

2014-01-01

Isomorphic biphasic algal life cycles often occur in the environment at ploidy abundance ratios (Haploid:Diploid) different from 1. Its spatial variability occurs within populations related to intertidal height and hydrodynamic stress, possibly reflecting the niche partitioning driven by their diverging adaptation to the environment argued necessary for their prevalence (evolutionary stability). Demographic models based in matrix algebra were developed to investigate which vital rates may efficiently generate an H:D variability at a fine spatial resolution. It was also taken into account time variation and type of life strategy. Ploidy dissimilarities in fecundity rates set an H:D spatial structure miss-fitting the ploidy fitness ratio. The same happened with ploidy dissimilarities in ramet growth whenever reproductive output dominated the population demography. Only through ploidy dissimilarities in looping rates (stasis, breakage and clonal growth) did the life cycle respond to a spatially heterogeneous environment efficiently creating a niche partition. Marginal locations were more sensitive than central locations. Related results have been obtained experimentally and numerically for widely different life cycles from the plant and animal kingdoms. Spore dispersal smoothed the effects of ploidy dissimilarities in fertility and enhanced the effects of ploidy dissimilarities looping rates. Ploidy dissimilarities in spore dispersal could also create the necessary niche partition, both over the space and time dimensions, even in spatial homogeneous environments and without the need for conditional differentiation of the ramets. Fine scale spatial variability may be the key for the prevalence of isomorphic biphasic life cycles, which has been neglected so far.

Regulation of the Demographic Structure in Isomorphic Biphasic Life Cycles at the Spatial Fine Scale

PubMed Central

Vieira, Vasco Manuel Nobre de Carvalho da Silva; Mateus, Marcos Duarte

2014-01-01

Isomorphic biphasic algal life cycles often occur in the environment at ploidy abundance ratios (Haploid:Diploid) different from 1. Its spatial variability occurs within populations related to intertidal height and hydrodynamic stress, possibly reflecting the niche partitioning driven by their diverging adaptation to the environment argued necessary for their prevalence (evolutionary stability). Demographic models based in matrix algebra were developed to investigate which vital rates may efficiently generate an H:D variability at a fine spatial resolution. It was also taken into account time variation and type of life strategy. Ploidy dissimilarities in fecundity rates set an H:D spatial structure miss-fitting the ploidy fitness ratio. The same happened with ploidy dissimilarities in ramet growth whenever reproductive output dominated the population demography. Only through ploidy dissimilarities in looping rates (stasis, breakage and clonal growth) did the life cycle respond to a spatially heterogeneous environment efficiently creating a niche partition. Marginal locations were more sensitive than central locations. Related results have been obtained experimentally and numerically for widely different life cycles from the plant and animal kingdoms. Spore dispersal smoothed the effects of ploidy dissimilarities in fertility and enhanced the effects of ploidy dissimilarities looping rates. Ploidy dissimilarities in spore dispersal could also create the necessary niche partition, both over the space and time dimensions, even in spatial homogeneous environments and without the need for conditional differentiation of the ramets. Fine scale spatial variability may be the key for the prevalence of isomorphic biphasic life cycles, which has been neglected so far. PMID:24658603

Application of Inter-Simple Sequence Repeat Markers in the Analysis of Populations of the Chagas Disease Vector Triatoma infestans (Hemiptera, Reduviidae)

PubMed Central

Pérez de Rosas, Alicia R.; Restelli, María F.; Fernández, Cintia J.; Blariza, María J.; García, Beatriz A.

2017-01-01

Here we apply inter-simple sequence repeat (ISSR) markers to explore the fine-scale genetic structure and dispersal in populations of Triatoma infestans. Five selected primers from 30 primers were used to amplify ISSRs by polymerase chain reaction. A total of 90 polymorphic bands were detected across 134 individuals captured from 11 peridomestic sites from the locality of San Martín (Capayán Department, Catamarca Province, Argentina). Significant levels of genetic differentiation suggest limited gene flow among sampling sites. Spatial autocorrelation analysis confirms that dispersal occurs on the scale of ∼469 m, suggesting that insecticide spraying should be extended at least within a radius of ∼500 m around the infested area. Moreover, Bayesian clustering algorithms indicated genetic exchange among different sites analyzed, supporting the hypothesis of an important role of peridomestic structures in the process of reinfestation. PMID:28115670

Clonal growth and fine-scale genetic structure in tanoak (Notholithocarpus densiflorus: Fagaceae)

Treesearch

Richard S. Dodd; Wasima Mayer; Alejandro Nettel; Zara Afzal-Rafii

2013-01-01

The combination of sprouting and reproduction by seed can have important consequences on fine-scale spatial distribution of genetic structure (SGS). SGS is an important consideration for species’ restoration because it determines the minimum distance among seed trees to maximize genetic diversity while not prejudicing locally adapted genotypes. Local environmental...

Fine-scale population dynamics in a marine fish species inferred from dynamic state-space models.

PubMed

Rogers, Lauren A; Storvik, Geir O; Knutsen, Halvor; Olsen, Esben M; Stenseth, Nils C

2017-07-01

Identifying the spatial scale of population structuring is critical for the conservation of natural populations and for drawing accurate ecological inferences. However, population studies often use spatially aggregated data to draw inferences about population trends and drivers, potentially masking ecologically relevant population sub-structure and dynamics. The goals of this study were to investigate how population dynamics models with and without spatial structure affect inferences on population trends and the identification of intrinsic drivers of population dynamics (e.g. density dependence). Specifically, we developed dynamic, age-structured, state-space models to test different hypotheses regarding the spatial structure of a population complex of coastal Atlantic cod (Gadus morhua). Data were from a 93-year survey of juvenile (age 0 and 1) cod sampled along >200 km of the Norwegian Skagerrak coast. We compared two models: one which assumes all sampled cod belong to one larger population, and a second which assumes that each fjord contains a unique population with locally determined dynamics. Using the best supported model, we then reconstructed the historical spatial and temporal dynamics of Skagerrak coastal cod. Cross-validation showed that the spatially structured model with local dynamics had better predictive ability. Furthermore, posterior predictive checks showed that a model which assumes one homogeneous population failed to capture the spatial correlation pattern present in the survey data. The spatially structured model indicated that population trends differed markedly among fjords, as did estimates of population parameters including density-dependent survival. Recent biomass was estimated to be at a near-record low all along the coast, but the finer scale model indicated that the decline occurred at different times in different regions. Warm temperatures were associated with poor recruitment, but local changes in habitat and fishing pressure may have played a role in driving local dynamics. More generally, we demonstrated how state-space models can be used to test evidence for population spatial structure based on survey time-series data. Our study shows the importance of considering spatially structured dynamics, as the inferences from such an approach can lead to a different ecological understanding of the drivers of population declines, and fundamentally different management actions to restore populations. © 2017 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.

Sex-specific morphological and physiological differences in the moss Ceratodon purpureus (Dicranales).

PubMed

Slate, Mandy L; Rosenstiel, Todd N; Eppley, Sarah M

2017-11-10

Dioecy and sexual dimorphism occur in many terrestrial plant species but are especially widespread among the bryophytes. Despite the prevalence of dioecy in non-vascular plants, surprisingly little is known about how fine-scale sex-specific cell and leaf morphological traits are correlated with sex-specific physiology and population sex ratios. Such data are critical to understanding the inter-relationship between sex-specific morphological and physiological characters and how their relationship influences population structure. In this study, these data types were assessed to determine how they vary across three populations within one moss species and whether fine-scale morphological traits scale up to physiological and sex ratio characteristics. Twenty cell-, leaf- and canopy-level traits and two photochemical measurements were compared between sexes and populations of the dioecious moss Ceratodon purpureus . Field population-expressed sex ratios were obtained for the same populations. Male and female plants differed in cell, leaf and photochemical measures. These sexual dimorphisms were female biased, with females having larger and thicker leaves and greater values for chlorophyll fluorescence-based, leaf photochemistry measurements than males. Female traits were also more variable than male traits. Interestingly, field population sex ratios were significantly male biased in two study populations and female biased in the third study population. The results demonstrate that the larger morphology and the greater physiological output of female C. purpureus gametophytes compared with males occurs across populations and is likely to have significant effects on resource allocation and biotic interactions. However, this high level of dimorphism does not explain population sex ratio variation in the three study populations tested. This research lays the groundwork for future studies on how differential sex-specific variation in cell and leaf traits influences bryophyte plant fitness. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Ultra-Fine Scale Spatially-Integrated Mapping of Habitat and Occupancy Using Structure-From-Motion.

PubMed

McDowall, Philip; Lynch, Heather J

2017-01-01

Organisms respond to and often simultaneously modify their environment. While these interactions are apparent at the landscape extent, the driving mechanisms often occur at very fine spatial scales. Structure-from-Motion (SfM), a computer vision technique, allows the simultaneous mapping of organisms and fine scale habitat, and will greatly improve our understanding of habitat suitability, ecophysiology, and the bi-directional relationship between geomorphology and habitat use. SfM can be used to create high-resolution (centimeter-scale) three-dimensional (3D) habitat models at low cost. These models can capture the abiotic conditions formed by terrain and simultaneously record the position of individual organisms within that terrain. While coloniality is common in seabird species, we have a poor understanding of the extent to which dense breeding aggregations are driven by fine-scale active aggregation or limited suitable habitat. We demonstrate the use of SfM for fine-scale habitat suitability by reconstructing the locations of nests in a gentoo penguin colony and fitting models that explicitly account for conspecific attraction. The resulting digital elevation models (DEMs) are used as covariates in an inhomogeneous hybrid point process model. We find that gentoo penguin nest site selection is a function of the topography of the landscape, but that nests are far more aggregated than would be expected based on terrain alone, suggesting a strong role of behavioral aggregation in driving coloniality in this species. This integrated mapping of organisms and fine scale habitat will greatly improve our understanding of fine-scale habitat suitability, ecophysiology, and the complex bi-directional relationship between geomorphology and habitat use.

Fine-scale population genetic structure of arctic foxes (Vulpes lagopus) in the High Arctic.

PubMed

Lai, Sandra; Quiles, Adrien; Lambourdière, Josie; Berteaux, Dominique; Lalis, Aude

2017-12-01

The arctic fox (Vulpes lagopus) is a circumpolar species inhabiting all accessible Arctic tundra habitats. The species forms a panmictic population over areas connected by sea ice, but recently, kin clustering and population differentiation were detected even in regions where sea ice was present. The purpose of this study was to examine the genetic structure of a population in the High Arctic using a robust panel of highly polymorphic microsatellites. We analyzed the genotypes of 210 individuals from Bylot Island, Nunavut, Canada, using 15 microsatellite loci. No pattern of isolation-by-distance was detected, but a spatial principal component analysis (sPCA) revealed the presence of genetic subdivisions. Overall, the sPCA revealed two spatially distinct genetic clusters corresponding to the northern and southern parts of the study area, plus another subdivision within each of these two clusters. The north-south genetic differentiation partly matched the distribution of a snow goose colony, which could reflect a preference for settling into familiar ecological environments. Secondary clusters may result from higher-order social structures (neighbourhoods) that use landscape features to delimit their borders. The cryptic genetic subdivisions found in our population may highlight ecological processes deserving further investigations in arctic foxes at larger, regional spatial scales.

Fine-scale population structure in Atlantic salmon from Maine's Penobscot River drainage

USGS Publications Warehouse

Spidle, A.P.; Bane, Schill W.; Lubinski, B.A.; King, T.L.

2001-01-01

We report a survey of micro satellite DNA variation in Atlantic salmon from the unimpounded lower reaches of Maine's Penobscot River. Our analysis indicates that Atlantic salmon in the Penobscot River are distinct from other populations that have little or no history of human-mediated repopulation, including two of its tributaries, Cove Brook and Kenduskeag Stream, another Maine river, the Ducktrap, and Canada's Miramichi and Gander rivers. Significant heterogeneity was detected in allele frequency among all three subpopulations sampled in the Penobscot drainage. The high resolution of the 12-locus suite was quantified using maximum likelihood assignment tests, which correctly identified the source of 90.4-96.1% of individuals from within the Penobscot drainage. Current populations are clearly isolated from each other, however we are unable to determine from the present data whether the populations in Cove Brook and Kenduskeag Stream are recently diverged from populations stocked into the Penobscot River over the last century, or are aboriginal in origin. The degree of population structure identified in the Penobscot drainage is noteworthy in light of its lengthy history of systematic restocking, the geographic proximity of the subpopulations, and the extent of the differentiation. Similar population structure on this extremely limited geographic scale could exist among Atlantic salmon runs elsewhere in Maine and throughout the species' range and should be taken into account for future management decisions.

Fire structures pine serotiny at different scales.

PubMed

Hernández-Serrano, Ana; Verdú, Miguel; González-Martínez, Santiago C; Pausas, Juli G

2013-12-01

Serotiny (delayed seed release with the consequent accumulation of a canopy seedbank) confers fitness benefits in environments with crown-fire regimes. Thus, we predicted that serotiny level should be higher in populations recurrently subjected to crown-fires than in populations where crown-fires are rare. In addition, under a high frequency of fires, space and resources are recurrently available, permitting recruitment around each mother to follow the seed rain shadow. Thus, we also predicted spatial aggregation of serotiny within populations. We compared serotiny, considering both the proportion and the age of serotinous cones, in populations living in contrasting fire regimes for two iconic Mediterranean pine species (Pinus halepensis, P. pinaster). We framed our results by quantitatively comparing the strength of the fire-serotiny relationship with previous studies worldwide. For the two species, populations living under high crown-fire recurrence regimes had a higher serotiny level than those populations where the recurrence of crown-fires was low. For P. halepensis (the species with higher serotiny), populations in high fire recurrence regimes had higher fine-scale spatial aggregation of serotiny than those inhabiting low fire recurrence systems. The strength of the observed fire-serotiny relationship in P. halepensis is among the highest in published literature. Fire regime shapes serotiny level among populations, and in populations with high serotiny, recurrent fires maintain a significant spatial structure for this trait. Consequently, fire has long-term evolutionary implications at different scales, emphasizing its prominent role in shaping the ecology of pines.

A regional-scale, high resolution dynamical malaria model that accounts for population density, climate and surface hydrology.

PubMed

Tompkins, Adrian M; Ermert, Volker

2013-02-18

The relative roles of climate variability and population related effects in malaria transmission could be better understood if regional-scale dynamical malaria models could account for these factors. A new dynamical community malaria model is introduced that accounts for the temperature and rainfall influences on the parasite and vector life cycles which are finely resolved in order to correctly represent the delay between the rains and the malaria season. The rainfall drives a simple but physically based representation of the surface hydrology. The model accounts for the population density in the calculation of daily biting rates. Model simulations of entomological inoculation rate and circumsporozoite protein rate compare well to data from field studies from a wide range of locations in West Africa that encompass both seasonal endemic and epidemic fringe areas. A focus on Bobo-Dioulasso shows the ability of the model to represent the differences in transmission rates between rural and peri-urban areas in addition to the seasonality of malaria. Fine spatial resolution regional integrations for Eastern Africa reproduce the malaria atlas project (MAP) spatial distribution of the parasite ratio, and integrations for West and Eastern Africa show that the model grossly reproduces the reduction in parasite ratio as a function of population density observed in a large number of field surveys, although it underestimates malaria prevalence at high densities probably due to the neglect of population migration. A new dynamical community malaria model is publicly available that accounts for climate and population density to simulate malaria transmission on a regional scale. The model structure facilitates future development to incorporate migration, immunity and interventions.

A regional-scale, high resolution dynamical malaria model that accounts for population density, climate and surface hydrology

PubMed Central

2013-01-01

Background The relative roles of climate variability and population related effects in malaria transmission could be better understood if regional-scale dynamical malaria models could account for these factors. Methods A new dynamical community malaria model is introduced that accounts for the temperature and rainfall influences on the parasite and vector life cycles which are finely resolved in order to correctly represent the delay between the rains and the malaria season. The rainfall drives a simple but physically based representation of the surface hydrology. The model accounts for the population density in the calculation of daily biting rates. Results Model simulations of entomological inoculation rate and circumsporozoite protein rate compare well to data from field studies from a wide range of locations in West Africa that encompass both seasonal endemic and epidemic fringe areas. A focus on Bobo-Dioulasso shows the ability of the model to represent the differences in transmission rates between rural and peri-urban areas in addition to the seasonality of malaria. Fine spatial resolution regional integrations for Eastern Africa reproduce the malaria atlas project (MAP) spatial distribution of the parasite ratio, and integrations for West and Eastern Africa show that the model grossly reproduces the reduction in parasite ratio as a function of population density observed in a large number of field surveys, although it underestimates malaria prevalence at high densities probably due to the neglect of population migration. Conclusions A new dynamical community malaria model is publicly available that accounts for climate and population density to simulate malaria transmission on a regional scale. The model structure facilitates future development to incorporate migration, immunity and interventions. PMID:23419192

Sea surface currents and geographic isolation shape the genetic population structure of a coral reef fish in the Indian Ocean.

PubMed

Huyghe, Filip; Kochzius, Marc

2018-01-01

In this contribution, we determine the genetic population structure in the Skunk Clownfish (Amphiprion akallopsisos) across the Indian Ocean, and on a smaller geographic scale in the Western Indian Ocean (WIO). Highly restricted gene flow was discovered between populations on either side of the Indian Ocean using the control region as a mitochondrial marker (mtDNA). We verify this conclusion using 13 microsatellite markers and infer fine scale genetic structuring within the WIO. In total 387 samples from 21 sites were analysed using mtDNA and 13 microsatellite loci. Analysis included estimation of genetic diversity and population differentiation. A haplotype network was inferred using mtDNA. Nuclear markers were used in Bayesian clustering and a principal component analysis. Both markers confirmed strong genetic differentiation between WIO and Eastern Indian Ocean (EIO) populations, and a shallower population structure among Malagasy and East African mainland populations. Limited gene flow across the Mozambique Channel may be explained by its complex oceanography, which could cause local retention of larvae, limiting dispersal between Madagascar and the East African coast. Two other potential current-mediated barriers to larval dispersal suggested in the WIO, the split of the SEC at approximately 10° S and the convergence of the Somali Current with the East African Coast Current at approximately 3° S, were not found to form a barrier to gene flow in this species.

Sea surface currents and geographic isolation shape the genetic population structure of a coral reef fish in the Indian Ocean

PubMed Central

Kochzius, Marc

2018-01-01

In this contribution, we determine the genetic population structure in the Skunk Clownfish (Amphiprion akallopsisos) across the Indian Ocean, and on a smaller geographic scale in the Western Indian Ocean (WIO). Highly restricted gene flow was discovered between populations on either side of the Indian Ocean using the control region as a mitochondrial marker (mtDNA). We verify this conclusion using 13 microsatellite markers and infer fine scale genetic structuring within the WIO. In total 387 samples from 21 sites were analysed using mtDNA and 13 microsatellite loci. Analysis included estimation of genetic diversity and population differentiation. A haplotype network was inferred using mtDNA. Nuclear markers were used in Bayesian clustering and a principal component analysis. Both markers confirmed strong genetic differentiation between WIO and Eastern Indian Ocean (EIO) populations, and a shallower population structure among Malagasy and East African mainland populations. Limited gene flow across the Mozambique Channel may be explained by its complex oceanography, which could cause local retention of larvae, limiting dispersal between Madagascar and the East African coast. Two other potential current-mediated barriers to larval dispersal suggested in the WIO, the split of the SEC at approximately 10° S and the convergence of the Somali Current with the East African Coast Current at approximately 3° S, were not found to form a barrier to gene flow in this species. PMID:29522547

Effects of population succession on demographic and genetic processes: predictions and tests in the daylily Hemerocallis thunbergii (Liliaceae).

PubMed

Chung, Mi Yoon; Nason, John D; Chung, Myong Gi

2007-07-01

Spatial genetic structure within plant populations is influenced by variation in demographic processes through space and time, including a population's successional status. To determine how demographic structure and fine-scale genetic structure (FSGS) change with stages in a population's successional history, we studied Hemerocallis thunbergii (Liliaceae), a nocturnal flowering and hawkmoth-pollinated herbaceous perennial with rapid population turnover dynamics. We examined nine populations assigned to three successive stages of population succession: expansion, maturation, and senescence. We developed stage-specific expectations for within-population demographic and genetic structure, and then for each population quantified the spatial aggregation of individuals and genotypes using spatial autocorrelation methods (nonaccumulative O-ring and kinship statistics, respectively), and at the landscape level measured inbreeding and genetic structure using Wright's F-statistics. Analyses using the O-ring statistic revealed significant aggregation of individuals at short spatial scales in expanding and senescing populations, in particular, which may reflect restricted seed dispersal around maternal individuals combined with relatively low local population densities at these stages. Significant FSGS was found for three of four expanding, no mature, and only one senescing population, a pattern generally consistent with expectations of successional processes. Although allozyme genetic diversity was high within populations (mean %P = 78.9 and H(E) = 0.281), landscape-level differentiation among sites was also high (F(ST) = 0.166) and all populations exhibited a significant deficit of heterozygotes relative to Hardy-Weinberg expectations (range F = 0.201-0.424, mean F(IS) = 0.321). Within populations, F was not correlated with the degree of FSGS, thus suggesting inbreeding due primarily to selfing as opposed to mating among close relatives in spatially structured populations. Our results demonstrate considerable variation in the spatial distribution of individuals and patterns and magnitude of FSGS in H. thunbergii populations across the landscape. This variation is generally consistent with succession-stage-specific differences in ecological processes operating within these populations.

Multiscale 3-D shape representation and segmentation using spherical wavelets.

PubMed

Nain, Delphine; Haker, Steven; Bobick, Aaron; Tannenbaum, Allen

2007-04-01

This paper presents a novel multiscale shape representation and segmentation algorithm based on the spherical wavelet transform. This work is motivated by the need to compactly and accurately encode variations at multiple scales in the shape representation in order to drive the segmentation and shape analysis of deep brain structures, such as the caudate nucleus or the hippocampus. Our proposed shape representation can be optimized to compactly encode shape variations in a population at the needed scale and spatial locations, enabling the construction of more descriptive, nonglobal, nonuniform shape probability priors to be included in the segmentation and shape analysis framework. In particular, this representation addresses the shortcomings of techniques that learn a global shape prior at a single scale of analysis and cannot represent fine, local variations in a population of shapes in the presence of a limited dataset. Specifically, our technique defines a multiscale parametric model of surfaces belonging to the same population using a compact set of spherical wavelets targeted to that population. We further refine the shape representation by separating into groups wavelet coefficients that describe independent global and/or local biological variations in the population, using spectral graph partitioning. We then learn a prior probability distribution induced over each group to explicitly encode these variations at different scales and spatial locations. Based on this representation, we derive a parametric active surface evolution using the multiscale prior coefficients as parameters for our optimization procedure to naturally include the prior for segmentation. Additionally, the optimization method can be applied in a coarse-to-fine manner. We apply our algorithm to two different brain structures, the caudate nucleus and the hippocampus, of interest in the study of schizophrenia. We show: 1) a reconstruction task of a test set to validate the expressiveness of our multiscale prior and 2) a segmentation task. In the reconstruction task, our results show that for a given training set size, our algorithm significantly improves the approximation of shapes in a testing set over the Point Distribution Model, which tends to oversmooth data. In the segmentation task, our validation shows our algorithm is computationally efficient and outperforms the Active Shape Model algorithm, by capturing finer shape details.

Multiscale 3-D Shape Representation and Segmentation Using Spherical Wavelets

PubMed Central

Nain, Delphine; Haker, Steven; Bobick, Aaron

2013-01-01

This paper presents a novel multiscale shape representation and segmentation algorithm based on the spherical wavelet transform. This work is motivated by the need to compactly and accurately encode variations at multiple scales in the shape representation in order to drive the segmentation and shape analysis of deep brain structures, such as the caudate nucleus or the hippocampus. Our proposed shape representation can be optimized to compactly encode shape variations in a population at the needed scale and spatial locations, enabling the construction of more descriptive, nonglobal, nonuniform shape probability priors to be included in the segmentation and shape analysis framework. In particular, this representation addresses the shortcomings of techniques that learn a global shape prior at a single scale of analysis and cannot represent fine, local variations in a population of shapes in the presence of a limited dataset. Specifically, our technique defines a multiscale parametric model of surfaces belonging to the same population using a compact set of spherical wavelets targeted to that population. We further refine the shape representation by separating into groups wavelet coefficients that describe independent global and/or local biological variations in the population, using spectral graph partitioning. We then learn a prior probability distribution induced over each group to explicitly encode these variations at different scales and spatial locations. Based on this representation, we derive a parametric active surface evolution using the multiscale prior coefficients as parameters for our optimization procedure to naturally include the prior for segmentation. Additionally, the optimization method can be applied in a coarse-to-fine manner. We apply our algorithm to two different brain structures, the caudate nucleus and the hippocampus, of interest in the study of schizophrenia. We show: 1) a reconstruction task of a test set to validate the expressiveness of our multiscale prior and 2) a segmentation task. In the reconstruction task, our results show that for a given training set size, our algorithm significantly improves the approximation of shapes in a testing set over the Point Distribution Model, which tends to oversmooth data. In the segmentation task, our validation shows our algorithm is computationally efficient and outperforms the Active Shape Model algorithm, by capturing finer shape details. PMID:17427745

Strong population structure in the marine sponge Crambe crambe (Poecilosclerida) as revealed by microsatellite markers.

PubMed

Duran, S; Pascual, M; Estoup, A; Turon, X

2004-03-01

Different categories of molecular markers have been used so far to study the population structure of sponges. However, these markers often did not have the resolution power to address precisely questions on structuring processes, especially at the intrapopulational level. In this study we show that microsatellites fulfil these expectations, allowing a fine description of population structure at different geographical scales in the marine sponge Crambe crambe. Specimens were collected in 11 locations, representing most of the Atlanto-Mediterranean range of the species, and were analysed at six loci. As expected for a sessile invertebrate with lecitotrophic larvae, high levels of between-population structure were found (FST = 0.18) and a significant isolation-by-distance pattern was observed. A strong genetic structure was also found within sampled sites (FIS = 0.21) that may be explained by several factors including inbreeding, selfing and the Wahlund effect. In spite of a sampling design planned to avoid the sampling of clones, genotypically identical individuals for the six loci were found in some locations. The significance of these potential clones is discussed and their effect on the observed pattern of population structure assessed. Patterns of allelic distribution within populations suggest the possibility of a recent colonization of the Atlantic range from the Mediterranean Sea.

Variations in Grain-Scale Sediment Structure in a Gravel-Bed Channel as a Function of Fine Sediment Content and Morphological Location

NASA Astrophysics Data System (ADS)

Voepel, H.; Ahmed, S. I.; Hodge, R. A.; Leyland, J.; Sear, D. A.

2016-12-01

One of the major causes of uncertainty in estimates of bedload transport rates in gravel bed rivers is a lack of understanding of grain-scale sediment structure, and the impact that this structure has on bed stability. Furthermore, grain-scale structure varies throughout a channel and over time in ways that have not been fully quantified. Our research aims to quantify variations in sediment structure caused by two key variables; morphological location within a riffle-pool sequence (reflecting variation in hydraulic conditions), and the fine sediment content of the gravel bed (sand and clay). We report results from a series of flume experiments in which we water-worked a gravel bed with a riffle-pool morphology. The fine sediment content of the bed was incrementally increased over a series of runs from gravel only, to coarse sand, fine sand and two concentrations of clay. After each experimental run intact samples of the bed at different locations were extracted and the internal structure of the bed was measured using non-destructive, micro-focus X-ray computed tomography (CT) imaging. The CT images were processed to measure the properties of individual grains, including volume, center of mass, dimension, and contact points. From these data we were able to quantify the sediment structure through metrics including measurement of grain pivot angles, grain exposure and protrusion, and vertical variation in bed porosity and fine sediment content. Metrics derived from the CT data were verified using data from grain counts and tilt-table measurements on co-located samples. Comparison of the metrics across different morphological locations and fine sediment content demonstrates how these factors affect the bed structure. These results have implications for the development of sediment entrainment models for gravel bed rivers.

Ultra-Fine Scale Spatially-Integrated Mapping of Habitat and Occupancy Using Structure-From-Motion

PubMed Central

McDowall, Philip; Lynch, Heather J.

2017-01-01

Organisms respond to and often simultaneously modify their environment. While these interactions are apparent at the landscape extent, the driving mechanisms often occur at very fine spatial scales. Structure-from-Motion (SfM), a computer vision technique, allows the simultaneous mapping of organisms and fine scale habitat, and will greatly improve our understanding of habitat suitability, ecophysiology, and the bi-directional relationship between geomorphology and habitat use. SfM can be used to create high-resolution (centimeter-scale) three-dimensional (3D) habitat models at low cost. These models can capture the abiotic conditions formed by terrain and simultaneously record the position of individual organisms within that terrain. While coloniality is common in seabird species, we have a poor understanding of the extent to which dense breeding aggregations are driven by fine-scale active aggregation or limited suitable habitat. We demonstrate the use of SfM for fine-scale habitat suitability by reconstructing the locations of nests in a gentoo penguin colony and fitting models that explicitly account for conspecific attraction. The resulting digital elevation models (DEMs) are used as covariates in an inhomogeneous hybrid point process model. We find that gentoo penguin nest site selection is a function of the topography of the landscape, but that nests are far more aggregated than would be expected based on terrain alone, suggesting a strong role of behavioral aggregation in driving coloniality in this species. This integrated mapping of organisms and fine scale habitat will greatly improve our understanding of fine-scale habitat suitability, ecophysiology, and the complex bi-directional relationship between geomorphology and habitat use. PMID:28076351

A New Multibeam Sonar Technique for Evaluating Fine-Scale Fish Behavior Near Hydroelectric Dam Guidance Structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Robert L.; Simmons, Mary Ann; Simmons, Carver S.

2002-03-07

This book chapter describes a Dual-Head Multibeam Sonar (DHMS) system developed by Battelle and deployed at two dam sites on the Snake and Columbia rivers in Washington State to evaluate the fine-scale (

The Effect of Experimental Geometry and Initial Conditions on the Shape of Coherent Population Trapping Resonances on the Fine Structure Levels of Thallium Atoms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karagodova, T.Ya.

2005-06-15

Specific features of the coherent population trapping effect are considered in the generalized {lambda} system whose lower levels are the magnetic sublevels of the fine structure levels of the thallium atom. Numerical experiments were performed aimed at examination of the coherent population trapping for the case of nontrivial, but feasible, initial populations of the upper metastable fine structure level. Such populations may be obtained, for example, due to the photodissociation of TlBr molecules. The possibility of reducing the number of resonances of the coherent population trapping in a multilevel system, which may be useful for high-resolution spectroscopy, is demonstrated. Itmore » is shown that the magnitude and shape of the resonances can be controlled by varying the orientation of the polarization vectors of the light field components with respect to each other and to a magnetic field. In addition, studying the shape of the coherent population trapping resonances for the atoms obtained by photodissociation of molecules may provide information about these molecules.« less

Exploring seascape genetics and kinship in the reef sponge Stylissa carteri in the Red Sea

PubMed Central

Giles, Emily C; Saenz-Agudelo, Pablo; Hussey, Nigel E; Ravasi, Timothy; Berumen, Michael L

2015-01-01

A main goal of population geneticists is to study patterns of gene flow to gain a better understanding of the population structure in a given organism. To date most efforts have been focused on studying gene flow at either broad scales to identify barriers to gene flow and isolation by distance or at fine spatial scales in order to gain inferences regarding reproduction and local dispersal. Few studies have measured connectivity at multiple spatial scales and have utilized novel tools to test the influence of both environment and geography on shaping gene flow in an organism. Here a seascape genetics approach was used to gain insight regarding geographic and ecological barriers to gene flow of a common reef sponge, Stylissa carteri in the Red Sea. Furthermore, a small-scale (<1 km) analysis was also conducted to infer reproductive potential in this organism. At the broad scale, we found that sponge connectivity is not structured by geography alone, but rather, genetic isolation in the southern Red Sea correlates strongly with environmental heterogeneity. At the scale of a 50-m transect, spatial autocorrelation analyses and estimates of full-siblings revealed that there is no deviation from random mating. However, at slightly larger scales (100–200 m) encompassing multiple transects at a given site, a greater proportion of full-siblings was found within sites versus among sites in a given location suggesting that mating and/or dispersal are constrained to some extent at this spatial scale. This study adds to the growing body of literature suggesting that environmental and ecological variables play a major role in the genetic structure of marine invertebrate populations. PMID:26257865

Predation Risk Shapes Social Networks in Fission-Fusion Populations

PubMed Central

Kelley, Jennifer L.; Morrell, Lesley J.; Inskip, Chloe; Krause, Jens; Croft, Darren P.

2011-01-01

Predation risk is often associated with group formation in prey, but recent advances in methods for analysing the social structure of animal societies make it possible to quantify the effects of risk on the complex dynamics of spatial and temporal organisation. In this paper we use social network analysis to investigate the impact of variation in predation risk on the social structure of guppy shoals and the frequency and duration of shoal splitting (fission) and merging (fusion) events. Our analyses revealed that variation in the level of predation risk was associated with divergent social dynamics, with fish in high-risk populations displaying a greater number of associations with overall greater strength and connectedness than those from low-risk sites. Temporal patterns of organisation also differed according to predation risk, with fission events more likely to occur over two short time periods (5 minutes and 20 minutes) in low-predation fish and over longer time scales (>1.5 hours) in high-predation fish. Our findings suggest that predation risk influences the fine-scale social structure of prey populations and that the temporal aspects of organisation play a key role in defining social systems. PMID:21912627

Zoonotic Babesia microti in the northeastern U.S.: Evidence for the expansion of a specific parasite lineage

PubMed Central

Molloy, Philip; Weeks, Karen

2018-01-01

The recent range expansion of human babesiosis in the northeastern United States, once found only in restricted coastal sites, is not well understood. This study sought to utilize a large number of samples to examine the population structure of the parasites on a fine scale to provide insights into the mode of emergence across the region. 228 B. microti samples collected in endemic northeastern U.S. sites were genotyped using published Variable number tandem repeat (VNTR) markers. The genetic diversity and population structure were analysed on a geographic scale using Phyloviz and TESS, programs that utilize two different methods to identify population membership without predefined population data. Three distinct populations were detected in northeastern US, each dominated by a single ancestral type. In contrast to the limited range of the Nantucket and Cape Cod populations, the mainland population dominated from New Jersey eastward to Boston. Ancestral populations of B. microti were sufficiently isolated to differentiate into distinct populations. Despite this, a single population was detected across a large geographic area of the northeast that historically had at least 3 distinct foci of transmission, central New Jersey, Long Island and southeastern Connecticut. We conclude that a single B. microti genotype has expanded across the northeastern U.S. The biological attributes associated with this parasite genotype that have contributed to such a selective sweep remain to be identified. PMID:29565993

Genetic co-structuring in host-parasite systems: Empirical data from raccoons and raccoon ticks

DOE PAGES

Dharmarajan, Guha; Beasley, James C.; Beatty, William S.; ...

2016-03-31

Many aspects of parasite biology critically depend on their hosts, and understanding how host-parasite populations are co-structured can help improve our understanding of the ecology of parasites, their hosts, and host-parasite interactions. Here, this study utilized genetic data collected from raccoons (Procyon lotor), and a specialist parasite, the raccoon tick (Ixodes texanus), to test for genetic co-structuring of host-parasite populations at both landscape and host scales. At the landscape scale, our analyses revealed a significant correlation between genetic and geographic distance matrices (i.e., isolation by distance) in ticks, but not their hosts. While there are several mechanisms that could leadmore » to a stronger pattern of isolation by distance in tick vs. raccoon datasets, our analyses suggest that at least one reason for the above pattern is the substantial increase in statistical power (due to the ≈8-fold increase in sample size) afforded by sampling parasites. Host-scale analyses indicated higher relatedness between ticks sampled from related vs. unrelated raccoons trapped within the same habitat patch, a pattern likely driven by increased contact rates between related hosts. Lastly, by utilizing fine-scale genetic data from both parasites and hosts, our analyses help improve our understanding of epidemiology and host ecology.« less

Fine-Scale Genetic Structure of Monilinia fructicola During Brown Rot Epidemics Within Individual Peach Tree Canopies.

PubMed

Everhart, S E; Scherm, H

2015-04-01

The purpose of this study was to determine the fine-scale genetic structure of populations of the brown rot pathogen Monilinia fructicola within individual peach tree canopies to better understand within-tree plant pathogen diversity and to complement previous work on spatiotemporal development of brown rot disease at the canopy level. Across 3 years in a total of six trees, we monitored disease development, collected isolates from every M. fructicola symptom during the course of the season, and created high-resolution three-dimensional maps of all symptom and isolate locations within individual canopies using an electromagnetic digitizer. Each canopy population (65 to 173 isolates per tree) was characterized using a set of 13 microsatellite markers and analyzed for evidence of spatial genetic autocorrelation among isolates during the epidemic phase of the disease. Results showed high genetic diversity (average uh=0.529) and high genotypic diversity (average D=0.928) within canopies. The percentage of unique multilocus genotypes within trees was greater for blossom blight isolates (78.2%) than for fruit rot isolates (51.3%), indicating a greater contribution of clonal reproduction during the preharvest epidemic. For fruit rot isolates, between 54.2 and 81.7% of isolates were contained in one to four dominant clonal genotypes per tree having at least 10 members. All six fruit rot populations showed positive and significant spatial genetic autocorrelation for distance classes between 0.37 and 1.48 m. Despite high levels of within-tree pathogen diversity, the contribution of locally available inoculum combined with short-distance dispersal is likely the main factor generating clonal population foci and associated spatial genetic clustering within trees.

Coupling fine-scale root and canopy structure using ground-based remote sensing

Treesearch

Brady Hardiman; Christopher Gough; John Butnor; Gil Bohrer; Matteo Detto; Peter Curtis

2017-01-01

Ecosystem physical structure, defined by the quantity and spatial distribution of biomass, influences a range of ecosystem functions. Remote sensing tools permit the non-destructive characterization of canopy and root features, potentially providing opportunities to link above- and belowground structure at fine spatial resolution in...

Quantum-gravity predictions for the fine-structure constant

NASA Astrophysics Data System (ADS)

Eichhorn, Astrid; Held, Aaron; Wetterich, Christof

2018-07-01

Asymptotically safe quantum fluctuations of gravity can uniquely determine the value of the gauge coupling for a large class of grand unified models. In turn, this makes the electromagnetic fine-structure constant calculable. The balance of gravity and matter fluctuations results in a fixed point for the running of the gauge coupling. It is approached as the momentum scale is lowered in the transplanckian regime, leading to a uniquely predicted value of the gauge coupling at the Planck scale. The precise value of the predicted fine-structure constant depends on the matter content of the grand unified model. It is proportional to the gravitational fluctuation effects for which computational uncertainties remain to be settled.

The Genetics of Mexico Recapitulates Native American Substructure and Affects Biomedical Traits

PubMed Central

Moreno-Estrada, Andrés; Gignoux, Christopher R.; Fernández-López, Juan Carlos; Zakharia, Fouad; Sikora, Martin; Contreras, Alejandra V.; Acuña-Alonzo, Victor; Sandoval, Karla; Eng, Celeste; Romero-Hidalgo, Sandra; Ortiz-Tello, Patricia; Robles, Victoria; Kenny, Eimear E.; Nuño-Arana, Ismael; Barquera-Lozano, Rodrigo; Macín-Pérez, Gastón; Granados-Arriola, Julio; Huntsman, Scott; Galanter, Joshua M.; Via, Marc; Ford, Jean G.; Chapela, Rocío; Rodriguez-Cintron, William; Rodríguez-Santana, Jose R.; Romieu, Isabelle; Sienra-Monge, Juan José; Navarro, Blanca del Rio; London, Stephanie J.; Ruiz-Linares, Andrés; Garcia-Herrera, Rodrigo; Estrada, Karol; Hidalgo-Miranda, Alfredo; Jimenez-Sanchez, Gerardo; Carnevale, Alessandra; Soberón, Xavier; Canizales-Quinteros, Samuel; Rangel-Villalobos, Héctor; Silva-Zolezzi, Irma; Burchard, Esteban Gonzalez; Bustamante, Carlos D.

2014-01-01

Mexico harbors great cultural and ethnic diversity, yet fine-scale patterns of human genome-wide variation from this region remain largely uncharacterized. We studied genomic variation within Mexico from over 1,000 individuals representing 20 indigenous and 11 mestizo populations. We found striking genetic stratification among indigenous populations within Mexico at varying degrees of geographic isolation. Some groups were as differentiated as Europeans are from East Asians. Pre-Columbian genetic substructure is recapitulated in the indigenous ancestry of admixed mestizo individuals across the country. Furthermore, two independently phenotyped cohorts of Mexicans and Mexican Americans showed a significant association between sub-continental ancestry and lung function. Thus, accounting for fine-scale ancestry patterns is critical for medical and population genetic studies within Mexico, in Mexican-descent populations, and likely in many other populations worldwide. PMID:24926019

Application of pinch-and-swell structure rheology gauge to determine rock paleo-rheological parameters in Taili, western Liaoning, NE China

NASA Astrophysics Data System (ADS)

Sun, Zhengquan; Zeng, Zuoxun; Wu, Linbo; Xu, Shaopeng; Yang, Shuang; Chen, Deli; Wang, Jianxiu

2017-05-01

New results, in combination with previously published ones, reveal that when the Stress Exponent of the Competent layer (SEC) ranges from 1 to 10 (1 < n < 10), Pinch-and-Swell structure Rheology Gauge (PSRG) can only be available under the condition that the Viscosity ratio between the Competent layer and its corresponding Matrix layer (VCM) is larger than 10. Therefore, we made the attempt to calculate the viscosity ratio of pinch-and-swell structure of competent layer to the related matrix and stress exponent. Based on this knowledge, we applied this gauge to calculate SECs and VCMs of eight types of pinch-and-swell structures, which are widely developed in the Taili area of the west Liaoning Province in China. Statistical analysis of the SEC resulted in intervals of four types of competent layers, that is, Medium-scale Granitic coarse-to-pegmatitic Veins, Small-scale Augen Granite aplite Veins, Small-scale Granite aplite Veins, and Small-scale Augen Quartz-K-feldspar veins, with intervals of [3.50, 4.63], [2.64, 4.29], [2.70, 3.51], and [2.50, 3.36] respectively. The preferred intervals of VCM of the five types of pinch-and-swell structures, Small-scale Augen Granite aplite Veins + Fine-grained Biotite-Hornblende-plagioclase Gneiss, Medium-scale Granitic coarse-to-pegmatitic Veins + Fine-grained Biotite-Hornblende-plagioclase Gneiss, Small-scale Augen Granite aplite Veins + medium-to-fine-grained granitic gneiss, Medium-scale Granitic coarse-to-pegmatitic Veins + medium-to-fine-grained granitic gneiss, and Small-scale Augen Granite aplite Veins + fine-grained biotite-plagioclase gneiss, are [19.98, 62.51], [15.90, 61.17], [26.72, 93.27], [22.21, 107.26], and [76.33, 309.39] respectively. The similarities between these calculated SEC statistical preferred intervals and the physical experimental results verify the validity of the PSRG. The competent layers of the pinch-and-swell structures were presented in this study as power-law flow with SEC values that increased with the thickness of the layer. Grain-size plays an important role in the rheology of pinch-and-swell structures. The results offer a case for the application of PSRG and determine the key rock rheological parameters of North China Craton for future related studies.

Population genomics reveals structure at the individual, host-tree scale and persistence of genotypic variants of the undomesticated yeast Saccharomyces paradoxus in a natural woodland.

PubMed

Xia, Wenjing; Nielly-Thibault, Lou; Charron, Guillaume; Landry, Christian R; Kasimer, Dahlia; Anderson, James B; Kohn, Linda M

2017-02-01

Genetic diversity in experimental, domesticated and wild populations of the related yeasts, Saccharomyces cerevisiae and Saccharomyces paradoxus, has been well described at the global scale. We investigated the population genomics of a local population on a small spatial scale to address two main questions. First, is there genomic variation in a S. paradoxus population at a spatial scale spanning centimetres (microsites) to tens of metres? Second, does the distribution of genomic variants persist over time? Our sample consisted of 42 S. paradoxus strains from 2014 and 43 strains from 2015 collected from the same 72 microsites around four host trees (Quercus rubra and Quercus alba) within 1 km 2 in a mixed hardwood forest in southern Ontario. Six additional S. paradoxus strains recovered from adjacent maple and beech trees in 2015 are also included in the sample. Whole-genome sequencing and genomic SNP analysis revealed five differentiated groups (clades) within the sampled area. The signal of persistence of genotypes in their microsites from 2014 to 2015 was highly significant. Isolates from the same tree tended to be more related than strains from different trees, with limited evidence of dispersal between trees. In growth assays, one genotype had a significantly longer lag phase than the other strains. Our results indicate that different clades coexist at fine spatial scale and that population structure persists over at least a one-year interval in these wild yeasts, suggesting the efficacy of yearly sampling to follow longer term genetic dynamics in future studies. © 2016 John Wiley & Sons Ltd.

Altered fish community and feeding behaviour in close proximity to boat moorings in an urban estuary.

PubMed

Lanham, Brendan S; Vergés, Adriana; Hedge, Luke H; Johnston, Emma L; Poore, Alistair G B

2018-04-01

Coastal urbanization has led to large-scale transformation of estuaries, with artificial structures now commonplace. Boat moorings are known to reduce seagrass cover, but little is known about their effect on fish communities. We used underwater video to quantify abundance, diversity, composition and feeding behaviour of fish assemblages on two scales: with increasing distance from moorings on fine scales, and among locations where moorings were present or absent. Fish were less abundant in close proximity to boat moorings, and the species composition varied on fine scales, leading to lower predation pressure near moorings. There was no relationship at the location with seagrass. On larger scales, we detected no differences in abundance or community composition among locations where moorings were present or absent. These findings show a clear impact of moorings on fish and highlight the importance of fine-scale assessments over location-scale comparisons in the detection of the effects of artificial structures. Copyright © 2018 Elsevier Ltd. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dharmarajan, Guha; Beasley, James C.; Beatty, William S.

Many aspects of parasite biology critically depend on their hosts, and understanding how host-parasite populations are co-structured can help improve our understanding of the ecology of parasites, their hosts, and host-parasite interactions. Here, this study utilized genetic data collected from raccoons (Procyon lotor), and a specialist parasite, the raccoon tick (Ixodes texanus), to test for genetic co-structuring of host-parasite populations at both landscape and host scales. At the landscape scale, our analyses revealed a significant correlation between genetic and geographic distance matrices (i.e., isolation by distance) in ticks, but not their hosts. While there are several mechanisms that could leadmore » to a stronger pattern of isolation by distance in tick vs. raccoon datasets, our analyses suggest that at least one reason for the above pattern is the substantial increase in statistical power (due to the ≈8-fold increase in sample size) afforded by sampling parasites. Host-scale analyses indicated higher relatedness between ticks sampled from related vs. unrelated raccoons trapped within the same habitat patch, a pattern likely driven by increased contact rates between related hosts. Lastly, by utilizing fine-scale genetic data from both parasites and hosts, our analyses help improve our understanding of epidemiology and host ecology.« less

Local topography shapes fine-scale spatial genetic structure in the Arkansas Valley evening primrose, Oenothera harringtonii (Onagraceae).

PubMed

Rhodes, Matthew K; Fant, Jeremie B; Skogen, Krissa A

2014-01-01

Identifying factors that shape the spatial distribution of genetic variation is crucial to understanding many population- and landscape-level processes. In this study, we explore fine-scale spatial genetic structure in Oenothera harringtonii (Onagraceae), an insect-pollinated, gravity-dispersed herb endemic to the grasslands of south-central and southeastern Colorado, USA. We genotyped 315 individuals with 11 microsatellite markers and utilized a combination of spatial autocorrelation analyses and landscape genetic models to relate life history traits and landscape features to dispersal processes. Spatial genetic structure was consistent with theoretical expectations of isolation by distance, but this pattern was weak (Sp = 0.00374). Anisotropic analyses indicated that spatial genetic structure was markedly directional, in this case consistent with increased dispersal along prominent slopes. Landscape genetic models subsequently confirmed that spatial genetic variation was significantly influenced by local topographic heterogeneity, specifically that geographic distance, elevation and aspect were important predictors of spatial genetic structure. Among these variables, geographic distance was ~68% more important than elevation in describing spatial genetic variation, and elevation was ~42% more important than aspect after removing the effect of geographic distance. From these results, we infer a mechanism of hydrochorous seed dispersal along major drainages aided by seasonal monsoon rains. Our findings suggest that landscape features may shape microevolutionary processes at much finer spatial scales than typically considered, and stress the importance of considering how particular dispersal vectors are influenced by their environmental context. © The American Genetic Association 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Introducing close-range photogrammetry for characterizing forest understory plant diversity and surface fuel structure at fine scales

Treesearch

Benjamin C. Bright; E. Louise Loudermilk; Scott M. Pokswinski; Andrew T. Hudak; Joseph J. O' Brien

2016-01-01

Methods characterizing fine-scale fuels and plant diversity can advance understanding of plant-fire interactions across scales and help in efforts to monitor important ecosystems such as longleaf pine (Pinus palustris Mill.) forests of the southeastern United States. Here, we evaluate the utility of close-range photogrammetry for measuring fuels and plant...

CFD MODELING OF FINE SCALE FLOW AND TRANSPORT IN THE HOUSTON METROPOLITAN AREA, TEXAS

EPA Science Inventory

Fine scale modeling of flows and air quality in Houston, Texas is being performed; the use of computational fluid dynamics (CFD) modeling is being applied to investigate the influence of morphologic structures on the within-grid transport and dispersion of sources in grid models ...

Clustering of 770,000 genomes reveals post-colonial population structure of North America

NASA Astrophysics Data System (ADS)

Han, Eunjung; Carbonetto, Peter; Curtis, Ross E.; Wang, Yong; Granka, Julie M.; Byrnes, Jake; Noto, Keith; Kermany, Amir R.; Myres, Natalie M.; Barber, Mathew J.; Rand, Kristin A.; Song, Shiya; Roman, Theodore; Battat, Erin; Elyashiv, Eyal; Guturu, Harendra; Hong, Eurie L.; Chahine, Kenneth G.; Ball, Catherine A.

2017-02-01

Despite strides in characterizing human history from genetic polymorphism data, progress in identifying genetic signatures of recent demography has been limited. Here we identify very recent fine-scale population structure in North America from a network of over 500 million genetic (identity-by-descent, IBD) connections among 770,000 genotyped individuals of US origin. We detect densely connected clusters within the network and annotate these clusters using a database of over 20 million genealogical records. Recent population patterns captured by IBD clustering include immigrants such as Scandinavians and French Canadians; groups with continental admixture such as Puerto Ricans; settlers such as the Amish and Appalachians who experienced geographic or cultural isolation; and broad historical trends, including reduced north-south gene flow. Our results yield a detailed historical portrait of North America after European settlement and support substantial genetic heterogeneity in the United States beyond that uncovered by previous studies.

Clustering of 770,000 genomes reveals post-colonial population structure of North America

PubMed Central

Han, Eunjung; Carbonetto, Peter; Curtis, Ross E.; Wang, Yong; Granka, Julie M.; Byrnes, Jake; Noto, Keith; Kermany, Amir R.; Myres, Natalie M.; Barber, Mathew J.; Rand, Kristin A.; Song, Shiya; Roman, Theodore; Battat, Erin; Elyashiv, Eyal; Guturu, Harendra; Hong, Eurie L.; Chahine, Kenneth G.; Ball, Catherine A.

2017-01-01

Despite strides in characterizing human history from genetic polymorphism data, progress in identifying genetic signatures of recent demography has been limited. Here we identify very recent fine-scale population structure in North America from a network of over 500 million genetic (identity-by-descent, IBD) connections among 770,000 genotyped individuals of US origin. We detect densely connected clusters within the network and annotate these clusters using a database of over 20 million genealogical records. Recent population patterns captured by IBD clustering include immigrants such as Scandinavians and French Canadians; groups with continental admixture such as Puerto Ricans; settlers such as the Amish and Appalachians who experienced geographic or cultural isolation; and broad historical trends, including reduced north-south gene flow. Our results yield a detailed historical portrait of North America after European settlement and support substantial genetic heterogeneity in the United States beyond that uncovered by previous studies. PMID:28169989

Clustering of 770,000 genomes reveals post-colonial population structure of North America.

PubMed

Han, Eunjung; Carbonetto, Peter; Curtis, Ross E; Wang, Yong; Granka, Julie M; Byrnes, Jake; Noto, Keith; Kermany, Amir R; Myres, Natalie M; Barber, Mathew J; Rand, Kristin A; Song, Shiya; Roman, Theodore; Battat, Erin; Elyashiv, Eyal; Guturu, Harendra; Hong, Eurie L; Chahine, Kenneth G; Ball, Catherine A

2017-02-07

Despite strides in characterizing human history from genetic polymorphism data, progress in identifying genetic signatures of recent demography has been limited. Here we identify very recent fine-scale population structure in North America from a network of over 500 million genetic (identity-by-descent, IBD) connections among 770,000 genotyped individuals of US origin. We detect densely connected clusters within the network and annotate these clusters using a database of over 20 million genealogical records. Recent population patterns captured by IBD clustering include immigrants such as Scandinavians and French Canadians; groups with continental admixture such as Puerto Ricans; settlers such as the Amish and Appalachians who experienced geographic or cultural isolation; and broad historical trends, including reduced north-south gene flow. Our results yield a detailed historical portrait of North America after European settlement and support substantial genetic heterogeneity in the United States beyond that uncovered by previous studies.

Environmental factors influence both abundance and genetic diversity in a widespread bird species

PubMed Central

Liu, Yang; Webber, Simone; Bowgen, Katharine; Schmaltz, Lucie; Bradley, Katharine; Halvarsson, Peter; Abdelgadir, Mohanad; Griesser, Michael

2013-01-01

Genetic diversity is one of the key evolutionary variables that correlate with population size, being of critical importance for population viability and the persistence of species. Genetic diversity can also have important ecological consequences within populations, and in turn, ecological factors may drive patterns of genetic diversity. However, the relationship between the genetic diversity of a population and how this interacts with ecological processes has so far only been investigated in a few studies. Here, we investigate the link between ecological factors, local population size, and allelic diversity, using a field study of a common bird species, the house sparrow (Passer domesticus). We studied sparrows outside the breeding season in a confined small valley dominated by dispersed farms and small-scale agriculture in southern France. Population surveys at 36 locations revealed that sparrows were more abundant in locations with high food availability. We then captured and genotyped 891 house sparrows at 10 microsatellite loci from a subset of these locations (N = 12). Population genetic analyses revealed weak genetic structure, where each locality represented a distinct substructure within the study area. We found that food availability was the main factor among others tested to influence the genetic structure between locations. These results suggest that ecological factors can have strong impacts on both population size per se and intrapopulation genetic variation even at a small scale. On a more general level, our data indicate that a patchy environment and low dispersal rate can result in fine-scale patterns of genetic diversity. Given the importance of genetic diversity for population viability, combining ecological and genetic data can help to identify factors limiting population size and determine the conservation potential of populations. PMID:24363897

A Modeling Framework for Improved Characterization of Near-Road Exposure at Fine Scales

EPA Science Inventory

Traffic-related air pollutants could cause adverse health impact to communities near roadways. To estimate the population risk and locate "hotspots" in the near-road environment, quantifying the exposure at a fine spatial resolution is essential. A new state-of-the-art ...

A modified dual-level algorithm for large-scale three-dimensional Laplace and Helmholtz equation

NASA Astrophysics Data System (ADS)

Li, Junpu; Chen, Wen; Fu, Zhuojia

2018-01-01

A modified dual-level algorithm is proposed in the article. By the help of the dual level structure, the fully-populated interpolation matrix on the fine level is transformed to a local supported sparse matrix to solve the highly ill-conditioning and excessive storage requirement resulting from fully-populated interpolation matrix. The kernel-independent fast multipole method is adopted to expediting the solving process of the linear equations on the coarse level. Numerical experiments up to 2-million fine-level nodes have successfully been achieved. It is noted that the proposed algorithm merely needs to place 2-3 coarse-level nodes in each wavelength per direction to obtain the reasonable solution, which almost down to the minimum requirement allowed by the Shannon's sampling theorem. In the real human head model example, it is observed that the proposed algorithm can simulate well computationally very challenging exterior high-frequency harmonic acoustic wave propagation up to 20,000 Hz.

Greater sage-grouse population trends across Wyoming

USGS Publications Warehouse

Edmunds, David; Aldridge, Cameron L.; O'Donnell, Michael; Monroe, Adrian

2018-01-01

The scale at which analyses are performed can have an effect on model results and often one scale does not accurately describe the ecological phenomena of interest (e.g., population trends) for wide-ranging species: yet, most ecological studies are performed at a single, arbitrary scale. To best determine local and regional trends for greater sage-grouse (Centrocercus urophasianus) in Wyoming, USA, we modeled density-independent and -dependent population growth across multiple spatial scales relevant to management and conservation (Core Areas [habitat encompassing approximately 83% of the sage-grouse population on ∼24% of surface area in Wyoming], local Working Groups [7 regional areas for which groups of local experts are tasked with implementing Wyoming's statewide sage-grouse conservation plan at the local level], Core Area status (Core Area vs. Non-Core Area) by Working Groups, and Core Areas by Working Groups). Our goal was to determine the influence of fine-scale population trends (Core Areas) on larger-scale populations (Working Group Areas). We modeled the natural log of change in population size ( peak M lek counts) by time to calculate the finite rate of population growth (λ) for each population of interest from 1993 to 2015. We found that in general when Core Area status (Core Area vs. Non-Core Area) was investigated by Working Group Area, the 2 populations trended similarly and agreed with the overall trend of the Working Group Area. However, at the finer scale where Core Areas were analyzed separately, Core Areas within the same Working Group Area often trended differently and a few large Core Areas could influence the overall Working Group Area trend and mask trends occurring in smaller Core Areas. Relatively close fine-scale populations of sage-grouse can trend differently, indicating that large-scale trends may not accurately depict what is occurring across the landscape (e.g., local effects of gas and oil fields may be masked by increasing larger populations). 

Species Associations in a Species-Rich Subtropical Forest Were Not Well-Explained by Stochastic Geometry of Biodiversity

PubMed Central

Wang, Qinggang; Bao, Dachuan; Guo, Yili; Lu, Junmeng; Lu, Zhijun; Xu, Yaozhan; Zhang, Kuihan; Liu, Haibo; Meng, Hongjie; Jiang, Mingxi; Qiao, Xiujuan; Huang, Handong

2014-01-01

The stochastic dilution hypothesis has been proposed to explain species coexistence in species-rich communities. The relative importance of the stochastic dilution effects with respect to other effects such as competition and habitat filtering required to be tested. In this study, using data from a 25-ha species-rich subtropical forest plot with a strong topographic structure at Badagongshan in central China, we analyzed overall species associations and fine-scale species interactions between 2,550 species pairs. The result showed that: (1) the proportion of segregation in overall species association analysis at 2 m neighborhood in this plot followed the prediction of the stochastic dilution hypothesis that segregations should decrease with species richness but that at 10 m neighborhood was higher than the prediction. (2) The proportion of no association type was lower than the expectation of stochastic dilution hypothesis. (3) Fine-scale species interaction analyses using Heterogeneous Poisson processes as null models revealed a high proportion (47%) of significant species effects. However, the assumption of separation of scale of this method was not fully met in this plot with a strong fine-scale topographic structure. We also found that for species within the same families, fine-scale positive species interactions occurred more frequently and negative ones occurred less frequently than expected by chance. These results suggested effects of environmental filtering other than species interaction in this forest. (4) We also found that arbor species showed a much higher proportion of significant fine-scale species interactions (66%) than shrub species (18%). We concluded that the stochastic dilution hypothesis only be partly supported and environmental filtering left discernible spatial signals in the spatial associations between species in this species-rich subtropical forest with a strong topographic structure. PMID:24824996

Species associations in a species-rich subtropical forest were not well-explained by stochastic geometry of biodiversity.

PubMed

Wang, Qinggang; Bao, Dachuan; Guo, Yili; Lu, Junmeng; Lu, Zhijun; Xu, Yaozhan; Zhang, Kuihan; Liu, Haibo; Meng, Hongjie; Jiang, Mingxi; Qiao, Xiujuan; Huang, Handong

2014-01-01

The stochastic dilution hypothesis has been proposed to explain species coexistence in species-rich communities. The relative importance of the stochastic dilution effects with respect to other effects such as competition and habitat filtering required to be tested. In this study, using data from a 25-ha species-rich subtropical forest plot with a strong topographic structure at Badagongshan in central China, we analyzed overall species associations and fine-scale species interactions between 2,550 species pairs. The result showed that: (1) the proportion of segregation in overall species association analysis at 2 m neighborhood in this plot followed the prediction of the stochastic dilution hypothesis that segregations should decrease with species richness but that at 10 m neighborhood was higher than the prediction. (2) The proportion of no association type was lower than the expectation of stochastic dilution hypothesis. (3) Fine-scale species interaction analyses using Heterogeneous Poisson processes as null models revealed a high proportion (47%) of significant species effects. However, the assumption of separation of scale of this method was not fully met in this plot with a strong fine-scale topographic structure. We also found that for species within the same families, fine-scale positive species interactions occurred more frequently and negative ones occurred less frequently than expected by chance. These results suggested effects of environmental filtering other than species interaction in this forest. (4) We also found that arbor species showed a much higher proportion of significant fine-scale species interactions (66%) than shrub species (18%). We concluded that the stochastic dilution hypothesis only be partly supported and environmental filtering left discernible spatial signals in the spatial associations between species in this species-rich subtropical forest with a strong topographic structure.

Heavy precipitation episodes in the Western Mediterranean : Use of a semi-Lagrangian advection model for the fine-scale description of upper-level troughs

NASA Astrophysics Data System (ADS)

Gauthier, N.; Claud, C.; Funatsu, B. M.; Chaboureau, J.-P.; Argence, S.; Lambert, D.; Richard, E.; Hauchecorne, A.; Arbogast, P.; Maynard, K.

2009-09-01

Heavy precipitation events over the Mediterranean Sea are generally associated with upper-level troughs. The mesoscale structures of such troughs are however not well reproduced by the atmospheric analyses due to inappropriate spatial resolution. We propose here to use a semi-Lagrangian advection model called MIMOSA (Modélisation Isentrope du transport Méso-échelle de l'Ozone Stratosphérique par Advection) initially developed to describe stratospheric filaments, to calculate fine-scale Potential Vorticity (PV) fields on isentropic surfaces near the tropopause. After a description of MIMOSA, we will focus on the model-generated PV fields for several high impact weather cases that occurred over the Western Mediterreanean Sea. We will demonstrate the ability of MIMOSA to resolve fine scale structures of upper-level troughs considering the Algiers' flash flood, which occurred on November 2001, and then a heavy precipitation event over southeast France on the 5-6 September 2005. Finally, with a PV inversion method, we will show the impact of the fine scales PV structures as depicted by MIMOSA to improve the numerical simulation of a « hurricane » that hit Italy in September 2006, both in terms of surface pressure and precipitation forecasts.

[Ultraviolet spectroscopic study on the fine structures in the solar polar hole].

PubMed

Zhang, Min; Wang, Dong; Liu, Guo-Hong

2014-07-01

Fine structures in the south solar polar coronal hole were observed by N IV line of SOHO/SUMER spectrograph. The scales of the fine structures range spatially range from 1 arcsec to several arcsecs, temporally from 1 min to several minutes, and parts of them are in strip shape along the slit direction. The line-of-sight velocity of them is up to tens of km x s(-1) with red and blue shift intercrossed occasionally, which appear periodically as long as 100 minutes in some regions. Part of the fine structures can be clearly observed at the Ne V III line with higher formation temperature in the same spectral window. The time and location of some fine structures with high velocity in the Ne V III spectrum are almost the same as that in N IV spectrum, but they are extended and diffused in the Ne V III spectrum. Some fine structures have non-Gaussian profiles with the line-of-sight Doppler velocities up to 150 km x s(-1) in the N IV blue/red wings, which is similar with the explosive events in the transition region. In the past, explosive events are small-scale dynamic phenomena often observed in the quiet-sun (QS) region, while their properties in coronal holes (CHs) remain unclear. Here, we find the EE-like events with strong dynamics in the south solar polar coronal hole by N IV line of SOHO/SUMER spectrograph.

Marked population structure and recent migration in the critically endangered Sumatran orangutan (Pongo abelii).

PubMed

Nater, Alexander; Arora, Natasha; Greminger, Maja P; van Schaik, Carel P; Singleton, Ian; Wich, Serge A; Fredriksson, Gabriella; Perwitasari-Farajallah, Dyah; Pamungkas, Joko; Krützen, Michael

2013-01-01

A multitude of factors influence how natural populations are genetically structured, including dispersal barriers, inhomogeneous habitats, and social organization. Such population subdivision is of special concern in endangered species, as it may lead to reduced adaptive potential and inbreeding in local subpopulations, thus increasing the risk of future extinctions. With only 6600 animals left in the wild, Sumatran orangutans (Pongo abelii) are among the most endangered, but also most enigmatic, great ape species. In order to infer the fine-scale population structure and connectivity of Sumatran orangutans, we analyzed the most comprehensive set of samples to date, including mitochondrial hyper-variable region I haplotypes for 123 individuals and genotypes of 27 autosomal microsatellite markers for 109 individuals. For both mitochondrial and autosomal markers, we found a pronounced population structure, caused by major rivers, mountain ridges, and the Toba caldera. We found that genetic diversity and corresponding long-term effective population size estimates vary strongly among sampling regions for mitochondrial DNA, but show remarkable similarity for autosomal markers, hinting at male-driven long-distance gene flow. In support of this, we identified several individuals that were most likely sired by males originating from other genetic clusters. Our results highlight the effect of natural barriers in shaping the genetic structure of great ape populations, but also point toward important dispersal corridors on northern Sumatra that allow for genetic exchange.

Feral pig populations are structured at fine spatial scales in tropical Queensland, Australia.

PubMed

Lopez, Jobina; Hurwood, David; Dryden, Bart; Fuller, Susan

2014-01-01

Feral pigs occur throughout tropical far north Queensland, Australia and are a significant threat to biodiversity and World Heritage values, agriculture and are a vector of infectious diseases. One of the constraints on long-lasting, local eradication of feral pigs is the process of reinvasion into recently controlled areas. This study examined the population genetic structure of feral pigs in far north Queensland to identify the extent of movement and the scale at which demographically independent management units exist. Genetic analysis of 328 feral pigs from the Innisfail to Tully region of tropical Queensland was undertaken. Seven microsatellite loci were screened and Bayesian clustering methods used to infer population clusters. Sequence variation at the mitochondrial DNA control region was examined to identify pig breed. Significant population structure was identified in the study area at a scale of 25 to 35 km, corresponding to three demographically independent management units (MUs). Distinct natural or anthropogenic barriers were not found, but environmental features such as topography and land use appear to influence patterns of gene flow. Despite the strong, overall pattern of structure, some feral pigs clearly exhibited ancestry from a MU outside of that from which they were sampled indicating isolated long distance dispersal or translocation events. Furthermore, our results suggest that gene flow is restricted among pigs of domestic Asian and European origin and non-random mating influences management unit boundaries. We conclude that the three MUs identified in this study should be considered as operational units for feral pig control in far north Queensland. Within a MU, coordinated and simultaneous control is required across farms, rainforest areas and National Park Estates to prevent recolonisation from adjacent localities.

Design of a 9K illumina BeadChip for polar bears (Ursus maritimus) from RAD and transcriptome sequencing.

PubMed

Malenfant, René M; Coltman, David W; Davis, Corey S

2015-05-01

Single-nucleotide polymorphisms (SNPs) offer numerous advantages over anonymous markers such as microsatellites, including improved estimation of population parameters, finer-scale resolution of population structure and more precise genomic dissection of quantitative traits. However, many SNPs are needed to equal the resolution of a single microsatellite, and reliable large-scale genotyping of SNPs remains a challenge in nonmodel species. Here, we document the creation of a 9K Illumina Infinium BeadChip for polar bears (Ursus maritimus), which will be used to investigate: (i) the fine-scale population structure among Canadian polar bears and (ii) the genomic architecture of phenotypic traits in the Western Hudson Bay subpopulation. To this end, we used restriction-site associated DNA (RAD) sequencing from 38 bears across their circumpolar range, as well as blood/fat transcriptome sequencing of 10 individuals from Western Hudson Bay. Six-thousand RAD SNPs and 3000 transcriptomic SNPs were selected for the chip, based primarily on genomic spacing and gene function respectively. Of the 9000 SNPs ordered from Illumina, 8042 were successfully printed, and - after genotyping 1450 polar bears - 5441 of these SNPs were found to be well clustered and polymorphic. Using this array, we show rapid linkage disequilibrium decay among polar bears, we demonstrate that in a subsample of 78 individuals, our SNPs detect known genetic structure more clearly than 24 microsatellites genotyped for the same individuals and that these results are not driven by the SNP ascertainment scheme. Here, we present one of the first large-scale genotyping resources designed for a threatened species. © 2014 John Wiley & Sons Ltd.

Gravity Wave Interactions with Fine Structures in the Mesosphere and Lower Thermosphere

NASA Astrophysics Data System (ADS)

Mixa, Tyler; Fritts, David; Bossert, Katrina; Laughman, Brian; Wang, Ling; Lund, Thomas; Kantha, Lakshmi

2017-04-01

An anelastic numerical model is used to probe the influences of fine layering structures on gravity wave propagation in the Mesosphere and Lower Thermosphere (MLT). Recent lidar observations confirm the presence of persistent layered structures in the MLT that have sharp stratification and vertical scales below 1km. Gravity waves propagating through finely layered environments can excite and modulate the evolution of small scale instabilities that redefine the layering structure in these regions. Such layers in turn filter the outgoing wave spectra, promote ducting or reflection, hasten the onset of self-acceleration dynamics, and encourage wave/mean-flow interactions via energy and momentum transport. Using high resolution simulations of a localized gravity wave packet in a deep atmosphere, we identify the relative impacts of various wave and mean flow parameters to improve our understanding of these dynamics and complement recent state-of-the-art observations.

Fine-scale population structure in a desert amphibian: landscape genetics of the black toad (Bufo exsul).

PubMed

Wang, Ian J

2009-09-01

Environmental variables can strongly influence a variety of intra- and inter-population processes, including demography, population structure and gene flow. When environmental conditions are particularly harsh for a certain species, investigating these effects is important to understanding how populations persist under difficult conditions. Furthermore, species inhabiting challenging environments present excellent opportunities to examine the effects of complex landscapes on population processes because these effects will often be more pronounced. In this study, I use 16 microsatellite loci to examine population structure, gene flow and demographic history in the black toad, Bufo exsul, which has one of the most restricted natural ranges of any amphibian. Bufo exsul inhabits four springs in the Deep Springs Valley high desert basin and has never been observed more than several meters from any source of water. My results reveal limited gene flow and moderately high levels of population structure (F(ST) = 0.051-0.063) between all but the two closest springs. I found that the geographic distance across the arid scrub habitat between springs is significantly correlated with genetic structure when distance accounts for topography and barriers to dispersal. I also found very low effective population sizes (N(e) = 7-30) and substantial evidence for historical population bottlenecks in all four populations. Together, these results suggest that the desert landscape and B. exsul's high habitat specificity contribute significantly to population structure and demography in this species and emphasize the importance of considering behavioural and landscape data in conservation genetic studies of natural systems.

A genetic atlas of human admixture history.

PubMed

Hellenthal, Garrett; Busby, George B J; Band, Gavin; Wilson, James F; Capelli, Cristian; Falush, Daniel; Myers, Simon

2014-02-14

Modern genetic data combined with appropriate statistical methods have the potential to contribute substantially to our understanding of human history. We have developed an approach that exploits the genomic structure of admixed populations to date and characterize historical mixture events at fine scales. We used this to produce an atlas of worldwide human admixture history, constructed by using genetic data alone and encompassing over 100 events occurring over the past 4000 years. We identified events whose dates and participants suggest they describe genetic impacts of the Mongol empire, Arab slave trade, Bantu expansion, first millennium CE migrations in Eastern Europe, and European colonialism, as well as unrecorded events, revealing admixture to be an almost universal force shaping human populations.

Patch-Scale Effects of Equine Disturbance on Arthropod Assemblages and Vegetation Structure in Subalpine Wetlands

NASA Astrophysics Data System (ADS)

Holmquist, Jeffrey G.; Schmidt-Gengenbach, Jutta; Ballenger, Elizabeth A.

2014-06-01

Assessments of vertebrate disturbance to plant and animal assemblages often contrast grazed versus ungrazed meadows or other larger areas of usage, and this approach can be powerful. Random sampling of such habitats carries the potential, however, for smaller, more intensely affected patches to be missed and for other responses that are only revealed at smaller scales to also escape detection. We instead sampled arthropod assemblages and vegetation structure at the patch scale (400-900 m2 patches) within subalpine wet meadows of Yosemite National Park (USA), with the goal of determining if there were fine-scale differences in magnitude and directionality of response at three levels of grazing intensity. Effects were both stronger and more nuanced than effects evidenced by previous random sampling of paired grazed and ungrazed meadows: (a) greater negative effects on vegetation structure and fauna in heavily used patches, but (b) some positive effects on fauna in lightly grazed patches, suggested by trends for mean richness and total and population abundances. Although assessment of disturbance at either patch or landscape scales should be appropriate, depending on the management question at hand, our patch-scale work demonstrated that there can be strong local effects on the ecology of these wetlands that may not be detected by comparing larger scale habitats.

Patterns of population genetic variation in sympatric chiltoniid amphipods within a calcrete aquifer reveal a dynamic subterranean environment

PubMed Central

Bradford, T M; Adams, M; Guzik, M T; Humphreys, W F; Austin, A D; Cooper, S JB

2013-01-01

Calcrete aquifers from the Yilgarn region of arid central Western Australia contain an assemblage of obligate groundwater invertebrate species that are each endemic to single aquifers. Fine-scale phylogeographic and population genetic analyses of three sympatric and independently derived species of amphipod (Chiltoniidae) were carried out to determine whether there were common patterns of population genetic structure or evidence for past geographic isolation of populations within a single calcrete aquifer. Genetic diversity in amphipod mitochondrial DNA (cytochrome c oxidase subunit I gene) and allozymes were examined across a 3.5 km2 region of the Sturt Meadows calcrete, which contains a grid of 115 bore holes (=wells). Stygobiont amphipods were found to have high levels of mitochondrial haplotype diversity coupled with low nucleotide diversity. Mitochondrial phylogeographic structuring was found between haplogroups for one of the chiltoniid species, which also showed population structuring for nuclear markers. Signatures of population expansion in two of the three species, match previous findings for diving beetles at the same site, indicating that the system is dynamic. We propose isolation of populations in refugia within the calcrete, followed by expansion events, as the most likely source of intraspecific genetic diversity, due to changes in water level influencing gene flow across the calcrete. PMID:23549336

Fine-scale characteristics of interplanetary sector

NASA Technical Reports Server (NTRS)

Behannon, K. W.; Neubauer, F. M.; Barnstoff, H.

1980-01-01

The structure of the interplanetary sector boundaries observed by Helios 1 within sector transition regions was studied. Such regions consist of intermediate (nonspiral) average field orientations in some cases, as well as a number of large angle directional discontinuities (DD's) on the fine scale (time scales 1 hour). Such DD's are found to be more similar to tangential than rotational discontinuities, to be oriented on average more nearly perpendicular than parallel to the ecliptic plane to be accompanied usually by a large dip ( 80%) in B and, with a most probable thickness of 3 x 10 to the 4th power km, significantly thicker previously studied. It is hypothesized that the observed structures represent multiple traversals of the global heliospheric current sheet due to local fluctuations in the position of the sheet. There is evidence that such fluctuations are sometimes produced by wavelike motions or surface corrugations of scale length 0.05 - 0.1 AU superimposed on the large scale structure.

Application of a predator-prey overlap metric to determine the impact of sub-grid scale feeding dynamics on ecosystem productivity

NASA Astrophysics Data System (ADS)

Greer, A. T.; Woodson, C. B.

2016-02-01

Because of the complexity and extremely large size of marine ecosystems, research attention has a strong focus on modelling the system through space and time to elucidate processes driving ecosystem state. One of the major weaknesses of current modelling approaches is the reliance on a particular grid cell size (usually 10's of km in the horizontal & water column mean) to capture the relevant processes, even though empirical research has shown that marine systems are highly structured on fine scales, and this structure can persist over relatively long time scales (days to weeks). Fine-scale features can have a strong influence on the predator-prey interactions driving trophic transfer. Here we apply a statistic, the AB ratio, used to quantify increased predator production due to predator-prey overlap on fine scales in a manner that is computationally feasible for larger scale models. We calculated the AB ratio for predator-prey distributions throughout the scientific literature, as well as for data obtained with a towed plankton imaging system, demonstrating that averaging across a typical model grid cell neglects the fine-scale predator-prey overlap that is an essential component of ecosystem productivity. Organisms from a range of trophic levels and oceanographic regions tended to overlap with their prey both in the horizontal and vertical dimensions. When predator swimming over a diel cycle was incorporated, the amount of production indicated by the AB ratio increased substantially. For the plankton image data, the AB ratio was higher with increasing sampling resolution, especially when prey were highly aggregated. We recommend that ecosystem models incorporate more fine-scale information both to more accurately capture trophic transfer processes and to capitalize on the increasing sampling resolution and data volume from empirical studies.

Integrating High-Resolution Datasets to Target Mitigation Efforts for Improving Air Quality and Public Health in Urban Neighborhoods

PubMed Central

Shandas, Vivek; Voelkel, Jackson; Rao, Meenakshi; George, Linda

2016-01-01

Reducing exposure to degraded air quality is essential for building healthy cities. Although air quality and population vary at fine spatial scales, current regulatory and public health frameworks assess human exposures using county- or city-scales. We build on a spatial analysis technique, dasymetric mapping, for allocating urban populations that, together with emerging fine-scale measurements of air pollution, addresses three objectives: (1) evaluate the role of spatial scale in estimating exposure; (2) identify urban communities that are disproportionately burdened by poor air quality; and (3) estimate reduction in mobile sources of pollutants due to local tree-planting efforts using nitrogen dioxide. Our results show a maximum value of 197% difference between cadastrally-informed dasymetric system (CIDS) and standard estimations of population exposure to degraded air quality for small spatial extent analyses, and a lack of substantial difference for large spatial extent analyses. These results provide the foundation for improving policies for managing air quality, and targeting mitigation efforts to address challenges of environmental justice. PMID:27527205

Fine-scale mapping of a locus for severe bipolar mood disorder on chromosome 18p11.3 in the Costa Rican population

PubMed Central

McInnes, L. Alison; Service, Susan K.; Reus, Victor I.; Barnes, Glenn; Charlat, Olga; Jawahar, Satya; Lewitzky, Steve; Yang, Qing; Duong, Quyen; Spesny, Mitzi; Araya, Carmen; Araya, Xinia; Gallegos, Alvaro; Meza, Luis; Molina, Julio; Ramirez, Rolando; Mendez, Roxana; Silva, Sandra; Fournier, Eduardo; Batki, Steven L.; Mathews, Carol A.; Neylan, Thomas; Glatt, Charles E.; Escamilla, Michael A.; Luo, David; Gajiwala, Paresh; Song, Terry; Crook, Stephen; Nguyen, Jasmine B.; Roche, Erin; Meyer, Joanne M.; Leon, Pedro; Sandkuijl, Lodewijk A.; Freimer, Nelson B.; Chen, Hong

2001-01-01

We have searched for genes predisposing to bipolar disorder (BP) by studying individuals with the most extreme form of the affected phenotype, BP-I, ascertained from the genetically isolated population of the Central Valley of Costa Rica (CVCR). The results of a previous linkage analysis on two extended CVCR BP-I pedigrees, CR001 and CR004, and of linkage disequilibrium (LD) analyses of a CVCR population sample of BP-I patients implicated a candidate region on 18p11.3. We further investigated this region by creating a physical map and developing 4 new microsatellite and 26 single-nucleotide polymorphism markers for typing in the pedigree and population samples. We report the results of fine-scale association analyses in the population sample, as well as evaluation of haplotypes in pedigree CR001. Our results suggest a candidate region containing six genes but also highlight the complexities of LD mapping of common disorders. PMID:11572994

Effect of a delta tab on fine scale mixing in a turbulent two-stream shear layer

NASA Technical Reports Server (NTRS)

Foss, J. K.; Zaman, K. B. M. Q.

1996-01-01

The fine scale mixing produced by a delta tab in a shear layer has been studied experimentally. The tab was placed at the trailing edge of a splitter plate which produced a turbulent two-stream mixing layer. The tab apex tilted downstream and into the high speed stream. Hot-wire measurements in the 3-D space behind the tab detailed the three velocity components as well as the small scale population distributions. These small scale eddies, which represent the peak in the dissipation spectrum, were identified and counted using the Peak-Valley-Counting technique. It was found that the small scale populations were greater in the shear region behind the tab, with the greatest increase occurring where the shear layer underwent a sharp turn. This location was near, but not coincident, with the core of the streamwise vortex, and away from the region exhibiting maximum turbulence intensity. Moreover, the tab increased the most probably frequency and strain rate of the small scales. It made the small scales smaller and more energetic.

Satellite-Scale Snow Water Equivalent Assimilation into a High-Resolution Land Surface Model

NASA Technical Reports Server (NTRS)

De Lannoy, Gabrielle J.M.; Reichle, Rolf H.; Houser, Paul R.; Arsenault, Kristi R.; Verhoest, Niko E.C.; Paulwels, Valentijn R.N.

2009-01-01

An ensemble Kalman filter (EnKF) is used in a suite of synthetic experiments to assimilate coarse-scale (25 km) snow water equivalent (SWE) observations (typical of satellite retrievals) into fine-scale (1 km) model simulations. Coarse-scale observations are assimilated directly using an observation operator for mapping between the coarse and fine scales or, alternatively, after disaggregation (re-gridding) to the fine-scale model resolution prior to data assimilation. In either case observations are assimilated either simultaneously or independently for each location. Results indicate that assimilating disaggregated fine-scale observations independently (method 1D-F1) is less efficient than assimilating a collection of neighboring disaggregated observations (method 3D-Fm). Direct assimilation of coarse-scale observations is superior to a priori disaggregation. Independent assimilation of individual coarse-scale observations (method 3D-C1) can bring the overall mean analyzed field close to the truth, but does not necessarily improve estimates of the fine-scale structure. There is a clear benefit to simultaneously assimilating multiple coarse-scale observations (method 3D-Cm) even as the entire domain is observed, indicating that underlying spatial error correlations can be exploited to improve SWE estimates. Method 3D-Cm avoids artificial transitions at the coarse observation pixel boundaries and can reduce the RMSE by 60% when compared to the open loop in this study.

Influence of habitat discontinuity, geographical distance, and oceanography on fine-scale population genetic structure of copper rockfish (Sebastes caurinus).

PubMed

Johansson, M L; Banks, M A; Glunt, K D; Hassel-Finnegan, H M; Buonaccorsi, V P

2008-07-01

The copper rockfish is a benthic, nonmigratory, temperate rocky reef marine species with pelagic larvae and juveniles. A previous range-wide study of the population-genetic structure of copper rockfish revealed a pattern consistent with isolation-by-distance. This could arise from an intrinsically limited dispersal capability in the species or from regularly-spaced extrinsic barriers that restrict gene flow (offshore jets that advect larvae offshore and/or habitat patchiness). Tissue samples were collected along the West Coast of the contiguous USA between Neah Bay, WA and San Diego, CA, with dense sampling along Oregon. At the whole-coast scale (approximately 2200 km), significant population subdivision (F(ST) = 0.0042), and a significant correlation between genetic and geographical distance were observed based on 11 microsatellite DNA loci. Population divergence was also significant among Oregon collections (approximately 450 km, F(ST) = 0.001). Hierarchical amova identified a weak but significant 130-km habitat break as a possible barrier to gene flow within Oregon, across which we estimated that dispersal (N(e)m) is half that of the coast-wide average. However, individual-based Bayesian analyses failed to identify more than a single population along the Oregon coast. In addition, no correlation between pairwise population genetic and geographical distances was detected at this scale. The offshore jet at Cape Blanco was not a significant barrier to gene flow in this species. These findings are consistent with low larval dispersal distances calculated in previous studies on this species, support a mesoscale dispersal model, and highlight the importance of continuity of habitat and adult population size in maintaining gene flow.

The role of gene flow in shaping genetic structures of the subtropical conifer species Araucaria angustifolia.

PubMed

Stefenon, V M; Gailing, O; Finkeldey, R

2008-05-01

The morphological features of pollen and seed of Araucaria angustifolia have led to the proposal of limited gene dispersal for this species. We used nuclear microsatellite and AFLP markers to assess patterns of genetic variation in six natural populations at the intra- and inter-population level, and related our findings to gene dispersal in this species. Estimates of both fine-scale spatial genetic structure (SGS) and migration rate suggest relatively short-distance gene dispersal. However, gene dispersal differed among populations, and effects of more efficient dispersal within population were observed in at least one stand. In addition, even though some seed dispersal may be aggregated in this principally barochorous species, reasonable secondary seed dispersal, presumably facilitated by animals, and overlap of seed shadows within populations is suggested. Overall, no correlation was observed between levels of SGS and inbreeding, density or age structure, except that a higher level of SGS was revealed for the population with a higher number of juvenile individuals. A low estimate for the number of migrants per generation between two neighbouring populations implies limited gene flow. We expect that stepping-stone pollen flow may have contributed to low genetic differentiation among populations observed in a previous survey. Thus, strategies for maintenance of gene flow among remnant populations should be considered in order to avoid degrading effects of population fragmentation on the evolution of A. angustifolia.

Contrasting patterns of fine-scale herb layer species composition in temperate forests

NASA Astrophysics Data System (ADS)

Chudomelová, Markéta; Zelený, David; Li, Ching-Feng

2017-04-01

Although being well described at the landscape level, patterns in species composition of forest herb layer are rarely studied at smaller scales. Here, we examined fine-scale environmental determinants and spatial structures of herb layer communities in thermophilous oak- and hornbeam dominated forests of the south-eastern part of the Czech Republic. Species composition of herb layer vegetation and environmental variables were recorded within a fixed grid of 2 × 2 m subplots regularly distributed within 1-ha quadrate plots in three forest stands. For each site, environmental models best explaining species composition were constructed using constrained ordination analysis. Spatial eigenvector mapping was used to model and account for spatial structures in community variation. Mean Ellenberg indicator values calculated for each subplot were used for ecological interpretation of spatially structured residual variation. The amount of variation explained by environmental and spatial models as well as the selection of variables with the best explanatory power differed among sites. As an important environmental factor, relative elevation was common to all three sites, while pH and canopy openness were shared by two sites. Both environmental and community variation was mostly coarse-scaled, as was the spatially structured portion of residual variation. When corrected for bias due to spatial autocorrelation, those environmental factors with already weak explanatory power lost their significance. Only a weak evidence of possibly omitted environmental predictor was found for autocorrelated residuals of site models using mean Ellenberg indicator values. Community structure was determined by different factors at different sites. The relative importance of environmental filtering vs. spatial processes was also site specific, implying that results of fine-scale studies tend to be shaped by local conditions. Contrary to expectations based on other studies, overall dominance of spatial processes at fine scale has not been detected. Ecologists should keep this in mind when making generalizations about community dynamics.

Spatial heterogeneity in ecologically important climate variables at coarse and fine scales in a high-snow mountain landscape.

PubMed

Ford, Kevin R; Ettinger, Ailene K; Lundquist, Jessica D; Raleigh, Mark S; Hille Ris Lambers, Janneke

2013-01-01

Climate plays an important role in determining the geographic ranges of species. With rapid climate change expected in the coming decades, ecologists have predicted that species ranges will shift large distances in elevation and latitude. However, most range shift assessments are based on coarse-scale climate models that ignore fine-scale heterogeneity and could fail to capture important range shift dynamics. Moreover, if climate varies dramatically over short distances, some populations of certain species may only need to migrate tens of meters between microhabitats to track their climate as opposed to hundreds of meters upward or hundreds of kilometers poleward. To address these issues, we measured climate variables that are likely important determinants of plant species distributions and abundances (snow disappearance date and soil temperature) at coarse and fine scales at Mount Rainier National Park in Washington State, USA. Coarse-scale differences across the landscape such as large changes in elevation had expected effects on climatic variables, with later snow disappearance dates and lower temperatures at higher elevations. However, locations separated by small distances (∼20 m), but differing by vegetation structure or topographic position, often experienced differences in snow disappearance date and soil temperature as great as locations separated by large distances (>1 km). Tree canopy gaps and topographic depressions experienced later snow disappearance dates than corresponding locations under intact canopy and on ridges. Additionally, locations under vegetation and on topographic ridges experienced lower maximum and higher minimum soil temperatures. The large differences in climate we observed over small distances will likely lead to complex range shift dynamics and could buffer species from the negative effects of climate change.

Spatial Heterogeneity in Ecologically Important Climate Variables at Coarse and Fine Scales in a High-Snow Mountain Landscape

PubMed Central

Ford, Kevin R.; Ettinger, Ailene K.; Lundquist, Jessica D.; Raleigh, Mark S.; Hille Ris Lambers, Janneke

2013-01-01

Climate plays an important role in determining the geographic ranges of species. With rapid climate change expected in the coming decades, ecologists have predicted that species ranges will shift large distances in elevation and latitude. However, most range shift assessments are based on coarse-scale climate models that ignore fine-scale heterogeneity and could fail to capture important range shift dynamics. Moreover, if climate varies dramatically over short distances, some populations of certain species may only need to migrate tens of meters between microhabitats to track their climate as opposed to hundreds of meters upward or hundreds of kilometers poleward. To address these issues, we measured climate variables that are likely important determinants of plant species distributions and abundances (snow disappearance date and soil temperature) at coarse and fine scales at Mount Rainier National Park in Washington State, USA. Coarse-scale differences across the landscape such as large changes in elevation had expected effects on climatic variables, with later snow disappearance dates and lower temperatures at higher elevations. However, locations separated by small distances (∼20 m), but differing by vegetation structure or topographic position, often experienced differences in snow disappearance date and soil temperature as great as locations separated by large distances (>1 km). Tree canopy gaps and topographic depressions experienced later snow disappearance dates than corresponding locations under intact canopy and on ridges. Additionally, locations under vegetation and on topographic ridges experienced lower maximum and higher minimum soil temperatures. The large differences in climate we observed over small distances will likely lead to complex range shift dynamics and could buffer species from the negative effects of climate change. PMID:23762277

CONSTRAINTS ON SPATIAL VARIATIONS IN THE FINE-STRUCTURE CONSTANT FROM PLANCK

DOE Office of Scientific and Technical Information (OSTI.GOV)

O'Bryan, Jon; Smidt, Joseph; De Bernardis, Francesco

2015-01-01

We use the cosmic microwave background (CMB) anisotropy data from Planck to constrain the spatial fluctuations of the fine-structure constant α at a redshift of 1100. We use a quadratic estimator to measure the four-point correlation function of the CMB temperature anisotropies and extract the angular power spectrum fine-structure constant spatial variations projected along the line of sight at the last scattering surface. At tens of degree angular scales and above, we constrain the fractional rms fluctuations of the fine-structure constant to be (δα/α){sub rms} < 3.4 × 10{sup –3} at the 68% confidence level. We find no evidence formore » a spatially varying α at a redshift of 10{sup 3}.« less

QUIESCENT PROMINENCES IN THE ERA OF ALMA: SIMULATED OBSERVATIONS USING THE 3D WHOLE-PROMINENCE FINE STRUCTURE MODEL

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gunár, Stanislav; Heinzel, Petr; Mackay, Duncan H.

2016-12-20

We use the detailed 3D whole-prominence fine structure model to produce the first simulated high-resolution ALMA observations of a modeled quiescent solar prominence. The maps of synthetic brightness temperature and optical thickness shown in the present paper are produced using a visualization method for synthesis of the submillimeter/millimeter radio continua. We have obtained the simulated observations of both the prominence at the limb and the filament on the disk at wavelengths covering a broad range that encompasses the full potential of ALMA. We demonstrate here extent to which the small-scale and large-scale prominence and filament structures will be visible inmore » the ALMA observations spanning both the optically thin and thick regimes. We analyze the relationship between the brightness and kinetic temperature of the prominence plasma. We also illustrate the opportunities ALMA will provide for studying the thermal structure of the prominence plasma from the cores of the cool prominence fine structure to the prominence–corona transition region. In addition, we show that detailed 3D modeling of entire prominences with their numerous fine structures will be important for the correct interpretation of future ALMA observations of prominences.« less

Recovering the fine structures in solar images

NASA Technical Reports Server (NTRS)

Karovska, Margarita; Habbal, S. R.; Golub, L.; Deluca, E.; Hudson, Hugh S.

1994-01-01

Several examples of the capability of the blind iterative deconvolution (BID) technique to recover the real point spread function, when limited a priori information is available about its characteristics. To demonstrate the potential of image post-processing for probing the fine scale and temporal variability of the solar atmosphere, the BID technique is applied to different samples of solar observations from space. The BID technique was originally proposed for correction of the effects of atmospheric turbulence on optical images. The processed images provide a detailed view of the spatial structure of the solar atmosphere at different heights in regions with different large-scale magnetic field structures.

Population genetics of the understory fishtail palm Chamaedorea ernesti-augusti in Belize: high genetic connectivity with local differentiation

PubMed Central

Cibrián-Jaramillo, Angélica; Bacon, Christine D; Garwood, Nancy C; Bateman, Richard M; Thomas, Meredith M; Russell, Steve; Bailey, C Donovan; Hahn, William J; Bridgewater, Samuel GM; DeSalle, Rob

2009-01-01

Background Developing a greater understanding of population genetic structure in lowland tropical plant species is highly relevant to our knowledge of increasingly fragmented forests and to the conservation of threatened species. Specific studies are particularly needed for taxa whose population dynamics are further impacted by human harvesting practices. One such case is the fishtail or xaté palm (Chamaedorea ernesti-augusti) of Central America, whose wild-collected leaves are becoming progressively more important to the global ornamental industry. We use microsatellite markers to describe the population genetics of this species in Belize and test the effects of climate change and deforestation on its recent and historical effective population size. Results We found high levels of inbreeding coupled with moderate or high allelic diversity within populations. Overall high gene flow was observed, with a north and south gradient and ongoing differentiation at smaller spatial scales. Immigration rates among populations were more difficult to discern, with minimal evidence for isolation by distance. We infer a tenfold reduction in effective population size ca. 10,000 years ago, but fail to detect changes attributable to Mayan or contemporary deforestation. Conclusion Populations of C. ernesti-augusti are genetically heterogeneous demes at a local spatial scale, but are widely connected at a regional level in Belize. We suggest that the inferred patterns in population genetic structure are the result of the colonization of this species into Belize following expansion of humid forests in combination with demographic and mating patterns. Within populations, we hypothesize that low aggregated population density over large areas, short distance pollen dispersal via thrips, low adult survival, and low fruiting combined with early flowering may contribute towards local inbreeding via genetic drift. Relatively high levels of regional connectivity are likely the result of animal-mediated long-distance seed dispersal. The greatest present threat to the species is the potential onset of inbreeding depression as the result of increased human harvesting activities. Future genetic studies in understory palms should focus on both fine-scale and landscape-level genetic structure. PMID:19818141

New Multilocus Variable-Number Tandem-Repeat Analysis (MLVA) Scheme for Fine-Scale Monitoring and Microevolution-Related Study of Ralstonia pseudosolanacearum Phylotype I Populations

PubMed Central

Guinard, Jérémy; Latreille, Anne; Guérin, Fabien; Poussier, Stéphane

2016-01-01

ABSTRACT Bacterial wilt caused by the Ralstonia solanacearum species complex (RSSC) is considered one of the most harmful plant diseases in the world. Special attention should be paid to R. pseudosolanacearum phylotype I due to its large host range, its worldwide distribution, and its high evolutionary potential. So far, the molecular epidemiology and population genetics of this bacterium are poorly understood. Until now, the genetic structure of the RSSC has been analyzed on the worldwide and regional scales. Emerging questions regarding evolutionary forces in RSSC adaptation to hosts now require genetic markers that are able to monitor RSSC field populations. In this study, we aimed to evaluate the multilocus variable-number tandem-repeat analysis (MLVA) approach for its ability to discriminate genetically close phylotype I strains and for population genetics studies. We developed a new MLVA scheme (MLVA-7) allowing us to genotype 580 R. pseudosolanacearum phylotype I strains extracted from susceptible and resistant hosts and from different habitats (stem, soil, and rhizosphere). Based on specificity, polymorphism, and the amplification success rate, we selected seven fast-evolving variable-number tandem-repeat (VNTR) markers. The newly developed MLVA-7 scheme showed higher discriminatory power than the previously published MLVA-13 scheme when applied to collections sampled from the same location on different dates and to collections from different locations on very small scales. Our study provides a valuable tool for fine-scale monitoring and microevolution-related study of R. pseudosolanacearum phylotype I populations. IMPORTANCE Understanding the evolutionary dynamics of adaptation of plant pathogens to new hosts or ecological niches has become a key point for the development of innovative disease management strategies, including durable resistance. Whereas the molecular mechanisms underlying virulence or pathogenicity changes have been studied thoroughly, the population genetics of plant pathogen adaptation remains an open, unexplored field, especially for plant-pathogenic bacteria. MLVA has become increasingly popular for epidemiosurveillance and molecular epidemiology studies of plant pathogens. However, this method has been used mostly for genotyping and identification on a regional or global scale. In this study, we developed a new MLVA scheme, targeting phylotype I of the soilborne Ralstonia solanacearum species complex (RSSC), specifically to address the bacterial population genetics on the field scale. Such a MLVA scheme, based on fast-evolving loci, may be a tool of choice for field experimental evolution and spatial genetics studies. PMID:28003195

Seafloor Tectonic Fabric from Satellite Altimetry

NASA Astrophysics Data System (ADS)

Smith, Walter H. F.

Ocean floor structures with horizontal scales of 10 to a few hundred kilometers and vertical scales of 100 m or more generate sea surface gravity anomalies observable with satellite altimetry. Prior to 1990, altimeter data resolved only tectonic lineaments, some seamounts, and some aspects of mid-ocean ridge structure. New altimeter data available since mid-1995 resolve 10-km--scale structures over nearly all the world's oceans. These data are the basis of new global bathymetric maps and have been interpreted as exhibiting complexities in the sea floor spreading process including ridge jumps, propagating rifts, and variations in magma supply. This chapter reviews the satellite altimetry technique and its resolution of tectonic structures, gives examples of intriguing tectonic phenomena, and shows that structures as small as abyssal hills are partially resolved. A new result obtained here is that the amplitude of the fine-scale (10--80 km) roughness of old ocean floor is spreading-rate dependent in the same that it is at mid-ocean ridges, suggesting that fine-scale tectonic fabric is generated nearly exclusively by ridge-axis processes.

Increased fire frequency promotes stronger spatial genetic structure and natural selection at regional and local scales in Pinus halepensis Mill

PubMed Central

González-Martínez, Santiago C.; Navascués, Miguel; Burgarella, Concetta; Mosca, Elena; Lorenzo, Zaida; Zabal-Aguirre, Mario; Vendramin, Giovanni G.; Verdú, Miguel; Pausas, Juli G.

2017-01-01

Background and Aims The recurrence of wildfires is predicted to increase due to global climate change, resulting in severe impacts on biodiversity and ecosystem functioning. Recurrent fires can drive plant adaptation and reduce genetic diversity; however, the underlying population genetic processes have not been studied in detail. In this study, the neutral and adaptive evolutionary effects of contrasting fire regimes were examined in the keystone tree species Pinus halepensis Mill. (Aleppo pine), a fire-adapted conifer. The genetic diversity, demographic history and spatial genetic structure were assessed at local (within-population) and regional scales for populations exposed to different crown fire frequencies. Methods Eight natural P. halepensis stands were sampled in the east of the Iberian Peninsula, five of them in a region exposed to frequent crown fires (HiFi) and three of them in an adjacent region with a low frequency of crown fires (LoFi). Samples were genotyped at nine neutral simple sequence repeats (SSRs) and at 251 single nucleotide polymorphisms (SNPs) from coding regions, some of them potentially important for fire adaptation. Key Results Fire regime had no effects on genetic diversity or demographic history. Three high-differentiation outlier SNPs were identified between HiFi and LoFi stands, suggesting fire-related selection at the regional scale. At the local scale, fine-scale spatial genetic structure (SGS) was overall weak as expected for a wind-pollinated and wind-dispersed tree species. HiFi stands displayed a stronger SGS than LoFi stands at SNPs, which probably reflected the simultaneous post-fire recruitment of co-dispersed related seeds. SNPs with exceptionally strong SGS, a proxy for microenvironmental selection, were only reliably identified under the HiFi regime. Conclusions An increasing fire frequency as predicted due to global change can promote increased SGS with stronger family structures and alter natural selection in P. halepensis and in plants with similar life history traits. PMID:28159988

Fine-Granularity Functional Interaction Signatures for Characterization of Brain Conditions

PubMed Central

Hu, Xintao; Zhu, Dajiang; Lv, Peili; Li, Kaiming; Han, Junwei; Wang, Lihong; Shen, Dinggang; Guo, Lei; Liu, Tianming

2014-01-01

In the human brain, functional activity occurs at multiple spatial scales. Current studies on functional brain networks and their alterations in brain diseases via resting-state functional magnetic resonance imaging (rs-fMRI) are generally either at local scale (regionally confined analysis and inter-regional functional connectivity analysis) or at global scale (graph theoretic analysis). In contrast, inferring functional interaction at fine-granularity sub-network scale has not been adequately explored yet. Here our hypothesis is that functional interaction measured at fine-granularity subnetwork scale can provide new insight into the neural mechanisms of neurological and psychological conditions, thus offering complementary information for healthy and diseased population classification. In this paper, we derived fine-granularity functional interaction (FGFI) signatures in subjects with Mild Cognitive Impairment (MCI) and Schizophrenia by diffusion tensor imaging (DTI) and rsfMRI, and used patient-control classification experiments to evaluate the distinctiveness of the derived FGFI features. Our experimental results have shown that the FGFI features alone can achieve comparable classification performance compared with the commonly used inter-regional connectivity features. However, the classification performance can be substantially improved when FGFI features and inter-regional connectivity features are integrated, suggesting the complementary information achieved from the FGFI signatures. PMID:23319242

Multiple drivers, scales, and interactions influence southern Appalachian stream salamander occupancy

Treesearch

Kristen K. Cecala; John C. Maerz; Brian J. Halstead; John R. Frisch; Ted L. Gragson; Jeffrey Hepinstall-Cymerman; David S. Leigh; C. Rhett Jackson; James T. Peterson; Catherine M. Pringle

2018-01-01

Understanding how factors that vary in spatial scale relate to population abundance is vital to forecasting species responses to environmental change. Stream and river ecosystems are inherently hierarchical, potentially resulting in organismal responses to fine‐scale changes in patch characteristics that are conditional on the watershed context. Here, we...

Three Types of Earth's Inner Core Boundary

NASA Astrophysics Data System (ADS)

Tian, D.; Wen, L.

2017-12-01

The Earth's inner core boundary (ICB) is the site where the liquid outer core solidifies and the solid inner core grows. Thus, the fine-scale structure of the ICB is important for our understanding of the thermo-compositional state of the Earth's core. In this study, we collect a large set of seismic records with high-quality pre-critical PKiKP and PcP phase pairs, recorded by two dense seismic arrays, Hi-net in Japan and USArray in US. This dataset samples the ICB regions beneath East Asia, Mexico and the Bering Sea. We use differential travel times, amplitude ratios and waveform differences between PKiKP and PcP phases to constrain fine-scale structure of the ICB. The sampled ICB can be grouped into three types based on their seismic characteristics: (1) a simple ICB with a flat and sharp boundary, (2) a bumpy ICB with topographic height changes of 10 km, and (3) a localized mushy ICB with laterally varying thicknesses of 4-8 km. The laterally varying fine-scale structure of the ICB indicates existence of complex small-scale forces at the surface and a laterally varying solidification process of the inner core due to lateral variation of thermo-compositional condition near the ICB.

Origin of fine structure of the giant dipole resonance in s d -shell nuclei

NASA Astrophysics Data System (ADS)

Fearick, R. W.; Erler, B.; Matsubara, H.; von Neumann-Cosel, P.; Richter, A.; Roth, R.; Tamii, A.

2018-04-01

A set of high-resolution zero-degree inelastic proton scattering data on 24Mg, 28Si, 32S, and 40Ca provides new insight into the long-standing puzzle of the origin of fragmentation of the giant dipole resonance (GDR) in s d -shell nuclei. Understanding is achieved by comparison with random phase approximation calculations for deformed nuclei using for the first time a realistic nucleon-nucleon interaction derived from the Argonne V18 potential with the unitary correlation operator method and supplemented by a phenomenological three-nucleon contact interaction. A wavelet analysis allows one to extract significant scales both in the data and calculations characterizing the fine structure of the GDR. The fair agreement for scales in the range of a few hundred keV supports the surmise that the fine structure arises from ground-state deformation driven by α clustering.

Ultrafast exciton fine structure relaxation dynamics in lead chalcogenide nanocrystals.

PubMed

Johnson, Justin C; Gerth, Kathrine A; Song, Qing; Murphy, James E; Nozik, Arthur J; Scholes, Gregory D

2008-05-01

The rates of fine structure relaxation in PbS, PbSe, and PbTe nanocrystals were measured on a femtosecond time scale as a function of temperature with no applied magnetic field by cross-polarized transient grating spectroscopy (CPTG) and circularly polarized pump-probe spectroscopy. The relaxation rates among exciton fine structure states follow trends with nanocrystal composition and size that are consistent with the expected influence of material dependent spin-orbit coupling, confinement enhanced electron-hole exchange interaction, and splitting between L valleys that are degenerate in the bulk. The size dependence of the fine structure relaxation rate is considerably different from what is observed for small CdSe nanocrystals, which appears to result from the unique material properties of the highly confined lead chalcogenide quantum dots. Modeling and qualitative considerations lead to conclusions about the fine structure of the lowest exciton absorption band, which has a potentially significant bearing on photophysical processes that make these materials attractive for practical purposes.

Global MLST of Salmonella Typhi Revisited in Post-genomic Era: Genetic Conservation, Population Structure, and Comparative Genomics of Rare Sequence Types.

PubMed

Yap, Kien-Pong; Ho, Wing S; Gan, Han M; Chai, Lay C; Thong, Kwai L

2016-01-01

Typhoid fever, caused by Salmonella enterica serovar Typhi, remains an important public health burden in Southeast Asia and other endemic countries. Various genotyping methods have been applied to study the genetic variations of this human-restricted pathogen. Multilocus sequence typing (MLST) is one of the widely accepted methods, and recently, there is a growing interest in the re-application of MLST in the post-genomic era. In this study, we provide the global MLST distribution of S. Typhi utilizing both publicly available 1,826 S. Typhi genome sequences in addition to performing conventional MLST on S. Typhi strains isolated from various endemic regions spanning over a century. Our global MLST analysis confirms the predominance of two sequence types (ST1 and ST2) co-existing in the endemic regions. Interestingly, S. Typhi strains with ST8 are currently confined within the African continent. Comparative genomic analyses of ST8 and other rare STs with genomes of ST1/ST2 revealed unique mutations in important virulence genes such as flhB, sipC, and tviD that may explain the variations that differentiate between seemingly successful (widespread) and unsuccessful (poor dissemination) S. Typhi populations. Large scale whole-genome phylogeny demonstrated evidence of phylogeographical structuring and showed that ST8 may have diverged from the earlier ancestral population of ST1 and ST2, which later lost some of its fitness advantages, leading to poor worldwide dissemination. In response to the unprecedented increase in genomic data, this study demonstrates and highlights the utility of large-scale genome-based MLST as a quick and effective approach to narrow the scope of in-depth comparative genomic analysis and consequently provide new insights into the fine scale of pathogen evolution and population structure.

Spatio-temporal population structuring and genetic diversity retention in depleted Atlantic Bluefin tuna of the Mediterranean Sea

PubMed Central

Riccioni, Giulia; Landi, Monica; Ferrara, Giorgia; Milano, Ilaria; Cariani, Alessia; Zane, Lorenzo; Sella, Massimo; Barbujani, Guido; Tinti, Fausto

2010-01-01

Fishery genetics have greatly changed our understanding of population dynamics and structuring in marine fish. In this study, we show that the Atlantic Bluefin tuna (ABFT, Thunnus thynnus), an oceanic predatory species exhibiting highly migratory behavior, large population size, and high potential for dispersal during early life stages, displays significant genetic differences over space and time, both at the fine and large scales of variation. We compared microsatellite variation of contemporary (n = 256) and historical (n = 99) biological samples of ABFTs of the central-western Mediterranean Sea, the latter dating back to the early 20th century. Measures of genetic differentiation and a general heterozygote deficit suggest that differences exist among population samples, both now and 96–80 years ago. Thus, ABFTs do not represent a single panmictic population in the Mediterranean Sea. Statistics designed to infer changes in population size, both from current and past genetic variation, suggest that some Mediterranean ABFT populations, although still not severely reduced in their genetic potential, might have suffered from demographic declines. The short-term estimates of effective population size are straddled on the minimum threshold (effective population size = 500) indicated to maintain genetic diversity and evolutionary potential across several generations in natural populations. PMID:20080643

Strained spiral vortex model for turbulent fine structure

NASA Technical Reports Server (NTRS)

Lundgren, T. S.

1982-01-01

A model for the intermittent fine structure of high Reynolds number turbulence is proposed. The model consists of slender axially strained spiral vortex solutions of the Navier-Stokes equation. The tightening of the spiral turns by the differential rotation of the induced swirling velocity produces a cascade of velocity fluctuations to smaller scale. The Kolmogorov energy spectrum is a result of this model.

Theory and data for simulating fine-scale human movement in an urban environment

PubMed Central

Perkins, T. Alex; Garcia, Andres J.; Paz-Soldán, Valerie A.; Stoddard, Steven T.; Reiner, Robert C.; Vazquez-Prokopec, Gonzalo; Bisanzio, Donal; Morrison, Amy C.; Halsey, Eric S.; Kochel, Tadeusz J.; Smith, David L.; Kitron, Uriel; Scott, Thomas W.; Tatem, Andrew J.

2014-01-01

Individual-based models of infectious disease transmission depend on accurate quantification of fine-scale patterns of human movement. Existing models of movement either pertain to overly coarse scales, simulate some aspects of movement but not others, or were designed specifically for populations in developed countries. Here, we propose a generalizable framework for simulating the locations that an individual visits, time allocation across those locations, and population-level variation therein. As a case study, we fit alternative models for each of five aspects of movement (number, distance from home and types of locations visited; frequency and duration of visits) to interview data from 157 residents of the city of Iquitos, Peru. Comparison of alternative models showed that location type and distance from home were significant determinants of the locations that individuals visited and how much time they spent there. We also found that for most locations, residents of two neighbourhoods displayed indistinguishable preferences for visiting locations at various distances, despite differing distributions of locations around those neighbourhoods. Finally, simulated patterns of time allocation matched the interview data in a number of ways, suggesting that our framework constitutes a sound basis for simulating fine-scale movement and for investigating factors that influence it. PMID:25142528

A genetic atlas of human admixture history

PubMed Central

Hellenthal, Garrett; Busby, George B.J.; Band, Gavin; Wilson, James F.; Capelli, Cristian

2014-01-01

Modern genetic data combined with appropriate statistical methods have the potential to contribute substantially to our understanding of human history. We have developed an approach that exploits the genomic structure of admixed populations to date and characterize historical mixture events at fine scales. We used this to produce an atlas of worldwide human admixture history, constructed using genetic data alone and encompassing over 100 events occurring over the past 4,000 years. We identify events whose dates and participants suggest they describe genetic impacts of the Mongol Empire, Arab slave trade, Bantu expansion, first millennium CE migrations in eastern Europe, and European colonialism, as well as unrecorded events, revealing admixture to be an almost universal force shaping human populations. PMID:24531965

Development of fine-resolution analyses and expanded large-scale forcing properties. Part I: Methodology and evaluation

DOE PAGES

Li, Zhijin; Vogelmann, Andrew M.; Feng, Sha; ...

2015-01-20

We produce fine-resolution, three-dimensional fields of meteorological and other variables for the U.S. Department of Energy’s Atmospheric Radiation Measurement (ARM) Southern Great Plains site. The Community Gridpoint Statistical Interpolation system is implemented in a multiscale data assimilation (MS-DA) framework that is used within the Weather Research and Forecasting model at a cloud-resolving resolution of 2 km. The MS-DA algorithm uses existing reanalysis products and constrains fine-scale atmospheric properties by assimilating high-resolution observations. A set of experiments show that the data assimilation analysis realistically reproduces the intensity, structure, and time evolution of clouds and precipitation associated with a mesoscale convective system.more » Evaluations also show that the large-scale forcing derived from the fine-resolution analysis has an overall accuracy comparable to the existing ARM operational product. For enhanced applications, the fine-resolution fields are used to characterize the contribution of subgrid variability to the large-scale forcing and to derive hydrometeor forcing, which are presented in companion papers.« less

From broadscale patterns to fine-scale processes: habitat structure influences genetic differentiation in the pitcher plant midge across multiple spatial scales.

PubMed

Rasic, Gordana; Keyghobadi, Nusha

2012-01-01

The spatial scale at which samples are collected and analysed influences the inferences that can be drawn from landscape genetic studies. We examined genetic structure and its landscape correlates in the pitcher plant midge, Metriocnemus knabi, an inhabitant of the purple pitcher plant, Sarracenia purpurea, across several spatial scales that are naturally delimited by the midge's habitat (leaf, plant, cluster of plants, bog and system of bogs). We analysed 11 microsatellite loci in 710 M. knabi larvae from two systems of bogs in Algonquin Provincial Park (Canada) and tested the hypotheses that variables related to habitat structure are associated with genetic differentiation in this midge. Up to 54% of variation in individual-based genetic distances at several scales was explained by broadscale landscape variables of bog size, pitcher plant density within bogs and connectivity of pitcher plant clusters. Our results indicate that oviposition behaviour of females at fine scales, as inferred from the spatial locations of full-sib larvae, and spatially limited gene flow at broad scales represent the important processes underlying observed genetic patterns in M. knabi. Broadscale landscape features (bog size and plant density) appear to influence oviposition behaviour of midges, which in turn influences the patterns of genetic differentiation observed at both fine and broad scales. Thus, we inferred linkages among genetic patterns, landscape patterns and ecological processes across spatial scales in M. knabi. Our results reinforce the value of exploring such links simultaneously across multiple spatial scales and landscapes when investigating genetic diversity within a species. © 2011 Blackwell Publishing Ltd.

Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds.

PubMed

Kawakami, Takeshi; Mugal, Carina F; Suh, Alexander; Nater, Alexander; Burri, Reto; Smeds, Linnéa; Ellegren, Hans

2017-08-01

Recombination rate is heterogeneous across the genome of various species and so are genetic diversity and differentiation as a consequence of linked selection. However, we still lack a clear picture of the underlying mechanisms for regulating recombination. Here we estimated fine-scale population recombination rate based on the patterns of linkage disequilibrium across the genomes of multiple populations of two closely related flycatcher species (Ficedula albicollis and F. hypoleuca). This revealed an overall conservation of the recombination landscape between these species at the scale of 200 kb, but we also identified differences in the local rate of recombination despite their recent divergence (<1 million years). Genetic diversity and differentiation were associated with recombination rate in a lineage-specific manner, indicating differences in the extent of linked selection between species. We detected 400-3,085 recombination hotspots per population. Location of hotspots was conserved between species, but the intensity of hotspot activity varied between species. Recombination hotspots were primarily associated with CpG islands (CGIs), regardless of whether CGIs were at promoter regions or away from genes. Recombination hotspots were also associated with specific transposable elements (TEs), but this association appears indirect due to shared preferences of the transposition machinery and the recombination machinery for accessible open chromatin regions. Our results suggest that CGIs are a major determinant of the localization of recombination hotspots, and we propose that both the distribution of TEs and fine-scale variation in recombination rate may be associated with the evolution of the epigenetic landscape. © 2017 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Fine- and hyperfine-structure effects in molecular photoionization. I. General theory and direct photoionization.

PubMed

Germann, Matthias; Willitsch, Stefan

2016-07-28

We develop a model for predicting fine- and hyperfine intensities in the direct photoionization of molecules based on the separability of electron and nuclear spin states from vibrational-electronic states. Using spherical tensor algebra, we derive highly symmetrized forms of the squared photoionization dipole matrix elements from which we derive the salient selection and propensity rules for fine- and hyperfine resolved photoionizing transitions. Our theoretical results are validated by the analysis of the fine-structure resolved photoelectron spectrum of O2 reported by Palm and Merkt [Phys. Rev. Lett. 81, 1385 (1998)] and are used for predicting hyperfine populations of molecular ions produced by photoionization.

Thermal stability analysis of the fine structure of solar prominences

NASA Technical Reports Server (NTRS)

Demoulin, Pascal; Malherbe, Jean-Marie; Schmieder, Brigitte; Raadu, Mickael A.

1986-01-01

The linear thermal stability of a 2D periodic structure (alternatively hot and cold) in a uniform magnetic field is analyzed. The energy equation includes wave heating (assumed proportional to density), radiative cooling and both conduction parallel and orthogonal to magnetic lines. The equilibrium is perturbed at constant gas pressure. With parallel conduction only, it is found to be unstable when the length scale 1// is greater than 45 Mn. In that case, orthogonal conduction becomes important and stabilizes the structure when the length scale is smaller than 5 km. On the other hand, when the length scale is greater than 5 km, the thermal equilibrium is unstable, and the corresponding time scale is about 10,000 s: this result may be compared to observations showing that the lifetime of the fine structure of solar prominences is about one hour; consequently, our computations suggest that the size of the unresolved threads could be of the order of 10 km only.

Stable genetic structure and connectivity in pollution-adapted and nearby pollution-sensitive populations of Fundulus heteroclitus

PubMed Central

Biancani, Leann M.; Flight, Patrick A.; Nacci, Diane E.; Rand, David M.; Crawford, Douglas L.; Oleksiak, Marjorie F.

2018-01-01

Populations of the non-migratory estuarine fish Fundulus heteroclitus inhabiting the heavily polluted New Bedford Harbour (NBH) estuary have shown inherited tolerance to local pollutants introduced to their habitats in the past 100 years. Here we examine two questions: (i) Is there pollution-driven selection on the mitochondrial genome across a fine geographical scale? and (ii) What is the pattern of migration among sites spanning a strong pollution gradient? Whole mitochondrial genomes were analysed for 133 F. heteroclitus from seven nearby collection sites: four sites along the NBH pollution cline (approx. 5 km distance), which had pollution-adapted fish, as well as one site adjacent to the pollution cline and two relatively unpolluted sites about 30 km away, which had pollution-sensitive fish. Additionally, we used microsatellite analyses to quantify genetic variation over three F. heteroclitus generations in both pollution-adapted and sensitive individuals collected from two sites at two different time points (1999/2000 and 2007/2008). Our results show no evidence for a selective sweep of mtDNA in the polluted sites. Moreover, mtDNA analyses revealed that both pollution-adapted and sensitive populations harbour similar levels of genetic diversity. We observed a high level of non-synonymous mutations in the most polluted site. This is probably associated with a reduction in Ne and concomitant weakening of purifying selection, a demographic expansion following a pollution-related bottleneck or increased mutation rates. Our demographic analyses suggest that isolation by distance influences the distribution of mtDNA genetic variation between the pollution cline and the clean populations at broad spatial scales. At finer scales, population structure is patchy, and neither spatial distance, pollution concentration or pollution tolerance is a good predictor of mtDNA variation. Lastly, microsatellite analyses revealed stable population structure over the last decade. PMID:29892357

A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome

PubMed Central

Mathias, Rasika Ann; Taub, Margaret A.; Gignoux, Christopher R.; Fu, Wenqing; Musharoff, Shaila; O'Connor, Timothy D.; Vergara, Candelaria; Torgerson, Dara G.; Pino-Yanes, Maria; Shringarpure, Suyash S.; Huang, Lili; Rafaels, Nicholas; Boorgula, Meher Preethi; Johnston, Henry Richard; Ortega, Victor E.; Levin, Albert M.; Song, Wei; Torres, Raul; Padhukasahasram, Badri; Eng, Celeste; Mejia-Mejia, Delmy-Aracely; Ferguson, Trevor; Qin, Zhaohui S.; Scott, Alan F.; Yazdanbakhsh, Maria; Wilson, James G.; Marrugo, Javier; Lange, Leslie A.; Kumar, Rajesh; Avila, Pedro C.; Williams, L. Keoki; Watson, Harold; Ware, Lorraine B.; Olopade, Christopher; Olopade, Olufunmilayo; Oliveira, Ricardo; Ober, Carole; Nicolae, Dan L.; Meyers, Deborah; Mayorga, Alvaro; Knight-Madden, Jennifer; Hartert, Tina; Hansel, Nadia N.; Foreman, Marilyn G.; Ford, Jean G.; Faruque, Mezbah U.; Dunston, Georgia M.; Caraballo, Luis; Burchard, Esteban G.; Bleecker, Eugene; Araujo, Maria Ilma; Herrera-Paz, Edwin Francisco; Gietzen, Kimberly; Grus, Wendy E.; Bamshad, Michael; Bustamante, Carlos D.; Kenny, Eimear E.; Hernandez, Ryan D.; Beaty, Terri H.; Ruczinski, Ingo; Akey, Joshua; Campbell, Monica; Chavan, Sameer; Foster, Cassandra; Gao, Li; Horowitz, Edward; Ortiz, Romina; Potee, Joseph; Gao, Jingjing; Hu, Yijuan; Hansen, Mark; Deshpande, Aniket; Locke, Devin P.; Grammer, Leslie; Kim, Kwang-YounA; Schleimer, Robert; De La Vega, Francisco M.; Szpiech, Zachary A.; Oluwole, Oluwafemi; Arinola, Ganiyu; Correa, Adolfo; Musani, Solomon; Chong, Jessica; Nickerson, Deborah; Reiner, Alexander; Maul, Pissamai; Maul, Trevor; Martinez, Beatriz; Meza, Catherine; Ayestas, Gerardo; Landaverde-Torres, Pamela; Erazo, Said Omar Leiva; Martinez, Rosella; Mayorga, Luis F.; Ramos, Hector; Saenz, Allan; Varela, Gloria; Vasquez, Olga Marina; Samms-Vaughan, Maureen; Wilks, Rainford J.; Adegnika, Akim; Ateba-Ngoa, Ulysse; Barnes, Kathleen C.

2016-01-01

The African Diaspora in the Western Hemisphere represents one of the largest forced migrations in history and had a profound impact on genetic diversity in modern populations. To date, the fine-scale population structure of descendants of the African Diaspora remains largely uncharacterized. Here we present genetic variation from deeply sequenced genomes of 642 individuals from North and South American, Caribbean and West African populations, substantially increasing the lexicon of human genomic variation and suggesting much variation remains to be discovered in African-admixed populations in the Americas. We summarize genetic variation in these populations, quantifying the postcolonial sex-biased European gene flow across multiple regions. Moreover, we refine estimates on the burden of deleterious variants carried across populations and how this varies with African ancestry. Our data are an important resource for empowering disease mapping studies in African-admixed individuals and will facilitate gene discovery for diseases disproportionately affecting individuals of African ancestry. PMID:27725671

Contrasting effects of landscape features on genetic structure in different geographic regions in the ornate dragon lizard, Ctenophorus ornatus.

PubMed

Levy, Esther; Tomkins, Joseph L; Lebas, Natasha R; Kennington, W Jason

2013-08-01

Habitat fragmentation can have profound effects on the distribution of genetic variation within and between populations. Previously, we showed that in the ornate dragon lizard, Ctenophorus ornatus, lizards residing on outcrops that are separated by cleared agricultural land are significantly more isolated and hold less genetic variation than lizards residing on neighbouring outcrops connected by undisturbed native vegetation. Here, we extend the fine-scale study to examine the pattern of genetic variation and population structure across the species' range. Using a landscape genetics approach, we test whether land clearing for agricultural purposes has affected the population structure of the ornate dragon lizard. We found significant genetic differentiation between outcrop populations (FST  = 0.12), as well as isolation by distance within each geographic region. In support of our previous study, land clearing was associated with higher genetic divergences between outcrops and lower genetic variation within outcrops, but only in the region that had been exposed to intense agriculture for the longest period of time. No other landscape features influenced population structure in any geographic region. These results show that the effects of landscape features can vary across species' ranges and suggest there may be a temporal lag in response to contemporary changes in land use. These findings therefore highlight the need for caution when assessing the impact of contemporary land use practices on genetic variation and population structure. © 2013 John Wiley & Sons Ltd.

Spatial genetic structure within populations and management implications of the South American species Acacia aroma (Fabaceae).

PubMed

Pometti, Carolina; Bessega, Cecilia; Cialdella, Ana; Ewens, Mauricio; Saidman, Beatriz; Vilardi, Juan

2018-01-01

The identification of factors that structure intraspecific diversity is of particular interest for biological conservation and restoration ecology. All rangelands in Argentina are currently experiencing some form of deterioration or desertification. Acacia aroma is a multipurpose species widely distributed throughout this country. In this study, we used the AFLP technique to study genetic diversity, population genetic structure, and fine-scale spatial genetic structure in 170 individuals belonging to 6 natural Argentinean populations. With 401 loci, the mean heterozygosity (HE = 0.2) and the mean percentage of polymorphic loci (PPL = 62.1%) coefficients indicated that the genetic variation is relatively high in A. aroma. The analysis with STRUCTURE showed that the number of clusters (K) was 3. With Geneland analysis, the number of clusters was K = 4, sharing the same grouping as STRUCTURE but dividing one population into two groups. When studying SGS, significant structure was detected in 3 of 6 populations. The neighbourhood size in these populations ranged from 15.2 to 64.3 individuals. The estimated gene dispersal distance depended on the effective population density and disturbance level and ranged from 45 to 864 m. The combined results suggest that a sampling strategy, which aims to maintain a considerable part of the variability contained in natural populations sampled here, would include at least 3 units defined by the clusters analyses that exhibit particular genetic properties. Moreover, the current SGS analysis suggests that within the wider management units/provinces, seed collection from A. aroma should target trees separated by a minimum distance of 50 m but preferably 150 m to reduce genetic relatedness among seeds from different trees.

Spatial genetic structure within populations and management implications of the South American species Acacia aroma (Fabaceae)

PubMed Central

Bessega, Cecilia; Cialdella, Ana; Ewens, Mauricio; Saidman, Beatriz; Vilardi, Juan

2018-01-01

The identification of factors that structure intraspecific diversity is of particular interest for biological conservation and restoration ecology. All rangelands in Argentina are currently experiencing some form of deterioration or desertification. Acacia aroma is a multipurpose species widely distributed throughout this country. In this study, we used the AFLP technique to study genetic diversity, population genetic structure, and fine-scale spatial genetic structure in 170 individuals belonging to 6 natural Argentinean populations. With 401 loci, the mean heterozygosity (HE = 0.2) and the mean percentage of polymorphic loci (PPL = 62.1%) coefficients indicated that the genetic variation is relatively high in A. aroma. The analysis with STRUCTURE showed that the number of clusters (K) was 3. With Geneland analysis, the number of clusters was K = 4, sharing the same grouping as STRUCTURE but dividing one population into two groups. When studying SGS, significant structure was detected in 3 of 6 populations. The neighbourhood size in these populations ranged from 15.2 to 64.3 individuals. The estimated gene dispersal distance depended on the effective population density and disturbance level and ranged from 45 to 864 m. The combined results suggest that a sampling strategy, which aims to maintain a considerable part of the variability contained in natural populations sampled here, would include at least 3 units defined by the clusters analyses that exhibit particular genetic properties. Moreover, the current SGS analysis suggests that within the wider management units/provinces, seed collection from A. aroma should target trees separated by a minimum distance of 50 m but preferably 150 m to reduce genetic relatedness among seeds from different trees. PMID:29389969

Coupling fine-scale root and canopy structure using ground-based remote sensing

DOE PAGES

Hardiman, Brady S.; Gough, Christopher M.; Butnor, John R.; ...

2017-02-21

Ecosystem physical structure, defined by the quantity and spatial distribution of biomass, influences a range of ecosystem functions. Remote sensing tools permit the non-destructive characterization of canopy and root features, potentially providing opportunities to link above- and belowground structure at fine spatial resolution in functionally meaningful ways. To test this possibility, we employed ground-based portable canopy LiDAR (PCL) and ground penetrating radar (GPR) along co-located transects in forested sites spanning multiple stages of ecosystem development and, consequently, of structural complexity. We examined canopy and root structural data for coherence (i.e., correlation in the frequency of spatial variation) at multiple spatialmore » scales 10 m within each site using wavelet analysis. Forest sites varied substantially in vertical canopy and root structure, with leaf area index and root mass more becoming even vertically as forests aged. In all sites, above- and belowground structure, characterized as mean maximum canopy height and root mass, exhibited significant coherence at a scale of 3.5–4 m, and results suggest that the scale of coherence may increase with stand age. Our findings demonstrate that canopy and root structure are linked at characteristic spatial scales, which provides the basis to optimize scales of observation. Lastly, our study highlights the potential, and limitations, for fusing LiDAR and radar technologies to quantitatively couple above- and belowground ecosystem structure.« less

Coupling fine-scale root and canopy structure using ground-based remote sensing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hardiman, Brady S.; Gough, Christopher M.; Butnor, John R.

Ecosystem physical structure, defined by the quantity and spatial distribution of biomass, influences a range of ecosystem functions. Remote sensing tools permit the non-destructive characterization of canopy and root features, potentially providing opportunities to link above- and belowground structure at fine spatial resolution in functionally meaningful ways. To test this possibility, we employed ground-based portable canopy LiDAR (PCL) and ground penetrating radar (GPR) along co-located transects in forested sites spanning multiple stages of ecosystem development and, consequently, of structural complexity. We examined canopy and root structural data for coherence (i.e., correlation in the frequency of spatial variation) at multiple spatialmore » scales 10 m within each site using wavelet analysis. Forest sites varied substantially in vertical canopy and root structure, with leaf area index and root mass more becoming even vertically as forests aged. In all sites, above- and belowground structure, characterized as mean maximum canopy height and root mass, exhibited significant coherence at a scale of 3.5–4 m, and results suggest that the scale of coherence may increase with stand age. Our findings demonstrate that canopy and root structure are linked at characteristic spatial scales, which provides the basis to optimize scales of observation. Lastly, our study highlights the potential, and limitations, for fusing LiDAR and radar technologies to quantitatively couple above- and belowground ecosystem structure.« less

Relative contributions of neutral and non-neutral genetic differentiation to inform conservation of steelhead trout across highly variable landscapes

PubMed Central

Matala, Andrew P; Ackerman, Michael W; Campbell, Matthew R; Narum, Shawn R

2014-01-01

Mounting evidence of climatic effects on riverine environments and adaptive responses of fishes have elicited growing conservation concerns. Measures to rectify population declines include assessment of local extinction risk, population ecology, viability, and genetic differentiation. While conservation planning has been largely informed by neutral genetic structure, there has been a dearth of critical information regarding the role of non-neutral or functional genetic variation. We evaluated genetic variation among steelhead trout of the Columbia River Basin, which supports diverse populations distributed among dynamic landscapes. We categorized 188 SNP loci as either putatively neutral or candidates for divergent selection (non-neutral) using a multitest association approach. Neutral variation distinguished lineages and defined broad-scale population structure consistent with previous studies, but fine-scale resolution was also detected at levels not previously observed. Within distinct coastal and inland lineages, we identified nine and 22 candidate loci commonly associated with precipitation or temperature variables and putatively under divergent selection. Observed patterns of non-neutral variation suggest overall climate is likely to shape local adaptation (e.g., potential rapid evolution) of steelhead trout in the Columbia River region. Broad geographic patterns of neutral and non-neutral variation demonstrated here can be used to accommodate priorities for regional management and inform long-term conservation of this species. PMID:25067950

Is isolation by adaptation driving genetic divergence among proximate Dolly Varden char populations?

PubMed Central

Bond, Morgan H; Crane, Penelope A; Larson, Wesley A; Quinn, Tom P

2014-01-01

Numerous studies of population genetics in salmonids and other anadromous fishes have revealed that population structure is generally organized into geographic hierarchies (isolation by distance), but significant structure can exist in proximate populations due to varying selective pressures (isolation by adaptation). In Chignik Lakes, Alaska, anadromous Dolly Varden char (Salvelinus malma) spawn in nearly all accessible streams throughout the watershed, including those draining directly to an estuary, Chignik Lagoon, into larger rivers, and into lakes. Collections of Dolly Varden fry from 13 streams throughout the system revealed low levels of population structure among streams emptying into freshwater. However, much stronger genetic differentiation was detected between streams emptying into freshwater and streams flowing directly into estuarine environments. This fine-scale reproductive isolation without any physical barriers to migration is likely driven by differences in selection pressures across freshwater and estuarine environments. Estuary tributaries had fewer larger, older juveniles, suggesting an alternative life history of smolting and migration to the marine environment at a much smaller size than occurs in the other populations. Therefore, genetic data were consistent with a scenario where isolation by adaptation occurs between populations of Dolly Varden in the study system, and ecological data suggest that this isolation may partially be a result of a novel Dolly Varden life history of seawater tolerance at a smaller size than previously recognized. PMID:25360283

Contrasting responses to a climate regime change by sympatric, ice-dependent predators.

PubMed

Younger, Jane L; van den Hoff, John; Wienecke, Barbara; Hindell, Mark; Miller, Karen J

2016-03-15

Models that predict changes in the abundance and distribution of fauna under future climate change scenarios often assume that ecological niche and habitat availability are the major determinants of species' responses to climate change. However, individual species may have very different capacities to adapt to environmental change, as determined by intrinsic factors such as their dispersal ability, genetic diversity, generation time and rate of evolution. These intrinsic factors are usually excluded from forecasts of species' abundance and distribution changes. We aimed to determine the importance of these factors by comparing the impact of the most recent climate regime change, the late Pleistocene glacial-interglacial transition, on two sympatric, ice-dependent meso-predators, the emperor penguin (Aptenodytes forsteri) and Weddell seal (Leptonychotes weddellii). We reconstructed the population trend of emperor penguins and Weddell seals in East Antarctica over the past 75,000 years using mitochondrial DNA sequences and an extended Bayesian skyline plot method. We also assessed patterns of contemporary population structure and genetic diversity. Despite their overlapping distributions and shared dependence on sea ice, our genetic data revealed very different responses to climate warming between these species. The emperor penguin population grew rapidly following the glacial-interglacial transition, but the size of the Weddell seal population did not change. The expansion of emperor penguin numbers during the warm Holocene may have been facilitated by their higher dispersal ability and gene flow among colonies, and fine-scale differences in preferred foraging locations. The vastly different climate change responses of two sympatric ice-dependent predators suggests that differing adaptive capacities and/or fine-scale niche differences can play a major role in species' climate change responses, and that adaptive capacity should be considered alongside niche and distribution in future species forecasts.

Human impact in naturally patched small populations: genetic structure and conservation of the burrowing rodent, tuco-tuco (Ctenomys lami).

PubMed

Lopes, Carla M; de Freitas, Thales R O

2012-01-01

Isolated or semi-isolated small populations are commonly found among species, due to a naturally patchy occupancy of suitable habitats or also as a result of habitat alterations. These populations are subject to an increased risk of local extinction because they are more vulnerable to demographic, genetic, and environmental stochasticity. Considering that natural areas have been becoming progressively more fragmented and smaller, understanding the genetic structure and evolutionary dynamics of small populations is critical. Ctenomys lami has 26 karyotypes distributed in a small area (936 km(2)) continually modified by human actions. We assessed the genetic geographical structure of this species, examining 178 specimens sampled on a fine scale, using information from chromosomal variability, mitochondrial DNA control region and cytochrome c oxidase subunit I sequences, and 14 microsatellite loci. The observed isolation-by-distance pattern and a clinal genetic variation suggest a stepping-stone population model. The results did not indicate genetic structuring associated with distinct karyotypes. However, mitochondrial and nuclear molecular markers demonstrated the existence of 2 demes, which are not completely isolated but are probably reinforced by a geographical barrier. The vulnerability of C. lami is greater than previously supposed, and our data support the designation of one Evolutionary Significant Unit and one Management Unit, and also the inclusion of this species' conservation status as vulnerable.

The complex roles of space and environment in structuring functional, taxonomic and phylogenetic beta diversity of frogs in the Atlantic Forest

PubMed Central

Luiz, Amom Mendes; Sawaya, Ricardo J.

2018-01-01

Ecological communities are complex entities that can be maintained and structured by niche-based processes such as environmental conditions, and spatial processes such as dispersal. Thus, diversity patterns may be shaped simultaneously at different spatial scales by very distinct processes. Herein we assess whether and how functional, taxonomic, and phylogenetic beta diversities of frog tadpoles are explained by environmental and/or spatial predictors. We implemented a distance–based redundancy analysis to explore variation in components of beta diversity explained by pure environmental and pure spatial predictors, as well as their interactions, at both fine and broad spatial scales. Our results indicated important but complex roles of spatial and environmental predictors in structuring phylogenetic, taxonomic and functional beta diversities. The pure fine-scales spatial fraction was more important in structuring all beta diversity components, especially to functional and taxonomical spatial turnover. Environmental variables such as canopy cover and vegetation structure were important predictors of all components, but especially to functional and taxonomic beta diversity. We emphasize that distinct factors related to environment and space are affecting distinct components of beta diversity in different ways. Although weaker, phylogenetic beta diversity, which is structured more on biogeographical scales, and thus can be represented by spatially structured processes, was more related to broad spatial processes than other components. However, selected fine-scale spatial predictors denoted negative autocorrelation, which may be revealing the existence of differences in unmeasured habitat variables among samples. Although overall important, local environmental-based processes explained better functional and taxonomic beta diversity, as these diversity components carry an important ecological value. We highlight the importance of assessing different components of diversity patterns at different scales by spatially explicit models in order to improve our understanding of community structure and help to unravel the complex nature of biodiversity. PMID:29672575

Elevation as a barrier: genetic structure for an Atlantic rain forest tree (Bathysa australis) in the Serra do Mar mountain range, SE Brazil.

PubMed

Reis, Talita Soares; Ciampi-Guillardi, Maísa; Bajay, Miklos Maximiliano; de Souza, Anete Pereira; Dos Santos, Flavio Antonio Maës

2015-05-01

Distance and discrete geographic barriers play a role in isolating populations, as seed and pollen dispersal become limited. Nearby populations without any geographic barrier between them may also suffer from ecological isolation driven by habitat heterogeneity, which may promote divergence by local adaptation and drift. Likewise, elevation gradients may influence the genetic structure and diversity of populations, particularly those marginally distributed. Bathysa australis (Rubiaceae) is a widespread tree along the elevation gradient of the Serra do Mar, SE Brazil. This self-compatible species is pollinated by bees and wasps and has autochoric seeds, suggesting restricted gene dispersal. We investigated the distribution of genetic diversity in six B. australis populations at two extreme sites along an elevation gradient: a lowland site (80-216 m) and an upland site (1010-1100 m.a.s.l.). Nine microsatellite loci were used to test for genetic structure and to verify differences in genetic diversity between sites. We found a marked genetic structure on a scale as small as 6 km (F ST = 0.21), and two distinct clusters were identified, each corresponding to a site. Although B. australis is continuously distributed along the elevation gradient, we have not observed a gene flow between the extreme populations. This might be related to B. australis biological features and creates a potential scenario for adaptation to the different conditions imposed by the elevation gradient. We failed to find an isolation-by-distance pattern; although on the fine scale, all populations showed spatial autocorrelation until ∼10-20 m. Elevation difference was a relevant factor though, but we need further sampling effort to check its correlation with genetic distance. The lowland populations had a higher allelic richness and showed higher rare allele counts than the upland ones. The upland site may be more selective, eliminating rare alleles, as we did not find any evidence for bottleneck.

Direct and indirect genetic and fine-scale location effects on breeding date in song sparrows.

PubMed

Germain, Ryan R; Wolak, Matthew E; Arcese, Peter; Losdat, Sylvain; Reid, Jane M

2016-11-01

Quantifying direct and indirect genetic effects of interacting females and males on variation in jointly expressed life-history traits is central to predicting microevolutionary dynamics. However, accurately estimating sex-specific additive genetic variances in such traits remains difficult in wild populations, especially if related individuals inhabit similar fine-scale environments. Breeding date is a key life-history trait that responds to environmental phenology and mediates individual and population responses to environmental change. However, no studies have estimated female (direct) and male (indirect) additive genetic and inbreeding effects on breeding date, and estimated the cross-sex genetic correlation, while simultaneously accounting for fine-scale environmental effects of breeding locations, impeding prediction of microevolutionary dynamics. We fitted animal models to 38 years of song sparrow (Melospiza melodia) phenology and pedigree data to estimate sex-specific additive genetic variances in breeding date, and the cross-sex genetic correlation, thereby estimating the total additive genetic variance while simultaneously estimating sex-specific inbreeding depression. We further fitted three forms of spatial animal model to explicitly estimate variance in breeding date attributable to breeding location, overlap among breeding locations and spatial autocorrelation. We thereby quantified fine-scale location variances in breeding date and quantified the degree to which estimating such variances affected the estimated additive genetic variances. The non-spatial animal model estimated nonzero female and male additive genetic variances in breeding date (sex-specific heritabilities: 0·07 and 0·02, respectively) and a strong, positive cross-sex genetic correlation (0·99), creating substantial total additive genetic variance (0·18). Breeding date varied with female, but not male inbreeding coefficient, revealing direct, but not indirect, inbreeding depression. All three spatial animal models estimated small location variance in breeding date, but because relatedness and breeding location were virtually uncorrelated, modelling location variance did not alter the estimated additive genetic variances. Our results show that sex-specific additive genetic effects on breeding date can be strongly positively correlated, which would affect any predicted rates of microevolutionary change in response to sexually antagonistic or congruent selection. Further, we show that inbreeding effects on breeding date can also be sex specific and that genetic effects can exceed phenotypic variation stemming from fine-scale location-based variation within a wild population. © 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.

Genetic structure among greater white-fronted goose populations of the Pacific Flyway

USGS Publications Warehouse

Ely, Craig R.; Wilson, Robert E.; Talbot, Sandra L.

2017-01-01

An understanding of the genetic structure of populations in the wild is essential for long-term conservation and stewardship in the face of environmental change. Knowledge of the present-day distribution of genetic lineages (phylogeography) of a species is especially important for organisms that are exploited or utilize habitats that may be jeopardized by human intervention, including climate change. Here, we describe mitochondrial (mtDNA) and nuclear genetic (microsatellite) diversity among three populations of a migratory bird, the greater white-fronted goose (Anser albifrons), which breeds discontinuously in western and southwestern Alaska and winters in the Pacific Flyway of North America. Significant genetic structure was evident at both marker types. All three populations were differentiated for mtDNA, whereas microsatellite analysis only differentiated geese from the Cook Inlet Basin. In sexual reproducing species, nonrandom mate selection, when occurring in concert with fine-scale resource partitioning, can lead to phenotypic and genetic divergence as we observed in our study. If mate selection does not occur at the time of reproduction, which is not uncommon in long-lived organisms, then mechanisms influencing the true availability of potential mates may be obscured, and the degree of genetic and phenotypic diversity may appear incongruous with presumed patterns of gene flow. Previous investigations revealed population-specific behavioral, temporal, and spatial mechanisms that likely influence the amount of gene flow measured among greater white-fronted goose populations. The degree of observed genetic structuring aligns well with our current understanding of population differences pertaining to seasonal movements, social structure, pairing behavior, and resource partitioning.

Assessment of Population Exposure to Coarse and Fine Particulate Matter in the Urban Areas of Chennai, India.

PubMed

Prasannavenkatesh, Ramachandran; Andimuthu, Ramachandran; Kandasamy, Palanivelu; Rajadurai, Geetha; Kumar, Divya Subash; Radhapriya, Parthasarathy; Ponnusamy, Malini

2015-01-01

Research outcomes from the epidemiological studies have found that the course (PM10) and the fine particulate matter (PM2.5) are mainly responsible for various respiratory health effects for humans. The population-weighted exposure assessment is used as a vital decision-making tool to analyze the vulnerable areas where the population is exposed to critical concentrations of pollutants. Systemic sampling was carried out at strategic locations of Chennai to estimate the various concentration levels of particulate pollution during November 2013-January 2014. The concentration of the pollutants was classified based on the World Health Organization interim target (IT) guidelines. Using geospatial information systems the pollution and the high-resolution population data were interpolated to study the extent of the pollutants at the urban scale. The results show that approximately 28% of the population resides in vulnerable locations where the coarse particulate matter exceeds the prescribed standards. Alarmingly, the results of the analysis of fine particulates show that about 94% of the inhabitants live in critical areas where the concentration of the fine particulates exceeds the IT guidelines. Results based on human exposure analysis show the vulnerability is more towards the zones which are surrounded by prominent sources of pollution.

Assessment of Population Exposure to Coarse and Fine Particulate Matter in the Urban Areas of Chennai, India

PubMed Central

Prasannavenkatesh, Ramachandran; Andimuthu, Ramachandran; Kandasamy, Palanivelu; Rajadurai, Geetha; Subash Kumar, Divya; Radhapriya, Parthasarathy; Ponnusamy, Malini

2015-01-01

Research outcomes from the epidemiological studies have found that the course (PM10) and the fine particulate matter (PM2.5) are mainly responsible for various respiratory health effects for humans. The population-weighted exposure assessment is used as a vital decision-making tool to analyze the vulnerable areas where the population is exposed to critical concentrations of pollutants. Systemic sampling was carried out at strategic locations of Chennai to estimate the various concentration levels of particulate pollution during November 2013–January 2014. The concentration of the pollutants was classified based on the World Health Organization interim target (IT) guidelines. Using geospatial information systems the pollution and the high-resolution population data were interpolated to study the extent of the pollutants at the urban scale. The results show that approximately 28% of the population resides in vulnerable locations where the coarse particulate matter exceeds the prescribed standards. Alarmingly, the results of the analysis of fine particulates show that about 94% of the inhabitants live in critical areas where the concentration of the fine particulates exceeds the IT guidelines. Results based on human exposure analysis show the vulnerability is more towards the zones which are surrounded by prominent sources of pollution. PMID:26258167

Fine- and hyperfine-structure effects in molecular photoionization. I. General theory and direct photoionization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Germann, Matthias; Willitsch, Stefan, E-mail: stefan.willitsch@unibas.ch

2016-07-28

We develop a model for predicting fine- and hyperfine intensities in the direct photoionization of molecules based on the separability of electron and nuclear spin states from vibrational-electronic states. Using spherical tensor algebra, we derive highly symmetrized forms of the squared photoionization dipole matrix elements from which we derive the salient selection and propensity rules for fine- and hyperfine resolved photoionizing transitions. Our theoretical results are validated by the analysis of the fine-structure resolved photoelectron spectrum of O{sub 2} reported by Palm and Merkt [Phys. Rev. Lett. 81, 1385 (1998)] and are used for predicting hyperfine populations of molecular ionsmore » produced by photoionization.« less

Scale-dependent effects of nonnative plant invasion on host-seeking tick abundance

PubMed Central

Adalsteinsson, Solny A.; D’Amico, Vincent; Shriver, W. Gregory; Brisson, Dustin; Buler, Jeffrey J.

2016-01-01

Nonnative, invasive shrubs can affect human disease risk through direct and indirect effects on vector populations. Multiflora rose (Rosa multiflora) is a common invader within eastern deciduous forests where tick-borne disease (e.g. Lyme disease) rates are high. We tested whether R. multiflora invasion affects blacklegged tick (Ixodes scapularis) abundance, and at what scale. We sampled host-seeking ticks at two spatial scales: fine-scale, within R. multiflora-invaded forest fragments; and patch scale, among R. multiflora-invaded and R. multiflora-free forest fragments. At a fine scale, we trapped 2.3 times more ticks under R. multiflora compared to paired traps 25 m away from R. multiflora. At the patch scale, we trapped 3.2 times as many ticks in R. multiflora-free forests compared to R. multiflora-invaded forests. Thus, ticks are concentrated beneath R. multiflora within invaded forests, but uninvaded forests support significantly more ticks. Among all covariates tested, leaf litter volume was the best predictor of tick abundance; at the patch scale, R. multiflora-invaded forests had less leaf litter than uninvaded forests. We suggest that leaf litter availability at the patch-scale plays a greater role in constraining tick abundance than the fine-scale, positive effect of invasive shrubs. PMID:27088044

Fine-structure-resolution for Rovibrational Excitation of CN Due to H2

NASA Astrophysics Data System (ADS)

Byrd, Nat; Yang, Benhui H.; Stancil, Phillip C.

2018-06-01

Diatomic molecules can be readily excited in interstellar environments exposed to intense UV radiation, such as the inner rim of a protoplanetary disk. Non-thermal populations of excited rovibrational levels can result, for example, following decay from electronically excited states to the electronic ground state. Competition between radiative decay and collisional processes, mostly due to H2, determine the resulting rovibrational emission spectrum. For CN, and other open-shell molecules, the resulting spectrum will be complicated due to fine-structure splitting of the rotational levels. In some cases, fine-structure resolution has been previously computed for rotational transitions in atom- or diatom-diatom collisional processes. Here we present the first fine-structure resolution for vibrational deexcitation for CN colliding with H2. The collisional cross sections were computed using a 6D potential energy surface with a full close-coupling approach. Fine-structure resolution is obtained by adopting an angular momentum recoupling scheme to transform the scattering matrices to a recoupled basis. Here we present low-energy calculations for the v=1 to 0 transition.This work was supported by NASA Grant NNX16AF09G.

Connecting traces of galaxy evolution: the missing core mass-morphological fine structure relation

NASA Astrophysics Data System (ADS)

Bonfini, P.; Bitsakis, T.; Zezas, A.; Duc, P.-A.; Iodice, E.; González-Martín, O.; Bruzual, G.; González Sanoja, A. J.

2018-01-01

Deep exposure imaging of early-type galaxies (ETGs) are revealing the second-order complexity of these objects, which have been long considered uniform, dispersion-supported spheroidals. `Fine structure' features (e.g. ripples, plumes, tidal tails, rings) as well as depleted stellar cores (i.e. central light deficits) characterize a number of massive ETG galaxies, and can be interpreted as the result of galaxy-galaxy interactions. We discuss how the time-scale for the evolution of cores and fine structures are comparable, and hence it is expected that they develop in parallel after the major interaction event which shaped the ETG. Using archival data, we compare the `depleted stellar mass' (i.e. the mass missing from the depleted stellar core) against the prominence of the fine structure features, and observe that they correlate inversely. This result confirms our expectation that, while the supermassive black hole (SMBH) binary (constituted by the SMBHs of the merger progenitors) excavates the core via three-body interactions, the gravitational potential of the newborn galaxy relaxes, and the fine structures fade below detection levels. We expect the inverse correlation to hold at least within the first Gyr from the merger which created the SMBH binary; after then, the fine structure evolves independently.

SHIPS: Spectral Hierarchical Clustering for the Inference of Population Structure in Genetic Studies

PubMed Central

Bouaziz, Matthieu; Paccard, Caroline; Guedj, Mickael; Ambroise, Christophe

2012-01-01

Inferring the structure of populations has many applications for genetic research. In addition to providing information for evolutionary studies, it can be used to account for the bias induced by population stratification in association studies. To this end, many algorithms have been proposed to cluster individuals into genetically homogeneous sub-populations. The parametric algorithms, such as Structure, are very popular but their underlying complexity and their high computational cost led to the development of faster parametric alternatives such as Admixture. Alternatives to these methods are the non-parametric approaches. Among this category, AWclust has proven efficient but fails to properly identify population structure for complex datasets. We present in this article a new clustering algorithm called Spectral Hierarchical clustering for the Inference of Population Structure (SHIPS), based on a divisive hierarchical clustering strategy, allowing a progressive investigation of population structure. This method takes genetic data as input to cluster individuals into homogeneous sub-populations and with the use of the gap statistic estimates the optimal number of such sub-populations. SHIPS was applied to a set of simulated discrete and admixed datasets and to real SNP datasets, that are data from the HapMap and Pan-Asian SNP consortium. The programs Structure, Admixture, AWclust and PCAclust were also investigated in a comparison study. SHIPS and the parametric approach Structure were the most accurate when applied to simulated datasets both in terms of individual assignments and estimation of the correct number of clusters. The analysis of the results on the real datasets highlighted that the clusterings of SHIPS were the more consistent with the population labels or those produced by the Admixture program. The performances of SHIPS when applied to SNP data, along with its relatively low computational cost and its ease of use make this method a promising solution to infer fine-scale genetic patterns. PMID:23077494

Are patterns of fine-scale spatial genetic structure consistent between sites within tropical tree species?

PubMed Central

Smith, James R.; Ghazoul, Jaboury; Burslem, David F. R. P.; Itoh, Akira; Khoo, Eyen; Lee, Soon Leong; Maycock, Colin R.; Nanami, Satoshi; Ng, Kevin Kit Siong; Kettle, Chris J.

2018-01-01

Documenting the scale and intensity of fine-scale spatial genetic structure (FSGS), and the processes that shape it, is relevant to the sustainable management of genetic resources in timber tree species, particularly where logging or fragmentation might disrupt gene flow. In this study we assessed patterns of FSGS in three species of Dipterocarpaceae (Parashorea tomentella, Shorea leprosula and Shorea parvifolia) across four different tropical rain forests in Malaysia using nuclear microsatellite markers. Topographic heterogeneity varied across the sites. We hypothesised that forests with high topographic heterogeneity would display increased FSGS among the adult populations driven by habitat associations. This hypothesis was not supported for S. leprosula and S. parvifolia which displayed little variation in the intensity and scale of FSGS between sites despite substantial variation in topographic heterogeneity. Conversely, the intensity of FSGS for P. tomentella was greater at a more topographically heterogeneous than a homogeneous site, and a significant difference in the overall pattern of FSGS was detected between sites for this species. These results suggest that local patterns of FSGS may in some species be shaped by habitat heterogeneity in addition to limited gene flow by pollen and seed dispersal. Site factors can therefore contribute to the development of FSGS. Confirming consistency in species’ FSGS amongst sites is an important step in managing timber tree genetic diversity as it provides confidence that species specific management recommendations based on species reproductive traits can be applied across a species’ range. Forest managers should take into account the interaction between reproductive traits and site characteristics, its consequences for maintaining forest genetic resources and how this might influence natural regeneration across species if management is to be sustainable. PMID:29547644

The evolutionary and ecological consequences of animal social networks: emerging issues.

PubMed

Kurvers, Ralf H J M; Krause, Jens; Croft, Darren P; Wilson, Alexander D M; Wolf, Max

2014-06-01

The first generation of research on animal social networks was primarily aimed at introducing the concept of social networks to the fields of animal behaviour and behavioural ecology. More recently, a diverse body of evidence has shown that social fine structure matters on a broader scale than initially expected, affecting many key ecological and evolutionary processes. Here, we review this development. We discuss the effects of social network structure on evolutionary dynamics (genetic drift, fixation probabilities, and frequency-dependent selection) and social evolution (cooperation and between-individual behavioural differences). We discuss how social network structure can affect important coevolutionary processes (host-pathogen interactions and mutualisms) and population stability. We also discuss the potentially important, but poorly studied, role of social network structure on dispersal and invasion. Throughout, we highlight important areas for future research. Copyright © 2014 Elsevier Ltd. All rights reserved.

Effect of mechanical fragmentation of sphagnum on population density and structure of micromycete communities

NASA Astrophysics Data System (ADS)

Semenova, T. A.; Golovchenko, A. V.

2017-07-01

The population density and taxonomic structure of micromycetes were monitored for six months in a model experiment with natural and mechanically fragmented (fine and coarse) samples of sphagnum. Sphagnum fragmentation favored an increase in the number of micromycetes only during the first week of the experiment. On the average, the number of micromycetes in fine-fragmented samples was two times greater than that in the coarse-fragmented samples. The diversity of micromycetes increased in the fragmented samples of sphagnum owing to the activation of some species, which remained in the inactive state as spores in the peat before fragmentation.

Structural dynamics of tropical moist forest gaps

Treesearch

Maria O. Hunter; Michael Keller; Douglas Morton; Bruce Cook; Michael Lefsky; Mark Ducey; Scott Saleska; Raimundo Cosme de Oliveira; Juliana Schietti

2015-01-01

Gap phase dynamics are the dominant mode of forest turnover in tropical forests. However, gap processes are infrequently studied at the landscape scale. Airborne lidar data offer detailed information on three-dimensional forest structure, providing a means to characterize fine-scale (1 m) processes in tropical forests over large areas. Lidar-based estimates of forest...

Carbon cycling in fine roots of several mature forests: results using either locally-derived or bomb-derived radiocarbon enrichment

NASA Astrophysics Data System (ADS)

Gaudinski, J. B.; Riley, W. J.; Torn, M. S.; Dawson, T. E.; Trumbore, S. E.; Joslin, J. D.; Majdi, H.; Hanson, P. J.; Swanston, C.

2008-12-01

This work seeks to improve our ability to quantify C cycling rates in fine roots of trees in mature deciduous and coniferous forests. We use two different types of atmospheric 14CO2 enrichment to trace the time elapsed since C in plant tissues was fixed from the atmosphere by photosynthesis. The first uses a local enrichment of 14CO2 which occurred in early summer 1999, at the Oak Ridge Reservation, Tennessee. The second, employed at three different sites, uses the global enrichment in background atmospheric 14CO2 caused by thermonuclear weapons testing (bomb-14C). In both cases we employ a new model (Radix1.0) to track C and 14C fluxes through fine root populations. Radix simulates two live-root populations (the longer-lived one having structural and non-structural C components), two dead-root pools, non-normally distributed root mortality turnover times, a stored C pool, seasonal growth and respiration patterns, a best-fit to measurements approach to estimate model parameters, and Monte Carlo uncertainty analysis. Our results show that: (1) New fine-root growth contains a lot of stored C (~55%) but it is young in age (0.7 y). (2) The effect of stored reserves on estimated ages of fine roots is unlikely to be large in most natural abundance isotope studies. However, models should take stored reserves into account, particularly for pulse labeling studies and fast-cycling roots (< 1 y). (3) Radiocarbon values show a stronger correlation with position on the root branch system than they do with diameter or depth in the soil profile. (4) Live fine root dynamics are well described by a short-lived and a long-lived population, with mean turnover times <1 y and ~12 y, respectively. (5) Dead root decomposition is best modeled with (at least) two pools, with moderate (~2 y) and slow (~10 y) decomposition turnover times. (6) Root respiration has a large effect on fine root biomass and isotopic composition, and should be included in ecosystem C and isotope models. (7) It is important to distinguish structural from non-structural components in the long-lived root pool. Otherwise the 14C signature of root respiration is significantly different than atmospheric. We conclude that realistic quantification of C flows through fine roots requires a model with a level of complexity similar to Radix. Moreover, future root research efforts should seek to sample and sort roots by position on the root branch system rather than by diameter size class and improve estimates of root respiration within fine root populations.

Distributions of soil phosphorus in China's densely populated village landscapes

Treesearch

Jiaguo Jiao; Erle C. Ellis; Ian Yesilonis; Junxi Wu; Hongqing Wang; Huixin Li; Linzhang Yang

2010-01-01

Purpose Village landscapes, which integrate small-scale agriculture with housing, forestry and a host of other land use practices, cover more than 2x106 km2 across China. Village lands tend to be managed at very fine spatial scales (≤30 m), with managers altering soil fertility and even terrain by terracing,...

Roads, interrupted dispersal, and genetic diversity in timber rattlesnakes.

PubMed

Clark, Rulon W; Brown, William S; Stechert, Randy; Zamudio, Kelly R

2010-08-01

Anthropogenic habitat modification often creates barriers to animal movement, transforming formerly contiguous habitat into a patchwork of habitat islands with low connectivity. Roadways are a feature of most landscapes that can act as barriers or filters to migration among local populations. Even small and recently constructed roads can have a significant impact on population genetic structure of some species, but not others. We developed a research approach that combines fine-scale molecular genetics with behavioral and ecological data to understand the impacts of roads on population structure and connectivity. We used microsatellite markers to characterize genetic variation within and among populations of timber rattlesnakes (Crotalus horridus) occupying communal hibernacula (dens) in regions bisected by roadways. We examined the impact of roads on seasonal migration, genetic diversity, and gene flow among populations. Snakes in hibernacula isolated by roads had significantly lower genetic diversity and higher genetic differentiation than snakes in hibernacula in contiguous habitat. Genetic-assignment analyses revealed that interruption to seasonal migration was the mechanism underlying these patterns. Our results underscore the sizeable impact of roads on this species, despite their relatively recent construction at our study sites (7 to 10 generations of rattlesnakes), the utility of population genetics for studies of road ecology, and the need for mitigating effects of roads.

Cheetahs and wild dogs show contrasting patterns of suppression by lions.

PubMed

Swanson, Alexandra; Caro, Tim; Davies-Mostert, Harriet; Mills, Michael G L; Macdonald, David W; Borner, Markus; Masenga, Emmanuel; Packer, Craig

2014-11-01

Top predators can dramatically suppress populations of smaller predators, with cascading effects throughout communities, and this pressure is often unquestioningly accepted as a constraint on mesopredator populations. In this study, we reassess whether African lions suppress populations of cheetahs and African wild dogs and examine possible mechanisms for coexistence between these species. Using long-term records from Serengeti National Park, we tested 30 years of population data for evidence of mesopredator suppression, and we examined six years of concurrent radio-telemetry data for evidence of large-scale spatial displacement. The Serengeti lion population nearly tripled between 1966 and 1998; during this time, wild dogs declined but cheetah numbers remained largely unchanged. Prior to their local extinction, wild dogs primarily occupied low lion density areas and apparently abandoned the long-term study area as the lion population 'saturated' the region. In contrast, cheetahs mostly utilized areas of high lion density, and the stability of the cheetah population indicates that neither high levels of lion-inflicted mortality nor behavioural avoidance inflict sufficient demographic consequences to translate into population-level effects. Population data from fenced reserves in southern Africa revealed a similar contrast between wild dogs and cheetahs in their ability to coexist with lions. These findings demonstrate differential responses of subordinate species within the same guild and challenge a widespread perception that lions undermine cheetah conservation efforts. Paired with several recent studies that document fine-scale lion-avoidance by cheetahs, this study further highlights fine-scale spatial avoidance as a possible mechanism for mitigating mesopredator suppression. © 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.

Population Structure of Two Rabies Hosts Relative to the Known Distribution of Rabies Virus Variants in Alaska

PubMed Central

Goldsmith, Elizabeth W.; Renshaw, Benjamin; Clement, Christopher J.; Himschoot, Elizabeth A.; Hundertmark, Kris J.; Hueffer, Karsten

2015-01-01

For pathogens that infect multiple species the distinction between reservoir hosts and spillover hosts is often difficult. In Alaska, three variants of the arctic rabies virus exist with distinct spatial distributions. We test the hypothesis that rabies virus variant distribution corresponds to the population structure of the primary rabies hosts in Alaska, arctic foxes (Vulpes lagopus) and red foxes (V. vulpes) in order to possibly distinguish reservoir and spill over hosts. We used mitochondrial DNA (mtDNA) sequence and nine microsatellites to assess population structure in those two species. mtDNA structure did not correspond to rabies virus variant structure in either species. Microsatellite analyses gave varying results. Bayesian clustering found 2 groups of arctic foxes in the coastal tundra region, but for red foxes it identified tundra and boreal types. Spatial Bayesian clustering and spatial principal components analysis identified 3 and 4 groups of arctic foxes, respectively, closely matching the distribution of rabies virus variants in the state. Red foxes, conversely, showed eight clusters comprising 2 regions (boreal and tundra) with much admixture. These results run contrary to previous beliefs that arctic fox show no fine-scale spatial population structure. While we cannot rule out that the red fox is part of the maintenance host community for rabies in Alaska, the distribution of virus variants appears to be driven primarily by the artic fox Therefore we show that host population genetics can be utilized to distinguish between maintenance and spillover hosts when used in conjunction with other approaches. PMID:26661691

Population structure of two rabies hosts relative to the known distribution of rabies virus variants in Alaska.

PubMed

Goldsmith, Elizabeth W; Renshaw, Benjamin; Clement, Christopher J; Himschoot, Elizabeth A; Hundertmark, Kris J; Hueffer, Karsten

2016-02-01

For pathogens that infect multiple species, the distinction between reservoir hosts and spillover hosts is often difficult. In Alaska, three variants of the arctic rabies virus exist with distinct spatial distributions. We tested the hypothesis that rabies virus variant distribution corresponds to the population structure of the primary rabies hosts in Alaska, arctic foxes (Vulpes lagopus) and red foxes (Vulpes vulpes) to possibly distinguish reservoir and spillover hosts. We used mitochondrial DNA (mtDNA) sequence and nine microsatellites to assess population structure in those two species. mtDNA structure did not correspond to rabies virus variant structure in either species. Microsatellite analyses gave varying results. Bayesian clustering found two groups of arctic foxes in the coastal tundra region, but for red foxes it identified tundra and boreal types. Spatial Bayesian clustering and spatial principal components analysis identified 3 and 4 groups of arctic foxes, respectively, closely matching the distribution of rabies virus variants in the state. Red foxes, conversely, showed eight clusters comprising two regions (boreal and tundra) with much admixture. These results run contrary to previous beliefs that arctic fox show no fine-scale spatial population structure. While we cannot rule out that the red fox is part of the maintenance host community for rabies in Alaska, the distribution of virus variants appears to be driven primarily by the arctic fox. Therefore, we show that host population genetics can be utilized to distinguish between maintenance and spillover hosts when used in conjunction with other approaches. © 2015 John Wiley & Sons Ltd.

A ubiquitous method for street scale spatial data collection and analysis in challenging urban environments: mapping health risks using spatial video in Haiti

PubMed Central

2013-01-01

Background Fine-scale and longitudinal geospatial analysis of health risks in challenging urban areas is often limited by the lack of other spatial layers even if case data are available. Underlying population counts, residential context, and associated causative factors such as standing water or trash locations are often missing unless collected through logistically difficult, and often expensive, surveys. The lack of spatial context also hinders the interpretation of results and designing intervention strategies structured around analytical insights. This paper offers a ubiquitous spatial data collection approach using a spatial video that can be used to improve analysis and involve participatory collaborations. A case study will be used to illustrate this approach with three health risks mapped at the street scale for a coastal community in Haiti. Methods Spatial video was used to collect street and building scale information, including standing water, trash accumulation, presence of dogs, cohort specific population characteristics, and other cultural phenomena. These data were digitized into Google Earth and then coded and analyzed in a GIS using kernel density and spatial filtering approaches. The concentrations of these risks around area schools which are sometimes sources of diarrheal disease infection because of the high concentration of children and variable sanitary practices will show the utility of the method. In addition schools offer potential locations for cholera education interventions. Results Previously unavailable fine scale health risk data vary in concentration across the town, with some schools being proximate to greater concentrations of the mapped risks. The spatial video is also used to validate coded data and location specific risks within these “hotspots”. Conclusions Spatial video is a tool that can be used in any environment to improve local area health analysis and intervention. The process is rapid and can be repeated in study sites through time to track spatio-temporal dynamics of the communities. Its simplicity should also be used to encourage local participatory collaborations. PMID:23587358

A ubiquitous method for street scale spatial data collection and analysis in challenging urban environments: mapping health risks using spatial video in Haiti.

PubMed

Curtis, Andrew; Blackburn, Jason K; Widmer, Jocelyn M; Morris, J Glenn

2013-04-15

Fine-scale and longitudinal geospatial analysis of health risks in challenging urban areas is often limited by the lack of other spatial layers even if case data are available. Underlying population counts, residential context, and associated causative factors such as standing water or trash locations are often missing unless collected through logistically difficult, and often expensive, surveys. The lack of spatial context also hinders the interpretation of results and designing intervention strategies structured around analytical insights. This paper offers a ubiquitous spatial data collection approach using a spatial video that can be used to improve analysis and involve participatory collaborations. A case study will be used to illustrate this approach with three health risks mapped at the street scale for a coastal community in Haiti. Spatial video was used to collect street and building scale information, including standing water, trash accumulation, presence of dogs, cohort specific population characteristics, and other cultural phenomena. These data were digitized into Google Earth and then coded and analyzed in a GIS using kernel density and spatial filtering approaches. The concentrations of these risks around area schools which are sometimes sources of diarrheal disease infection because of the high concentration of children and variable sanitary practices will show the utility of the method. In addition schools offer potential locations for cholera education interventions. Previously unavailable fine scale health risk data vary in concentration across the town, with some schools being proximate to greater concentrations of the mapped risks. The spatial video is also used to validate coded data and location specific risks within these "hotspots". Spatial video is a tool that can be used in any environment to improve local area health analysis and intervention. The process is rapid and can be repeated in study sites through time to track spatio-temporal dynamics of the communities. Its simplicity should also be used to encourage local participatory collaborations.

Spawning site selection and contingent behavior in Common Snook, Centropomus undecimalis.

PubMed

Lowerre-Barbieri, Susan; Villegas-Ríos, David; Walters, Sarah; Bickford, Joel; Cooper, Wade; Muller, Robert; Trotter, Alexis

2014-01-01

Reproductive behavior affects spatial population structure and our ability to manage for sustainability in marine and diadromous fishes. In this study, we used fishery independent capture-based sampling to evaluate where Common Snook occurred in Tampa Bay and if it changed with spawning season, and passive acoustic telemetry to assess fine scale behavior at an inlet spawning site (2007-2009). Snook concentrated in three areas during the spawning season only one of which fell within the expected spawning habitat. Although in lower numbers, they remained in these areas throughout the winter months. Acoustically-tagged snook (n = 31) showed two seasonal patterns at the spawning site: Most fish occurred during the spawning season but several fish displayed more extended residency, supporting the capture-based findings that Common Snook exhibit facultative catadromy. Spawning site selection for iteroparous, multiple-batch spawning fishes occurs at the lifetime, annual, or intra-annual temporal scales. In this study we show colonization of a new spawning site, indicating that lifetime spawning site fidelity of Common Snook is not fixed at this fine spatial scale. However, individuals did exhibit annual and intra-seasonal spawning site fidelity to this new site over the three years studied. The number of fish at the spawning site increased in June and July (peak spawning months) and on new and full lunar phases indicating within population variability in spawning and movement patterns. Intra-seasonal patterns of detection also differed significantly with sex. Common Snook exhibited divergent migration tactics and habitat use at the annual and estuarine scales, with contingents using different overwintering habitat. Migration tactics also varied at the spawning site at the intra-seasonal scale and with sex. These results have important implications for understanding how reproductive behavior affects spatio-temporal patterns of fish abundance and their resilience to disturbance events and fishing pressure.

The genetic structure of fermentative vineyard-associated Saccharomyces cerevisiae populations revealed by microsatellite analysis.

PubMed

Schuller, Dorit; Casal, Margarida

2007-02-01

From the analysis of six polymorphic microsatellite loci performed in 361 Saccharomyces cerevisiae isolates, 93 alleles were identified, 52 of them being described for the first time. All these isolates have a distinct mtDNA RFLP pattern. They are derived from a pool of 1620 isolates obtained from spontaneous fermentations of grapes collected in three vineyards of the Vinho Verde Region in Portugal, during the 2001-2003 harvest seasons. For all loci analyzed, observed heterozygosity was 3-4 times lower than the expected value supposing a Hardy-Weinberg equilibrium (random mating and no evolutionary mechanisms acting), indicating a clonal structure and strong populational substructuring. Genetic differences among S. cerevisiae populations were apparent mainly from gradations in allele frequencies rather than from distinctive "diagnostic" genotypes, and the accumulation of small allele-frequency differences across six loci allowed the identification of population structures. Genetic differentiation in the same vineyard in consecutive years was of the same order of magnitude as the differences verified among the different vineyards. Correlation of genetic differentiation with the distance between sampling points within a vineyard suggested a pattern of isolation-by-distance, where genetic divergence in a vineyard increased with size. The continuous use of commercial yeasts has a limited influence on the autochthonous fermentative yeast population collected from grapes and may just slightly change populational structures of strains isolated from sites very close to the winery where they have been used. The present work is the first large-scale approach using microsatellite typing allowing a very fine resolution of indigenous S. cerevisiae populations isolated from vineyards.

A nanobuffer reporter library for fine-scale imaging and perturbation of endocytic organelles | Office of Cancer Genomics

Cancer.gov

Endosomes, lysosomes and related catabolic organelles are a dynamic continuum of vacuolar structures that impact a number of cell physiological processes such as protein/lipid metabolism, nutrient sensing and cell survival. Here we develop a library of ultra-pH-sensitive fluorescent nanoparticles with chemical properties that allow fine-scale, multiplexed, spatio-temporal perturbation and quantification of catabolic organelle maturation at single organelle resolution to support quantitative investigation of these processes in living cells.

Increased fire frequency promotes stronger spatial genetic structure and natural selection at regional and local scales in Pinus halepensis Mill.

PubMed

Budde, Katharina B; González-Martínez, Santiago C; Navascués, Miguel; Burgarella, Concetta; Mosca, Elena; Lorenzo, Zaida; Zabal-Aguirre, Mario; Vendramin, Giovanni G; Verdú, Miguel; Pausas, Juli G; Heuertz, Myriam

2017-04-01

The recurrence of wildfires is predicted to increase due to global climate change, resulting in severe impacts on biodiversity and ecosystem functioning. Recurrent fires can drive plant adaptation and reduce genetic diversity; however, the underlying population genetic processes have not been studied in detail. In this study, the neutral and adaptive evolutionary effects of contrasting fire regimes were examined in the keystone tree species Pinus halepensis Mill. (Aleppo pine), a fire-adapted conifer. The genetic diversity, demographic history and spatial genetic structure were assessed at local (within-population) and regional scales for populations exposed to different crown fire frequencies. Eight natural P. halepensis stands were sampled in the east of the Iberian Peninsula, five of them in a region exposed to frequent crown fires (HiFi) and three of them in an adjacent region with a low frequency of crown fires (LoFi). Samples were genotyped at nine neutral simple sequence repeats (SSRs) and at 251 single nucleotide polymorphisms (SNPs) from coding regions, some of them potentially important for fire adaptation. Fire regime had no effects on genetic diversity or demographic history. Three high-differentiation outlier SNPs were identified between HiFi and LoFi stands, suggesting fire-related selection at the regional scale. At the local scale, fine-scale spatial genetic structure (SGS) was overall weak as expected for a wind-pollinated and wind-dispersed tree species. HiFi stands displayed a stronger SGS than LoFi stands at SNPs, which probably reflected the simultaneous post-fire recruitment of co-dispersed related seeds. SNPs with exceptionally strong SGS, a proxy for microenvironmental selection, were only reliably identified under the HiFi regime. An increasing fire frequency as predicted due to global change can promote increased SGS with stronger family structures and alter natural selection in P. halepensis and in plants with similar life history traits. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Fine-scaled human genetic structure revealed by SNP microarrays.

PubMed

Xing, Jinchuan; Watkins, W Scott; Witherspoon, David J; Zhang, Yuhua; Guthery, Stephen L; Thara, Rangaswamy; Mowry, Bryan J; Bulayeva, Kazima; Weiss, Robert B; Jorde, Lynn B

2009-05-01

We report an analysis of more than 240,000 loci genotyped using the Affymetrix SNP microarray in 554 individuals from 27 worldwide populations in Africa, Asia, and Europe. To provide a more extensive and complete sampling of human genetic variation, we have included caste and tribal samples from two states in South India, Daghestanis from eastern Europe, and the Iban from Malaysia. Consistent with observations made by Charles Darwin, our results highlight shared variation among human populations and demonstrate that much genetic variation is geographically continuous. At the same time, principal components analyses reveal discernible genetic differentiation among almost all identified populations in our sample, and in most cases, individuals can be clearly assigned to defined populations on the basis of SNP genotypes. All individuals are accurately classified into continental groups using a model-based clustering algorithm, but between closely related populations, genetic and self-classifications conflict for some individuals. The 250K data permitted high-level resolution of genetic variation among Indian caste and tribal populations and between highland and lowland Daghestani populations. In particular, upper-caste individuals from Tamil Nadu and Andhra Pradesh form one defined group, lower-caste individuals from these two states form another, and the tribal Irula samples form a third. Our results emphasize the correlation of genetic and geographic distances and highlight other elements, including social factors that have contributed to population structure.

Contrasting population genetic structure among freshwater-resident and anadromous lampreys: the role of demographic history, differential dispersal and anthropogenic barriers to movement

PubMed Central

Bracken, Fiona S A; Hoelzel, A Rus; Hume, John B; Lucas, Martyn C

2015-01-01

The tendency of many species to abandon migration remains a poorly understood aspect of evolutionary biology that may play an important role in promoting species radiation by both allopatric and sympatric mechanisms. Anadromy inherently offers an opportunity for the colonization of freshwater environments, and the shift from an anadromous to a wholly freshwater life history has occurred in many families of fishes. Freshwater-resident forms have arisen repeatedly among lampreys (within the Petromyzontidae and Mordaciidae), and there has been much debate as to whether anadromous lampreys, and their derived freshwater-resident analogues, constitute distinct species or are divergent ecotypes of polymorphic species. Samples of 543 European river lamprey Lampetra fluviatilis (mostly from anadromous populations) and freshwater European brook lamprey Lampetra planeri from across 18 sites, primarily in the British Isles, were investigated for 13 polymorphic microsatellite DNA loci, and 108 samples from six of these sites were sequenced for 829 bp of mitochondrial DNA (mtDNA). We found contrasting patterns of population structure for mtDNA and microsatellite DNA markers, such that low diversity and little structure were seen for all populations for mtDNA (consistent with a recent founder expansion event), while fine-scale structuring was evident for nuclear markers. Strong differentiation for microsatellite DNA loci was seen among freshwater-resident L. planeri populations and between L. fluviatilis and L. planeri in most cases, but little structure was evident among anadromous L. fluviatilis populations. We conclude that postglacial colonization founded multiple freshwater-resident populations with strong habitat fidelity and limited dispersal tendencies that became highly differentiated, a pattern that was likely intensified by anthropogenic barriers. PMID:25689694

Adaptive Genetic Divergence Despite Significant Isolation-by-Distance in Populations of Taiwan Cow-Tail Fir (Keteleeria davidiana var. formosana)

PubMed Central

Shih, Kai-Ming; Chang, Chung-Te; Chung, Jeng-Der; Chiang, Yu-Chung; Hwang, Shih-Ying

2018-01-01

Double digest restriction site-associated DNA sequencing (ddRADseq) is a tool for delivering genome-wide single nucleotide polymorphism (SNP) markers for non-model organisms useful in resolving fine-scale population structure and detecting signatures of selection. This study performs population genetic analysis, based on ddRADseq data, of a coniferous species, Keteleeria davidiana var. formosana, disjunctly distributed in northern and southern Taiwan, for investigation of population adaptive divergence in response to environmental heterogeneity. A total of 13,914 SNPs were detected and used to assess genetic diversity, FST outlier detection, population genetic structure, and individual assignments of five populations (62 individuals) of K. davidiana var. formosana. Principal component analysis (PCA), individual assignments, and the neighbor-joining tree were successful in differentiating individuals between northern and southern populations of K. davidiana var. formosana, but apparent gene flow between the southern DW30 population and northern populations was also revealed. Fifteen of 23 highly differentiated SNPs identified were found to be strongly associated with environmental variables, suggesting isolation-by-environment (IBE). However, multiple matrix regression with randomization analysis revealed strong IBE as well as significant isolation-by-distance. Environmental impacts on divergence were found between populations of the North and South regions and also between the two southern neighboring populations. BLASTN annotation of the sequences flanking outlier SNPs gave significant hits for three of 23 markers that might have biological relevance to mitochondrial homeostasis involved in the survival of locally adapted lineages. Species delimitation between K. davidiana var. formosana and its ancestor, K. davidiana, was also examined (72 individuals). This study has produced highly informative population genomic data for the understanding of population attributes, such as diversity, connectivity, and adaptive divergence associated with large- and small-scale environmental heterogeneity in K. davidiana var. formosana. PMID:29449860

A Comparative Analysis of Genetic Diversity and Structure in Jaguars (Panthera onca), Pumas (Puma concolor), and Ocelots (Leopardus pardalis) in Fragmented Landscapes of a Critical Mesoamerican Linkage Zone.

PubMed

Wultsch, Claudia; Waits, Lisette P; Kelly, Marcella J

2016-01-01

With increasing anthropogenic impact and landscape change, terrestrial carnivore populations are becoming more fragmented. Thus, it is crucial to genetically monitor wild carnivores and quantify changes in genetic diversity and gene flow in response to these threats. This study combined the use of scat detector dogs and molecular scatology to conduct the first genetic study on wild populations of multiple Neotropical felids coexisting across a fragmented landscape in Belize, Central America. We analyzed data from 14 polymorphic microsatellite loci in 1053 scat samples collected from wild jaguars (Panthera onca), pumas (Puma concolor), and ocelots (Leopardus pardalis). We assessed levels of genetic diversity, defined potential genetic clusters, and examined gene flow for the three target species on a countrywide scale using a combination of individual- and population-based analyses. Wild felids in Belize showed moderate levels of genetic variation, with jaguars having the lowest diversity estimates (HE = 0.57 ± 0.02; AR = 3.36 ± 0.09), followed by pumas (HE = 0.57 ± 0.08; AR = 4.20 ± 0.16), and ocelots (HE = 0.63 ± 0.03; AR = 4.16 ± 0.08). We observed low to moderate levels of genetic differentiation for all three target species, with jaguars showing the lowest degree of genetic subdivision across the country, followed by ocelots and pumas. Although levels of genetic diversity and gene flow were still fairly high, we detected evidence of fine-scale genetic subdivision, indicating that levels of genetic connectivity for wild felids in Belize are likely to decrease if habitat loss and fragmentation continue at the current rate. Our study demonstrates the value of understanding fine-scale patterns of gene flow in multiple co-occurring felid species of conservation concern, which is vital for wildlife movement corridor planning and prioritizing future conservation and management efforts within human-impacted landscapes.

A Comparative Analysis of Genetic Diversity and Structure in Jaguars (Panthera onca), Pumas (Puma concolor), and Ocelots (Leopardus pardalis) in Fragmented Landscapes of a Critical Mesoamerican Linkage Zone

PubMed Central

Wultsch, Claudia; Waits, Lisette P.; Kelly, Marcella J.

2016-01-01

With increasing anthropogenic impact and landscape change, terrestrial carnivore populations are becoming more fragmented. Thus, it is crucial to genetically monitor wild carnivores and quantify changes in genetic diversity and gene flow in response to these threats. This study combined the use of scat detector dogs and molecular scatology to conduct the first genetic study on wild populations of multiple Neotropical felids coexisting across a fragmented landscape in Belize, Central America. We analyzed data from 14 polymorphic microsatellite loci in 1053 scat samples collected from wild jaguars (Panthera onca), pumas (Puma concolor), and ocelots (Leopardus pardalis). We assessed levels of genetic diversity, defined potential genetic clusters, and examined gene flow for the three target species on a countrywide scale using a combination of individual- and population-based analyses. Wild felids in Belize showed moderate levels of genetic variation, with jaguars having the lowest diversity estimates (HE = 0.57 ± 0.02; AR = 3.36 ± 0.09), followed by pumas (HE = 0.57 ± 0.08; AR = 4.20 ± 0.16), and ocelots (HE = 0.63 ± 0.03; AR = 4.16 ± 0.08). We observed low to moderate levels of genetic differentiation for all three target species, with jaguars showing the lowest degree of genetic subdivision across the country, followed by ocelots and pumas. Although levels of genetic diversity and gene flow were still fairly high, we detected evidence of fine-scale genetic subdivision, indicating that levels of genetic connectivity for wild felids in Belize are likely to decrease if habitat loss and fragmentation continue at the current rate. Our study demonstrates the value of understanding fine-scale patterns of gene flow in multiple co-occurring felid species of conservation concern, which is vital for wildlife movement corridor planning and prioritizing future conservation and management efforts within human-impacted landscapes. PMID:26974968

Integration of ALOS/PALSAR backscatter with a LiDAR-derived canopy height map to quantify forest fragmentation

NASA Astrophysics Data System (ADS)

Pinto, N.; Dubayah, R.; Simard, M.; Fatoyinbo, T. E.

2011-12-01

Habitat loss is the main predictor of species extinctions and must be characterized in high-biodiversity ecosystems where land cover change is pervasive. Forests' ability to support viable animal populations is typically modeled as a function of the presence of linkages or corridors, and quantified with fragmentation metrics. In this scenario, small forest patches and linear (e.g. riparian) zones can act as keystone structures. Fine-resolution, all-weather Synthetic Aperture Radar (SAR) data from ALOS/PALSAR is well-suited to resolve forest fragments in tropical sites. This study summarizes a technique for integrating fragmentation metrics from ALOS/PALSAR with vertical structure data from ICESat/GLAS to produce fine-resolution (30 m) forest habitat metrics that capture both local quality (canopy height) as well as spatial context and multi-scale connectivity. We illustrate our approach with backscatter images acquired over the Brazilian Atlantic Forest, a biodiversity hotspot. ALOS/PALSAR 1.1 images acquired over the dry season were calibrated to calculate gamma naught and map forest cover via tresholding. We employ network algorithms to locate dispersal bottlenecks between conservation units. The location of keystone structures is compared against a model that uses coarse (500m) percent tree cover as an input.

Range expansion through fragmented landscapes under a variable climate

PubMed Central

Bennie, Jonathan; Hodgson, Jenny A; Lawson, Callum R; Holloway, Crispin TR; Roy, David B; Brereton, Tom; Thomas, Chris D; Wilson, Robert J

2013-01-01

Ecological responses to climate change may depend on complex patterns of variability in weather and local microclimate that overlay global increases in mean temperature. Here, we show that high-resolution temporal and spatial variability in temperature drives the dynamics of range expansion for an exemplar species, the butterfly Hesperia comma. Using fine-resolution (5 m) models of vegetation surface microclimate, we estimate the thermal suitability of 906 habitat patches at the species' range margin for 27 years. Population and metapopulation models that incorporate this dynamic microclimate surface improve predictions of observed annual changes to population density and patch occupancy dynamics during the species' range expansion from 1982 to 2009. Our findings reveal how fine-scale, short-term environmental variability drives rates and patterns of range expansion through spatially localised, intermittent episodes of expansion and contraction. Incorporating dynamic microclimates can thus improve models of species range shifts at spatial and temporal scales relevant to conservation interventions. PMID:23701124

Spectral structure and stability studies on microstructure-fiber continuum

NASA Astrophysics Data System (ADS)

Gu, Xun; Kimmel, Mark; Zeek, Erik; Shreenath, Aparna P.; Trebino, Rick P.; Windeler, Robert S.

2003-07-01

Although previous direct measurements of the microstructure-fiber continuum have all showed a smooth and stable spectrum, our cross-correlation frequency-resolved optical gating (XFROG) full-intensity-and-phase characterization of the continuum pulse, utilizing sum-frequency-generation with a pre-characterized reference pulse and the angle-dithered-crystal technique, indicates that fine-scale spectral structure exists on a single-shot basis, contrary to previous observations. In particular, deep and fine oscillations are found in the retrieved spectrum, and the retrieved trace contains a "measles" pattern, whereas the measured trace and the independently-measured spectrum are rather smooth. The discrepancy is shown to be the result of unstable single-shot spectral structure. Although the XFROG measurement is not able to directly measure the single-shot fine structure in the trace, the redundancy of information in FROG traces enables the retrieval algorithm to correctly recognize the existence of the spectral fine structure, and restore the structure in the retrieved trace and spectrum. Numerical simulations have supported our hypothesis, and we directly observed the fine spectral structure in single-shot measurements of the continuum spectrum and the structure was seen to be highly unstable, the continuum spectrum appearing smooth only when many shots are averaged. Despite the structure and instability in the continuum spectrum, coherence experiments also reveal that the spectral phase is rather stable, being able to produce well-defined spectral fringes across the entire continuum bandwidth.

High-resolution observations of active region moss and its dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morton, R. J.; McLaughlin, J. A., E-mail: richard.morton@northumbria.ac.uk

2014-07-10

The High Resolution Coronal Imager has provided the sharpest view of the EUV corona to date. In this paper, we exploit its impressive resolving power to provide the first analysis of the fine-scale structure of moss in an active region. The data reveal that the moss is made up of a collection of fine threads that have widths with a mean and standard deviation of 440 ± 190 km (FWHM). The brightest moss emission is located at the visible head of the fine-scale structure and the fine structure appears to extend into the lower solar atmosphere. The emission decreases alongmore » the features, implying that the lower sections are most likely dominated by cooler transition region plasma. These threads appear to be the cool, lower legs of the hot loops. In addition, the increased resolution allows for the first direct observation of physical displacements of the moss fine structure in a direction transverse to its central axis. Some of these transverse displacements demonstrate periodic behavior, which we interpret as a signature of kink (Alfvénic) waves. Measurements of the properties of the transverse motions are made and the wave motions have means and standard deviations of 55 ± 37 km for the transverse displacement amplitude, 77 ± 33 s for the period, and 4.7 ± 2.5 km s{sup –1} for the velocity amplitude. The presence of waves in the transition region of hot loops could have important implications for the heating of active regions.« less

Fine-scale genetic structure arises during range expansion of an invasive gecko.

PubMed

Short, Kristen Harfmann; Petren, Kenneth

2011-01-01

Processes of range expansion are increasingly important in light of current concerns about invasive species and range shifts due to climate change. Theoretical studies suggest that genetic structuring may occur during range expansion. Ephemeral genetic structure can have important evolutionary implications, such as propagating genetic changes along the wave front of expansion, yet few studies have shown evidence of such structure. We tested the hypothesis that genetic structure arises during range expansion in Hemidactylus mabouia, a nocturnal African gecko recently introduced to Florida, USA. Twelve highly variable microsatellite loci were used to screen 418 individuals collected from 43 locations from four sampling sites across Florida, representing a gradient from earlier (∼1990s) to very recent colonization. We found earlier colonized locations had little detectable genetic structure and higher allelic richness than more recently colonized locations. Genetic structuring was pronounced among locations at spatial scales of tens to hundreds of meters near the leading edge of range expansion. Despite the rapid pace of range expansion in this introduced gecko, dispersal is limited among many suitable habitat patches. Fine-scale genetic structure is likely the result of founder effects during colonization of suitable habitat patches. It may be obscured over time and by scale-dependent modes of dispersal. Further studies are needed to determine if such genetic structure affects adaptation and trait evolution in range expansions and range shifts.

Unprecedented Fine Structure of a Solar Flare Revealed by the 1.6 m New Solar Telescope

PubMed Central

Jing, Ju; Xu, Yan; Cao, Wenda; Liu, Chang; Gary, Dale; Wang, Haimin

2016-01-01

Solar flares signify the sudden release of magnetic energy and are sources of so called space weather. The fine structures (below 500 km) of flares are rarely observed and are accessible to only a few instruments world-wide. Here we present observation of a solar flare using exceptionally high resolution images from the 1.6 m New Solar Telescope (NST) equipped with high order adaptive optics at Big Bear Solar Observatory (BBSO). The observation reveals the process of the flare in unprecedented detail, including the flare ribbon propagating across the sunspots, coronal rain (made of condensing plasma) streaming down along the post-flare loops, and the chromosphere’s response to the impact of coronal rain, showing fine-scale brightenings at the footpoints of the falling plasma. Taking advantage of the resolving power of the NST, we measure the cross-sectional widths of flare ribbons, post-flare loops and footpoint brighenings, which generally lie in the range of 80–200 km, well below the resolution of most current instruments used for flare studies. Confining the scale of such fine structure provides an essential piece of information in modeling the energy transport mechanism of flares, which is an important issue in solar and plasma physics. PMID:27071459

Fine-Scale Cartography of Human Impacts along French Mediterranean Coasts: A Relevant Map for the Management of Marine Ecosystems

PubMed Central

Holon, Florian; Mouquet, Nicolas; Boissery, Pierre; Bouchoucha, Marc; Delaruelle, Gwenaelle; Tribot, Anne-Sophie; Deter, Julie

2015-01-01

Ecosystem services provided by oceans and seas support most human needs but are threatened by human activities. Despite existing maps illustrating human impacts on marine ecosystems, information remains either large-scale but rough and insufficient for stakeholders (1 km² grid, lack of data along the coast) or fine-scale but fragmentary and heterogeneous in methodology. The objectives of this study are to map and quantify the main pressures exerted on near-coast marine ecosystems, at a large spatial scale though in fine and relevant resolution for managers (one pixel = 20 x 20 m). It focuses on the French Mediterranean coast (1,700 km of coastline including Corsica) at a depth of 0 to 80 m. After completing and homogenizing data presently available under GIS on the bathymetry and anthropogenic pressures but also on the seabed nature and ecosystem vulnerability, we provide a fine modeling of the extent and impacts of 10 anthropogenic pressures on marine habitats. The considered pressures are man-made coastline, boat anchoring, aquaculture, urban effluents, industrial effluents, urbanization, agriculture, coastline erosion, coastal population and fishing. A 1:10 000 continuous habitat map is provided considering 11 habitat classes. The marine bottom is mostly covered by three habitats: infralittoral soft bottom, Posidonia oceanica meadows and circalittoral soft bottom. Around two thirds of the bottoms are found within medium and medium high cumulative impact categories. Seagrass meadows are the most impacted habitats. The most important pressures (in area and intensity) are urbanization, coastal population, coastal erosion and man-made coastline. We also identified areas in need of a special management interest. This work should contribute to prioritize environmental needs, as well as enhance the development of indicators for the assessment of the ecological status of coastal systems. It could also help better apply and coordinate management measures at a relevant scale for biodiversity conservation. PMID:26266542

Fine-Scale Cartography of Human Impacts along French Mediterranean Coasts: A Relevant Map for the Management of Marine Ecosystems.

PubMed

Holon, Florian; Mouquet, Nicolas; Boissery, Pierre; Bouchoucha, Marc; Delaruelle, Gwenaelle; Tribot, Anne-Sophie; Deter, Julie

2015-01-01

Ecosystem services provided by oceans and seas support most human needs but are threatened by human activities. Despite existing maps illustrating human impacts on marine ecosystems, information remains either large-scale but rough and insufficient for stakeholders (1 km² grid, lack of data along the coast) or fine-scale but fragmentary and heterogeneous in methodology. The objectives of this study are to map and quantify the main pressures exerted on near-coast marine ecosystems, at a large spatial scale though in fine and relevant resolution for managers (one pixel = 20 x 20 m). It focuses on the French Mediterranean coast (1,700 km of coastline including Corsica) at a depth of 0 to 80 m. After completing and homogenizing data presently available under GIS on the bathymetry and anthropogenic pressures but also on the seabed nature and ecosystem vulnerability, we provide a fine modeling of the extent and impacts of 10 anthropogenic pressures on marine habitats. The considered pressures are man-made coastline, boat anchoring, aquaculture, urban effluents, industrial effluents, urbanization, agriculture, coastline erosion, coastal population and fishing. A 1:10 000 continuous habitat map is provided considering 11 habitat classes. The marine bottom is mostly covered by three habitats: infralittoral soft bottom, Posidonia oceanica meadows and circalittoral soft bottom. Around two thirds of the bottoms are found within medium and medium high cumulative impact categories. Seagrass meadows are the most impacted habitats. The most important pressures (in area and intensity) are urbanization, coastal population, coastal erosion and man-made coastline. We also identified areas in need of a special management interest. This work should contribute to prioritize environmental needs, as well as enhance the development of indicators for the assessment of the ecological status of coastal systems. It could also help better apply and coordinate management measures at a relevant scale for biodiversity conservation.

Directional genetic selection by pulp mill effluent on multiple natural populations of three-spined stickleback (Gasterosteus aculeatus).

PubMed

Lind, Emma E; Grahn, Mats

2011-05-01

Contamination can cause a rapid environmental change which may require populations to respond with evolutionary changes. To evaluate the effects of pulp mill effluents on population genetics, we sampled three-spined sticklebacks (Gasterosteus aculeatus) near four pulp mills and four adjacent reference sites and analyzed Amplified Fragment Length Polymorphism (AFLP) to compare genetic variability. A fine scale genetic structure was detected and samples from polluted sites separated from reference sites in multidimensional scaling plots (P<0.005, 1000 permutations) and locus-by-locus Analysis of Molecular Variance (AMOVA) further confirmed that habitats are significantly separated (F(ST)=0.021, P<0.01, 1023 permutations). The amount of genetic variation between populations did not differ between habitats, and populations from both habitats had similar levels of heterozygosity (polluted sites Nei's Hs=0.11, reference sites Nei's Hs=0.11). Still, pairwise F(ST): s between three, out of four, pairs of polluted-reference sites were significant. A F(ST)-outlier analysis showed that 21 (8.4%) loci were statistically different from a neutral distribution at the P<0.05 level and therefore indicated to be under divergent selection. When removing 13 F(ST)-outlier loci, significant at the P<0.01 level, differentiation between habitats disappeared in a multidimensional scaling plot. In conclusion, pulp mill effluence has acted as a selective agent on natural populations of G. aculeatus, causing a convergence in genotype composition change at multiple sites in an open environment. © The Author(s) 2011. This article is published with open access at Springerlink.com

Genetic Diversity in Introduced Golden Mussel Populations Corresponds to Vector Activity

PubMed Central

Ghabooli, Sara; Zhan, Aibin; Sardiña, Paula; Paolucci, Esteban; Sylvester, Francisco; Perepelizin, Pablo V.; Briski, Elizabeta; Cristescu, Melania E.; MacIsaac, Hugh J.

2013-01-01

We explored possible links between vector activity and genetic diversity in introduced populations of Limnoperna fortunei by characterizing the genetic structure in native and introduced ranges in Asia and South America. We surveyed 24 populations: ten in Asia and 14 in South America using the mitochondrial cytochrome c oxidase subunit I (COI) gene, as well as eight polymorphic microsatellite markers. We performed population genetics and phylogenetic analyses to investigate population genetic structure across native and introduced regions. Introduced populations in Asia exhibit higher genetic diversity (H E = 0.667–0.746) than those in South America (H E = 0.519–0.575), suggesting higher introduction effort for the former populations. We observed pronounced geographical structuring in introduced regions, as indicated by both mitochondrial and nuclear markers based on multiple genetic analyses including pairwise ФST, F ST, Bayesian clustering method, and three-dimensional factorial correspondence analyses. Pairwise F ST values within both Asia (F ST = 0.017–0.126, P = 0.000–0.009) and South America (F ST = 0.004–0.107, P = 0.000–0.721) were lower than those between continents (F ST = 0.180–0.319, P = 0.000). Fine-scale genetic structuring was also apparent among introduced populations in both Asia and South America, suggesting either multiple introductions of distinct propagules or strong post-introduction selection and demographic stochasticity. Higher genetic diversity in Asia as compared to South America is likely due to more frequent propagule transfers associated with higher shipping activities between source and donor regions within Asia. This study suggests that the intensity of human-mediated introduction vectors influences patterns of genetic diversity in non-indigenous species. PMID:23533614

On the Feedback Phenomenon of an Impinging Jet

DTIC Science & Technology

1979-09-01

the double-structured nature of turbulent flows: time dependent quasi- ordered large scale structures, and fine-scale random structures. Numerous ...downstream and upstream waves d Nozzle diameter f Frequency (Hz) Gf Normalized power si.c ,ur’ of i G ,(f) Normalized cr,- tr bee -en i(t) and J(t) I ,j xiv...1975) suggested that these quasi- ordered structures are deterministic, in the sense that they have a characteristic shape, size and convection motion

Molecular Dynamics Simulations and Classical Multidimensional Scaling Unveil New Metastable States in the Conformational Landscape of CDK2

PubMed Central

Pisani, Pasquale; Rastelli, Giulio

2016-01-01

Protein kinases are key regulatory nodes in cellular networks and their function has been shown to be intimately coupled with their structural flexibility. However, understanding the key structural mechanisms of large conformational transitions remains a difficult task. CDK2 is a crucial regulator of cell cycle. Its activity is finely tuned by Cyclin E/A and the catalytic segment phosphorylation, whereas its deregulation occurs in many types of cancer. ATP competitive inhibitors have failed to be approved for clinical use due to toxicity issues raised by a lack of selectivity. However, in the last few years type III allosteric inhibitors have emerged as an alternative strategy to selectively modulate CDK2 activity. In this study we have investigated the conformational variability of CDK2. A low dimensional conformational landscape of CDK2 was modeled using classical multidimensional scaling on a set of 255 crystal structures. Microsecond-scale plain and accelerated MD simulations were used to populate this landscape by using an out-of-sample extension of multidimensional scaling. CDK2 was simulated in the apo-form and in complex with the allosteric inhibitor 8-anilino-1-napthalenesulfonic acid (ANS). The apo-CDK2 landscape analysis showed a conformational equilibrium between an Src-like inactive conformation and an active-like form. These two states are separated by different metastable states that share hybrid structural features with both forms of the kinase. In contrast, the CDK2/ANS complex landscape is compatible with a conformational selection picture where the binding of ANS in proximity of the αC helix causes a population shift toward the inactive conformation. Interestingly, the new metastable states could enlarge the pool of candidate structures for the development of selective allosteric CDK2 inhibitors. The method here presented should not be limited to the CDK2 case but could be used to systematically unmask similar mechanisms throughout the human kinome. PMID:27100206

Molecular Dynamics Simulations and Classical Multidimensional Scaling Unveil New Metastable States in the Conformational Landscape of CDK2.

PubMed

Pisani, Pasquale; Caporuscio, Fabiana; Carlino, Luca; Rastelli, Giulio

2016-01-01

Protein kinases are key regulatory nodes in cellular networks and their function has been shown to be intimately coupled with their structural flexibility. However, understanding the key structural mechanisms of large conformational transitions remains a difficult task. CDK2 is a crucial regulator of cell cycle. Its activity is finely tuned by Cyclin E/A and the catalytic segment phosphorylation, whereas its deregulation occurs in many types of cancer. ATP competitive inhibitors have failed to be approved for clinical use due to toxicity issues raised by a lack of selectivity. However, in the last few years type III allosteric inhibitors have emerged as an alternative strategy to selectively modulate CDK2 activity. In this study we have investigated the conformational variability of CDK2. A low dimensional conformational landscape of CDK2 was modeled using classical multidimensional scaling on a set of 255 crystal structures. Microsecond-scale plain and accelerated MD simulations were used to populate this landscape by using an out-of-sample extension of multidimensional scaling. CDK2 was simulated in the apo-form and in complex with the allosteric inhibitor 8-anilino-1-napthalenesulfonic acid (ANS). The apo-CDK2 landscape analysis showed a conformational equilibrium between an Src-like inactive conformation and an active-like form. These two states are separated by different metastable states that share hybrid structural features with both forms of the kinase. In contrast, the CDK2/ANS complex landscape is compatible with a conformational selection picture where the binding of ANS in proximity of the αC helix causes a population shift toward the inactive conformation. Interestingly, the new metastable states could enlarge the pool of candidate structures for the development of selective allosteric CDK2 inhibitors. The method here presented should not be limited to the CDK2 case but could be used to systematically unmask similar mechanisms throughout the human kinome.

The role of chromosomal rearrangements and geographical barriers in the divergence of lineages in a South American subterranean rodent (Rodentia: Ctenomyidae: Ctenomys minutus)

PubMed Central

Lopes, C M; Ximenes, S S F; Gava, A; de Freitas, T R O

2013-01-01

Identifying factors and the extent of their roles in the differentiation of populations is of great importance for understanding the evolutionary process in which a species is involved. Ctenomys minutus is a highly karyotype–polymorphic subterranean rodent, with diploid numbers ranging from 42 to 50 and autosomal arm numbers (ANs) ranging from 68 to 80, comprising a total of 45 karyotypes described so far. This species inhabits the southern Brazilian coastal plain, which has a complex geological history, with several potential geographical barriers acting on different time scales. We assessed the geographical genetic structure of C. minutus, examining 340 individuals over the entire distributional range and using information from chromosomal rearrangements, mitochondrial DNA (mtDNA) sequences and 14 microsatellite loci. The mtDNA results revealed seven main haplogroups, with the most recent common ancestors dating from the Pleistocene, whereas clustering methods defined 12 populations. Some boundaries of mtDNA haplogroups and population clusters can be associated with potential geographical barriers to gene flow. The isolation-by-distance pattern also has an important role in fine-scale genetic differentiation, which is strengthened by the narrowness of the coastal plain and by common features of subterranean rodents (that is, small fragmented populations and low dispersal rates), which limit gene flow among populations. A step-by-step mechanism of chromosomal evolution can be suggested for this species, mainly associated with the metapopulation structure, genetic drift and the geographical features of the southern Brazilian coastal plain. However, chromosomal variations have no or very little role in the diversification of C. minutus populations. PMID:23759727

Temporal Organization of Sound Information in Auditory Memory.

PubMed

Song, Kun; Luo, Huan

2017-01-01

Memory is a constructive and organizational process. Instead of being stored with all the fine details, external information is reorganized and structured at certain spatiotemporal scales. It is well acknowledged that time plays a central role in audition by segmenting sound inputs into temporal chunks of appropriate length. However, it remains largely unknown whether critical temporal structures exist to mediate sound representation in auditory memory. To address the issue, here we designed an auditory memory transferring study, by combining a previously developed unsupervised white noise memory paradigm with a reversed sound manipulation method. Specifically, we systematically measured the memory transferring from a random white noise sound to its locally temporal reversed version on various temporal scales in seven experiments. We demonstrate a U-shape memory-transferring pattern with the minimum value around temporal scale of 200 ms. Furthermore, neither auditory perceptual similarity nor physical similarity as a function of the manipulating temporal scale can account for the memory-transferring results. Our results suggest that sounds are not stored with all the fine spectrotemporal details but are organized and structured at discrete temporal chunks in long-term auditory memory representation.

Feedbacks Between Soil Structure and Microbial Activities in Soil

NASA Astrophysics Data System (ADS)

Bailey, V. L.; Smith, A. P.; Fansler, S.; Varga, T.; Kemner, K. M.; McCue, L. A.

2017-12-01

Soil structure provides the physical framework for soil microbial habitats. The connectivity and size distribution of soil pores controls the microbial access to nutrient resources for growth and metabolism. Thus, a crucial component of soil research is how a soil's three-dimensional structure and organization influences its biological potential on a multitude of spatial and temporal scales. In an effort to understand microbial processes at scale more consistent with a microbial community, we have used soil aggregates as discrete units of soil microbial habitats. Our research has shown that mean pore diameter (x-ray computed tomography) of soil aggregates varies with the aggregate diameter itself. Analyzing both the bacterial composition (16S) and enzyme activities of individual aggregates showed significant differences in the relative abundances of key members the microbial communities associated with high enzyme activities compared to those with low activities, even though we observed no differences in the size of the biomass, nor in the overall richness or diversity of these communities. We hypothesize that resources and substrates have stimulated key populations in the aggregates identified as highly active, and as such, we conducted further research that explored how such key populations (i.e. fungal or bacterial dominated populations) alter pathways of C accumulation in aggregate size domains and microbial C utilization. Fungi support and stabilize soil structure through both physical and chemical effects of their hyphal networks. In contrast, bacterial-dominated communities are purported to facilitate micro- and fine aggregate stabilization. Here we quantify the direct effects fungal versus bacterial dominated communities on aggregate formation (both the rate of aggregation and the quality, quantity and distribution of SOC contained within aggregates). A quantitative understanding of the different mechanisms through which fungi or bacteria shape aggregate formation could alter how we currently treat our predictions of soil biogeochemistry. Current predictions are largely site- or biome-specific; quantitative mechanisms could underpin "rules" that operate at the pore-scale leading to more robust, mechanistic models.

FRB microstructure revealed by the real-time detection of FRB170827

NASA Astrophysics Data System (ADS)

Farah, W.; Flynn, C.; Bailes, M.; Jameson, A.; Bannister, K. W.; Barr, E. D.; Bateman, T.; Bhandari, S.; Caleb, M.; Campbell-Wilson, D.; Chang, S.-W.; Deller, A.; Green, A. J.; Hunstead, R.; Jankowski, F.; Keane, E.; Macquart, J.-P.; Möller, A.; Onken, C. A.; Osłowski, S.; Parthasarathy, A.; Plant, K.; Ravi, V.; Shannon, R. M.; Tucker, B. E.; Venkatraman Krishnan, V.; Wolf, C.

2018-07-01

We report a new fast radio burst (FRB) discovered in real-time as part of the UTMOST project at the Molonglo Observatory Synthesis Radio Telescope. FRB170827 was first detected with our low-latency (<24 s) and machine-learning based FRB detection system. The FRB discovery was accompanied by the capture of voltage data at the native time and frequency resolution of the observing system, enabling coherent dedispersion and detailed off-line analysis that have unveiled fine temporal and frequency structure. The dispersion measure (DM) of 176.80 ± 0.04 pc cm-3 is the lowest of the FRB population. The Milky Way contribution along the line of sight is ˜40 pc cm-3, leaving an excess DM of ˜145 pc cm-3. The FRB has a fluence >20 ± 7 Jy ms, and is narrow with a width of ˜400 s at 10 per cent of its maximum amplitude. However, the burst shows three temporal components, the narrowest of which is ˜30 s, and a scattering time-scale of 4.1 ± 2.7 s. The FRB shows spectral modulations on frequency scales of 1.5 MHz and 0.1 MHz. Both are prominent in the dynamic spectrum, which shows a very bright region of emission between 841 and 843 MHz, and weaker and patchy emission across the entire band. We show that the fine spectral structure could arise in the FRB host galaxy, or its immediate vicinity.

Direct Numerical Simulation of a Temporally Evolving Incompressible Plane Wake: Effect of Initial Conditions on Evolution and Topology

NASA Technical Reports Server (NTRS)

Sondergaard, R.; Cantwell, B.; Mansour, N.

1997-01-01

Direct numerical simulations have been used to examine the effect of the initial disturbance field on the development of three-dimensionality and the transition to turbulence in the incompressible plane wake. The simulations were performed using a new numerical method for solving the time-dependent, three-dimensional, incompressible Navier-Stokes equations in flows with one infinite and two periodic directions. The method uses standard Fast Fourier Transforms and is applicable to cases where the vorticity field is compact in the infinite direction. Initial disturbances fields examined were combinations of two-dimensional waves and symmetric pairs of 60 deg oblique waves at the fundamental, subharmonic, and sub-subharmonic wavelengths. The results of these simulations indicate that the presence of 60 deg disturbances at the subharmonic streamwise wavelength results in the development of strong coherent three-dimensional structures. The resulting strong three-dimensional rate-of-strain triggers the growth of intense fine scale motions. Wakes initiated with 60 deg disturbances at the fundamental streamwise wavelength develop weak coherent streamwise structures, and do not develop significant fine scale motions, even at high Reynolds numbers. The wakes which develop strong three-dimensional structures exhibit growth rates on par with experimentally observed turbulent plane wakes. Wakes which develop only weak three-dimensional structures exhibit significantly lower late time growth rates. Preliminary studies of wakes initiated with an oblique fundamental and a two-dimensional subharmonic, which develop asymmetric coherent oblique structures at the subharmonic wavelength, indicate that significant fine scale motions only develop if the resulting oblique structures are above an angle of approximately 45 deg.

Population Genetic Structure and Demographic History of Atrina pectinata Based on Mitochondrial DNA and Microsatellite Markers

PubMed Central

Xue, Dong-Xiu; Wang, Hai-Yan; Zhang, Tao; Liu, Jin-Xian

2014-01-01

The pen shell, Atrina pectinata, is one of the commercial bivalves in East Asia and thought to be recently affected by anthropogenic pressure (habitat destruction and/or fishing pressure). Information on its population genetic structure is crucial for the conservation of A. pectinata. Considering its long pelagic larval duration and iteroparity with high fecundity, the genetic structure for A. pectinata could be expected to be weak at a fine scale. However, the unusual oceanography in the coasts of China and Korea suggests potential for restricted dispersal of pelagic larvae and geographical differentiation. In addition, environmental changes associated with Pleistocene sea level fluctuations on the East China Sea continental shelf may also have strongly influenced historical population demography and genetic diversity of marine organisms. Here, partial sequences of the mitochondrial Cytochrome c oxidase subunit I (COI) gene and seven microsatellite loci were used to estimate population genetic structure and demographic history of seven samples from Northern China coast and one sample from North Korea coast. Despite high levels of genetic diversity within samples, there was no genetic differentiation among samples from Northern China coast and low but significant genetic differentiation between some of the Chinese samples and the North Korean sample. A late Pleistocene population expansion, probably after the Last Glacial Maximum, was also demonstrated for A. pectinata samples. No recent genetic bottleneck was detected in any of the eight samples. We concluded that both historical recolonization (through population range expansion and demographic expansion in the late Pleistocene) and current gene flow (through larval dispersal) were responsible for the weak level of genetic structure detected in A. pectinata. PMID:24789175

Elk resource selection at parturition sites, Black Hills, South Dakota

Treesearch

Chadwick P. Lehman; Mark A. Rumble; Christopher T. Rota; Benjamin J. Bird; Dillon T. Fogarty; Joshua J. Millspaugh

2015-01-01

We studied elk (Cervus canadensis nelsoni) parturition sites at coarse (314-km2 and 7-km2) and fine (0.2-ha) scales in the Black Hills, South Dakota, 2011-2013, following a period of population decline and poor calf recruitment. Our objective was to test whether female elk selected parturition sites across spatial scales in association with forage, terrain...

Assessing Clark's nutcracker seed-caching flights using maternally inherited mitochondrial DNA of whitebark pine

Treesearch

Bryce A. Richardson; Ned B. Klopfenstein; Steven J. Brunsfeld

2002-01-01

Maternally inherited mitochondrial DNA haplotypes in whitebark pine (Pinus albicaulis Engelm.) were used to examine the maternal genetic structure at three hierarchical spatial scales: fine scale, coarse scale, and interpopulation. These data were used to draw inferences into Clark’s nutcracker (Nucifraga columbiana Wilson)...

The Recombination Landscape in Wild House Mice Inferred Using Population Genomic Data.

PubMed

Booker, Tom R; Ness, Rob W; Keightley, Peter D

2017-09-01

Characterizing variation in the rate of recombination across the genome is important for understanding several evolutionary processes. Previous analysis of the recombination landscape in laboratory mice has revealed that the different subspecies have different suites of recombination hotspots. It is unknown, however, whether hotspots identified in laboratory strains reflect the hotspot diversity of natural populations or whether broad-scale variation in the rate of recombination is conserved between subspecies. In this study, we constructed fine-scale recombination rate maps for a natural population of the Eastern house mouse, Mus musculus castaneus We performed simulations to assess the accuracy of recombination rate inference in the presence of phase errors, and we used a novel approach to quantify phase error. The spatial distribution of recombination events is strongly positively correlated between our castaneus map, and a map constructed using inbred lines derived predominantly from M. m. domesticus Recombination hotspots in wild castaneus show little overlap, however, with the locations of double-strand breaks in wild-derived house mouse strains. Finally, we also find that genetic diversity in M. m. castaneus is positively correlated with the rate of recombination, consistent with pervasive natural selection operating in the genome. Our study suggests that recombination rate variation is conserved at broad scales between house mouse subspecies, but it is not strongly conserved at fine scales. Copyright © 2017 by the Genetics Society of America.

Fine structures of wing scales in Sasakia charonda butterflies as photonic crystals.

PubMed

Matejková-Plskova, J; Shiojiri, S; Shiojiri, M

2009-11-01

We investigate the microstructure of scales in the wings of male Sasakia charonda charonda butterflies by scanning electron microscopy with the aid of optical microscopy. Six types of scales are identified: B1, W1 and R1 in brown background yellow spots and red spots, respectively; B2 in iridescent purple-blue and W2 in white pearl, both of which characterize the male and B3 in the wing edges. The B1, W1 and R1 scales are almost the same in structure and the B2 and W2 scales are almost the same. The difference among the B, W and R scales is in species and content of pigment. The B1, W1 and R1 scales have only two layers of cuticle lapped on the ridges. In contrast with them, the B2 and W2 scales have seven multilayers of cuticle piled on the ridge. The multiple interference of light that occurs among these cuticle layers, spaced with air layers, generates the significant iridescence of the B2 and W2 scales. Thus, the characteristic purple-blue of the male wings is ascribed to the combination of the structural and chemical colouration in the B2 scales with melanin. The photonic crystals of these scales may be applicable to fine light manipulators such as reflection elements in laser diodes. B3 has many holes between the ridges and no multilayers of cuticle on the ridges. These structures may play any role in aerodynamically easy flight and/or in drainage of wet wings.

Interactions of multi-scale heterogeneity in the lithosphere: Australia

NASA Astrophysics Data System (ADS)

Kennett, B. L. N.; Yoshizawa, K.; Furumura, T.

2017-10-01

Understanding the complex heterogeneity of the continental lithosphere involves a wide variety of spatial scales and the synthesis of multiple classes of information. Seismic surface waves and multiply reflected body waves provide the main constraints on broad-scale structure, and bounds on the extent of the lithosphere-asthenosphere transition (LAT) can be found from the vertical gradients of S wavespeed. Information on finer-scale structures comes through body wave studies, including detailed seismic tomography and P-wave reflectivity extracted from stacked autocorrelograms of continuous component records. With the inclusion of deterministic large-scale structure and realistic medium-scale stochastic features fine-scale variations are subdued. The resulting multi-scale heterogeneity model for the Australian region gives a good representation of the character of observed seismograms and their geographic variations and matches the observations of P-wave reflectivity. P reflections in the 0.5-3.0 Hz band in the uppermost mantle suggest variations on vertical scales of a few hundred metres with amplitudes of the order of 1%. Interference of waves reflected or converted at sequences of such modest variations in physical properties produce relatively simple behaviour for lower frequencies, which can suggest simpler structures than are actually present. Vertical changes in the character of fine-scale heterogeneity can produce apparent discontinuities. In Central Australia a 'mid-lithospheric discontinuity' can be tracked via changes in frequency content of station reflectivity, with links to the broad-scale pattern of wavespeed gradients and, in particular, the gradients of radial anisotropy. Comparisons with xenolith results from southeastern Australia indicate a strong tie between geochemical stratification and P-wave reflectivity.

Low incidence of clonality in cold water corals revealed through the novel use of standardized protocol adapted to deep sea sampling

USGS Publications Warehouse

Becheler, Ronan; Cassone, Anne-Laure; Noel, Philippe; Mouchel, Olivier; Morrison, Cheryl L.; Arnaud-Haond, Sophie

2017-01-01

Sampling in the deep sea is a technical challenge, which has hindered the acquisition of robust datasets that are necessary to determine the fine-grained biological patterns and processes that may shape genetic diversity. Estimates of the extent of clonality in deep-sea species, despite the importance of clonality in shaping the local dynamics and evolutionary trajectories, have been largely obscured by such limitations. Cold-water coral reefs along European margins are formed mainly by two reef-building species, Lophelia pertusa and Madrepora oculata. Here we present a fine-grained analysis of the genotypic and genetic composition of reefs occurring in the Bay of Biscay, based on an innovative deep-sea sampling protocol. This strategy was designed to be standardized, random, and allowed the georeferencing of all sampled colonies. Clonal lineages discriminated through their Multi-Locus Genotypes (MLG) at 6–7 microsatellite markers could thus be mapped to assess the level of clonality and the spatial spread of clonal lineages. High values of clonal richness were observed for both species across all sites suggesting a limited occurrence of clonality, which likely originated through fragmentation. Additionally, spatial autocorrelation analysis underlined the possible occurrence of fine-grained genetic structure in several populations of both L. pertusa and M. oculata. The two cold-water coral species examined had contrasting patterns of connectivity among canyons, with among-canyon genetic structuring detected in M. oculata, whereas L. pertusa was panmictic at the canyon scale. This study exemplifies that a standardized, random and georeferenced sampling strategy, while challenging, can be applied in the deep sea, and associated benefits outlined here include improved estimates of fine grained patterns of clonality and dispersal that are comparable across sites and among species.

Low incidence of clonality in cold water corals revealed through the novel use of a standardized protocol adapted to deep sea sampling

NASA Astrophysics Data System (ADS)

Becheler, Ronan; Cassone, Anne-Laure; Noël, Philippe; Mouchel, Olivier; Morrison, Cheryl L.; Arnaud-Haond, Sophie

2017-11-01

Sampling in the deep sea is a technical challenge, which has hindered the acquisition of robust datasets that are necessary to determine the fine-grained biological patterns and processes that may shape genetic diversity. Estimates of the extent of clonality in deep-sea species, despite the importance of clonality in shaping the local dynamics and evolutionary trajectories, have been largely obscured by such limitations. Cold-water coral reefs along European margins are formed mainly by two reef-building species, Lophelia pertusa and Madrepora oculata. Here we present a fine-grained analysis of the genotypic and genetic composition of reefs occurring in the Bay of Biscay, based on an innovative deep-sea sampling protocol. This strategy was designed to be standardized, random, and allowed the georeferencing of all sampled colonies. Clonal lineages discriminated through their Multi-Locus Genotypes (MLG) at 6-7 microsatellite markers could thus be mapped to assess the level of clonality and the spatial spread of clonal lineages. High values of clonal richness were observed for both species across all sites suggesting a limited occurrence of clonality, which likely originated through fragmentation. Additionally, spatial autocorrelation analysis underlined the possible occurrence of fine-grained genetic structure in several populations of both L. pertusa and M. oculata. The two cold-water coral species examined had contrasting patterns of connectivity among canyons, with among-canyon genetic structuring detected in M. oculata, whereas L. pertusa was panmictic at the canyon scale. This study exemplifies that a standardized, random and georeferenced sampling strategy, while challenging, can be applied in the deep sea, and associated benefits outlined here include improved estimates of fine grained patterns of clonality and dispersal that are comparable across sites and among species.

USE OF CITIZEN BIRD POPULATION MONITORING DATA FOR ECOLOGICAL RISK ASSESSMENT

EPA Science Inventory

Birds are among the most conspicuous and easily monitored indicators of environmental health and change. Although volunteer avian monitoring ('citizen science') programs provide unique opportunities to gather data at fine and broad geographic scales simultaneously, and over long...

Partially natural two Higgs doublet models

DOE PAGES

Draper, Patrick; Haber, Howard E.; Ruderman, Joshua T.

2016-06-21

It is possible that the electroweak scale is low due to the fine-tuning of microscopic parameters, which can result from selection effects. The experimental discovery of new light fundamental scalars other than the Standard Model Higgs boson would seem to disfavor this possibility, since generically such states imply parametrically worse fine-tuning with no compelling connection to selection effects. We discuss counterexamples where the Higgs boson is light because of fine-tuning, and a second scalar doublet is light because a discrete symmetry relates its mass to the mass of the Standard Model Higgs boson. Our examples require new vectorlike fermions atmore » the electroweak scale, and the models possess a rich electroweak vacuum structure. Furthermore, the mechanism that we discuss does not protect a small CP-odd Higgs mass in split or high-scale supersymmetry-breaking scenarios of the MSSM due to an incompatibility between the discrete symmetries and holomorphy.« less

Airframe-Jet Engine Integration Noise

NASA Technical Reports Server (NTRS)

Tam, Christopher; Antcliff, Richard R. (Technical Monitor)

2003-01-01

It has been found experimentally that the noise radiated by a jet mounted under the wing of an aircraft exceeds that of the same jet in a stand-alone environment. The increase in noise is referred to as jet engine airframe integration noise. The objectives of the present investigation are, (1) To obtain a better understanding of the physical mechanisms responsible for jet engine airframe integration noise or installation noise. (2) To develop a prediction model for jet engine airframe integration noise. It is known that jet mixing noise consists of two principal components. They are the noise from the large turbulence structures of the jet flow and the noise from the fine scale turbulence. In this investigation, only the effect of jet engine airframe interaction on the fine scale turbulence noise of a jet is studied. The fine scale turbulence noise is the dominant noise component in the sideline direction. Thus we limit out consideration primarily to the sideline.

Distribution of fine-scale mantle heterogeneity from observations of Pdiff coda

USGS Publications Warehouse

Earle, P.S.; Shearer, P.M.

2001-01-01

We present stacked record sections of Global Seismic Network data that image the average amplitude and polarization of the high-frequency Pdiff coda and investigate their implications on the depth extent of fine-scale (~10 km) mantle heterogeneity. The extended 1-Hz coda lasts for at least 150 sec and is observed to a distance of 130??. The coda's polarization angle is about the same as the main Pdiff arrival (4.4 sec/deg) and is nearly constant with time. Previous studies show that multiple scattering from heterogeneity restricted to the lowermost mantle generates an extended Pdiff coda with a constant polarization. Here we present an alternative model that satisfies our Pdiff observations. The model consists of single scattering from weak (~1%) fine-scale (~2 km) structures distributed throughout the mantle. Although this model is nonunique, it demonstrates that Pdiff coda observations do not preclude the existence of scattering contributions from the entire mantle.

[Species composition and point pattern analysis of standing trees in secondary Betula albosinensis forest in Xiaolongshan of west Qinling Mountains].

PubMed

Guo, Yao-xin; Kang, Bing; Li, Gang; Wang, De-xiang; Yang, Gai-he; Wang, Da-wei

2011-10-01

An investigation was conducted on the species composition and population diameter-class structure of a typical secondary Betula albo-sinensis forest in Xiaolongshan of west Qinling Mountains, and the spatial distribution pattern and interspecific correlations of the main populations were analyzed at multiple scales by the O-ring functions of single variable and double variables. In the test forest, B. albo-sinensis was obviously dominant, but from the analysis of DBH class distribution, the B. albo-sinensis seedlings were short of, and the natural regeneration was very poor. O the contrary, the regeneration of Abies fargesii and Populus davidianas was fine. B. albo-sinensis and Salix matsudana had a random distribution at almost all scales, while A. fargesii and P. davidianas were significantly clumped at small scale. B. albo-sinensis had positive correlations with A. fargesii and P. davidianas at medium scale, whereas S. matsudana had negative correlations with B. albo-sinensis, A. fargesii, and P. davidianas at small scale. No significant correlations were observed between other species. The findings suggested that the spatial distribution patterns of the tree species depended on their biological characteristics at small scale, but on the environmental heterogeneity at larger scales. In a period of future time, B. albo-sinensis would still be dominant, but from a long-term view, it was necessary to take some artificial measures to improve the regeneratio of B. albo-sinensis.

Separating the effects of environment and space on tree species distribution: from population to community.

PubMed

Lin, Guojun; Stralberg, Diana; Gong, Guiquan; Huang, Zhongliang; Ye, Wanhui; Wu, Linfang

2013-01-01

Quantifying the relative contributions of environmental conditions and spatial factors to species distribution can help improve our understanding of the processes that drive diversity patterns. In this study, based on tree inventory, topography and soil data from a 20-ha stem-mapped permanent forest plot in Guangdong Province, China, we evaluated the influence of different ecological processes at different spatial scales using canonical redundancy analysis (RDA) at the community level and multiple linear regression at the species level. At the community level, the proportion of explained variation in species distribution increased with grid-cell sizes, primarily due to a monotonic increase in the explanatory power of environmental variables. At the species level, neither environmental nor spatial factors were important determinants of overstory species' distributions at small cell sizes. However, purely spatial variables explained most of the variation in the distributions of understory species at fine and intermediate cell sizes. Midstory species showed patterns that were intermediate between those of overstory and understory species. At the 20-m cell size, the influence of spatial factors was stronger for more dispersal-limited species, suggesting that much of the spatial structuring in this community can be explained by dispersal limitation. Comparing environmental factors, soil variables had higher explanatory power than did topography for species distribution. However, both topographic and edaphic variables were highly spatial structured. Our results suggested that dispersal limitation has an important influence on fine-intermediate scale (from several to tens of meters) species distribution, while environmental variability facilitates species distribution at intermediate (from ten to tens of meters) and broad (from tens to hundreds of meters) scales.

Scattering - a probe to Earth's small scale structure

NASA Astrophysics Data System (ADS)

Rost, S.; Earle, P.

2009-05-01

Much of the short-period teleseismic wavefield shows strong evidence for scattered waves in extended codas trailing the main arrivals predicted by ray theory. This energy mainly originates from high-frequency body waves interacting with fine-scale volumetric heterogeneities in the Earth. Studies of this energy revealed much of what we know about Earth's structure at scale lengths around 10 km throughout the Earth from crust to core. From these data we can gain important information about the mineral-physical and geochemical constitution of the Earth that is inaccessible to many other seismic imaging techniques. Previous studies used scattered energy related to PKP, PKiKP, and Pdiff to identify and map the small-scale structure of the mantle and core. We will present observations related to the core phases PKKP and P'P' to study fine-scale mantle heterogeneities. These phases are maximum travel-time phases with respect to perturbations at their reflection points. This allows observation of the scattered energy as precursors to the main phase avoiding common problems with traditional coda phases which arrive after the main pulse. The precursory arrival of the scattered energy allows the separation between deep Earth and crustal contributions to the scattered wavefield for certain source-receiver configurations. Using the information from these scattered phases we identify regions of the mantle that shows increased scattering potential likely linked to larger scale mantle structure identified in seismic tomography and geodynamical models.

Fine-Scale Habitat Heterogeneity Influences Occupancy in Terrestrial Mammals in a Temperate Region of Australia

PubMed Central

Stirnemann, Ingrid; Mortelliti, Alessio; Gibbons, Philip; Lindenmayer, David B.

2015-01-01

Vegetation heterogeneity is an inherent feature of most ecosystems, characterises the structure of habitat, and is considered an important driver of species distribution patterns. However, quantifying fine-scale heterogeneity of vegetation cover can be time consuming, and therefore it is seldom measured. Here, we determine if heterogeneity is worthwhile measuring, in addition to the amount of cover, when examining species distribution patterns. Further, we investigated the effect of the surrounding landscape heterogeneity on species occupancy. We tested the effect of cover and heterogeneity of trees and shrubs, and the context of the surrounding landscape (number of habitats and distance to an ecotone) on site occupancy of three mammal species (the black wallaby [Wallabia bicolor], the long-nosed bandicoot [Perameles nasuta], and the bush rat [Rattus fuscipes]) within a naturally heterogeneous landscape in a temperate region of Australia. We found that fine-scale heterogeneity of vegetation attributes is an important driver of mammal occurrence of two of these species. Further, we found that, although all three species responded positively to vegetation heterogeneity, different mammals vary in their response to different types of vegetation heterogeneity measurement. For example, the black wallaby responded to the proximity of an ecotone, and the bush rat and the long-nosed bandicoot responded to fine-scale heterogeneity of small tree cover, whereas none of the mammals responded to broad scale heterogeneity (i.e., the number of habitat types). Our results highlight the influence of methodological decisions, such as how heterogeneity vegetation is measured, in quantifying species responses to habitat structures. The findings confirm the importance of choosing meaningful heterogeneity measures when modelling the factors influencing occupancy of the species of interest. PMID:26394327

Development of eighteen microsatellite loci in walleye (Sander vitreus)

USGS Publications Warehouse

Coykendall, D. Katharine; Morrison, Cheryl L.; Stott, Wendylee; Springmann, Marcus J.

2014-01-01

A suite of tri- and tetra-nucleotide microsatellite loci were developed for walleye (Sander vitreus) from 454 pyrosequencing data. Eighteen of the 50 primer sets tested amplified consistently in 35 walleye from two lakes on Isle Royale, Lake Superior: Chickenbone Lake and Whittlesey Lake. The loci displayed moderate levels of allelic diversity (average 5.5 alleles/locus) and heterozygosity (average 35.8 %). Levels of genetic diversity were sufficient to produce unique multi-locus genotypes and detect phylogeographic structuring as individuals assigned back to their population of origin. Cross-species amplification within S. canadensis(sauger) was successful for 15 loci, and 11 loci were diagnostic to species. The loci characterized here will be useful for detecting fine-scale spatial structuring, resolving the taxonomic status of Sander species and sub-species, and detecting walleye/sauger hybrids.

A Compendium of Scale Surface Microstructures: Ni(pt)al Coatings Oxidized at 1150 C for 2000 1-h Cycles

NASA Technical Reports Server (NTRS)

Smialek, James L.; Garg, Anita

2010-01-01

The surface structure of scales formed on Ni(Pt)Al coatings was characterized by SEM/EDS/BSE in plan view. Two nominally identical {100} samples of aluminide coated CMSX4 single crystal were oxidized at 1150 C for 2000 1-h cycles and were found to produce somewhat disparate behavior. One sample, with less propensity for coating grain boundary ridge deformation, presented primarily alpha-Al2O3 scale structures, with minimal weight loss and spallation. The original scale structure, still retained over most of the sample, consisted of the classic theta-alpha transformation-induced ridge network structure, with approx. 25 nm crystallographic steps and terraces indicative of surface rearrangement to low energy alumina planes. The scale grain boundary ridges were often decorated with a fine, uniform distribution of (Hf,Ti)O2 particles. Another sample, producing steady state weight losses, exhibited much interfacial spallation and a complex assortment of different structures. Broad areas of interfacial spalling, crystallographically-faceted (Ni,Co)(Al,Cr)2O4 spinel, with an alpha-Al2O3 base scale, were the dominant features. Other regions exhibited nodular spinel grains, with fine or (Ta,Ti)-rich (rutile) particles decorating or interspersed with the spinel. While these features were consistent with a coating that presented more deformation at extruded grain boundaries, the root cause of the different behavior between the duplicate samples could not be conclusively identified.

Fungal biomineralization of montmorillonite and goethite to short-range-ordered minerals

NASA Astrophysics Data System (ADS)

Li, Huan; Hu, Shuijin; Polizzotto, Matthew L.; Chang, Xiaoli; Shen, Qirong; Ran, Wei; Yu, Guanghui

2016-10-01

Highly reactive nano-scale minerals, e.g., short-range-ordered minerals (SROs) and other nanoparticles, play an important role in soil carbon (C) retention. Yet, the mechanisms that govern biomineralization from bulk minerals to highly reactive nano-scale minerals remain largely unexplored, which critically hinders our efforts toward managing nano-scale minerals for soil C retention. Here we report the results from a study that explores structural changes during Aspergillus fumigatus Z5 transformation of montmorillonite and goethite to SROs. We examined the morphology and structure of nano-scale minerals, using high-resolution transmission electron microscopy, time-resolved solid-state 27Al and 29Si NMR, and Fe K-edge X-ray absorption fine structure spectroscopy combined with two dimensional correlation spectroscopy (2D COS) analysis. Our results showed that after a 48-h cultivation of montmorillonite and goethite with Z5, new biogenic intracellular and extracellular reactive nano-scale minerals with a size of 3-5 nm became abundant. Analysis of 2D COS further suggested that montmorillonite and goethite were the precursors of the dominant biogenic nano-scale minerals. Carbon 1s near edge X-ray absorption fine structure (NEXAFS) spectra and their deconvolution results demonstrated that during fungus Z5 growth, carboxylic C (288.4-289.1 eV) was the dominant organic group, accounting for approximately 34% and 59% in the medium and aggregates, respectively. This result suggested that high percentage of the production of organic acids during the growth of Z5 was the driving factor for structural changes during biomineralization. This is, to the best of our knowledge, the first report of the structural characterization of nano-scale minerals by 2D COS, highlighting its potential to elucidate biomineralization pathways and thus identify the precursors of nano-scale minerals.

Fine-scale analysis of genetic structure in the brooding coral Seriatopora hystrix from the Red Sea

NASA Astrophysics Data System (ADS)

Maier, E.; Tollrian, R.; Nürnberger, B.

2009-09-01

The dispersal of gametes and larvae plays a key role in the population dynamics of sessile marine invertebrates. Species with internal fertilisation are often associated with very localised larval dispersal, which may cause small-scale patterns of neutral genetic variation. This study on the brooding coral Seriatopora hystrix from the Red Sea focused on the smallest possible scale: Two S. hystrix stands (~100 colonies each) near Dahab were completely sampled, mapped and analysed at five microsatellite markers. The sexual mode of reproduction, the likely occurrence of selfing and the level of immigration were in agreement with previous studies on this species. Contrary to previous findings, both stands were in Hardy-Weinberg proportions. Also, no evidence for spatially restricted larval dispersal within the sampled areas was found. Differences between this and previous studies on S. hystrix could reflect variation in life history or varying environmental conditions, which opens intriguing questions for future research.

E nergetic, Dynamics And Fine-Scale Structure Of The Sun's Magnetized Atmosphere, Observational Strategies For The Solar Orbiter

NASA Astrophysics Data System (ADS)

Kjeldseth-Moe, O.

2007-01-01

We look at so me known fine stru cture features, or processes on the Sun th at goes on at a small scale, notably explosive even ts and blinkers. From th eir proper ties we dr aw up a list of ob- servational strateg ies for the So lar Orbiter, based on how we could extend our knowledge of these f eatures. W e then show examples from other f eatures and processes on a small scale in cluding specu lations on th e possibility that th e upper solar atmosph ere consist of hy- per fine reso lution elemen ts much smaller than the pr esen t limit of r esolu tion at ultrav iolet or X-ray wavelengths, i.e. 725 km on the Sun. The applicab ility of the So lar Orbiter instru- ments and observation strateg ies for deter min- ing th e properties of the v arious structures will be discussed. Finally we shall co mmen t on the importance of the out of eclip tic observ ation in the extended mission phase for studying the fast solar w ind in the polar coronal holes.

Investigating the Relationships between Canopy Characteristics and Snow Depth Distribution at Fine Scales: Preliminary Results from the SnowEX TLS Campaign

NASA Astrophysics Data System (ADS)

Glenn, N. F.; Uhlmann, Z.; Spaete, L.; Tennant, C.; Hiemstra, C. A.; McNamara, J.

2017-12-01

Predicting changes in forested seasonal snowpacks under altered climate scenarios is one of the most pressing hydrologic challenges facing today's society. Airborne- and satellite-based remote sensing methods hold the potential to transform measurements of terrestrial water stores in snowpack, improve process representations of snowpack accumulation and ablation, and to generate high quality predictions that inform potential strategies to better manage water resources. While the effects of forest on snowpack are well documented, many of the fine-scale processes influenced by the forest-canopy are not directly accounted for because most snow models don't explicitly represent canopy structure and canopy heterogeneity. This study investigates the influence of forest canopy on snowpack distribution at fine scales and quantifies the influence of canopy heterogeneity on snowpack accumulation and ablation processes. We use terrestrial laser scanning (TLS) data collected during the SnowEX campaign to discover how the relationships between canopy and snow distributions change across scales. Our sample scales range from individual trees to patches of trees across the Grand Mesa, CO, SnowEx site.

Predictors of malaria infection in a wild bird population: landscape-level analyses reveal climatic and anthropogenic factors.

PubMed

Gonzalez-Quevedo, Catalina; Davies, Richard G; Richardson, David S

2014-09-01

How the environment influences the transmission and prevalence of disease in a population of hosts is a key aspect of disease ecology. The role that environmental factors play in host-pathogen systems has been well studied at large scales, that is, differences in pathogen pressures among separate populations of hosts or across land masses. However, despite considerable understanding of how environmental conditions vary at fine spatial scales, the effect of these parameters on host-pathogen dynamics at such scales has been largely overlooked. Here, we used a combination of molecular screening and GIS-based analysis to investigate how environmental factors determine the distribution of malaria across the landscape in a population of Berthelot's pipit (Anthus berthelotii, Bolle 1862) on the island of Tenerife (Canary Islands, Spain) using spatially explicit models that account for spatial autocorrelation. Minimum temperature of the coldest month was found to be the most important predictor of malaria infection at the landscape scale across this population. Additionally, anthropogenic factors such as distance to artificial water reservoirs and distance to poultry farms were important predictors of malaria. A model including these factors, and the interaction between distance to artificial water reservoirs and minimum temperature, best explained the distribution of malaria infection in this system. These results suggest that levels of malaria infection in this endemic species may be artificially elevated by the impact of humans. Studies such as the one described here improve our understanding of how environmental factors, and their heterogeneity, affect the distribution of pathogens within wild populations. The results demonstrate the importance of measuring fine-scale variation - and not just regional effects - to understand how environmental variation can influence wildlife diseases. Such understanding is important for predicting the future spread and impact of disease and may help inform disease management programmes as well as the conservation of specific host species. © 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.

Coupling physics and biogeochemistry thanks to high-resolution observations of the phytoplankton community structure in the northwestern Mediterranean Sea

NASA Astrophysics Data System (ADS)

Marrec, Pierre; Grégori, Gérald; Doglioli, Andrea M.; Dugenne, Mathilde; Della Penna, Alice; Bhairy, Nagib; Cariou, Thierry; Hélias Nunige, Sandra; Lahbib, Soumaya; Rougier, Gilles; Wagener, Thibaut; Thyssen, Melilotus

2018-03-01

Fine-scale physical structures and ocean dynamics strongly influence and regulate biogeochemical and ecological processes. These processes are particularly challenging to describe and understand because of their ephemeral nature. The OSCAHR (Observing Submesoscale Coupling At High Resolution) campaign was conducted in fall 2015 in which a fine-scale structure (1-10 km/1-10 days) in the northwestern Mediterranean Ligurian subbasin was pre-identified using both satellite and numerical modeling data. Along the ship track, various variables were measured at the surface (temperature, salinity, chlorophyll a and nutrient concentrations) with ADCP current velocity. We also deployed a new model of the CytoSense automated flow cytometer (AFCM) optimized for small and dim cells, for near real-time characterization of the surface phytoplankton community structure of surface waters with a spatial resolution of a few kilometers and an hourly temporal resolution. For the first time with this optimized version of the AFCM, we were able to fully resolve Prochlorococcus picocyanobacteria in addition to the easily distinguishable Synechococcus. The vertical physical dynamics and biogeochemical properties of the studied area were investigated by continuous high-resolution CTD profiles thanks to a moving vessel profiler (MVP) during the vessel underway associated with a high-resolution pumping system deployed during fixed stations allowing sampling of the water column at a fine resolution (below 1 m). The observed fine-scale feature presented a cyclonic structure with a relatively cold core surrounded by warmer waters. Surface waters were totally depleted in nitrate and phosphate. In addition to the doming of the isopycnals by the cyclonic circulation, an intense wind event induced Ekman pumping. The upwelled subsurface cold nutrient-rich water fertilized surface waters and was marked by an increase in Chl a concentration. Prochlorococcus and pico- and nano-eukaryotes were more abundant in cold core waters, while Synechococcus dominated in warm boundary waters. Nanoeukaryotes were the main contributors ( > 50 %) in terms of pigment content (red fluorescence) and biomass. Biological observations based on the mean cell's red fluorescence recorded by AFCM combined with physical properties of surface waters suggest a distinct origin for two warm boundary waters. Finally, the application of a matrix growth population model based on high-frequency AFCM measurements in warm boundary surface waters provides estimates of in situ growth rate and apparent net primary production for Prochlorococcus (μ = 0.21 d-1, NPP = 0.11 mg C m-3 d-1) and Synechococcus (μ = 0.72 d-1, NPP = 2.68 mg C m-3 d-1), which corroborate their opposite surface distribution pattern. The innovative adaptive strategy applied during OSCAHR with a combination of several multidisciplinary and complementary approaches involving high-resolution in situ observations and sampling, remote-sensing and model simulations provided a deeper understanding of the marine biogeochemical dynamics through the first trophic levels.

Atomic Fine-Structure Diagnostic and Cooling Transitions for Far Infrared and Submillimeter Observations

NASA Astrophysics Data System (ADS)

Balance, Connor

Some of the strongest emission lines observed from a variety of astronomical sources originate from transitions between fine-structure levels in the ground term of neutral atoms and lowly-charged ions. These fine-structure levels are populated due to collisions with -, H+, H, He, and/or H2 depending on the temperature and ionization fraction of e the environment. As fine-structure excitation measurements are rare, modeling applications depend on theoretically determined rate coefficients. However, for many ions electron collision studies have not been performed for a decade or more, while over that time period the theoretical/computational methodology has significantly advanced. For heavy-particle collisions, very few systems have been studied. As a result, most models rely on estimates or on low-quality collisional data for fine-structure excitation. To significantly advance the state of fine-structure data for astrophysical models, we propose a collaborative effort in electron collisions, heavy-particle collisions, and quantum chemistry. Using the R-matrix method, fine-structure excitation due to electron collisions will be investigated for C, O, Ne^+, Ne^2+, Ar^+, Ar^2+, Fe, Fe^+, and Fe^2+. Fine-structure excitation due to heavy-particle collisions will be studied with a fully quantum molecular-orbital approach using potential energy surfaces computed with a multireference configuration-interaction method. The systems to be studied include: C/H^+, C/H2, O/H^+, O/H2, Ne^+/H, Ne^+/H2, Ne^2+/H, Ne^2+/H2, Fe/H^+, Fe^+/H, and Fe^2+/H. 2D rigid-rotor surfaces will be constructed for H2 collisions, internuclear distance dependent spin-orbit coupling will be computed in some cases, and all rate coefficients will be obtained for the temperature range 10-2000 K. The availability the proposed fine-structure excitation data will lead to deeper examination and understanding of the properties of many astrophysical environments, including young stellar objects, protoplanetary disks, planetary nebulae, photodissociation regions, active galactic nuclei, and x-ray dominated regions, hence elevating the scientific return from current (SOFIA, Spitzer, Herschel, HST) and upcoming (JWST) NASA IR/Submm astrophysics missions, as well as from ground-based telescopes.

Oceanographic connectivity and environmental correlates of genetic structuring in Atlantic herring in the Baltic Sea

PubMed Central

Teacher, Amber GF; André, Carl; Jonsson, Per R; Merilä, Juha

2013-01-01

Marine fish often show little genetic structuring in neutral marker genes, and Atlantic herring (Clupea harengus) in the Baltic Sea are no exception; historically, very low levels of population differentiation (FST ≍ 0.002) have been found, despite a high degree of interpopulation environmental heterogeneity in salinity and temperature. Recent exome sequencing and SNP studies have however shown that many loci are under selection in this system. Here, we combined population genetic analyses of a large number of transcriptome-derived microsatellite markers with oceanographic modelling to investigate genetic differentiation and connectivity in Atlantic herring at a relatively fine scale within the Baltic Sea. We found evidence for weak but robust and significant genetic structuring (FST = 0.008) explainable by oceanographic connectivity. Genetic differentiation was also associated with site differences in temperature and salinity, with the result driven by the locus Her14 which appears to be under directional selection (FST = 0.08). The results show that Baltic herring are genetically structured within the Baltic Sea, and highlight the role of oceanography and environmental factors in explaining this structuring. The results also have implications for the management of herring fisheries, the most economically important fishery in the Baltic Sea, suggesting that the current fisheries management units may be in need of revision. PMID:23745145

Strong spatial genetic structure in five tropical Piper species: should the Baker–Fedorov hypothesis be revived for tropical shrubs?

PubMed Central

Lasso, E; Dalling, J W; Bermingham, E

2011-01-01

Fifty years ago, Baker and Fedorov proposed that the high species diversity of tropical forests could arise from the combined effects of inbreeding and genetic drift leading to population differentiation and eventually to sympatric speciation. Decades of research, however have failed to support the Baker–Fedorov hypothesis (BFH), and it has now been discarded in favor of a paradigm where most trees are self-incompatible or strongly outcrossing, and where long-distance pollen dispersal prevents population drift. Here, we propose that several hyper-diverse genera of tropical herbs and shrubs, including Piper (>1,000 species), may provide an exception. Species in this genus often have aggregated, high-density populations with self-compatible breeding systems; characteristics which the BFH would predict lead to high local genetic differentiation. We test this prediction for five Piper species on Barro Colorado Island, Panama, using Amplified Fragment Length Polymorphism (AFLP) markers. All species showed strong genetic structure at both fine- and large-spatial scales. Over short distances (200–750 m) populations showed significant genetic differentiation (Fst 0.11–0.46, P < 0.05), with values of spatial genetic structure that exceed those reported for other tropical tree species (Sp = 0.03–0.136). This genetic structure probably results from the combined effects of limited seed and pollen dispersal, clonal spread, and selfing. These processes are likely to have facilitated the diversification of populations in response to local natural selection or genetic drift and may explain the remarkable diversity of this rich genus. PMID:22393518

Lens-Aided Multi-Angle Spectroscopy (LAMAS) Reveals Small-Scale Outflow Structure in Quasars

NASA Astrophysics Data System (ADS)

Green, Paul J.

2006-06-01

Spectral differences between lensed quasar image components are common. Since lensing is intrinsically achromatic, these differences are typically explained as the effect of either microlensing, or as light path time delays sampling intrinsic quasar spectral variability. Here we advance a novel third hypothesis: some spectral differences are due to small line-of-sight differences through quasar disk wind outflows. In particular, we propose that variable spectral differences seen only in component A of the widest separation lens SDSS J1004+4112 are due to differential absorption along the sight lines. The absorber properties required by this hypothesis are akin to known broad absorption line (BAL) outflows but must have a broader, smoother velocity profile. We interpret the observed C IV emission-line variability as further evidence for spatial fine structure transverse to the line of sight. Since outflows are likely to be rotating, such absorber fine structure can consistently explain some of the UV and X-ray variability seen in AGNs. The implications are many: (1) Spectroscopic differences in other lensed objects may be due to this ``lens-aided multi-angle spectroscopy'' (LAMAS). (2) Outflows have fine structure on size scales of arcseconds, as seen from the nucleus. (3) Assuming either broad absorption line region sizes proposed in recent wind models, or typically assumed continuum emission region sizes, LAMAS and/or variability provide broadly consistent absorber size scale estimates of ~1015 cm. (4) Very broad smooth absorption may be ubiquitous in quasar spectra, even when no obvious troughs are seen.

Prospects of Fine-Mapping Trait-Associated Genomic Regions by Using Summary Statistics from Genome-wide Association Studies.

PubMed

Benner, Christian; Havulinna, Aki S; Järvelin, Marjo-Riitta; Salomaa, Veikko; Ripatti, Samuli; Pirinen, Matti

2017-10-05

During the past few years, various novel statistical methods have been developed for fine-mapping with the use of summary statistics from genome-wide association studies (GWASs). Although these approaches require information about the linkage disequilibrium (LD) between variants, there has not been a comprehensive evaluation of how estimation of the LD structure from reference genotype panels performs in comparison with that from the original individual-level GWAS data. Using population genotype data from Finland and the UK Biobank, we show here that a reference panel of 1,000 individuals from the target population is adequate for a GWAS cohort of up to 10,000 individuals, whereas smaller panels, such as those from the 1000 Genomes Project, should be avoided. We also show, both theoretically and empirically, that the size of the reference panel needs to scale with the GWAS sample size; this has important consequences for the application of these methods in ongoing GWAS meta-analyses and large biobank studies. We conclude by providing software tools and by recommending practices for sharing LD information to more efficiently exploit summary statistics in genetics research. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Fine scale relationships between sex, life history, and dispersal of masu salmon

USGS Publications Warehouse

Kitanishi, Shigeru; Yamamoto, Toshiaki; Koizumi, Itsuro; Dunham, Jason B.; Higashi, Seigo

2012-01-01

Identifying the patterns and processes driving dispersal is critical for understanding population structure and dynamics. In many organisms, sex-biased dispersal is related to the type of mating system. Considerably less is known about the influence of life history variability on dispersal. Here we investigated patterns of dispersal in masu salmon (Oncorhynchus masou) to evaluate influences of sex and life history on dispersal. As expected, assignment tests and isolation by distance analysis revealed that dispersal of marine-migratory masu salmon was male-biased. However, dispersal of resident and migratory males did not follow our expectation and marine-migratory individuals dispersed more than residents. This may be because direct competition between marine-migratory and resident males is weak or that the cost of dispersal is smaller for marine-migratory individuals. This study revealed that both sex and migratory life history influence patterns of dispersal at a local scale in masu salmon.

Determining fine-scale migratory connectivity and habitat selection for a migratory songbird by using new GPS technology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fraser, Kevin C.; Shave, A.; Savage, A.

Migratory aerial insectivores are among the fastest declining avian group, but our understanding of these trends has been limited by poor knowledge of migratory connectivity and the identification of critical habitat across the vast distances they travel annually. Using new, archival GPS loggers, we tracked individual purple martins ( Progne subis) from breeding colonies across North America to determine precise (<10m) locations of migratory and overwintering roost locations in South America and to test hypotheses for fine-scale migratory connectivity and habitat use. We discovered weak migratory connectivity at the roost scale, and extensive, fine-scale mixing of birds in the Amazonmore » from distant (>2000 km) breeding sites, with some individuals sharing the same roosting trees. Despite vast tracts of contiguous forest in this region, birds occupied a much more limited habitat, with most (56%) roosts occurring on small habitat islands that were strongly associated with water. Only 17% of these roosts were in current protected areas. As a result, these data reflect a critical advance in our ability to remotely determine precise migratory connectivity and habitat selection across vast spatial scales, enhancing our understanding of population dynamics and enabling more effective conservation of species at risk.« less

Determining fine-scale migratory connectivity and habitat selection for a migratory songbird by using new GPS technology

DOE PAGES

Fraser, Kevin C.; Shave, A.; Savage, A.; ...

2016-07-27

Migratory aerial insectivores are among the fastest declining avian group, but our understanding of these trends has been limited by poor knowledge of migratory connectivity and the identification of critical habitat across the vast distances they travel annually. Using new, archival GPS loggers, we tracked individual purple martins ( Progne subis) from breeding colonies across North America to determine precise (<10m) locations of migratory and overwintering roost locations in South America and to test hypotheses for fine-scale migratory connectivity and habitat use. We discovered weak migratory connectivity at the roost scale, and extensive, fine-scale mixing of birds in the Amazonmore » from distant (>2000 km) breeding sites, with some individuals sharing the same roosting trees. Despite vast tracts of contiguous forest in this region, birds occupied a much more limited habitat, with most (56%) roosts occurring on small habitat islands that were strongly associated with water. Only 17% of these roosts were in current protected areas. As a result, these data reflect a critical advance in our ability to remotely determine precise migratory connectivity and habitat selection across vast spatial scales, enhancing our understanding of population dynamics and enabling more effective conservation of species at risk.« less

New microsatellite loci for Prosopis alba and P. chilensis (Fabaceae)1

PubMed Central

Bessega, Cecilia F.; Pometti, Carolina L.; Miller, Joe T.; Watts, Richard; Saidman, Beatriz O.; Vilardi, Juan C.

2013-01-01

• Premise of the study: As only six useful microsatellite loci that exhibit broad cross-amplification are so far available for Prosopis species, it is necessary to develop a larger number of codominant markers for population genetic studies. Simple sequence repeat (SSR) markers obtained for Prosopis species from a 454 pyrosequencing run were optimized and characterized for studies in P. alba and P. chilensis. • Methods and Results: Twelve markers that were successfully amplified showed polymorphism in P. alba and P. chilensis. The number of alleles per locus ranged between two and seven and heterozygosity estimates ranged from 0.2 to 0.8. Most of these loci cross-amplify in P. ruscifolia, P. flexuosa, P. kuntzei, P. glandulosa, and P. pallida. • Conclusions: These loci will enable genetic diversity studies of P. alba and P. chilensis and contribute to fine-scale population structure, indirect estimation of relatedness among individuals, and marker-assisted selection. PMID:25202541

Expectations on Hierarchical Scales of Discourse: Multifractality Predicts Both Short- and Long-Range Effects of Violating Gender Expectations in Text Reading

ERIC Educational Resources Information Center

Booth, Chase R.; Brown, Hannah L.; Eason, Elizabeth G.; Wallot, Sebastian; Kelty-Stephen, Damian G.

2018-01-01

Reader expectations form across hierarchical scales of discourse (e.g., from coarse to fine: genre, narrative, syntax). Cross-scale interactivity produces word reading times (RTs) with multifractal structure. After introducing multifractals, we test two hypotheses regarding their relevance to reader expectations: (1) multifractal evidence of…

Congenital amusia: a cognitive disorder limited to resolved harmonics and with no peripheral basis.

PubMed

Cousineau, Marion; Oxenham, Andrew J; Peretz, Isabelle

2015-01-01

Pitch plays a fundamental role in audition, from speech and music perception to auditory scene analysis. Congenital amusia is a neurogenetic disorder that appears to affect primarily pitch and melody perception. Pitch is normally conveyed by the spectro-temporal fine structure of low harmonics, but some pitch information is available in the temporal envelope produced by the interactions of higher harmonics. Using 10 amusic subjects and 10 matched controls, we tested the hypothesis that amusics suffer exclusively from impaired processing of spectro-temporal fine structure. We also tested whether the inability of amusics to process acoustic temporal fine structure extends beyond pitch by measuring sensitivity to interaural time differences, which also rely on temporal fine structure. Further tests were carried out on basic intensity and spectral resolution. As expected, pitch perception based on spectro-temporal fine structure was impaired in amusics; however, no significant deficits were observed in amusics' ability to perceive the pitch conveyed via temporal-envelope cues. Sensitivity to interaural time differences was also not significantly different between the amusic and control groups, ruling out deficits in the peripheral coding of temporal fine structure. Finally, no significant differences in intensity or spectral resolution were found between the amusic and control groups. The results demonstrate a pitch-specific deficit in fine spectro-temporal information processing in amusia that seems unrelated to temporal or spectral coding in the auditory periphery. These results are consistent with the view that there are distinct mechanisms dedicated to processing resolved and unresolved harmonics in the general population, the former being altered in congenital amusia while the latter is spared. Copyright © 2014 Elsevier Ltd. All rights reserved.

Schaffer Collateral Inputs to CA1 Excitatory and Inhibitory Neurons Follow Different Connectivity Rules.

PubMed

Kwon, Osung; Feng, Linqing; Druckmann, Shaul; Kim, Jinhyun

2018-05-30

Neural circuits, governed by a complex interplay between excitatory and inhibitory neurons, are the substrate for information processing, and the organization of synaptic connectivity in neural network is an important determinant of circuit function. Here, we analyzed the fine structure of connectivity in hippocampal CA1 excitatory and inhibitory neurons innervated by Schaffer collaterals (SCs) using mGRASP in male mice. Our previous study revealed spatially structured synaptic connectivity between CA3 and CA1 pyramidal cells (PCs). Surprisingly, parvalbumin-positive interneurons (PVs) showed a significantly more random pattern spatial structure. Notably, application of Peters' rule for synapse prediction by random overlap between axons and dendrites enhanced structured connectivity in PCs, but, by contrast, made the connectivity pattern in PVs more random. In addition, PCs in a deep sublayer of striatum pyramidale appeared more highly structured than PCs in superficial layers, and little or no sublayer specificity was found in PVs. Our results show that CA1 excitatory PCs and inhibitory PVs innervated by the same SC inputs follow different connectivity rules. The different organizations of fine scale structured connectivity in hippocampal excitatory and inhibitory neurons provide important insights into the development and functions of neural networks. SIGNIFICANCE STATEMENT Understanding how neural circuits generate behavior is one of the central goals of neuroscience. An important component of this endeavor is the mapping of fine-scale connection patterns that underlie, and help us infer, signal processing in the brain. Here, using our recently developed synapse detection technology (mGRASP and neuTube), we provide detailed profiles of synaptic connectivity in excitatory (CA1 pyramidal) and inhibitory (CA1 parvalbumin-positive) neurons innervated by the same presynaptic inputs (CA3 Schaffer collaterals). Our results reveal that these two types of CA1 neurons follow different connectivity patterns. Our new evidence for differently structured connectivity at a fine scale in hippocampal excitatory and inhibitory neurons provides a better understanding of hippocampal networks and will guide theoretical and experimental studies. Copyright © 2018 the authors 0270-6474/18/385140-13$15.00/0.

Coupling Satellite Data with Species Distribution and Connectivity Models as a Tool for Environmental Management and Planning in Matrix-Sensitive Species.

PubMed

Rödder, Dennis; Nekum, Sven; Cord, Anna F; Engler, Jan O

2016-07-01

Climate change and anthropogenic habitat fragmentation are considered major threats for global biodiversity. As a direct consequence, connectivity is increasingly disrupted in many species, which might have serious consequences that could ultimately lead to the extinction of populations. Although a large number of reserves and conservation sites are designated and protected by law, potential habitats acting as inter-population connectivity corridors are, however, mostly ignored in the common practice of environmental planning. In most cases, this is mainly caused by a lack of quantitative measures of functional connectivity available for the planning process. In this study, we highlight the use of fine-scale potential connectivity models (PCMs) derived from multispectral satellite data for the quantification of spatially explicit habitat corridors for matrix-sensitive species of conservation concern. This framework couples a species distribution model with a connectivity model in a two-step framework, where suitability maps from step 1 are transformed into maps of landscape resistance in step 2 filtered by fragmentation thresholds. We illustrate the approach using the sand lizard (Lacerta agilis L.) in the metropolitan area of Cologne, Germany, as a case study. Our model proved to be well suited to identify connected as well as completely isolated populations within the study area. Furthermore, due to its fine resolution, the PCM was also able to detect small linear structures known to be important for sand lizards' inter-population connectivity such as railroad embankments. We discuss the applicability and possible implementation of PCMs to overcome shortcomings in the common practice of environmental impact assessments.

Coupling Satellite Data with Species Distribution and Connectivity Models as a Tool for Environmental Management and Planning in Matrix-Sensitive Species

NASA Astrophysics Data System (ADS)

Rödder, Dennis; Nekum, Sven; Cord, Anna F.; Engler, Jan O.

2016-07-01

Climate change and anthropogenic habitat fragmentation are considered major threats for global biodiversity. As a direct consequence, connectivity is increasingly disrupted in many species, which might have serious consequences that could ultimately lead to the extinction of populations. Although a large number of reserves and conservation sites are designated and protected by law, potential habitats acting as inter-population connectivity corridors are, however, mostly ignored in the common practice of environmental planning. In most cases, this is mainly caused by a lack of quantitative measures of functional connectivity available for the planning process. In this study, we highlight the use of fine-scale potential connectivity models (PCMs) derived from multispectral satellite data for the quantification of spatially explicit habitat corridors for matrix-sensitive species of conservation concern. This framework couples a species distribution model with a connectivity model in a two-step framework, where suitability maps from step 1 are transformed into maps of landscape resistance in step 2 filtered by fragmentation thresholds. We illustrate the approach using the sand lizard ( Lacerta agilis L.) in the metropolitan area of Cologne, Germany, as a case study. Our model proved to be well suited to identify connected as well as completely isolated populations within the study area. Furthermore, due to its fine resolution, the PCM was also able to detect small linear structures known to be important for sand lizards' inter-population connectivity such as railroad embankments. We discuss the applicability and possible implementation of PCMs to overcome shortcomings in the common practice of environmental impact assessments.

IPUMS: Detailed global data on population characteristics

NASA Astrophysics Data System (ADS)

Kugler, T.

2017-12-01

Many new and exciting sources of data on human population distributions based on remote sensing, mobile technology, and other mechanisms are becoming available. These new data sources often provide fine scale spatial and/or temporal resolution. However, they typically focus on the location of population, with little or no information on population characteristics. The large and growing collection of data available through the IPUMS family of products complements datasets that provide spatial and temporal detail but little attribute detail by providing the full depth of characteristics covered by population censuses, including demographic, household structure, economic, employment, education, and housing characteristics. IPUMS International provides census microdata for 85 countries. Microdata provide the responses to every census question for each individual in a sample of households. Microdata identify the sub-national geographic unit in which a household is located, but for confidentiality reasons, identified units must include a minimum population, typically 20,000 people. Small-area aggregate data often describe much smaller geographic units, enabling study of detailed spatial patterns of population characteristics. However the structure of aggregate data tables is highly heterogeneous across countries, census years, and even topics within a given census, making these data difficult to work with in any systematic way. A recently funded project will assemble small-area aggregate population and agricultural census data published by national statistical offices. Through preliminary work collecting and cataloging over 10,000 tables, we have identified a small number of structural families that can be used to organize the many different structures. These structural families will form the basis for software tools to document and standardize the tables for ingest into a common database. Both the microdata and aggregate data are made available through IPUMS Terra, facilitating integration with land use, land cover, climate, and other environmental data. These data can be used to address pressing global challenges, such as food and water security, development and deforestation, and environmentally-influenced migration.

Impacts of insect disturbance on the structure, composition, and functioning of oak-pine forests

NASA Astrophysics Data System (ADS)

Medvigy, D.; Schafer, K. V.; Clark, K. L.

2011-12-01

Episodic disturbance is an essential feature of terrestrial ecosystems, and strongly modulates their structure, composition, and functioning. However, dynamic global vegetation models that are commonly used to make ecosystem and terrestrial carbon budget predictions rarely have an explicit representation of disturbance. One reason why disturbance is seldom included is that disturbance tends to operate on spatial scales that are much smaller than typical model resolutions. In response to this problem, the Ecosystem Demography model 2 (ED2) was developed as a way of tracking the fine-scale heterogeneity arising from disturbances. In this study, we used ED2 to simulate an oak-pine forest that experiences episodic defoliation by gypsy moth (Lymantria dispar L). The model was carefully calibrated against site-level data, and then used to simulate changes in ecosystem composition, structure, and functioning on century time scales. Compared to simulations that include gypsy moth defoliation, we show that simulations that ignore defoliation events lead to much larger ecosystem carbon stores and a larger fraction of deciduous trees relative to evergreen trees. Furthermore, we find that it is essential to preserve the fine-scale nature of the disturbance. Attempts to "smooth out" the defoliation event over an entire grid cells led to large biases in ecosystem structure and functioning.

Landscape management of fire and grazing regimes alters the fine-scale habitat utilisation by feral cats.

PubMed

McGregor, Hugh W; Legge, Sarah; Jones, Menna E; Johnson, Christopher N

2014-01-01

Intensification of fires and grazing by large herbivores has caused population declines in small vertebrates in many ecosystems worldwide. Impacts are rarely direct, and usually appear driven via indirect pathways, such as changes to predator-prey dynamics. Fire events and grazing may improve habitat and/or hunting success for the predators of small mammals, however, such impacts have not been documented. To test for such an interaction, we investigated fine-scale habitat selection by feral cats in relation to fire, grazing and small-mammal abundance. Our study was conducted in north-western Australia, where small mammal populations are sensitive to changes in fire and grazing management. We deployed GPS collars on 32 cats in landscapes with contrasting fire and grazing treatments. Fine-scale habitat selection was determined using discrete choice modelling of cat movements. We found that cats selected areas with open grass cover, including heavily-grazed areas. They strongly selected for areas recently burnt by intense fires, but only in habitats that typically support high abundance of small mammals. Intense fires and grazing by introduced herbivores created conditions that are favoured by cats, probably because their hunting success is improved. This mechanism could explain why, in northern Australia, impacts of feral cats on small mammals might have increased. Our results suggest the impact of feral cats could be reduced in most ecosystems by maximising grass cover, minimising the incidence of intense fires, and reducing grazing by large herbivores.

Landscape Management of Fire and Grazing Regimes Alters the Fine-Scale Habitat Utilisation by Feral Cats

PubMed Central

McGregor, Hugh W.; Legge, Sarah; Jones, Menna E.; Johnson, Christopher N.

2014-01-01

Intensification of fires and grazing by large herbivores has caused population declines in small vertebrates in many ecosystems worldwide. Impacts are rarely direct, and usually appear driven via indirect pathways, such as changes to predator-prey dynamics. Fire events and grazing may improve habitat and/or hunting success for the predators of small mammals, however, such impacts have not been documented. To test for such an interaction, we investigated fine-scale habitat selection by feral cats in relation to fire, grazing and small-mammal abundance. Our study was conducted in north-western Australia, where small mammal populations are sensitive to changes in fire and grazing management. We deployed GPS collars on 32 cats in landscapes with contrasting fire and grazing treatments. Fine-scale habitat selection was determined using discrete choice modelling of cat movements. We found that cats selected areas with open grass cover, including heavily-grazed areas. They strongly selected for areas recently burnt by intense fires, but only in habitats that typically support high abundance of small mammals. Intense fires and grazing by introduced herbivores created conditions that are favoured by cats, probably because their hunting success is improved. This mechanism could explain why, in northern Australia, impacts of feral cats on small mammals might have increased. Our results suggest the impact of feral cats could be reduced in most ecosystems by maximising grass cover, minimising the incidence of intense fires, and reducing grazing by large herbivores. PMID:25329902

Up, Down, and All Around: Scale-Dependent Spatial Variation in Rocky-Shore Communities of Fildes Peninsula, King George Island, Antarctica

PubMed Central

Valdivia, Nelson; Díaz, María J.; Holtheuer, Jorge; Garrido, Ignacio; Huovinen, Pirjo; Gómez, Iván

2014-01-01

Understanding the variation of biodiversity along environmental gradients and multiple spatial scales is relevant for theoretical and management purposes. Hereby, we analysed the spatial variability in diversity and structure of intertidal and subtidal macrobenthic Antarctic communities along vertical environmental stress gradients and across multiple horizontal spatial scales. Since biotic interactions and local topographic features are likely major factors for coastal assemblages, we tested the hypothesis that fine-scale processes influence the effects of the vertical environmental stress gradients on the macrobenthic diversity and structure. We used nested sampling designs in the intertidal and subtidal habitats, including horizontal spatial scales ranging from few centimetres to 1000s of metres along the rocky shore of Fildes Peninsula, King George Island. In both intertidal and subtidal habitats, univariate and multivariate analyses showed a marked vertical zonation in taxon richness and community structure. These patterns depended on the horizontal spatial scale of observation, as all analyses showed a significant interaction between height (or depth) and the finer spatial scale analysed. Variance and pseudo-variance components supported our prediction for taxon richness, community structure, and the abundance of dominant species such as the filamentous green alga Urospora penicilliformis (intertidal), the herbivore Nacella concinna (intertidal), the large kelp-like Himantothallus grandifolius (subtidal), and the red crustose red alga Lithothamnion spp. (subtidal). We suggest that in coastal ecosystems strongly governed by physical factors, fine-scale processes (e.g. biotic interactions and refugia availability) are still relevant for the structuring and maintenance of the local communities. The spatial patterns found in this study serve as a necessary benchmark to understand the dynamics and adaptation of natural assemblages in response to observed and predicted environmental changes in Antarctica. PMID:24956114

Fine Structures of Solar Radio Type III Bursts and Their Possible Relationship with Coronal Density Turbulence

NASA Astrophysics Data System (ADS)

Chen, Xingyao; Kontar, Eduard P.; Yu, Sijie; Yan, Yihua; Huang, Jing; Tan, Baolin

2018-03-01

Solar radio type III bursts are believed to be the most sensitive signatures of near-relativistic electron beam propagation in the corona. A solar radio type IIIb-III pair burst with fine frequency structures, observed by the Low Frequency Array (LOFAR) with high temporal (∼10 ms) and spectral (12.5 kHz) resolutions at 30–80 MHz, is presented. The observations show that the type III burst consists of many striae, which have a frequency scale of about 0.1 MHz in both the fundamental (plasma) and the harmonic (double plasma) emission. We investigate the effects of background density fluctuations based on the observation of striae structure to estimate the density perturbation in the solar corona. It is found that the spectral index of the density fluctuation spectrum is about ‑1.7, and the characteristic spatial scale of the density perturbation is around 700 km. This spectral index is very close to a Kolmogorov turbulence spectral index of ‑5/3, consistent with a turbulent cascade. This fact indicates that the coronal turbulence may play the important role of modulating the time structures of solar radio type III bursts, and the fine structure of radio type III bursts could provide a useful and unique tool to diagnose the turbulence in the solar corona.

Rocket measurements of mesospheric ionization irregularities

NASA Technical Reports Server (NTRS)

Stoltzfus, R. B.; Bowhill, S. A.

1985-01-01

The Langmuir probe technique for measurement of electron concentration in the mesosphere is capable of excellent altitude resolution, of order 1 m. Measurements from nine daytime rocket flights carrying an electron density fine structure experiment frequently show small scale ionization structures in the altitude region 70 to 90 km. The irregularities are believed to be the result of turbulent advection of ions and electrons. The fine structure experiment flown by the University of Illinois is described and methods of analyzing the collected data is presented. Theories of homogeneous, isotropic turbulence are reviewed. Power spectra of the measured irregularities are calculated and compared to spectra predicted by turbulence theories.

East-west genetic differentiation in Musk Ducks (Biziura lobata) of Australia suggests late Pleistocene divergence at the Nullarbor Plain

USGS Publications Warehouse

Guay, P.-J.; Chesser, R.T.; Mulder, R.A.; Afton, A.D.; Paton, D.C.; McCracken, K.G.

2010-01-01

Musk Ducks (Biziura lobata) are endemic to Australia and occur as two geographically isolated populations separated by the Nullarbor Plain, a vast arid region in southern Australia. We studied genetic variation in Musk Duck populations at coarse (eastern versus western Australia) and fine scales (four sites within eastern Australia). We found significant genetic structure between eastern and western Australia in the mtDNA control region (??ST = 0. 747), one nuclear intron (??ST = 0.193) and eight microsatellite loci (FST = 0.035). In contrast, there was little genetic structure between Kangaroo Island and adjacent mainland regions within eastern Australia. One small population of Musk Ducks in Victoria (Lake Wendouree) differed from both Kangaroo Island and the remainder of mainland eastern Australia, possibly due to genetic drift exacerbated by inbreeding and small population size. The observed low pairwise distance between the eastern and western mtDNA lineages (0.36%) suggests that they diverged near the end of the Pleistocene, a period characterised by frequent shifts between wet and arid conditions in central Australia. Our genetic results corroborate the display call divergence and Mathews' (Austral Avian Record 2:83-107, 1914) subspecies classification, and confirm that eastern and western populations of Musk Duck are currently isolated from each other. ?? 2010 Springer Science+Business Media B.V.

The underlying processes of a soil mite metacommunity on a small scale.

PubMed

Dong, Chengxu; Gao, Meixiang; Guo, Chuanwei; Lin, Lin; Wu, Donghui; Zhang, Limin

2017-01-01

Metacommunity theory provides an understanding of how ecological processes regulate local community assemblies. However, few field studies have evaluated the underlying mechanisms of a metacommunity on a small scale through revealing the relative roles of spatial and environmental filtering in structuring local community composition. Based on a spatially explicit sampling design in 2012 and 2013, this study aims to evaluate the underlying processes of a soil mite metacommunity on a small spatial scale (50 m) in a temperate deciduous forest located at the Maoershan Ecosystem Research Station, Northeast China. Moran's eigenvector maps (MEMs) were used to model independent spatial variables. The relative importance of spatial (including trend variables, i.e., geographical coordinates, and broad- and fine-scale spatial variables) and environmental factors in driving the soil mite metacommunity was determined by variation partitioning. Mantel and partial Mantel tests and a redundancy analysis (RDA) were also used to identify the relative contributions of spatial and environmental variables. The results of variation partitioning suggested that the relatively large and significant variance was a result of spatial variables (including broad- and fine-scale spatial variables and trend), indicating the importance of dispersal limitation and autocorrelation processes. The significant contribution of environmental variables was detected in 2012 based on a partial Mantel test, and soil moisture and soil organic matter were especially important for the soil mite metacommunity composition in both years. The study suggested that the soil mite metacommunity was primarily regulated by dispersal limitation due to broad-scale and neutral biotic processes at a fine-scale and that environmental filtering might be of subordinate importance. In conclusion, a combination of metacommunity perspectives between neutral and species sorting theories was suggested to be important in the observed structure of the soil mite metacommunity at the studied small scale.

The underlying processes of a soil mite metacommunity on a small scale

PubMed Central

Guo, Chuanwei; Lin, Lin; Wu, Donghui; Zhang, Limin

2017-01-01

Metacommunity theory provides an understanding of how ecological processes regulate local community assemblies. However, few field studies have evaluated the underlying mechanisms of a metacommunity on a small scale through revealing the relative roles of spatial and environmental filtering in structuring local community composition. Based on a spatially explicit sampling design in 2012 and 2013, this study aims to evaluate the underlying processes of a soil mite metacommunity on a small spatial scale (50 m) in a temperate deciduous forest located at the Maoershan Ecosystem Research Station, Northeast China. Moran’s eigenvector maps (MEMs) were used to model independent spatial variables. The relative importance of spatial (including trend variables, i.e., geographical coordinates, and broad- and fine-scale spatial variables) and environmental factors in driving the soil mite metacommunity was determined by variation partitioning. Mantel and partial Mantel tests and a redundancy analysis (RDA) were also used to identify the relative contributions of spatial and environmental variables. The results of variation partitioning suggested that the relatively large and significant variance was a result of spatial variables (including broad- and fine-scale spatial variables and trend), indicating the importance of dispersal limitation and autocorrelation processes. The significant contribution of environmental variables was detected in 2012 based on a partial Mantel test, and soil moisture and soil organic matter were especially important for the soil mite metacommunity composition in both years. The study suggested that the soil mite metacommunity was primarily regulated by dispersal limitation due to broad-scale and neutral biotic processes at a fine-scale and that environmental filtering might be of subordinate importance. In conclusion, a combination of metacommunity perspectives between neutral and species sorting theories was suggested to be important in the observed structure of the soil mite metacommunity at the studied small scale. PMID:28481906

Comment on: Polar Plumes and Fine-scale Coronal Structures - On the Interpretation of Coronal Radio Sounding Data by Patzold and Bird

NASA Technical Reports Server (NTRS)

Woo, R.; Habbal, S. R.

1998-01-01

Radio occultation measurements, which probe electron density over a wide dynamic range with high sensitivity and high spatial and temporal resolution reveal a solar corona permeated by a hierarchy of filamentary structures.

Global kinetic simulations of neoclassical toroidal viscosity in low-collisional perturbed tokamak plasmas

NASA Astrophysics Data System (ADS)

Matsuoka, Seikichi; Idomura, Yasuhiro; Satake, Shinsuke

2017-10-01

The neoclassical toroidal viscosity (NTV) caused by a non-axisymmetric magnetic field perturbation is numerically studied using two global kinetic simulations with different numerical approaches. Both simulations reproduce similar collisionality ( νb*) dependencies over wide νb * ranges. It is demonstrated that resonant structures in the velocity space predicted by the conventional superbanana-plateau theory exist in the small banana width limit, while the resonances diminish when the banana width becomes large. It is also found that fine scale structures are generated in the velocity space as νb* decreases in the large banana width simulations, leading to the νb* -dependency of the NTV. From the analyses of the particle orbit, it is found that the finite k∥ mode structure along the bounce motion appears owing to the finite orbit width, and it suffers from bounce phase mixing, suggesting the generation of the fine scale structures by the similar mechanism as the parallel phase mixing of passing particles.

Modeling and simulation of storm surge on Staten Island to understand inundation mitigation strategies

USGS Publications Warehouse

Kress, Michael E.; Benimoff, Alan I.; Fritz, William J.; Thatcher, Cindy A.; Blanton, Brian O.; Dzedzits, Eugene

2016-01-01

Hurricane Sandy made landfall on October 29, 2012, near Brigantine, New Jersey, and had a transformative impact on Staten Island and the New York Metropolitan area. Of the 43 New York City fatalities, 23 occurred on Staten Island. The borough, with a population of approximately 500,000, experienced some of the most devastating impacts of the storm. Since Hurricane Sandy, protective dunes have been constructed on the southeast shore of Staten Island. ADCIRC+SWAN model simulations run on The City University of New York's Cray XE6M, housed at the College of Staten Island, using updated topographic data show that the coast of Staten Island is still susceptible to tidal surge similar to those generated by Hurricane Sandy. Sandy hindcast simulations of storm surges focusing on Staten Island are in good agreement with observed storm tide measurements. Model results calculated from fine-scaled and coarse-scaled computational grids demonstrate that finer grids better resolve small differences in the topography of critical hydraulic control structures, which affect storm surge inundation levels. The storm surge simulations, based on post-storm topography obtained from high-resolution lidar, provide much-needed information to understand Staten Island's changing vulnerability to storm surge inundation. The results of fine-scale storm surge simulations can be used to inform efforts to improve resiliency to future storms. For example, protective barriers contain planned gaps in the dunes to provide for beach access that may inadvertently increase the vulnerability of the area.

Patterns of resting state connectivity in human primary visual cortical areas: a 7T fMRI study.

PubMed

Raemaekers, Mathijs; Schellekens, Wouter; van Wezel, Richard J A; Petridou, Natalia; Kristo, Gert; Ramsey, Nick F

2014-01-01

The nature and origin of fMRI resting state fluctuations and connectivity are still not fully known. More detailed knowledge on the relationship between resting state patterns and brain function may help to elucidate this matter. We therefore performed an in depth study of how resting state fluctuations map to the well known architecture of the visual system. We investigated resting state connectivity at both a fine and large scale within and across visual areas V1, V2 and V3 in ten human subjects using a 7Tesla scanner. We found evidence for several coexisting and overlapping connectivity structures at different spatial scales. At the fine-scale level we found enhanced connectivity between the same topographic locations in the fieldmaps of V1, V2 and V3, enhanced connectivity to the contralateral functional homologue, and to a lesser extent enhanced connectivity between iso-eccentric locations within the same visual area. However, by far the largest proportion of the resting state fluctuations occurred within large-scale bilateral networks. These large-scale networks mapped to some extent onto the architecture of the visual system and could thereby obscure fine-scale connectivity. In fact, most of the fine-scale connectivity only became apparent after the large-scale network fluctuations were filtered from the timeseries. We conclude that fMRI resting state fluctuations in the visual cortex may in fact be a composite signal of different overlapping sources. Isolating the different sources could enhance correlations between BOLD and electrophysiological correlates of resting state activity. © 2013 Elsevier Inc. All rights reserved.

Spatially explicit modeling in ecology: A review

USGS Publications Warehouse

DeAngelis, Donald L.; Yurek, Simeon

2017-01-01

The use of spatially explicit models (SEMs) in ecology has grown enormously in the past two decades. One major advancement has been that fine-scale details of landscapes, and of spatially dependent biological processes, such as dispersal and invasion, can now be simulated with great precision, due to improvements in computer technology. Many areas of modeling have shifted toward a focus on capturing these fine-scale details, to improve mechanistic understanding of ecosystems. However, spatially implicit models (SIMs) have played a dominant role in ecology, and arguments have been made that SIMs, which account for the effects of space without specifying spatial positions, have an advantage of being simpler and more broadly applicable, perhaps contributing more to understanding. We address this debate by comparing SEMs and SIMs in examples from the past few decades of modeling research. We argue that, although SIMs have been the dominant approach in the incorporation of space in theoretical ecology, SEMs have unique advantages for addressing pragmatic questions concerning species populations or communities in specific places, because local conditions, such as spatial heterogeneities, organism behaviors, and other contingencies, produce dynamics and patterns that usually cannot be incorporated into simpler SIMs. SEMs are also able to describe mechanisms at the local scale that can create amplifying positive feedbacks at that scale, creating emergent patterns at larger scales, and therefore are important to basic ecological theory. We review the use of SEMs at the level of populations, interacting populations, food webs, and ecosystems and argue that SEMs are not only essential in pragmatic issues, but must play a role in the understanding of causal relationships on landscapes.

Hierarchical Learning of Tree Classifiers for Large-Scale Plant Species Identification.

PubMed

Fan, Jianping; Zhou, Ning; Peng, Jinye; Gao, Ling

2015-11-01

In this paper, a hierarchical multi-task structural learning algorithm is developed to support large-scale plant species identification, where a visual tree is constructed for organizing large numbers of plant species in a coarse-to-fine fashion and determining the inter-related learning tasks automatically. For a given parent node on the visual tree, it contains a set of sibling coarse-grained categories of plant species or sibling fine-grained plant species, and a multi-task structural learning algorithm is developed to train their inter-related classifiers jointly for enhancing their discrimination power. The inter-level relationship constraint, e.g., a plant image must first be assigned to a parent node (high-level non-leaf node) correctly if it can further be assigned to the most relevant child node (low-level non-leaf node or leaf node) on the visual tree, is formally defined and leveraged to learn more discriminative tree classifiers over the visual tree. Our experimental results have demonstrated the effectiveness of our hierarchical multi-task structural learning algorithm on training more discriminative tree classifiers for large-scale plant species identification.

Inferring landscape-scale land-use impacts on rivers using data from mesocosm experiments and artificial neural networks.

PubMed

Magierowski, Regina H; Read, Steve M; Carter, Steven J B; Warfe, Danielle M; Cook, Laurie S; Lefroy, Edward C; Davies, Peter E

2015-01-01

Identifying land-use drivers of changes in river condition is complicated by spatial scale, geomorphological context, land management, and correlations among responding variables such as nutrients and sediments. Furthermore, variations in standard metrics, such as substratum composition, do not necessarily relate causally to ecological impacts. Consequently, the absence of a significant relationship between a hypothesised driver and a dependent variable does not necessarily indicate the absence of a causal relationship. We conducted a gradient survey to identify impacts of catchment-scale grazing by domestic livestock on river macroinvertebrate communities. A standard correlative approach showed that community structure was strongly related to the upstream catchment area under grazing. We then used data from a stream mesocosm experiment that independently quantified the impacts of nutrients and fine sediments on macroinvertebrate communities to train artificial neural networks (ANNs) to assess the relative influence of nutrients and fine sediments on the survey sites from their community composition. The ANNs developed to predict nutrient impacts did not find a relationship between nutrients and catchment area under grazing, suggesting that nutrients were not an important factor mediating grazing impacts on community composition, or that these ANNs had no generality or insufficient power at the landscape-scale. In contrast, ANNs trained to predict the impacts of fine sediments indicated a significant relationship between fine sediments and catchment area under grazing. Macroinvertebrate communities at sites with a high proportion of land under grazing were thus more similar to those resulting from high fine sediments in a mesocosm experiment than to those resulting from high nutrients. Our study confirms that 1) fine sediment is an important mediator of land-use impacts on river macroinvertebrate communities, 2) ANNs can successfully identify subtle effects and separate the effects of correlated variables, and 3) data from small-scale experiments can generate relationships that help explain landscape-scale patterns.

Inferring Landscape-Scale Land-Use Impacts on Rivers Using Data from Mesocosm Experiments and Artificial Neural Networks

PubMed Central

Magierowski, Regina H.; Read, Steve M.; Carter, Steven J. B.; Warfe, Danielle M.; Cook, Laurie S.; Lefroy, Edward C.; Davies, Peter E.

2015-01-01

Identifying land-use drivers of changes in river condition is complicated by spatial scale, geomorphological context, land management, and correlations among responding variables such as nutrients and sediments. Furthermore, variations in standard metrics, such as substratum composition, do not necessarily relate causally to ecological impacts. Consequently, the absence of a significant relationship between a hypothesised driver and a dependent variable does not necessarily indicate the absence of a causal relationship. We conducted a gradient survey to identify impacts of catchment-scale grazing by domestic livestock on river macroinvertebrate communities. A standard correlative approach showed that community structure was strongly related to the upstream catchment area under grazing. We then used data from a stream mesocosm experiment that independently quantified the impacts of nutrients and fine sediments on macroinvertebrate communities to train artificial neural networks (ANNs) to assess the relative influence of nutrients and fine sediments on the survey sites from their community composition. The ANNs developed to predict nutrient impacts did not find a relationship between nutrients and catchment area under grazing, suggesting that nutrients were not an important factor mediating grazing impacts on community composition, or that these ANNs had no generality or insufficient power at the landscape-scale. In contrast, ANNs trained to predict the impacts of fine sediments indicated a significant relationship between fine sediments and catchment area under grazing. Macroinvertebrate communities at sites with a high proportion of land under grazing were thus more similar to those resulting from high fine sediments in a mesocosm experiment than to those resulting from high nutrients. Our study confirms that 1) fine sediment is an important mediator of land-use impacts on river macroinvertebrate communities, 2) ANNs can successfully identify subtle effects and separate the effects of correlated variables, and 3) data from small-scale experiments can generate relationships that help explain landscape-scale patterns. PMID:25775245

Applications of random forest feature selection for fine-scale genetic population assignment.

PubMed

Sylvester, Emma V A; Bentzen, Paul; Bradbury, Ian R; Clément, Marie; Pearce, Jon; Horne, John; Beiko, Robert G

2018-02-01

Genetic population assignment used to inform wildlife management and conservation efforts requires panels of highly informative genetic markers and sensitive assignment tests. We explored the utility of machine-learning algorithms (random forest, regularized random forest and guided regularized random forest) compared with F ST ranking for selection of single nucleotide polymorphisms (SNP) for fine-scale population assignment. We applied these methods to an unpublished SNP data set for Atlantic salmon ( Salmo salar ) and a published SNP data set for Alaskan Chinook salmon ( Oncorhynchus tshawytscha ). In each species, we identified the minimum panel size required to obtain a self-assignment accuracy of at least 90% using each method to create panels of 50-700 markers Panels of SNPs identified using random forest-based methods performed up to 7.8 and 11.2 percentage points better than F ST -selected panels of similar size for the Atlantic salmon and Chinook salmon data, respectively. Self-assignment accuracy ≥90% was obtained with panels of 670 and 384 SNPs for each data set, respectively, a level of accuracy never reached for these species using F ST -selected panels. Our results demonstrate a role for machine-learning approaches in marker selection across large genomic data sets to improve assignment for management and conservation of exploited populations.

Band-Edge Exciton Fine Structure and Recombination Dynamics in InP/ZnS Colloidal Nanocrystals.

PubMed

Biadala, Louis; Siebers, Benjamin; Beyazit, Yasin; Tessier, Mickaël D; Dupont, Dorian; Hens, Zeger; Yakovlev, Dmitri R; Bayer, Manfred

2016-03-22

We report on a temperature-, time-, and spectrally resolved study of the photoluminescence of type-I InP/ZnS colloidal nanocrystals with varying core size. By studying the exciton recombination dynamics we assess the exciton fine structure in these systems. In addition to the typical bright-dark doublet, the photoluminescence stems from an upper bright state in spite of its large energy splitting (∼100 meV). This striking observation results from dramatically lengthened thermalization processes among the fine structure levels and points to optical-phonon bottleneck effects in InP/ZnS nanocrystals. Furthermore, our data show that the radiative recombination of the dark exciton scales linearly with the bright-dark energy splitting for CdSe and InP nanocrystals. This finding strongly suggests a universal dangling bonds-assisted recombination of the dark exciton in colloidal nanostructures.

Recent Demographic History and Present Fine-Scale Structure in the Northwest Atlantic Leatherback (Dermochelys coriacea) Turtle Population

PubMed Central

Molfetti, Érica; Torres Vilaça, Sibelle; Georges, Jean-Yves; Plot, Virginie; Delcroix, Eric; Le Scao, Rozen; Lavergne, Anne; Barrioz, Sébastien; dos Santos, Fabrício Rodrigues; de Thoisy, Benoît

2013-01-01

The leatherback turtle Dermochelys coriacea is the most widely distributed sea turtle species in the world. It exhibits complex life traits: female homing and migration, migrations of juveniles and males that remain poorly known, and a strong climatic influence on resources, breeding success and sex-ratio. It is consequently challenging to understand population dynamics. Leatherbacks are critically endangered, yet the group from the Northwest Atlantic is currently considered to be under lower risk than other populations while hosting some of the largest rookeries. Here, we investigated the genetic diversity and the demographic history of contrasted rookeries from this group, namely two large nesting populations in French Guiana, and a smaller one in the French West Indies. We used 10 microsatellite loci, of which four are newly isolated, and mitochondrial DNA sequences of the control region and cytochrome b. Both mitochondrial and nuclear markers revealed that the Northwest Atlantic stock of leatherbacks derives from a single ancestral origin, but show current genetic structuration at the scale of nesting sites, with the maintenance of migrants amongst rookeries. Low nuclear genetic diversities are related to founder effects that followed consequent bottlenecks during the late Pleistocene/Holocene. Most probably in response to climatic oscillations, with a possible influence of early human hunting, female effective population sizes collapsed from 2 million to 200. Evidence of founder effects and high numbers of migrants make it possible to reconsider the population dynamics of the species, formerly considered as a metapopulation model: we propose a more relaxed island model, which we expect to be a key element in the currently observed recovering of populations. Although these Northwest Atlantic rookeries should be considered as a single evolutionary unit, we stress that local conservation efforts remain necessary since each nesting site hosts part of the genetic diversity and species history. PMID:23516429

Role of buoyant flame dynamics in wildfire spread.

PubMed

Finney, Mark A; Cohen, Jack D; Forthofer, Jason M; McAllister, Sara S; Gollner, Michael J; Gorham, Daniel J; Saito, Kozo; Akafuah, Nelson K; Adam, Brittany A; English, Justin D

2015-08-11

Large wildfires of increasing frequency and severity threaten local populations and natural resources and contribute carbon emissions into the earth-climate system. Although wildfires have been researched and modeled for decades, no verifiable physical theory of spread is available to form the basis for the precise predictions needed to manage fires more effectively and reduce their environmental, economic, ecological, and climate impacts. Here, we report new experiments conducted at multiple scales that appear to reveal how wildfire spread derives from the tight coupling between flame dynamics induced by buoyancy and fine-particle response to convection. Convective cooling of the fine-sized fuel particles in wildland vegetation is observed to efficiently offset heating by thermal radiation until convective heating by contact with flames and hot gasses occurs. The structure and intermittency of flames that ignite fuel particles were found to correlate with instabilities induced by the strong buoyancy of the flame zone itself. Discovery that ignition in wildfires is critically dependent on nonsteady flame convection governed by buoyant and inertial interaction advances both theory and the physical basis for practical modeling.

Role of buoyant flame dynamics in wildfire spread

PubMed Central

Finney, Mark A.; Cohen, Jack D.; Forthofer, Jason M.; McAllister, Sara S.; Gollner, Michael J.; Gorham, Daniel J.; Saito, Kozo; Akafuah, Nelson K.; Adam, Brittany A.; English, Justin D.

2015-01-01

Large wildfires of increasing frequency and severity threaten local populations and natural resources and contribute carbon emissions into the earth-climate system. Although wildfires have been researched and modeled for decades, no verifiable physical theory of spread is available to form the basis for the precise predictions needed to manage fires more effectively and reduce their environmental, economic, ecological, and climate impacts. Here, we report new experiments conducted at multiple scales that appear to reveal how wildfire spread derives from the tight coupling between flame dynamics induced by buoyancy and fine-particle response to convection. Convective cooling of the fine-sized fuel particles in wildland vegetation is observed to efficiently offset heating by thermal radiation until convective heating by contact with flames and hot gasses occurs. The structure and intermittency of flames that ignite fuel particles were found to correlate with instabilities induced by the strong buoyancy of the flame zone itself. Discovery that ignition in wildfires is critically dependent on nonsteady flame convection governed by buoyant and inertial interaction advances both theory and the physical basis for practical modeling. PMID:26183227

Phylogeography of the American woodcock (Scolopax minor): Are management units based on band recovery data reflected in genetically based management units?

USGS Publications Warehouse

Rhymer, J.M.; McAuley, D.G.; Ziel, H.L.

2005-01-01

Information on population connectivity throughout the annual cycle has become more crucial, because populations of many migratory birds are in decline. One such species is the American Woodcock (Scolopax minor), which inhabits early-successional forests in eastern North America. Although band recoveries have proved useful for dividing populations of this game bird species into an Eastern Region and Central Region for management purposes, these data do not provide enough detail to determine the breeding population of origin of birds recovered on stopover and wintering areas. To obtain more fine-scale data, we undertook a phylogeographic study of American Woodcock populations throughout their primary breeding range in the eastern United States and Canada using mitochondrial DNA (mtDNA) sequences from the hypervariable control region I (CRI) and ND6 gene. Despite high haplotype diversity, nucleotide diversity was low and there was no phylogeographic structure among American Woodcock populations across the species range, with birds from many states and provinces in both management regions sharing identical haplotypes. Results suggest recent or ongoing gene flow among populations, with asymmetric movement of birds between migration flyways. As has been demonstrated for several other avian species in North America, American Woodcock appear to have undergone a rapid population expansion following the late Pleistocene glacial retreat. Thus, a combination of historical demographic factors and recent or ongoing gene flow mask any population structure based on mtDNA that might accrue from philopatry to breeding areas observed in studies of marked birds.

Relationships between population density, fine-scale genetic structure, mating system and pollen dispersal in a timber tree from African rainforests.

PubMed

Duminil, J; Daïnou, K; Kaviriri, D K; Gillet, P; Loo, J; Doucet, J-L; Hardy, O J

2016-03-01

Owing to the reduction of population density and/or the environmental changes it induces, selective logging could affect the demography, reproductive biology and evolutionary potential of forest trees. This is particularly relevant in tropical forests where natural population densities can be low and isolated trees may be subject to outcross pollen limitation and/or produce low-quality selfed seeds that exhibit inbreeding depression. Comparing reproductive biology processes and genetic diversity of populations at different densities can provide indirect evidence of the potential impacts of logging. Here, we analysed patterns of genetic diversity, mating system and gene flow in three Central African populations of the self-compatible legume timber species Erythrophleum suaveolens with contrasting densities (0.11, 0.68 and 1.72 adults per ha). The comparison of inbreeding levels among cohorts suggests that selfing is detrimental as inbred individuals are eliminated between seedling and adult stages. Levels of genetic diversity, selfing rates (∼16%) and patterns of spatial genetic structure (Sp ∼0.006) were similar in all three populations. However, the extent of gene dispersal differed markedly among populations: the average distance of pollen dispersal increased with decreasing density (from 200 m in the high-density population to 1000 m in the low-density one). Overall, our results suggest that the reproductive biology and genetic diversity of the species are not affected by current logging practices. However, further investigations need to be conducted in low-density populations to evaluate (1) whether pollen limitation may reduce seed production and (2) the regeneration potential of the species.

Multiple SNP Markers Reveal Fine-Scale Population and Deep Phylogeographic Structure in European Anchovy (Engraulis encrasicolus L.)

PubMed Central

Zarraonaindia, Iratxe; Iriondo, Mikel; Albaina, Aitor; Pardo, Miguel Angel; Manzano, Carmen; Grant, W. Stewart; Irigoien, Xabier; Estonba, Andone

2012-01-01

Geographic surveys of allozymes, microsatellites, nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) have detected several genetic subdivisions among European anchovy populations. However, these studies have been limited in their power to detect some aspects of population structure by the use of a single or a few molecular markers, or by limited geographic sampling. We use a multi-marker approach, 47 nDNA and 15 mtDNA single nucleotide polymorphisms (SNPs), to analyze 626 European anchovies from the whole range of the species to resolve shallow and deep levels of population structure. Nuclear SNPs define 10 genetic entities within two larger genetically distinctive groups associated with oceanic variables and different life-history traits. MtDNA SNPs define two deep phylogroups that reflect ancient dispersals and colonizations. These markers define two ecological groups. One major group of Iberian-Atlantic populations is associated with upwelling areas on narrow continental shelves and includes populations spawning and overwintering in coastal areas. A second major group includes northern populations in the North East (NE) Atlantic (including the Bay of Biscay) and the Mediterranean and is associated with wide continental shelves with local larval retention currents. This group tends to spawn and overwinter in oceanic areas. These two groups encompass ten populations that differ from previously defined management stocks in the Alboran Sea, Iberian-Atlantic and Bay of Biscay regions. In addition, a new North Sea-English Channel stock is defined. SNPs indicate that some populations in the Bay of Biscay are genetically closer to North Western (NW) Mediterranean populations than to other populations in the NE Atlantic, likely due to colonizations of the Bay of Biscay and NW Mediterranean by migrants from a common ancestral population. Northern NE Atlantic populations were subsequently established by migrants from the Bay of Biscay. Populations along the Iberian-Atlantic coast appear to have been founded by secondary waves of migrants from a southern refuge. PMID:22860082

The basis of orientation decoding in human primary visual cortex: fine- or coarse-scale biases?

PubMed

Maloney, Ryan T

2015-01-01

Orientation signals in human primary visual cortex (V1) can be reliably decoded from the multivariate pattern of activity as measured with functional magnetic resonance imaging (fMRI). The precise underlying source of these decoded signals (whether by orientation biases at a fine or coarse scale in cortex) remains a matter of some controversy, however. Freeman and colleagues (J Neurosci 33: 19695-19703, 2013) recently showed that the accuracy of decoding of spiral patterns in V1 can be predicted by a voxel's preferred spatial position (the population receptive field) and its coarse orientation preference, suggesting that coarse-scale biases are sufficient for orientation decoding. Whether they are also necessary for decoding remains an open question, and one with implications for the broader interpretation of multivariate decoding results in fMRI studies. Copyright © 2015 the American Physiological Society.

A Bi-Modal Distribution of ALHA77307 Matrix Olivine: Evidence for Fine-Grained Mixing from Multiple Reservoirs in the CO Formation Zone

NASA Technical Reports Server (NTRS)

Frank, D.; Zolensky, Michael E.; Brearley, A.; Le, L.

2011-01-01

The CO 3.0 chondrite ALHA77307 is thought to be the least metamorphosed of all the CO chondrites [1]. As such, the fine-grained (<30 m) olivine found in its matrix is a valuable resource for investigating the CO formation environment since its compositions should be primary. In the CO matrix, we indeed find a wide range of major element compositions (Fa(0.5-71)). However, more importantly, we find that the olivines make up two compositionally distinct populations (Fa(0.5-5) and Fa(21-71)). Grains from both populations are found within an extremely close proximity and we see no obvious evidence of two distinct lithologies within our samples. Therefore, we conclude that the olivine grains found in the ALHA77307 matrix must have crystallized within two unique formation conditions and were later mixed at a very fine scale during the accretion epoch. Here, we propose a possible explanation based on Cr and Mn concentrations in the olivine.

Cholera and shigellosis in Bangladesh: similarities and differences in population dynamics under climate forcing

NASA Astrophysics Data System (ADS)

Pascual, M.; Cash, B.; Reiner, R.; King, A.; Emch, M.; Yunus, M.; Faruque, A. S.

2012-12-01

The influence of climate variability on the population dynamics of infectious diseases is considered a large scale, regional, phenomenon, and as such, has been previously addressed for cholera with temporal models that do not incorporate fine-scale spatial structure. In our previous work, evidence for a role of ENSO (El Niño Southern Oscillation) on cholera in Bangladesh was elucidated, and shown to influence the regional climate through precipitation. With a probabilistic spatial model for cholera dynamics in the megacity of Dhaka, we found that the action of climate variability (ENSO and flooding) is localized: there is a climate-sensitive urban core that acts to propagate risk to the rest of the city. Here, we consider long-term surveillance data for shigellosis, another diarrheal disease that coexists with cholera in Bangladesh. We compare the patterns of association with climate variables for these two diseases in a rural setting, as well as the spatial structure in their spatio-temporal dynamics in an urban one. Evidence for similar patterns is presented, and discussed in the context of the differences in the routes of transmission of the two diseases and the proposed role of an environmental reservoir in cholera. The similarities provide evidence for a more general influence of hydrology and of socio-economic factors underlying human susceptibility and sanitary conditions.

Characterization, scaling, and partial representation of diffuse and discrete input junctions to CA3 hippocampus.

PubMed

Ascarrunz, F G; Kisley, M A; Flach, K A; Hamilton, R W; MacGregor, R J

1995-07-01

This paper applies a general mathematical system for characterizing and scaling functional connectivity and information flow across the diffuse (EC) and discrete (DG) input junctions to the CA3 hippocampus. Both gross connectivity and coordinated multiunit informational firing patterns are quantitatively characterized in terms of 32 defining parameters interrelated by 17 equations, and then scaled down according to rules for uniformly proportional scaling and for partial representation. The diffuse EC-CA3 junction is shown to be uniformly scalable with realistic representation of both essential spatiotemporal cooperativity and coordinated firing patterns down to populations of a few hundred neurons. Scaling of the discrete DG-CA3 junction can be effected with a two-step process, which necessarily deviates from uniform proportionality but nonetheless produces a valuable and readily interpretable reduced model, also utilizing a few hundred neurons in the receiving population. Partial representation produces a reduced model of only a portion of the full network where each model neuron corresponds directly to a biological neuron. The mathematical analysis illustrated here shows that although omissions and distortions are inescapable in such an application, satisfactorily complete and accurate models the size of pattern modules are possible. Finally, the mathematical characterization of these junctions generates a theory which sees the DG as a definer of the fine structure of embedded traces in the hippocampus and entire coordinated patterns of sequences of 14-cell links in CA3 as triggered by the firing of sequences of individual neurons in DG.

Spatial Structure of Seagrass Suggests That Size-Dependent Plant Traits Have a Strong Influence on the Distribution and Maintenance of Tropical Multispecies Meadows

PubMed Central

Ooi, Jillian L. S.; Van Niel, Kimberly P.; Kendrick, Gary A.; Holmes, Karen W.

2014-01-01

Background Seagrass species in the tropics occur in multispecies meadows. How these meadows are maintained through species co-existence and what their ecological drivers may be has been an overarching question in seagrass biogeography. In this study, we quantify the spatial structure of four co-existing species and infer potential ecological processes from these structures. Methods and Results Species presence/absence data were collected using underwater towed and dropped video cameras in Pulau Tinggi, Malaysia. The geostatistical method, utilizing semivariograms, was used to describe the spatial structure of Halophila spp, Halodule uninervis, Syringodium isoetifolium and Cymodocea serrulata. Species had spatial patterns that were oriented in the along-shore and across-shore directions, nested with larger species in meadow interiors, and consisted of multiple structures that indicate the influence of 2–3 underlying processes. The Linear Model of Coregionalization (LMC) was used to estimate the amount of variance contributing to the presence of a species at specific spatial scales. These distances were <2.5 m (micro-scale), 2.5–50 m (fine-scale) and >50 m (broad-scale) in the along-shore; and <2.5 m (micro-scale), 2.5–140 m (fine-scale) and >140 m (broad-scale) in the across-shore. The LMC suggests that smaller species (Halophila spp and H. uninervis) were most influenced by broad-scale processes such as hydrodynamics and water depth whereas large, localised species (S. isoetifolium and C. serrulata) were more influenced by finer-scale processes such as sediment burial, seagrass colonization and growth, and physical disturbance. Conclusion In this study, we provide evidence that spatial structure is distinct even when species occur in well-mixed multispecies meadows, and we suggest that size-dependent plant traits have a strong influence on the distribution and maintenance of tropical marine plant communities. This study offers a contrast from previous spatial models of seagrasses which have largely focused on monospecific temperate meadows. PMID:24497978

Spatial structure of seagrass suggests that size-dependent plant traits have a strong influence on the distribution and maintenance of tropical multispecies meadows.

PubMed

Ooi, Jillian L S; Van Niel, Kimberly P; Kendrick, Gary A; Holmes, Karen W

2014-01-01

Seagrass species in the tropics occur in multispecies meadows. How these meadows are maintained through species co-existence and what their ecological drivers may be has been an overarching question in seagrass biogeography. In this study, we quantify the spatial structure of four co-existing species and infer potential ecological processes from these structures. Species presence/absence data were collected using underwater towed and dropped video cameras in Pulau Tinggi, Malaysia. The geostatistical method, utilizing semivariograms, was used to describe the spatial structure of Halophila spp, Halodule uninervis, Syringodium isoetifolium and Cymodocea serrulata. Species had spatial patterns that were oriented in the along-shore and across-shore directions, nested with larger species in meadow interiors, and consisted of multiple structures that indicate the influence of 2-3 underlying processes. The Linear Model of Coregionalization (LMC) was used to estimate the amount of variance contributing to the presence of a species at specific spatial scales. These distances were <2.5 m (micro-scale), 2.5-50 m (fine-scale) and >50 m (broad-scale) in the along-shore; and <2.5 m (micro-scale), 2.5-140 m (fine-scale) and >140 m (broad-scale) in the across-shore. The LMC suggests that smaller species (Halophila spp and H. uninervis) were most influenced by broad-scale processes such as hydrodynamics and water depth whereas large, localised species (S. isoetifolium and C. serrulata) were more influenced by finer-scale processes such as sediment burial, seagrass colonization and growth, and physical disturbance. In this study, we provide evidence that spatial structure is distinct even when species occur in well-mixed multispecies meadows, and we suggest that size-dependent plant traits have a strong influence on the distribution and maintenance of tropical marine plant communities. This study offers a contrast from previous spatial models of seagrasses which have largely focused on monospecific temperate meadows.

The Atlantic-Mediterranean watershed, river basins and glacial history shape the genetic structure of Iberian poplars.

PubMed

Macaya-Sanz, D; Heuertz, M; López-de-Heredia, U; De-Lucas, A I; Hidalgo, E; Maestro, C; Prada, A; Alía, R; González-Martínez, S C

2012-07-01

Recent phylogeographic studies have elucidated the effects of Pleistocene glaciations and of Pre-Pleistocene events on populations from glacial refuge areas. This study investigates those effects in riparian trees (Populus spp.), whose particular features may convey enhanced resistance to climate fluctuations. We analysed the phylogeographic structure of 44 white (Populus alba), 13 black (Populus nigra) and two grey (Populus x canescens) poplar populations in the Iberian Peninsula using plastid DNA microsatellites and sequences. We also assessed fine-scale spatial genetic structure and the extent of clonality in four white and one grey poplar populations using nuclear microsatellites and we determined quantitative genetic differentiation (Q(ST) ) for growth traits in white poplar. Black poplar displayed higher regional diversity and lower differentiation than white poplar, reflecting its higher cold-tolerance. The dependence of white poplar on phreatic water was evidenced by strong differentiation between the Atlantic and Mediterranean drainage basins and among river basins, and by weaker isolation by distance within than among river basins. Our results suggest confinement to the lower river courses during glacial periods and moderate interglacial gene exchange along coastlines. In northern Iberian river basins, white poplar had lower diversity, fewer private haplotypes and larger clonal assemblies than in southern basins, indicating a stronger effect of glaciations in the north. Despite strong genetic structure and frequent asexual propagation in white poplar, some growth traits displayed adaptive divergence between drainage and river basins (Q(ST) >F(ST)), highlighting the remarkable capacity of riparian tree populations to adapt to regional environmental conditions. © 2012 Blackwell Publishing Ltd.

Small-Scale Habitat Structure Modulates the Effects of No-Take Marine Reserves for Coral Reef Macroinvertebrates

PubMed Central

Dumas, Pascal; Jimenez, Haizea; Peignon, Christophe; Wantiez, Laurent; Adjeroud, Mehdi

2013-01-01

No-take marine reserves are one of the oldest and most versatile tools used across the Pacific for the conservation of reef resources, in particular for invertebrates traditionally targeted by local fishers. Assessing their actual efficiency is still a challenge in complex ecosystems such as coral reefs, where reserve effects are likely to be obscured by high levels of environmental variability. The goal of this study was to investigate the potential interference of small-scale habitat structure on the efficiency of reserves. The spatial distribution of widely harvested macroinvertebrates was surveyed in a large set of protected vs. unprotected stations from eleven reefs located in New Caledonia. Abundance, density and individual size data were collected along random, small-scale (20×1 m) transects. Fine habitat typology was derived with a quantitative photographic method using 17 local habitat variables. Marine reserves substantially augmented the local density, size structure and biomass of the target species. Density of Trochus niloticus and Tridacna maxima doubled globally inside the reserve network; average size was greater by 10 to 20% for T. niloticus. We demonstrated that the apparent success of protection could be obscured by marked variations in population structure occurring over short distances, resulting from small-scale heterogeneity in the reef habitat. The efficiency of reserves appeared to be modulated by the availability of suitable habitats at the decimetric scale (“microhabitats”) for the considered sessile/low-mobile macroinvertebrate species. Incorporating microhabitat distribution could significantly enhance the efficiency of habitat surrogacy, a valuable approach in the case of conservation targets focusing on endangered or emblematic macroinvertebrate or relatively sedentary fish species PMID:23554965

Fine-Scale Map of Encyclopedia of DNA Elements Regions in the Korean Population

PubMed Central

Yoo, Yeon-Kyeong; Ke, Xiayi; Hong, Sungwoo; Jang, Hye-Yoon; Park, Kyunghee; Kim, Sook; Ahn, TaeJin; Lee, Yeun-Du; Song, Okryeol; Rho, Na-Young; Lee, Moon Sue; Lee, Yeon-Su; Kim, Jaeheup; Kim, Young J.; Yang, Jun-Mo; Song, Kyuyoung; Kimm, Kyuchan; Weir, Bruce; Cardon, Lon R.; Lee, Jong-Eun; Hwang, Jung-Joo

2006-01-01

The International HapMap Project aims to generate detailed human genome variation maps by densely genotyping single-nucleotide polymorphisms (SNPs) in CEPH, Chinese, Japanese, and Yoruba samples. This will undoubtedly become an important facility for genetic studies of diseases and complex traits in the four populations. To address how the genetic information contained in such variation maps is transferable to other populations, the Korean government, industries, and academics have launched the Korean HapMap project to genotype high-density Encyclopedia of DNA Elements (ENCODE) regions in 90 Korean individuals. Here we show that the LD pattern, block structure, haplotype diversity, and recombination rate are highly concordant between Korean and the two HapMap Asian samples, particularly Japanese. The availability of information from both Chinese and Japanese samples helps to predict more accurately the possible performance of HapMap markers in Korean disease-gene studies. Tagging SNPs selected from the two HapMap Asian maps, especially the Japanese map, were shown to be very effective for Korean samples. These results demonstrate that the HapMap variation maps are robust in related populations and will serve as an important resource for the studies of the Korean population in particular. PMID:16702437

Influences of geomorphology and geology on alpine treeline in the American West - More important than climatic influences?

USGS Publications Warehouse

Butler, D.R.; Malanson, G.P.; Walsh, S.J.; Fagre, D.B.

2007-01-01

The spatial distribution and pattern of alpine treeline in the American West reflect the overarching influences of geological history, lithology and structure, and geomorphic processes and landforms, and geologic and geomorphic factors—both forms and processes—can control the spatiotemporal response of the ecotone to climate change. These influences occur at spatial scales ranging from the continental scale to fine scale processes and landforms at the slope scale. Past geomorphic influences, particularly Pleistocene glaciation, have also left their impact on treeline, and treelines across the west are still adjusting to post-Pleistocene conditions within Pleistocene-created landforms. Current fine scale processes include solifluction and changes on relict solifluction and digging by animals. These processes should be examined in detail in future studies to facilitate a better understanding of where individual tree seedlings become established as a primary response of the ecotone to climate change.

Linking complex forest fuel structure and fire behavior at fine scales

Treesearch

EL Loudermilk; Joseph O' Brien; RJ Mitchell; JK Hiers; WP Cropper; S Grunwald; J Grego; J Fernandez

2012-01-01

Improved fire management of savannas and open woodlands requires better understanding of the fundamental connection between fuel heterogeneity, variation in fire behaviour and the influence of fire variation on vegetation feedbacks. In this study, we introduce a novel approach to predicting fire behaviour at the submetre scale, including measurements of forest...

A suture delta: the co-evolution of tectonics and sedimentology as a remnant ocean basin closes; the Indo Burman ranges, northeast India and Bangladesh

NASA Astrophysics Data System (ADS)

Sincavage, R.; Betka, P. M.; Seeber, L.; Steckler, M. S.; Zoramthara, C.

2017-12-01

The closure of an ocean basin involves the interplay of tectonics and sedimentology, whereby thick successions of fluvio-deltaic and shallow marine sediment accumulate in the closing gap between the subduction zone and passive margin. The transition from subduction to collision involves processes that are inherently time-transgressive and co-evolve to influence the nature of the developing tectonic wedge. The Indo-Burman Ranges (IBR) of eastern India present a unique opportunity to examine this scenario on a variety of spatial (10-2­­­-105 m2) and temporal (1 a-10 Ma) scales. Recent field mapping campaigns in the IBR have illuminated analogous depositional environments expressed in the Neogene outcrops of the IBR and the Holocene sediment archive of the Ganges-Brahmaputra-Meghna delta (GBMD). Six distinct lithofacies are present in shallow-marine to fluvial strata of the IBR, containing sedimentary structures that reflect depositional environments correlative with the modern delta. Cyclical alternations of fine sands and silts in packages on the order of 15-20 cm thick define part of the shallow-marine section (M2 facies) that we interpret to represent the foreset beds of the ancient subaqueous delta. The overall scale and sedimentary structures of M2 compare favorably with modern foreset deposits in the Bay of Bengal. Tan-orange medium-grained, well sorted fluvial sandstone that contain large scale (1-10 m) tabular and trough cross bedding represent large-river channel deposits (F2 facies) that overlie the shallow marine strata. F2 deposits bear a striking resemblance in scale and character to bar deposits along the modern Jamuna River. Preliminary grain size analyses on the F2 facies yield grain size distributions that are remarkably consistent with Brahmaputra-sourced mid-Holocene sediments from Sylhet basin within the GBMD. Current research on the GBMD has revealed quantifiable trends in bed thicknesses, downstream fining, and grain size within fluvial deposits. These data will be coupled with ongoing structural and geo- and thermochronology field studies of the IBR that aim to continue to reveal the structural and stratigraphic evolution of this geologically active and densely populated region.

SONEX: NASA SASS Ozone and Nitrogen Oxide Experiment

NASA Technical Reports Server (NTRS)

Newell, Reginald E.; Zhu, Yong; Cho, John; Hu, Yuanlong

1999-01-01

This final report follows closely on our 1998 Annual Progress Report which was forwarded to NASA on November 19, 1998. Rather than reiterate the material therein we note here the continuation of the various items covered. SONEX has proN,Ided a number of opportunities to learn more about the fine-scale structure of the atmosphere. Coupled with the MOZAIC work on layers we can synthesize a new 3-D view of the fine scales that influence atmospheric chemistry. As a side issue we are also relating the features to clear air turbulence which would be, we think, a useful connection for commercial aviation.

About the bears and the bees: Adaptive responses to asymmetric warfare

NASA Astrophysics Data System (ADS)

Ryan, Alex

Conventional military forces are organised to generate large scale effects against similarly structured adversaries. Asymmetric warfare is a 'game' between a conventional military force and a weaker adversary that is unable to match the scale of effects of the conventional force. In asymmetric warfare, an insurgents' strategy can be understood using a multi-scale perspective: by generating and exploiting fine scale complexity, insurgents prevent the conventional force from acting at the scale they are designed for. This paper presents a complex systems approach to the problem of asymmetric warfare, which shows how future force structures can be designed to adapt to environmental complexity at multiple scales and achieve full spectrum dominance.

About the bears and the bees: Adaptive responses to asymmetric warfare

NASA Astrophysics Data System (ADS)

Ryan, Alex

Conventional military forces are organised to generate large scale effects against similarly structured adversaries. Asymmetric warfare is a `game' between a conventional military force and a weaker adversary that is unable to match the scale of effects of the conventional force. In asymmetric warfare, an insurgents' strategy can be understood using a multi-scale perspective: by generating and exploiting fine scale complexity, insurgents prevent the conventional force from acting at the scale they are designed for. This paper presents a complex systems approach to the problem of asymmetric warfare, which shows how future force structures can be designed to adapt to environmental complexity at multiple scales and achieve full spectrum dominance.

Fine-Scale Community Structure Analysis of ANME in Nyegga Sediments with High and Low Methane Flux

PubMed Central

Roalkvam, Irene; Dahle, Håkon; Chen, Yifeng; Jørgensen, Steffen Leth; Haflidason, Haflidi; Steen, Ida Helene

2012-01-01

To obtain knowledge on how regional variations in methane seepage rates influence the stratification, abundance, and diversity of anaerobic methanotrophs (ANME), we analyzed the vertical microbial stratification in a gravity core from a methane micro-seeping area at Nyegga by using 454-pyrosequencing of 16S rRNA gene tagged amplicons and quantitative PCR. These data were compared with previously obtained data from the more active G11 pockmark, characterized by higher methane flux. A down core stratification and high relative abundance of ANME were observed in both cores, with transition from an ANME-2a/b dominated community in low-sulfide and low methane horizons to ANME-1 dominance in horizons near the sulfate-methane transition zone. The stratification was over a wider spatial region and at greater depth in the core with lower methane flux, and the total 16S rRNA copy numbers were two orders of magnitude lower than in the sediments at G11 pockmark. A fine-scale view into the ANME communities at each location was achieved through operational taxonomical units (OTU) clustering of ANME-affiliated sequences. The majority of ANME-1 sequences from both sampling sites clustered within one OTU, while ANME-2a/b sequences were represented in unique OTUs. We suggest that free-living ANME-1 is the most abundant taxon in Nyegga cold seeps, and also the main consumer of methane. The observation of specific ANME-2a/b OTUs at each location could reflect that organisms within this clade are adapted to different geochemical settings, perhaps due to differences in methane affinity. Given that the ANME-2a/b population could be sustained in less active seepage areas, this subgroup could be potential seed populations in newly developed methane-enriched environments. PMID:22715336

Fine line structures of ceramic films formed by patterning of metalorganic precursors using photolithography and ion beams

NASA Astrophysics Data System (ADS)

Hung, L. S.; Zheng, L. R.

1992-05-01

Fine line structures of ceramic thin films were fabricated by patterning of metalorganic precursors using photolithography and ion beams. A trilevel structure was developed with an outer resist layer to transfer patterns, a silver delineated layer as an implantation mask, and a planar resist layer protecting the precursor film from chemical attacking and sputtering. Ion irradiation through the Ag stencil rendered metal carboxylates insoluble in 2-ethylhexanoic acid, permitting patterning of the precursor film with patterning features on micron scales. The potential of this technique was demonstrated in patterning of Bi2Sr2CaCu2O(8+x) and Pb(Zr(0.53)Ti(0.47) thin films.

Disturbance and density-dependent processes (competition and facilitation) influence the fine-scale genetic structure of a tree species' population.

PubMed

Fajardo, Alex; Torres-Díaz, Cristian; Till-Bottraud, Irène

2016-01-01

Disturbances, dispersal and biotic interactions are three major drivers of the spatial distribution of genotypes within populations, the last of which has been less studied than the other two. This study aimed to determine the role of competition and facilitation in the degree of conspecific genetic relatedness of nearby individuals of tree populations. It was expected that competition among conspecifics will lead to low relatedness, while facilitation will lead to high relatedness (selection for high relatedness within clusters). The stand structure and spatial genetic structure (SGS) of trees were examined within old-growth and second-growth forests (including multi-stemmed trees at the edge of forests) of Nothofagus pumilio following large-scale fires in Patagonia, Chile. Genetic spatial autocorrelations were computed on a spatially explicit sampling of the forests using five microsatellite loci. As biotic plant interactions occur among immediate neighbours, mean nearest neighbour distance (MNND) among trees was computed as a threshold for distinguishing the effects of disturbances and biotic interactions. All forests exhibited a significant SGS for distances greater than the MNND. The old-growth forest genetic and stand structure indicated gap recolonization from nearby trees (significantly related trees at distances between 4 and 10 m). At distances smaller than the MNND, trees of the second-growth interior forest showed significantly lower relatedness, suggesting a fading of the recolonization structure by competition, whereas the second-growth edge forest showed a positive and highly significant relatedness among trees (higher among stems of a cluster than among stems of different clusters), resulting from facilitation. Biotic interactions are shown to influence the genetic composition of a tree population. However, facilitation can only persist if individuals are related. Thus, the genetic composition in turn influences what type of biotic interactions will take place among immediate neighbours in post-disturbance forests. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hehemann, Jan -Hendrik; Arevalo, Philip; Datta, Manoshi S.

Adaptive radiations are important drivers of niche filling, since they rapidly adapt a single clade of organisms to ecological opportunities. Although thought to be common for animals and plants, adaptive radiations have remained difficult to document for microbes in the wild. Here we describe a recent adaptive radiation leading to fine-scale ecophysiological differentiation in the degradation of an algal glycan in a clade of closely related marine bacteria. Horizontal gene transfer is the primary driver in the diversification of the pathway leading to several ecophysiologically differentiated Vibrionaceae populations adapted to different physical forms of alginate. Furthermore, pathway architecture is predictivemore » of function and ecology, underscoring that horizontal gene transfer without extensive regulatory changes can rapidly assemble fully functional pathways in microbes.« less

Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes

DOE PAGES

Hehemann, Jan -Hendrik; Arevalo, Philip; Datta, Manoshi S.; ...

2016-09-22

Adaptive radiations are important drivers of niche filling, since they rapidly adapt a single clade of organisms to ecological opportunities. Although thought to be common for animals and plants, adaptive radiations have remained difficult to document for microbes in the wild. Here we describe a recent adaptive radiation leading to fine-scale ecophysiological differentiation in the degradation of an algal glycan in a clade of closely related marine bacteria. Horizontal gene transfer is the primary driver in the diversification of the pathway leading to several ecophysiologically differentiated Vibrionaceae populations adapted to different physical forms of alginate. Furthermore, pathway architecture is predictivemore » of function and ecology, underscoring that horizontal gene transfer without extensive regulatory changes can rapidly assemble fully functional pathways in microbes.« less

Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes

PubMed Central

Hehemann, Jan-Hendrik; Arevalo, Philip; Datta, Manoshi S.; Yu, Xiaoqian; Corzett, Christopher H.; Henschel, Andreas; Preheim, Sarah P.; Timberlake, Sonia; Alm, Eric J.; Polz, Martin F.

2016-01-01

Adaptive radiations are important drivers of niche filling, since they rapidly adapt a single clade of organisms to ecological opportunities. Although thought to be common for animals and plants, adaptive radiations have remained difficult to document for microbes in the wild. Here we describe a recent adaptive radiation leading to fine-scale ecophysiological differentiation in the degradation of an algal glycan in a clade of closely related marine bacteria. Horizontal gene transfer is the primary driver in the diversification of the pathway leading to several ecophysiologically differentiated Vibrionaceae populations adapted to different physical forms of alginate. Pathway architecture is predictive of function and ecology, underscoring that horizontal gene transfer without extensive regulatory changes can rapidly assemble fully functional pathways in microbes. PMID:27653556

Rooting strategies in a subtropical savanna: a landscape-scale three-dimensional assessment.

PubMed

Zhou, Yong; Boutton, Thomas W; Wu, X Ben; Wright, Cynthia L; Dion, Anais L

2018-04-01

In resource-limited savannas, the distribution and abundance of fine roots play an important role in acquiring essential resources and structuring vegetation patterns and dynamics. However, little is known regarding the three-dimensional distribution of fine roots in savanna ecosystems at the landscape scale. We quantified spatial patterns of fine root density to a depth of 1.2 m in a subtropical savanna landscape using spatially specific sampling. Kriged maps revealed that fine root density was highest at the centers of woody patches, decreased towards the canopy edges, and reached lowest values within the grassland matrix throughout the entire soil profile. Lacunarity analyses indicated that spatial heterogeneities of fine root density decreased continuously to a depth of 50 cm and then increased in deeper portions of the soil profile across this landscape. This vertical pattern might be related to inherent differences in root distribution between trees/shrubs and herbaceous species, and the presence/absence of an argillic horizon across this landscape. The greater density of fine roots beneath woody patches in both upper and lower portions of the soil profile suggests an ability to acquire disproportionately more resources than herbaceous species, which may facilitate the development and persistence of woody patches across this landscape.

Spatially disaggregated population estimates in the absence of national population and housing census data

PubMed Central

Wardrop, N. A.; Jochem, W. C.; Bird, T. J.; Chamberlain, H. R.; Clarke, D.; Kerr, D.; Bengtsson, L.; Juran, S.; Seaman, V.; Tatem, A. J.

2018-01-01

Population numbers at local levels are fundamental data for many applications, including the delivery and planning of services, election preparation, and response to disasters. In resource-poor settings, recent and reliable demographic data at subnational scales can often be lacking. National population and housing census data can be outdated, inaccurate, or missing key groups or areas, while registry data are generally lacking or incomplete. Moreover, at local scales accurate boundary data are often limited, and high rates of migration and urban growth make existing data quickly outdated. Here we review past and ongoing work aimed at producing spatially disaggregated local-scale population estimates, and discuss how new technologies are now enabling robust and cost-effective solutions. Recent advances in the availability of detailed satellite imagery, geopositioning tools for field surveys, statistical methods, and computational power are enabling the development and application of approaches that can estimate population distributions at fine spatial scales across entire countries in the absence of census data. We outline the potential of such approaches as well as their limitations, emphasizing the political and operational hurdles for acceptance and sustainable implementation of new approaches, and the continued importance of traditional sources of national statistical data. PMID:29555739

Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population.

PubMed

Aykanat, Tutku; Johnston, Susan E; Orell, Panu; Niemelä, Eero; Erkinaro, Jaakko; Primmer, Craig R

2015-10-01

Despite decades of research assessing the genetic structure of natural populations, the biological meaning of low yet significant genetic divergence often remains unclear due to a lack of associated phenotypic and ecological information. At the same time, structured populations with low genetic divergence and overlapping boundaries can potentially provide excellent models to study adaptation and reproductive isolation in cases where high-resolution genetic markers and relevant phenotypic and life history information are available. Here, we combined single nucleotide polymorphism (SNP)-based population inference with extensive phenotypic and life history data to identify potential biological mechanisms driving fine-scale subpopulation differentiation in Atlantic salmon (Salmo salar) from the Teno River, a major salmon river in Europe. Two sympatrically occurring subpopulations had low but significant genetic differentiation (FST  = 0.018) and displayed marked differences in the distribution of life history strategies, including variation in juvenile growth rate, age at maturity and size within age classes. Large, late-maturing individuals were virtually absent from one of the two subpopulations, and there were significant differences in juvenile growth rates and size at age after oceanic migration between individuals in the respective subpopulations. Our findings suggest that different evolutionary processes affect each subpopulation and that hybridization and subsequent selection may maintain low genetic differentiation without hindering adaptive divergence. © 2015 John Wiley & Sons Ltd.

Longitudinal motor development of "apparently normal" high-risk infants at 18 months, 3 and 5 years.

PubMed

Goyen, Traci Anne; Lui, Kei

2002-12-01

Motor development appears to be more affected by premature birth than other developmental domains, however few studies have specifically investigated the development of gross and fine motor skills in this population. To examine longitudinal motor development in a group of "apparently normal" high-risk infants. Developmental follow-up clinic in a perinatal centre. Longitudinal observational cohort study. Fifty-eight infants born less than 29 weeks gestation and/or 1000 g and without disabilities detected at 12 months. Longitudinal gross and fine motor skills at 18 months, 3 and 5 years using the Peabody Developmental Motor Scales. The HOME scale provided information of the home environment as a stimulus for development. A large proportion (54% at 18 months, 47% at 3 years and 64% at 5 years) of children continued to have fine motor deficits from 18 months to 5 years. The proportion of infants with gross motor deficits significantly increased over this period (14%, 33% and 81%, p<0.001), particularly for the 'micropreemies' (born <750 g). In multivariate analyses, gross motor development was positively influenced by the quality of the home environment. A large proportion of high-risk infants continued to have fine motor deficits, reflecting an underlying problem with fine motor skills. The proportion of infants with gross motor deficits significantly increased, as test demands became more challenging. In addition, the development of gross and fine motor skills appears to be influenced differently by the home environment.

sGD: software for estimating spatially explicit indices of genetic diversity.

PubMed

Shirk, A J; Cushman, S A

2011-09-01

Anthropogenic landscape changes have greatly reduced the population size, range and migration rates of many terrestrial species. The small local effective population size of remnant populations favours loss of genetic diversity leading to reduced fitness and adaptive potential, and thus ultimately greater extinction risk. Accurately quantifying genetic diversity is therefore crucial to assessing the viability of small populations. Diversity indices are typically calculated from the multilocus genotypes of all individuals sampled within discretely defined habitat patches or larger regional extents. Importantly, discrete population approaches do not capture the clinal nature of populations genetically isolated by distance or landscape resistance. Here, we introduce spatial Genetic Diversity (sGD), a new spatially explicit tool to estimate genetic diversity based on grouping individuals into potentially overlapping genetic neighbourhoods that match the population structure, whether discrete or clinal. We compared the estimates and patterns of genetic diversity using patch or regional sampling and sGD on both simulated and empirical populations. When the population did not meet the assumptions of an island model, we found that patch and regional sampling generally overestimated local heterozygosity, inbreeding and allelic diversity. Moreover, sGD revealed fine-scale spatial heterogeneity in genetic diversity that was not evident with patch or regional sampling. These advantages should provide a more robust means to evaluate the potential for genetic factors to influence the viability of clinal populations and guide appropriate conservation plans. © 2011 Blackwell Publishing Ltd.

Computing local edge probability in natural scenes from a population of oriented simple cells

PubMed Central

Ramachandra, Chaithanya A.; Mel, Bartlett W.

2013-01-01

A key computation in visual cortex is the extraction of object contours, where the first stage of processing is commonly attributed to V1 simple cells. The standard model of a simple cell—an oriented linear filter followed by a divisive normalization—fits a wide variety of physiological data, but is a poor performing local edge detector when applied to natural images. The brain's ability to finely discriminate edges from nonedges therefore likely depends on information encoded by local simple cell populations. To gain insight into the corresponding decoding problem, we used Bayes's rule to calculate edge probability at a given location/orientation in an image based on a surrounding filter population. Beginning with a set of ∼ 100 filters, we culled out a subset that were maximally informative about edges, and minimally correlated to allow factorization of the joint on- and off-edge likelihood functions. Key features of our approach include a new, efficient method for ground-truth edge labeling, an emphasis on achieving filter independence, including a focus on filters in the region orthogonal rather than tangential to an edge, and the use of a customized parametric model to represent the individual filter likelihood functions. The resulting population-based edge detector has zero parameters, calculates edge probability based on a sum of surrounding filter influences, is much more sharply tuned than the underlying linear filters, and effectively captures fine-scale edge structure in natural scenes. Our findings predict nonmonotonic interactions between cells in visual cortex, wherein a cell may for certain stimuli excite and for other stimuli inhibit the same neighboring cell, depending on the two cells' relative offsets in position and orientation, and their relative activation levels. PMID:24381295

Relationships among vegetation structure, canopy composition, and avian richness patterns across an aspen-conifer forest gradient

Treesearch

Charles E. Swift; Kerri T. Vierling; Andrew T. Hudak; Lee A. Vierling

2017-01-01

Ecologists have a long-term interest in understanding the relative influence of vegetation composition and vegetation structure on avian diversity. LiDAR remote sensing is useful in studying local patterns of avian diversity because it characterizes fine-scale vegetation structure across broad extents. We used LiDAR, aerial and satellite imagery, and avian field data...

PROPERTIES AND MODELING OF UNRESOLVED FINE STRUCTURE LOOPS OBSERVED IN THE SOLAR TRANSITION REGION BY IRIS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brooks, David H.; Reep, Jeffrey W.; Warren, Harry P.

Recent observations from the Interface Region Imaging Spectrograph ( IRIS ) have discovered a new class of numerous low-lying dynamic loop structures, and it has been argued that they are the long-postulated unresolved fine structures (UFSs) that dominate the emission of the solar transition region. In this letter, we combine IRIS measurements of the properties of a sample of 108 UFSs (intensities, lengths, widths, lifetimes) with one-dimensional non-equilibrium ionization simulations, using the HYDRAD hydrodynamic model to examine whether the UFSs are now truly spatially resolved in the sense of being individual structures rather than being composed of multiple magnetic threads.more » We find that a simulation of an impulsively heated single strand can reproduce most of the observed properties, suggesting that the UFSs may be resolved, and the distribution of UFS widths implies that they are structured on a spatial scale of 133 km on average. Spatial scales of a few hundred kilometers appear to be typical for a range of chromospheric and coronal structures, and we conjecture that this could be an important clue for understanding the coronal heating process.« less

Promiscuity resolves constraints on social mate choice imposed by population viscosity.

PubMed

While, Geoffrey M; Uller, Tobias; Bordogna, Genevieve; Wapstra, Erik

2014-02-01

Population viscosity can have major consequences for adaptive evolution, in particular for phenotypes involved in social interactions. For example, population viscosity increases the probability of mating with close kin, resulting in selection for mechanisms that circumvent the potential negative consequences of inbreeding. Female promiscuity is often suggested to be one such mechanism. However, whether avoidance of genetically similar partners is a major selective force shaping patterns of promiscuity remains poorly supported by empirical data. Here, we show (i) that fine-scale genetic structure constrains social mate choice in a pair-bonding lizard, resulting in individuals pairing with genetically similar individuals, (ii) that these constraints are circumvented by multiple mating with less related individuals and (iii) that this results in increased heterozygosity of offspring. Despite this, we did not detect any significant effects of heterozygosity on offspring or adult fitness or a strong relationship between pair relatedness and female multiple mating. We discuss these results within the context of incorporating the genetic context dependence of mating strategies into a holistic understanding of mating system evolution. © 2013 John Wiley & Sons Ltd.

Habitat associations of sympatric red-tailed hawks and northern goshawks on the Kaibab Plateau

Treesearch

Frank A. La Sorte; R. William Mannan; Richard T. Reynolds; Teryl G. Grubb

2004-01-01

We investigated habitat association of sympatric red-tailed hawks (Buteo jamaicensis) and northern goshawks (Accipiter gentilis) at 2 spatial scales centered on nest sites: (1) fine-scale patterns of forest structure and topography within 16-m radius circles (0.08 ha), and (2) midscale patterns of forested and nonforested areas,...

A Simple Model for Fine Structure Transitions in Alkali-Metal Noble-Gas Collisions

DTIC Science & Technology

2015-03-01

63 33 Effect of Scaling the VRG(R) Radial Coupling Fit Parameter, V0, for KHe, KNe, and KAr...64 ix Figure Page 34 Effect of Scaling the VRG(R) Radial Coupling Fit Parameter, V0, for RbHe, RbNe, and...RbAr . . . . . . . . . . . . . . . . . . . . . . . . . 64 35 Effect of Scaling the VRG(R) Radial Coupling Fit Parameter, V0, for CsHe, CsNe, and CsAr

A matter of scale: apparent niche differentiation of diploid and tetraploid plants may depend on extent and grain of analysis.

PubMed

Kirchheimer, Bernhard; Schinkel, Christoph C F; Dellinger, Agnes S; Klatt, Simone; Moser, Dietmar; Winkler, Manuela; Lenoir, Jonathan; Caccianiga, Marco; Guisan, Antoine; Nieto-Lugilde, Diego; Svenning, Jens-Christian; Thuiller, Wilfried; Vittoz, Pascal; Willner, Wolfgang; Zimmermann, Niklaus E; Hörandl, Elvira; Dullinger, Stefan

2016-03-22

Emerging polyploids may depend on environmental niche shifts for successful establishment. Using the alpine plant Ranunculus kuepferi as a model system, we explore the niche shift hypothesis at different spatial resolutions and in contrasting parts of the species range. European Alps. We sampled 12 individuals from each of 102 populations of R. kuepferi across the Alps, determined their ploidy levels, derived coarse-grain (100 × 100 m) environmental descriptors for all sampling sites by downscaling WorldClim maps, and calculated fine-scale environmental descriptors (2 × 2 m) from indicator values of the vegetation accompanying the sampled individuals. Both coarse and fine-scale variables were further computed for 8239 vegetation plots from across the Alps. Subsequently, we compared niche optima and breadths of diploid and tetraploid cytotypes by combining principal components analysis and kernel smoothing procedures. Comparisons were done separately for coarse and fine-grain data sets and for sympatric, allopatric and the total set of populations. All comparisons indicate that the niches of the two cytotypes differ in optima and/or breadths, but results vary in important details. The whole-range analysis suggests differentiation along the temperature gradient to be most important. However, sympatric comparisons indicate that this climatic shift was not a direct response to competition with diploid ancestors. Moreover, fine-grained analyses demonstrate niche contraction of tetraploids, especially in the sympatric range, that goes undetected with coarse-grained data. Although the niche optima of the two cytotypes differ, separation along ecological gradients was probably less decisive for polyploid establishment than a shift towards facultative apomixis, a particularly effective strategy to avoid minority cytotype exclusion. In addition, our results suggest that coarse-grained analyses overestimate niche breadths of widely distributed taxa. Niche comparison analyses should hence be conducted at environmental data resolutions appropriate for the organism and question under study.

Genome-Wide SNP Discovery, Genotyping and Their Preliminary Applications for Population Genetic Inference in Spotted Sea Bass (Lateolabrax maculatus)

PubMed Central

Wang, Juan; Xue, Dong-Xiu; Zhang, Bai-Dong; Li, Yu-Long; Liu, Bing-Jian; Liu, Jin-Xian

2016-01-01

Next-generation sequencing and the collection of genome-wide single-nucleotide polymorphisms (SNPs) allow identifying fine-scale population genetic structure and genomic regions under selection. The spotted sea bass (Lateolabrax maculatus) is a non-model species of ecological and commercial importance and widely distributed in northwestern Pacific. A total of 22 648 SNPs was discovered across the genome of L. maculatus by paired-end sequencing of restriction-site associated DNA (RAD-PE) for 30 individuals from two populations. The nucleotide diversity (π) for each population was 0.0028±0.0001 in Dandong and 0.0018±0.0001 in Beihai, respectively. Shallow but significant genetic differentiation was detected between the two populations analyzed by using both the whole data set (FST = 0.0550, P < 0.001) and the putatively neutral SNPs (FST = 0.0347, P < 0.001). However, the two populations were highly differentiated based on the putatively adaptive SNPs (FST = 0.6929, P < 0.001). Moreover, a total of 356 SNPs representing 298 unique loci were detected as outliers putatively under divergent selection by FST-based outlier tests as implemented in BAYESCAN and LOSITAN. Functional annotation of the contigs containing putatively adaptive SNPs yielded hits for 22 of 55 (40%) significant BLASTX matches. Candidate genes for local selection constituted a wide array of functions, including binding, catalytic and metabolic activities, etc. The analyses with the SNPs developed in the present study highlighted the importance of genome-wide genetic variation for inference of population structure and local adaptation in L. maculatus. PMID:27336696

Genome-Wide SNP Discovery, Genotyping and Their Preliminary Applications for Population Genetic Inference in Spotted Sea Bass (Lateolabrax maculatus).

PubMed

Wang, Juan; Xue, Dong-Xiu; Zhang, Bai-Dong; Li, Yu-Long; Liu, Bing-Jian; Liu, Jin-Xian

2016-01-01

Next-generation sequencing and the collection of genome-wide single-nucleotide polymorphisms (SNPs) allow identifying fine-scale population genetic structure and genomic regions under selection. The spotted sea bass (Lateolabrax maculatus) is a non-model species of ecological and commercial importance and widely distributed in northwestern Pacific. A total of 22 648 SNPs was discovered across the genome of L. maculatus by paired-end sequencing of restriction-site associated DNA (RAD-PE) for 30 individuals from two populations. The nucleotide diversity (π) for each population was 0.0028±0.0001 in Dandong and 0.0018±0.0001 in Beihai, respectively. Shallow but significant genetic differentiation was detected between the two populations analyzed by using both the whole data set (FST = 0.0550, P < 0.001) and the putatively neutral SNPs (FST = 0.0347, P < 0.001). However, the two populations were highly differentiated based on the putatively adaptive SNPs (FST = 0.6929, P < 0.001). Moreover, a total of 356 SNPs representing 298 unique loci were detected as outliers putatively under divergent selection by FST-based outlier tests as implemented in BAYESCAN and LOSITAN. Functional annotation of the contigs containing putatively adaptive SNPs yielded hits for 22 of 55 (40%) significant BLASTX matches. Candidate genes for local selection constituted a wide array of functions, including binding, catalytic and metabolic activities, etc. The analyses with the SNPs developed in the present study highlighted the importance of genome-wide genetic variation for inference of population structure and local adaptation in L. maculatus.

Water balance and topography predict fire and forest structure patterns

Treesearch

Van R. Kane; James A. Lutz; C. Alina Cansler; Nicholas A. Povak; Derek J. Churchill; Douglas F. Smith; Jonathan T. Kane; Malcolm P. North

2015-01-01

Mountainous topography creates fine-scale environmental mosaics that vary in precipitation, temperature, insolation, and slope position. This mosaic in turn influences fuel accumulation and moisture and forest structure. We studied these the effects of varying environmental conditions across a 27,104 ha landscape within Yosemite National Park, California, USA, on the...

Comparison of human exposure model estimates of PM2.5 exposure variability using fine-scale CMAQ simulations from the Baltimore DISCOVER-AQ evaluation

EPA Science Inventory

Human exposure models estimate population distributions of exposure to air pollutants by combining ambient (outdoor) concentration data with human activity patterns to account for the time people spend in different locations (e.g., outdoors, indoors, in vehicles) and the various ...

Fine-scale analysis of Mount Graham red squirrel habitat following disturbance

Treesearch

David J. A. Wood; Sam Drake; Steve P. Rushton; Doug Rautenkranz; Peter W. W. Lurz; John L. Koprowski

2007-01-01

Habitat destruction and degradation are major factors in reducing abundance, placing populations and species in jeopardy. Monitoring changes to habitat and identifying locations of habitat for a species, after disturbance, can assist mitigation of the effects of humancaused or -amplified habitat disturbance. Like many areas in the western United States, the Pinaleno...

Vortex Filaments in Grids for Scalable, Fine Smoke Simulation.

PubMed

Meng, Zhang; Weixin, Si; Yinling, Qian; Hanqiu, Sun; Jing, Qin; Heng, Pheng-Ann

2015-01-01

Vortex modeling can produce attractive visual effects of dynamic fluids, which are widely applicable for dynamic media, computer games, special effects, and virtual reality systems. However, it is challenging to effectively simulate intensive and fine detailed fluids such as smoke with fast increasing vortex filaments and smoke particles. The authors propose a novel vortex filaments in grids scheme in which the uniform grids dynamically bridge the vortex filaments and smoke particles for scalable, fine smoke simulation with macroscopic vortex structures. Using the vortex model, their approach supports the trade-off between simulation speed and scale of details. After computing the whole velocity, external control can be easily exerted on the embedded grid to guide the vortex-based smoke motion. The experimental results demonstrate the efficiency of using the proposed scheme for a visually plausible smoke simulation with macroscopic vortex structures.

Grey-scale ultrasonography for monitoring industrial exposure to hepatotoxic agents.

PubMed

Taylor, K J; Williams, D M; Smith, P M; Duck, B W

1975-05-31

Industrial exposure to several potentially hepatotoxic agents, such as vinyl-chloride monomer may occur, and there is a need for non-vasive, diagnostic techniques to detect and monitor progressive pathological processes in liver or spleen. Grey-scale ultrasonography permits display of detailed anatomy and pathology in the liver, portal veins, and spleen. The combination of fine resolution, non-invasiveness, absence of ionising radiation hazard, and portable equipment makes the technique ideal for screening populations at risk.

Dynamics of land change in India: a fine-scale spatial analysis

NASA Astrophysics Data System (ADS)

Meiyappan, P.; Roy, P. S.; Sharma, Y.; Jain, A. K.; Ramachandran, R.; Joshi, P. K.

2015-12-01

Land is scarce in India: India occupies 2.4% of worlds land area, but supports over 1/6th of worlds human and livestock population. This high population to land ratio, combined with socioeconomic development and increasing consumption has placed tremendous pressure on India's land resources for food, feed, and fuel. In this talk, we present contemporary (1985 to 2005) spatial estimates of land change in India using national-level analysis of Landsat imageries. Further, we investigate the causes of the spatial patterns of change using two complementary lines of evidence. First, we use statistical models estimated at macro-scale to understand the spatial relationships between land change patterns and their concomitant drivers. This analysis using our newly compiled extensive socioeconomic database at village level (~630,000 units), is 100x higher in spatial resolution compared to existing datasets, and covers over 200 variables. The detailed socioeconomic data enabled the fine-scale spatial analysis with Landsat data. Second, we synthesized information from over 130 survey based case studies on land use drivers in India to complement our macro-scale analysis. The case studies are especially useful to identify unobserved variables (e.g. farmer's attitude towards risk). Ours is the most detailed analysis of contemporary land change in India, both in terms of national extent, and the use of detailed spatial information on land change, socioeconomic factors, and synthesis of case studies.

Fine scale mapping of the structure and composition of the Elkhorn Slough (California, USA) tidal plume

NASA Astrophysics Data System (ADS)

Fischer, Andrew M.; Ryan, John P.; Rienecker, Erich V.

2017-01-01

Fine scale mapping of the structure and composition of a tidal ebb plume from a highly modified coastal lagoon (Elkhorn Slough, California, USA) was conducted by combining in situ, observational data sets from surface underway mapping, autonomous underwater vehicle (AUV) profiles, drifter tracking and the analysis of plume structure indices. The results reveal a 6-m-deep, jet-like, sediment laden plume extending one km offshore at low tide, which becomes entrained in the prevailing nearshore circulation. The plume that exits the slough is significantly different from the water that enters the slough. The rapidly evolving discharge plume is associated with elevated and highly correlated (r = 0.93) concentrations of dissolved organic matter and nitrate. While dissolved constituents remain in the shallow plume and are transported northward with the prevailing current, sediment may settle quickly through the water column and can be transported southwestward with the littoral currents. This study illustrates the applications of AUVs, when coupled with additional datasets, for generating higher resolution observational snapshots of dynamic and ephemeral tidal plumes. The results provide unique perspective on small-scale dynamics of an estuarine plume and its influence on coastal ecology.

Signatures of Penumbral Magnetic Fields at Very High Spatial Resolution

NASA Astrophysics Data System (ADS)

Langhans, K.

2006-12-01

Full Stokes spectro-polarimetry, together with refined techniques to interpret the measurements and continual modeling efforts, have improved our understanding of sunspot penumbrae in the last years. In spite of this progress, an improvement in the spatial resolution of the observations is clearly needed to establish in a more direct way the fine structure of the penumbra. The discovery of dark penumbral cores by tet{l3 Sc02} suggests that we are starting to resolve the fundamental scales of the penumbra. Spectro-polarimetric measurements that are sensitive to the magnetic field in both the photosphere and higher layers, and obtained at a spatial resolution approaching 0.1 arcsec, may therefore allow us to draw firm conclusions about the fine scale organization of penumbral magnetic fields. In this paper I will discuss recent polarization measurements at very high spatial resolution, trying to reconcile the different scenarios put forward to explain the structure of the penumbra.

Cortical feedback signals generalise across different spatial frequencies of feedforward inputs.

PubMed

Revina, Yulia; Petro, Lucy S; Muckli, Lars

2017-09-22

Visual processing in cortex relies on feedback projections contextualising feedforward information flow. Primary visual cortex (V1) has small receptive fields and processes feedforward information at a fine-grained spatial scale, whereas higher visual areas have larger, spatially invariant receptive fields. Therefore, feedback could provide coarse information about the global scene structure or alternatively recover fine-grained structure by targeting small receptive fields in V1. We tested if feedback signals generalise across different spatial frequencies of feedforward inputs, or if they are tuned to the spatial scale of the visual scene. Using a partial occlusion paradigm, functional magnetic resonance imaging (fMRI) and multivoxel pattern analysis (MVPA) we investigated whether feedback to V1 contains coarse or fine-grained information by manipulating the spatial frequency of the scene surround outside an occluded image portion. We show that feedback transmits both coarse and fine-grained information as it carries information about both low (LSF) and high spatial frequencies (HSF). Further, feedback signals containing LSF information are similar to feedback signals containing HSF information, even without a large overlap in spatial frequency bands of the HSF and LSF scenes. Lastly, we found that feedback carries similar information about the spatial frequency band across different scenes. We conclude that cortical feedback signals contain information which generalises across different spatial frequencies of feedforward inputs. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Evaluating the efficacy of a landscape scale feral cat control program using camera traps and occupancy models.

PubMed

Comer, Sarah; Speldewinde, Peter; Tiller, Cameron; Clausen, Lucy; Pinder, Jeff; Cowen, Saul; Algar, Dave

2018-03-28

The impact of introduced predators is a major factor limiting survivorship and recruitment of many native Australian species. In particular, the feral cat and red fox have been implicated in range reductions and population declines of many conservation dependent species across Australia, including ground-nesting birds and small to medium-sized mammals. The impact of predation by feral cats since their introduction some 200 years ago has altered the structure of native fauna communities and led to the development of landscape-scale threat abatement via baiting programs with the feral cat bait, Eradicat. Demonstrating the effectiveness of broad-scale programs is essential for managers to fine tune delivery and timing of baiting. Efficacy of feral cat baiting at the Fortescue Marsh in the Pilbara, Western Australia was tested using camera traps and occupancy models. There was a significant decrease in probability of site occupancy in baited sites in each of the five years of this study, demonstrating both the effectiveness of aerial baiting for landscape-scale removal of feral cats, and the validity of camera trap monitoring techniques for detecting changes in feral cat occupancy during a five-year baiting program.

Increased level of linkage disequilibrium in rural compared with urban communities: a factor to consider in association-study design.

PubMed

Vitart, Veronique; Carothers, Andrew D; Hayward, Caroline; Teague, Peter; Hastie, Nicholas D; Campbell, Harry; Wright, Alan F

2005-05-01

Few studies have investigated genetic differentiation within nonisolate European populations, despite the initiation of large national sample collections such as U.K. Biobank. Here, we used short tandem repeat markers to explore fine-scale genetic structure and to examine the extent of linkage disequilibrium (LD) within national subpopulations. We studied 955 unrelated individuals of local ancestry from nine Scottish rural regions and the urban center of Edinburgh, as well as 96 unrelated individuals from the general U.K. population. Despite little overall differentiation on the basis of allele frequencies, there were clear differences among subpopulations in the extent of pairwise LD, measured between a subset of X-linked markers, that reflected presumed differences in the depths of the underlying genealogies within these subpopulations. Therefore, there are strategic advantages in studying rural subpopulations, in terms of increased power and reduced cost, that are lost by sampling across regions or within urban populations. Similar rural-urban contrasts are likely to exist in many other populations with stable rural subpopulations, which could influence the design of genetic association studies and national biobank data collections.

Novel tetra-nucleotide microsatellite DNA markers for assessing the evolutionary genetics and demographics of Northern Snakehead (Channa argus) invading North America

USGS Publications Warehouse

King, Timothy L.; Johnson, Robin L.

2011-01-01

We document the isolation and characterization of 19 tetra-nucleotide microsatellite DNA markers in northern snakehead (Channa argus) fish that recently colonized Meadow Lake, New York City, New York. These markers displayed moderate levels of allelic diversity (averaging 6.8 alleles/locus) and heterozygosity (averaging 74.2%). Demographic analyses suggested that the Meadow Lake collection has not achieved mutation-drift equilibrium. These results were consistent with instances of deviations from Hardy–Weinberg equilibrium and the presence of some linkage disequilibrium. A comparison of individual pair-wise distances suggested the presence of multiple differentiated groups of related individuals. Results of all analyses are consistent with a pattern of multiple, recent introductions. The microsatellite markers developed for C. argus yielded sufficient genetic diversity to potentially: (1) delineate kinship; (2) elucidate fine-scale population structure; (3) define management (eradication) units; (4) estimate dispersal rates; (5) estimate population sizes; and (6) provide unique demographic perspectives of control or eradication effectiveness.

Relationships between population density, fine-scale genetic structure, mating system and pollen dispersal in a timber tree from African rainforests

PubMed Central

Duminil, J; Daïnou, K; Kaviriri, D K; Gillet, P; Loo, J; Doucet, J-L; Hardy, O J

2016-01-01

Owing to the reduction of population density and/or the environmental changes it induces, selective logging could affect the demography, reproductive biology and evolutionary potential of forest trees. This is particularly relevant in tropical forests where natural population densities can be low and isolated trees may be subject to outcross pollen limitation and/or produce low-quality selfed seeds that exhibit inbreeding depression. Comparing reproductive biology processes and genetic diversity of populations at different densities can provide indirect evidence of the potential impacts of logging. Here, we analysed patterns of genetic diversity, mating system and gene flow in three Central African populations of the self-compatible legume timber species Erythrophleum suaveolens with contrasting densities (0.11, 0.68 and 1.72 adults per ha). The comparison of inbreeding levels among cohorts suggests that selfing is detrimental as inbred individuals are eliminated between seedling and adult stages. Levels of genetic diversity, selfing rates (∼16%) and patterns of spatial genetic structure (Sp ∼0.006) were similar in all three populations. However, the extent of gene dispersal differed markedly among populations: the average distance of pollen dispersal increased with decreasing density (from 200 m in the high-density population to 1000 m in the low-density one). Overall, our results suggest that the reproductive biology and genetic diversity of the species are not affected by current logging practices. However, further investigations need to be conducted in low-density populations to evaluate (1) whether pollen limitation may reduce seed production and (2) the regeneration potential of the species. PMID:26696137

STarlight Absorption Reduction through a Survey of Multiple Occulting Galaxies (STARSMOG)

NASA Astrophysics Data System (ADS)

Holwerda, Benne

2014-10-01

Dust absorption remains the poorest constrained parameter in both Cosmological distances and multi-wavelength studies of galaxy populations. A galaxy's dust distribution can be measured to great accuracy in the case of an overlapping pair of galaxies, i.e., when a foreground spiral galaxy accidentally overlaps a more distant, preferably elliptical galaxy. We have identified over 300 bona-fide overlapping pairs --well separated in redshift but close on the sky-- in the GAMA spectroscopic survey, taking advantage of its high completeness (98%) on small scales. We propose to map the fine-scale (~50pc) dust structure in these occulting galaxies, using HST/WFC3 SNAP observations. The resulting dust maps will (1) serve as an extinction probability for supernova lightcurve fits in similar type host galaxies, (2) strongly constrain the role of ISM structure in Spectral Energy Distribution models of spiral galaxies, and (3) map the level of ISM turbulence (through the spatial power-spectrum). We ask for SNAP observations with a parent list of 355 targets to ensure a complete and comprehensive coverage of each foreground galaxy mass, radius and inclination. The resulting extinction maps will serve as a library for SNIa measurements, galaxy SED modelling and ISM turbulence measurements.

Size-dependent characteristics of ultra-fine oxygen-enriched nanoparticles in austenitic steels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miao, Yinbin; Mo, Kun; Zhou, Zhangjian

2016-11-01

Here, a coordinated investigation of the elemental composition and morphology of ultra-fine-scale nanoparticles as a function of size within a variety of austenitic oxide dispersion-strengthened (ODS) steels is reported. Atom probe tomography was utilized to evaluate the elemental composition of these nanoparticles. Meanwhile, the crystal structures and orientation relationships were determined by high resolution transmission electron microscopy. The nanoparticles with sufficient size (>4 nm) to maintain a Y2Ti2-xO7-2x stoichiometry were found to have a pyrochlore structure, whereas smaller YxTiyOz nanoparticles lacked a well-defined structure. The size-dependent characteristics of the nanoparticles in austenitic ODS steels differ from those in ferritic/martensitic ODSmore » steels.« less

Reconstruction of vessel structures from serial whole slide sections of murine liver samples

NASA Astrophysics Data System (ADS)

Schwier, Michael; Hahn, Horst K.; Dahmen, Uta; Dirsch, Olaf

2013-03-01

Image-based analysis of the vascular structures of murine liver samples is an important tool for scientists to understand liver physiology and morphology. Typical assessment methods are MicroCT, which allows for acquiring images of the whole organ while lacking resolution for fine details, and confocal laser scanning microscopy, which allows detailed insights into fine structures while lacking the broader context. Imaging of histological serial whole slide sections is a recent technology able to fill this gap, since it provides a fine resolution up to the cellular level, but on a whole organ scale. However, whole slide imaging is a modality providing only 2D images. Therefore the challenge is to use stacks of serial sections from which to reconstruct the 3D vessel structures. In this paper we present a semi-automatic procedure to achieve this goal. We employ an automatic method that detects vessel structures based on continuity and shape characteristics. Furthermore it supports the user to perform manual corrections where required. With our methods we were able to successfully extract and reconstruct vessel structures from a stack of 100 and a stack of 397 serial sections of a mouse liver lobe, thus proving the potential of our approach.

Solar Cycle Fine Structure and Surface Rotation from Ca II K-Line Time Series Data

NASA Technical Reports Server (NTRS)

Scargle, Jeff; Keil, Steve; Worden, Pete

2011-01-01

Analysis of three and a half decades of data from the NSO/AFRL/Sac Peak K-line monitoring program yields evidence for four components to the variation: (a) the solar cycle, with considerable fine structure and a quasi-periodicity of 122.4 days; (b) a stochastic process, faster than (a) and largely independent of it, (c) a quasi-periodic signal due to rotational modulation, and of course (d) observational errors (shown to be quite small). Correlation and power spectrum analyses elucidate periodic and aperiodic variation of these chromospheric parameters. Time-frequency analysis is especially useful for extracting information about differential rotation, and in particular elucidates the connection between its behavior and fine structure of the solar cycle on approximately one-year time scales. These results further suggest that similar analyses will be useful at detecting and characterizing differential rotation in stars from stellar light-curves such as those being produced at NASA's Kepler observatory.

Identification of fine scale and landscape scale drivers of urban aboveground carbon stocks using high-resolution modeling and mapping.

PubMed

Mitchell, Matthew G E; Johansen, Kasper; Maron, Martine; McAlpine, Clive A; Wu, Dan; Rhodes, Jonathan R

2018-05-01

Urban areas are sources of land use change and CO 2 emissions that contribute to global climate change. Despite this, assessments of urban vegetation carbon stocks often fail to identify important landscape-scale drivers of variation in urban carbon, especially the potential effects of landscape structure variables at different spatial scales. We combined field measurements with Light Detection And Ranging (LiDAR) data to build high-resolution models of woody plant aboveground carbon across the urban portion of Brisbane, Australia, and then identified landscape scale drivers of these carbon stocks. First, we used LiDAR data to quantify the extent and vertical structure of vegetation across the city at high resolution (5×5m). Next, we paired this data with aboveground carbon measurements at 219 sites to create boosted regression tree models and map aboveground carbon across the city. We then used these maps to determine how spatial variation in land cover/land use and landscape structure affects these carbon stocks. Foliage densities above 5m height, tree canopy height, and the presence of ground openings had the strongest relationships with aboveground carbon. Using these fine-scale relationships, we estimate that 2.2±0.4 TgC are stored aboveground in the urban portion of Brisbane, with mean densities of 32.6±5.8MgCha -1 calculated across the entire urban land area, and 110.9±19.7MgCha -1 calculated within treed areas. Predicted carbon densities within treed areas showed strong positive relationships with the proportion of surrounding tree cover and how clumped that tree cover was at both 1km 2 and 1ha resolutions. Our models predict that even dense urban areas with low tree cover can have high carbon densities at fine scales. We conclude that actions and policies aimed at increasing urban carbon should focus on those areas where urban tree cover is most fragmented. Copyright © 2017 Elsevier B.V. All rights reserved.

Strong trans-Pacific break and local conservation units in the Galapagos shark (Carcharhinus galapagensis) revealed by genome-wide cytonuclear markers.

PubMed

Pazmiño, Diana A; Maes, Gregory E; Green, Madeline E; Simpfendorfer, Colin A; Hoyos-Padilla, E Mauricio; Duffy, Clinton J A; Meyer, Carl G; Kerwath, Sven E; Salinas-de-León, Pelayo; van Herwerden, Lynne

2018-05-01

The application of genome-wide cytonuclear molecular data to identify management and adaptive units at various spatio-temporal levels is particularly important for overharvested large predatory organisms, often characterized by smaller, localized populations. Despite being "near threatened", current understanding of habitat use and population structure of Carcharhinus galapagensis is limited to specific areas within its distribution. We evaluated population structure and connectivity across the Pacific Ocean using genome-wide single-nucleotide polymorphisms (~7200 SNPs) and mitochondrial control region sequences (945 bp) for 229 individuals. Neutral SNPs defined at least two genetically discrete geographic groups: an East Tropical Pacific (Mexico, east and west Galapagos Islands), and another central-west Pacific (Lord Howe Island, Middleton Reef, Norfolk Island, Elizabeth Reef, Kermadec, Hawaii and Southern Africa). More fine-grade population structure was suggested using outlier SNPs: west Pacific, Hawaii, Mexico, and Galapagos. Consistently, mtDNA pairwise Φ ST defined three regional stocks: east, central and west Pacific. Compared to neutral SNPs (F ST  = 0.023-0.035), mtDNA exhibited more divergence (Φ ST  = 0.258-0.539) and high overall genetic diversity (h = 0.794 ± 0.014; π = 0.004 ± 0.000), consistent with the longstanding eastern Pacific barrier between the east and central-west Pacific. Hawaiian and Southern African populations group within the west Pacific cluster. Effective population sizes were moderate/high for east/west populations (738 and 3421, respectively). Insights into the biology, connectivity, genetic diversity, and population demographics informs for improved conservation of this species, by delineating three to four conservation units across their Pacific distribution. Implementing such conservation management may be challenging, but is necessary to achieve long-term population resilience at basin and regional scales.

Improving predictions of large scale soil carbon dynamics: Integration of fine-scale hydrological and biogeochemical processes, scaling, and benchmarking

NASA Astrophysics Data System (ADS)

Riley, W. J.; Dwivedi, D.; Ghimire, B.; Hoffman, F. M.; Pau, G. S. H.; Randerson, J. T.; Shen, C.; Tang, J.; Zhu, Q.

2015-12-01

Numerical model representations of decadal- to centennial-scale soil-carbon dynamics are a dominant cause of uncertainty in climate change predictions. Recent attempts by some Earth System Model (ESM) teams to integrate previously unrepresented soil processes (e.g., explicit microbial processes, abiotic interactions with mineral surfaces, vertical transport), poor performance of many ESM land models against large-scale and experimental manipulation observations, and complexities associated with spatial heterogeneity highlight the nascent nature of our community's ability to accurately predict future soil carbon dynamics. I will present recent work from our group to develop a modeling framework to integrate pore-, column-, watershed-, and global-scale soil process representations into an ESM (ACME), and apply the International Land Model Benchmarking (ILAMB) package for evaluation. At the column scale and across a wide range of sites, observed depth-resolved carbon stocks and their 14C derived turnover times can be explained by a model with explicit representation of two microbial populations, a simple representation of mineralogy, and vertical transport. Integrating soil and plant dynamics requires a 'process-scaling' approach, since all aspects of the multi-nutrient system cannot be explicitly resolved at ESM scales. I will show that one approach, the Equilibrium Chemistry Approximation, improves predictions of forest nitrogen and phosphorus experimental manipulations and leads to very different global soil carbon predictions. Translating model representations from the site- to ESM-scale requires a spatial scaling approach that either explicitly resolves the relevant processes, or more practically, accounts for fine-resolution dynamics at coarser scales. To that end, I will present recent watershed-scale modeling work that applies reduced order model methods to accurately scale fine-resolution soil carbon dynamics to coarse-resolution simulations. Finally, we contend that creating believable soil carbon predictions requires a robust, transparent, and community-available benchmarking framework. I will present an ILAMB evaluation of several of the above-mentioned approaches in ACME, and attempt to motivate community adoption of this evaluation approach.

Dendrites are dispensable for basic motoneuron function but essential for fine tuning of behavior.

PubMed

Ryglewski, Stefanie; Kadas, Dimitrios; Hutchinson, Katie; Schuetzler, Natalie; Vonhoff, Fernando; Duch, Carsten

2014-12-16

Dendrites are highly complex 3D structures that define neuronal morphology and connectivity and are the predominant sites for synaptic input. Defects in dendritic structure are highly consistent correlates of brain diseases. However, the precise consequences of dendritic structure defects for neuronal function and behavioral performance remain unknown. Here we probe dendritic function by using genetic tools to selectively abolish dendrites in identified Drosophila wing motoneurons without affecting other neuronal properties. We find that these motoneuron dendrites are unexpectedly dispensable for synaptic targeting, qualitatively normal neuronal activity patterns during behavior, and basic behavioral performance. However, significant performance deficits in sophisticated motor behaviors, such as flight altitude control and switching between discrete courtship song elements, scale with the degree of dendritic defect. To our knowledge, our observations provide the first direct evidence that complex dendrite architecture is critically required for fine-tuning and adaptability within robust, evolutionarily constrained behavioral programs that are vital for mating success and survival. We speculate that the observed scaling of performance deficits with the degree of structural defect is consistent with gradual increases in intellectual disability during continuously advancing structural deficiencies in progressive neurological disorders.

A Genome-Wide Analysis of Populations from European Russia Reveals a New Pole of Genetic Diversity in Northern Europe

PubMed Central

Khrunin, Andrey V.; Khokhrin, Denis V.; Filippova, Irina N.; Esko, Tõnu; Nelis, Mari; Bebyakova, Natalia A.; Bolotova, Natalia L.; Klovins, Janis; Nikitina-Zake, Liene; Rehnström, Karola; Ripatti, Samuli; Schreiber, Stefan; Franke, Andre; Macek, Milan; Krulišová, Veronika; Lubinski, Jan; Metspalu, Andres; Limborska, Svetlana A.

2013-01-01

Several studies examined the fine-scale structure of human genetic variation in Europe. However, the European sets analyzed represent mainly northern, western, central, and southern Europe. Here, we report an analysis of approximately 166,000 single nucleotide polymorphisms in populations from eastern (northeastern) Europe: four Russian populations from European Russia, and three populations from the northernmost Finno-Ugric ethnicities (Veps and two contrast groups of Komi people). These were compared with several reference European samples, including Finns, Estonians, Latvians, Poles, Czechs, Germans, and Italians. The results obtained demonstrated genetic heterogeneity of populations living in the region studied. Russians from the central part of European Russia (Tver, Murom, and Kursk) exhibited similarities with populations from central–eastern Europe, and were distant from Russian sample from the northern Russia (Mezen district, Archangelsk region). Komi samples, especially Izhemski Komi, were significantly different from all other populations studied. These can be considered as a second pole of genetic diversity in northern Europe (in addition to the pole, occupied by Finns), as they had a distinct ancestry component. Russians from Mezen and the Finnic-speaking Veps were positioned between the two poles, but differed from each other in the proportions of Komi and Finnic ancestries. In general, our data provides a more complete genetic map of Europe accounting for the diversity in its most eastern (northeastern) populations. PMID:23505534

Seeking Signs of Life Preserved in Martian Silica

NASA Astrophysics Data System (ADS)

Ruff, S. W.; Farmer, J. D.; Van Kranendonk, M. J.; Campbell, K. A.; Djokic, T.; Damer, B.; Deamer, D. W.

2018-04-01

Hot spring nodular silica deposits on Earth, which resemble those discovered with the Spirit rover, preserve concentrated organics and fine-scale structures that could be searched for on Mars with the Mars 2020 rover and in returned samples.

Ground Layer Plant Species Turnover and Beta Diversity in Southern-European Old-Growth Forests

PubMed Central

Sabatini, Francesco Maria; Burrascano, Sabina; Tuomisto, Hanna; Blasi, Carlo

2014-01-01

Different assembly processes may simultaneously affect local-scale variation of species composition in temperate old-growth forests. Ground layer species diversity reflects chance colonization and persistence of low-dispersal species, as well as fine-scale environmental heterogeneity. The latter depends on both purely abiotic factors, such as soil properties and topography, and factors primarily determined by overstorey structure, such as light availability. Understanding the degree to which plant diversity in old-growth forests is associated with structural heterogeneity and/or to dispersal limitation will help assessing the effectiveness of silvicultural practices that recreate old-growth patterns and structures for the conservation or restoration of plant diversity. We used a nested sampling design to assess fine-scale species turnover, i.e. the proportion of species composition that changes among sampling units, across 11 beech-dominated old-growth forests in Southern Europe. For each stand, we also measured a wide range of environmental and structural variables that might explain ground layer species turnover. Our aim was to quantify the relative importance of dispersal limitation in comparison to that of stand structural heterogeneity while controlling for other sources of environmental heterogeneity. For this purpose, we used multiple regression on distance matrices at the within-stand extent, and mixed effect models at the extent of the whole dataset. Species turnover was best predicted by structural and environmental heterogeneity, especially by differences in light availability and in topsoil nutrient concentration and texture. Spatial distances were significant only in four out of eleven stands with a relatively low explanatory power. This suggests that structural heterogeneity is a more important driver of local-scale ground layer species turnover than dispersal limitation in southern European old-growth beech forests. PMID:24748155

Fine-scale genetic structure and social organization in female white-tailed deer

Treesearch

Christopher E. Comer; John C. Kilgo; Gino J. D' Angelo; Travis C. Glenn; Karl V. Miller

2005-01-01

Social behavior of white-tailed deer (Odocoileus virginianus) can have important management implications. The formation of matrilineal social groups among female deer has been documented and management strategies have been proposed based on this well-developed social structure. Using radiocollared (n = 17) and hunter or vehicle-killed (n = 21) does, we examined spatial...

Exploring fine-scale variability of stratospheric wind above the tropical la reunion island using rayleigh-mie doppler lidar

NASA Astrophysics Data System (ADS)

Khaykin, S. M.; Hauchecorne, A.; Cammas, J.-P.; Marqestaut, N.; Mariscal, J.-F.; Posny, F.; Payen, G.; Porteneuve, J.; Keckhut, P.

2018-04-01

A unique Rayleigh-Mie Doppler lidar capable of wind measurements in the 5-50 km altitude range is operated routinely at La Reunion island (21° S, 55° E) since 2015. We evaluate instrument's capacities in capturing fine structures in stratospheric wind profiles and their temporal and spatial variability through comparison with collocated radiosoundings and ECMWF analysis. Perturbations in the wind velocity are used to retrieve gravity wave frequency spectrum.

Rapid solidification of levitation melted Ni-Sn alloy droplets with high undercooling

NASA Technical Reports Server (NTRS)

Shiohara, Yuh; Flemings, Merton C.; Wu, Yanzhong; Piccone, Thomas J.

1985-01-01

Experimental results obtained by high-speed optical temperature sensing for the rapid solidification of highly undercooled, levitation-melted Ni-Sn alloy droplets are presented. These data suggest a solidification model proceeding according to overlapping steps: (1) dendritic growth within the bulk undercooled melt, (2) continued recalescence as supersaturation of the interdendritic liquid dissipates, (3) fine-scale remelting within the dendrites, (4) ripening of the fine structure, and (5) solidification of remaining liquid at the end of recalescence.

Urban Evolutionary Ecology and the Potential Benefits of Implementing Genomics.

PubMed

Schell, Christopher J

2018-02-14

Urban habitats are quickly becoming exceptional models to address adaptation under rapid environmental change, given the expansive temporal and spatial scales with which anthropogenic landscape conversion occurs. Urban ecologists in the last 10-15 years have done an extraordinary job of highlighting phenotypic patterns that correspond with urban living, as well as delineating urban population structure using traditional genetic markers. The underpinning genetic mechanisms that govern those phenotypic patterns, however, are less well established. Moreover, the power of traditional molecular studies is constrained by the number of markers being evaluated, which limits the potential to assess fine-scale population structure potentially common in urban areas. With the recent proliferation of low-cost, high-throughput sequencing methods, we can begin to address an emerging question in urban ecology: are species adapted to local optima within cities or are they expressing latent phenotypic plasticity? Here, I provide a comprehensive review of previous urban ecological studies, with special focus on the molecular ecology and phenotypic adjustments documented in urban terrestrial and amphibious fauna. I subsequently pinpoint areas in the literature that could benefit from a genomic investigation and briefly discuss the suitability of specific techniques in addressing eco-evolutionary questions within urban ecology. Though many challenges exist with implementing genomics into urban ecology, such studies provide an exceptional opportunity to advance our understanding of eco-evolutionary processes in metropolitan areas. © The American Genetic Association 2018. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Western Lake Erie Basin: Soft-data-constrained, NHDPlus resolution watershed modeling and exploration of applicable conservation scenarios.

PubMed

Yen, Haw; White, Michael J; Arnold, Jeffrey G; Keitzer, S Conor; Johnson, Mari-Vaughn V; Atwood, Jay D; Daggupati, Prasad; Herbert, Matthew E; Sowa, Scott P; Ludsin, Stuart A; Robertson, Dale M; Srinivasan, Raghavan; Rewa, Charles A

2016-11-01

Complex watershed simulation models are powerful tools that can help scientists and policy-makers address challenging topics, such as land use management and water security. In the Western Lake Erie Basin (WLEB), complex hydrological models have been applied at various scales to help describe relationships between land use and water, nutrient, and sediment dynamics. This manuscript evaluated the capacity of the current Soil and Water Assessment Tool (SWAT) to predict hydrological and water quality processes within WLEB at the finest resolution watershed boundary unit (NHDPlus) along with the current conditions and conservation scenarios. The process based SWAT model was capable of the fine-scale computation and complex routing used in this project, as indicated by measured data at five gaging stations. The level of detail required for fine-scale spatial simulation made the use of both hard and soft data necessary in model calibration, alongside other model adaptations. Limitations to the model's predictive capacity were due to a paucity of data in the region at the NHDPlus scale rather than due to SWAT functionality. Results of treatment scenarios demonstrate variable effects of structural practices and nutrient management on sediment and nutrient loss dynamics. Targeting treatment to acres with critical outstanding conservation needs provides the largest return on investment in terms of nutrient loss reduction per dollar spent, relative to treating acres with lower inherent nutrient loss vulnerabilities. Importantly, this research raises considerations about use of models to guide land management decisions at very fine spatial scales. Decision makers using these results should be aware of data limitations that hinder fine-scale model interpretation. Copyright © 2016 Elsevier B.V. All rights reserved.

Western Lake Erie Basin: Soft-data-constrained, NHDPlus resolution watershed modeling and exploration of applicable conservation scenarios

USGS Publications Warehouse

Yen, Haw; White, Michael J.; Arnold, Jeffrey G.; Keitzer, S. Conor; Johnson, Mari-Vaughn V; Atwood, Jay D.; Daggupati, Prasad; Herbert, Matthew E.; Sowa, Scott P.; Ludsin, Stuart A.; Robertson, Dale M.; Srinivasan, Raghavan; Rewa, Charles A.

2016-01-01

Complex watershed simulation models are powerful tools that can help scientists and policy-makers address challenging topics, such as land use management and water security. In the Western Lake Erie Basin (WLEB), complex hydrological models have been applied at various scales to help describe relationships between land use and water, nutrient, and sediment dynamics. This manuscript evaluated the capacity of the current Soil and Water Assessment Tool (SWAT2012) to predict hydrological and water quality processes within WLEB at the finest resolution watershed boundary unit (NHDPlus) along with the current conditions and conservation scenarios. The process based SWAT model was capable of the fine-scale computation and complex routing used in this project, as indicated by measured data at five gaging stations. The level of detail required for fine-scale spatial simulation made the use of both hard and soft data necessary in model calibration, alongside other model adaptations. Limitations to the model's predictive capacity were due to a paucity of data in the region at the NHDPlus scale rather than due to SWAT functionality. Results of treatment scenarios demonstrate variable effects of structural practices and nutrient management on sediment and nutrient loss dynamics. Targeting treatment to acres with critical outstanding conservation needs provides the largest return on investment in terms of nutrient loss reduction per dollar spent, relative to treating acres with lower inherent nutrient loss vulnerabilities. Importantly, this research raises considerations about use of models to guide land management decisions at very fine spatial scales. Decision makers using these results should be aware of data limitations that hinder fine-scale model interpretation.

The 8p23 inversion polymorphism determines local recombination heterogeneity across human populations.

PubMed

Alves, Joao M; Chikhi, Lounès; Amorim, António; Lopes, Alexandra M

2014-04-01

For decades, chromosomal inversions have been regarded as fascinating evolutionary elements as they are expected to suppress recombination between chromosomes with opposite orientations, leading to the accumulation of genetic differences between the two configurations over time. Here, making use of publicly available population genotype data for the largest polymorphic inversion in the human genome (8p23-inv), we assessed whether this inhibitory effect of inversion rearrangements led to significant differences in the recombination landscape of two homologous DNA segments, with opposite orientation. Our analysis revealed that the accumulation of genetic differentiation is positively correlated with the variation in recombination profiles. The observed recombination dissimilarity between inversion types is consistent across all populations analyzed and surpasses the effects of geographic structure, suggesting that both structures (orientations) have been evolving independently over an extended period of time, despite being subjected to the very same demographic history. Aside this mainly independent evolution, we also identified a short segment (350 kb, <10% of the whole inversion) in the central region of the inversion where the genetic divergence between the two structural haplotypes is diminished. Although it is difficult to demonstrate it, this could be due to gene flow (possibly via double-crossing over events), which is consistent with the higher recombination rates surrounding this segment. This study demonstrates for the first time that chromosomal inversions influence the recombination landscape at a fine-scale and highlights the role of these rearrangements as drivers of genome evolution.

Multi-scale interactions between local hydrography, seabed topography, and community assembly on cold-water coral reefs

NASA Astrophysics Data System (ADS)

Henry, L.-A.; Moreno Navas, J.; Roberts, J. M.

2013-04-01

We investigated how interactions between hydrography, topography and species ecology influence the assembly of species and functional traits across multiple spatial scales of a cold-water coral reef seascape. In a novel approach for these ecosystems, we used a spatially resolved complex three-dimensional flow model of hydrography to help explain assembly patterns. Forward-selection of distance-based Moran's eigenvector mapping (dbMEM) variables identified two submodels of spatial scales at which communities change: broad-scale (across reef) and fine-scale (within reef). Variance partitioning identified bathymetric and hydrographic gradients important in creating broad-scale assembly of species and traits. In contrast, fine-scale assembly was related more to processes that created spatially autocorrelated patches of fauna, such as philopatric recruitment in sessile fauna, and social interactions and food supply in scavenging detritivores and mobile predators. Our study shows how habitat modification of reef connectivity and hydrography by bottom fishing and renewable energy installations could alter the structure and function of an entire cold-water coral reef seascape.

An agent-based model of tsetse fly response to seasonal climatic drivers: Assessing the impact on sleeping sickness transmission rates.

PubMed

Alderton, Simon; Macleod, Ewan T; Anderson, Neil E; Palmer, Gwen; Machila, Noreen; Simuunza, Martin; Welburn, Susan C; Atkinson, Peter M

2018-02-01

This paper presents the development of an agent-based model (ABM) to incorporate climatic drivers which affect tsetse fly (G. m. morsitans) population dynamics, and ultimately disease transmission. The model was used to gain a greater understanding of how tsetse populations fluctuate seasonally, and investigate any response observed in Trypanosoma brucei rhodesiense human African trypanosomiasis (rHAT) disease transmission, with a view to gaining a greater understanding of disease dynamics. Such an understanding is essential for the development of appropriate, well-targeted mitigation strategies in the future. The ABM was developed to model rHAT incidence at a fine spatial scale along a 75 km transect in the Luangwa Valley, Zambia. The model incorporates climatic factors that affect pupal mortality, pupal development, birth rate, and death rate. In combination with fine scale demographic data such as ethnicity, age and gender for the human population in the region, as well as an animal census and a sample of daily routines, we create a detailed, plausible simulation model to explore tsetse population and disease transmission dynamics. The seasonally-driven model suggests that the number of infections reported annually in the simulation is likely to be a reasonable representation of reality, taking into account the high levels of under-detection observed. Similar infection rates were observed in human (0.355 per 1000 person-years (SE = 0.013)), and cattle (0.281 per 1000 cattle-years (SE = 0.025)) populations, likely due to the sparsity of cattle close to the tsetse interface. The model suggests that immigrant tribes and school children are at greatest risk of infection, a result that derives from the bottom-up nature of the ABM and conditioning on multiple constraints. This result could not be inferred using alternative population-level modelling approaches. In producing a model which models the tsetse population at a very fine resolution, we were able to analyse and evaluate specific elements of the output, such as pupal development and the progression of the teneral population, allowing the development of our understanding of the tsetse population as a whole. This is an important step in the production of a more accurate transmission model for rHAT which can, in turn, help us to gain a greater understanding of the transmission system as a whole.

Associations and dynamics of Vibrionaceae in the environment, from the genus to the population level

PubMed Central

Takemura, Alison F.; Chien, Diana M.; Polz, Martin F.

2013-01-01

The Vibrionaceae, which encompasses several potential pathogens, including V. cholerae, the causative agent of cholera, and V. vulnificus, the deadliest seafood-borne pathogen, are a well-studied family of marine bacteria that thrive in diverse habitats. To elucidate the environmental conditions under which vibrios proliferate, numerous studies have examined correlations with bulk environmental variables—e.g., temperature, salinity, nitrogen, and phosphate—and association with potential host organisms. However, how meaningful these environmental associations are remains unclear because data are fragmented across studies with variable sampling and analysis methods. Here, we synthesize findings about Vibrio correlations and physical associations using a framework of increasingly fine environmental and taxonomic scales, to better understand their dynamics in the wild. We first conduct a meta-analysis to determine trends with respect to bulk water environmental variables, and find that while temperature and salinity are generally strongly predictive correlates, other parameters are inconsistent and overall patterns depend on taxonomic resolution. Based on the hypothesis that dynamics may better correlate with more narrowly defined niches, we review evidence for specific association with plants, algae, zooplankton, and animals. We find that Vibrio are attached to many organisms, though evidence for enrichment compared to the water column is often lacking. Additionally, contrary to the notion that they flourish predominantly while attached, Vibrio can have, at least temporarily, a free-living lifestyle and even engage in massive blooms. Fine-scale sampling from the water column has enabled identification of such lifestyle preferences for ecologically cohesive populations, and future efforts will benefit from similar analysis at fine genetic and environmental sampling scales to describe the conditions, habitats, and resources shaping Vibrio dynamics. PMID:24575082

Unresolved fine-scale structure in solar coronal loop-tops

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scullion, E.; Van der Voort, L. Rouppe; Wedemeyer, S.

2014-12-10

New and advanced space-based observing facilities continue to lower the resolution limit and detect solar coronal loops in greater detail. We continue to discover even finer substructures within coronal loop cross-sections, in order to understand the nature of the solar corona. Here, we push this lower limit further to search for the finest coronal loop substructures, through taking advantage of the resolving power of the Swedish 1 m Solar Telescope/CRisp Imaging Spectro-Polarimeter (CRISP), together with co-observations from the Solar Dynamics Observatory/Atmospheric Image Assembly (AIA). High-resolution imaging of the chromospheric Hα 656.28 nm spectral line core and wings can, under certainmore » circumstances, allow one to deduce the topology of the local magnetic environment of the solar atmosphere where its observed. Here, we study post-flare coronal loops, which become filled with evaporated chromosphere that rapidly condenses into chromospheric clumps of plasma (detectable in Hα) known as a coronal rain, to investigate their fine-scale structure. We identify, through analysis of three data sets, large-scale catastrophic cooling in coronal loop-tops and the existence of multi-thermal, multi-stranded substructures. Many cool strands even extend fully intact from loop-top to footpoint. We discover that coronal loop fine-scale strands can appear bunched with as many as eight parallel strands within an AIA coronal loop cross-section. The strand number density versus cross-sectional width distribution, as detected by CRISP within AIA-defined coronal loops, most likely peaks at well below 100 km, and currently, 69% of the substructure strands are statistically unresolved in AIA coronal loops.« less

Spatially disaggregated population estimates in the absence of national population and housing census data.

PubMed

Wardrop, N A; Jochem, W C; Bird, T J; Chamberlain, H R; Clarke, D; Kerr, D; Bengtsson, L; Juran, S; Seaman, V; Tatem, A J

2018-04-03

Population numbers at local levels are fundamental data for many applications, including the delivery and planning of services, election preparation, and response to disasters. In resource-poor settings, recent and reliable demographic data at subnational scales can often be lacking. National population and housing census data can be outdated, inaccurate, or missing key groups or areas, while registry data are generally lacking or incomplete. Moreover, at local scales accurate boundary data are often limited, and high rates of migration and urban growth make existing data quickly outdated. Here we review past and ongoing work aimed at producing spatially disaggregated local-scale population estimates, and discuss how new technologies are now enabling robust and cost-effective solutions. Recent advances in the availability of detailed satellite imagery, geopositioning tools for field surveys, statistical methods, and computational power are enabling the development and application of approaches that can estimate population distributions at fine spatial scales across entire countries in the absence of census data. We outline the potential of such approaches as well as their limitations, emphasizing the political and operational hurdles for acceptance and sustainable implementation of new approaches, and the continued importance of traditional sources of national statistical data. Copyright © 2018 the Author(s). Published by PNAS.

Atomic data and line intensities for the S V ion

NASA Astrophysics Data System (ADS)

Iorga, C.; Stancalie, V.

2017-05-01

The energy levels, oscillator strengths, spontaneous radiative decay rates, lifetimes and electron impact collision strengths have been obtained for the [ Ne ] 3s nl, [ Ne ] 3p nl, [ Ne ] 3d nl configurations belonging to S V ion, with n ≤ 7 and l ≤ 4, resulting in 567 fine-structure levels. The calculations have been performed within the fully relativistic Flexible Atomic Code (FAC, Gu, 2008) framework and the distorted wave approximation. To attain the desired accuracy for the levels energy, the valence-valence and valence-core correlations have been taken care of by including 96 configuration state functions (CSFs) in the model, reaching a total of 3147 fine-structure levels. Two separate calculations have been performed with the local central potential computed for two different average configurations. A third calculation is also performed without the addition of the core-excited states in the atomic model for completeness. The effects of slightly different mean configurations and valence-core correlations on the energy levels and decay rates are investigated. The collision data have been computed employing the relativistic distorted-wave method along with the atomic model containing the 96 CSFs and corresponding to the ground state mean configuration. The collision strengths corresponding to excitation from the first four fine-structure levels are given for five energy values of the scattered electron 2.65, 6.18, 11.02, 17.36, 25.43 Rydberg, plus an additional variable small energy value near the threshold. A collisional-radiative model has been employed to solve the rate equations for the populations of the 567 fine-structure levels, for a temperature of LogTE(K) = 5.2 corresponding to the maximum abundance of S V, and at densities 106-1016cm-3, assuming a Maxwellian electron energy distribution function and black body radiation of temperature 6000 K and dilution factor 0.35 for the photon distribution function. The main processes responsible for the level population variations are the electron-impact collisional excitation and the radiative decay along with their inverse processes. As a result, the level populations along with the spectral high-line intensity ratios are provided.

Quantifying Spatial Genetic Structuring in Mesophotic Populations of the Precious Coral Corallium rubrum

PubMed Central

Costantini, Federica; Carlesi, Lorenzo; Abbiati, Marco

2013-01-01

While shallow water red coral populations have been overharvested in the past, nowadays, commercial harvesting shifted its pressure on mesophotic organisms. An understanding of red coral population structure, particularly larval dispersal patterns and connectivity among harvested populations is paramount to the viability of the species. In order to determine patterns of genetic spatial structuring of deep water Corallium rubrum populations, for the first time, colonies found between 58–118 m depth within the Tyrrhenian Sea were collected and analyzed. Ten microsatellite loci and two regions of mitochondrial DNA (mtMSH and mtC) were used to quantify patterns of genetic diversity within populations and to define population structuring at spatial scales from tens of metres to hundreds of kilometres. Microsatellites showed heterozygote deficiencies in all populations. Significant levels of genetic differentiation were observed at all investigated spatial scales, suggesting that populations are likely to be isolated. This differentiation may by the results of biological interactions, occurring within a small spatial scale and/or abiotic factors acting at a larger scale. Mitochondrial markers revealed significant genetic structuring at spatial scales greater then 100 km showing the occurrence of a barrier to gene flow between northern and southern Tyrrhenian populations. These findings provide support for the establishment of marine protected areas in the deep sea and off-shore reefs, in order to effectively maintain genetic diversity of mesophotic red coral populations. PMID:23646109

Quantifying spatial genetic structuring in mesophotic populations of the precious coral Corallium rubrum.

PubMed

Costantini, Federica; Carlesi, Lorenzo; Abbiati, Marco

2013-01-01

While shallow water red coral populations have been overharvested in the past, nowadays, commercial harvesting shifted its pressure on mesophotic organisms. An understanding of red coral population structure, particularly larval dispersal patterns and connectivity among harvested populations is paramount to the viability of the species. In order to determine patterns of genetic spatial structuring of deep water Corallium rubrum populations, for the first time, colonies found between 58-118 m depth within the Tyrrhenian Sea were collected and analyzed. Ten microsatellite loci and two regions of mitochondrial DNA (mtMSH and mtC) were used to quantify patterns of genetic diversity within populations and to define population structuring at spatial scales from tens of metres to hundreds of kilometres. Microsatellites showed heterozygote deficiencies in all populations. Significant levels of genetic differentiation were observed at all investigated spatial scales, suggesting that populations are likely to be isolated. This differentiation may by the results of biological interactions, occurring within a small spatial scale and/or abiotic factors acting at a larger scale. Mitochondrial markers revealed significant genetic structuring at spatial scales greater then 100 km showing the occurrence of a barrier to gene flow between northern and southern Tyrrhenian populations. These findings provide support for the establishment of marine protected areas in the deep sea and off-shore reefs, in order to effectively maintain genetic diversity of mesophotic red coral populations.

Hi-C First Results

NASA Technical Reports Server (NTRS)

Cirtain, Jonathan

2013-01-01

Hi-C obtained the highest spatial and temporal resolution observatoins ever taken in the solar corona. Hi-C reveals dynamics and structure at the limit of its temporal and spatial resolution. Hi-C observed ubiquitous fine-scale flows consistent with the local sound speed.

Haplotype Sharing Provides Insights into Fine-Scale Population History and Disease in Finland.

PubMed

Martin, Alicia R; Karczewski, Konrad J; Kerminen, Sini; Kurki, Mitja I; Sarin, Antti-Pekka; Artomov, Mykyta; Eriksson, Johan G; Esko, Tõnu; Genovese, Giulio; Havulinna, Aki S; Kaprio, Jaakko; Konradi, Alexandra; Korányi, László; Kostareva, Anna; Männikkö, Minna; Metspalu, Andres; Perola, Markus; Prasad, Rashmi B; Raitakari, Olli; Rotar, Oxana; Salomaa, Veikko; Groop, Leif; Palotie, Aarno; Neale, Benjamin M; Ripatti, Samuli; Pirinen, Matti; Daly, Mark J

2018-05-03

Finland provides unique opportunities to investigate population and medical genomics because of its adoption of unified national electronic health records, detailed historical and birth records, and serial population bottlenecks. We assembled a comprehensive view of recent population history (≤100 generations), the timespan during which most rare-disease-causing alleles arose, by comparing pairwise haplotype sharing from 43,254 Finns to that of 16,060 Swedes, Estonians, Russians, and Hungarians from geographically and linguistically adjacent countries with different population histories. We find much more extensive sharing in Finns, with at least one ≥ 5 cM tract on average between pairs of unrelated individuals. By coupling haplotype sharing with fine-scale birth records from more than 25,000 individuals, we find that although haplotype sharing broadly decays with geographical distance, there are pockets of excess haplotype sharing; individuals from northeast Finland typically share several-fold more of their genome in identity-by-descent segments than individuals from southwest regions. We estimate recent effective population-size changes through time across regions of Finland, and we find that there was more continuous gene flow as Finns migrated from southwest to northeast between the early- and late-settlement regions than was dichotomously described previously. Lastly, we show that haplotype sharing is locally enriched by an order of magnitude among pairs of individuals sharing rare alleles and especially among pairs sharing rare disease-causing variants. Our work provides a general framework for using haplotype sharing to reconstruct an integrative view of recent population history and gain insight into the evolutionary origins of rare variants contributing to disease. Copyright © 2018 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Light trapping structures in wing scales of butterfly Trogonoptera brookiana.

PubMed

Han, Zhiwu; Niu, Shichao; Shang, Chunhui; Liu, Zhenning; Ren, Luquan

2012-04-28

The fine optical structures in wing scales of Trogonoptera brookiana, a tropical butterfly exhibiting efficient light trapping effect, were carefully examined and the reflectivity was measured using reflectance spectrometry. The optimized 3D configuration of the coupling structure was determined using SEM and TEM data, and the light trapping mechanism of butterfly scales was studied. It is found that the front and back sides of butterfly wings possess different light trapping structures, but both can significantly increase the optical path and thus result in almost total absorption of all incident light. An optical model was created to check the properties of this light trapping structure. The simulated reflectance spectra are in concordance with the experimental ones. The results reliably confirm that these structures induce efficient light trapping effect. This functional "biomimetic structure" would have a potential value in wide engineering and optical applications. This journal is © The Royal Society of Chemistry 2012

Temperature-dependent body size effects determine population responses to climate warming.

PubMed

Lindmark, Max; Huss, Magnus; Ohlberger, Jan; Gårdmark, Anna

2018-02-01

Current understanding of animal population responses to rising temperatures is based on the assumption that biological rates such as metabolism, which governs fundamental ecological processes, scale independently with body size and temperature, despite empirical evidence for interactive effects. Here, we investigate the consequences of interactive temperature- and size scaling of vital rates for the dynamics of populations experiencing warming using a stage-structured consumer-resource model. We show that interactive scaling alters population and stage-specific responses to rising temperatures, such that warming can induce shifts in population regulation and stage-structure, influence community structure and govern population responses to mortality. Analysing experimental data for 20 fish species, we found size-temperature interactions in intraspecific scaling of metabolic rate to be common. Given the evidence for size-temperature interactions and the ubiquity of size structure in animal populations, we argue that accounting for size-specific temperature effects is pivotal for understanding how warming affects animal populations and communities. © 2017 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.

Landscape Pattern Determines Neighborhood Size and Structure within a Lizard Population

PubMed Central

Ryberg, Wade A.; Hill, Michael T.; Painter, Charles W.; Fitzgerald, Lee A.

2013-01-01

Although defining population structure according to discrete habitat patches is convenient for metapopulation theories, taking this approach may overlook structure within populations continuously distributed across landscapes. For example, landscape features within habitat patches direct the movement of organisms and define the density distribution of individuals, which can generate spatial structure and localized dynamics within populations as well as among them. Here, we use the neighborhood concept, which describes population structure relative to the scale of individual movements, to illustrate how localized dynamics within a population of lizards (Sceloporus arenicolus) arise in response to variation in landscape pattern within a continuous habitat patch. Our results emphasize links between individual movements at small scales and the emergence of spatial structure within populations which resembles metapopulation dynamics at larger scales. We conclude that population dynamics viewed in a landscape context must consider the explicit distribution and movement of individuals within continuous habitat as well as among habitat patches. PMID:23441217

Variations in grain-scale sediment structure and entrainment force in a gravel-bed channel as a function of fine sediment content and morphological location

NASA Astrophysics Data System (ADS)

Voepel, Hal; Ahmed, Sharif; Hodge, Rebecca; Leyland, Julian; Sear, David

2017-04-01

One of the major causes of uncertainty in estimates of bedload transport rates in gravel-bed rivers is a lack of understanding of grain-scale sediment structure, and the impact that this structure has on the force required to entrain sediment. There are at least two factors that standard entrainment models do not consider. The first is the way in which the spatial arrangement and orientation of grains and the resultant forces varies throughout a channel and over time, ways that have yet to be fully quantified. The second is that sediment entrainment is a 3D process, yet calculations of entrainment thresholds for sediment grains are typically based on 2D diagrams where we calculate static moments of force vectors about a pivot angle, represented as a single point rather than as a more realistic axis of rotation. Our research addresses these limitations by quantifying variations in 3D sediment structure and entrainment force requirements across two key parameters: morphological location within a riffle-pool sequence (reflecting variation in hydraulic conditions), and the fine sediment content of the gravel-bed (sand and clay). We report results from a series of flume experiments in which we water-worked a gravel-bed with a riffle-pool morphology containing varying amounts of fine sediment. After each experimental run intact samples of the bed at different locations were extracted and the internal structure of the bed was measured using non-destructive, micro-focus X-ray computed tomography (CT) imaging. The CT images were processed to measure the properties of individual grains, including volume, center of mass, dimension, and contact points. From these data we were able to quantify the sediment structure and entrainment force requirements through measurement of 3D metrics including grain pivot angles, grain exposure and protrusion. Comparison of the metrics across different morphological locations and fine sediment content demonstrates how these factors affect the bed structure and entrainment force requirement. These results have implications for the development of sediment entrainment models for gravel-bed rivers. Keywords: fluvial sediment, geomorphology, entrainment models, X-ray computed tomography, 3D imaging, vector mechanics

Genetic divergence and fine scale population structure of the common bottlenose dolphin (Tursiops truncatus, Montagu) found in the Gulf of Guayaquil, Ecuador

PubMed Central

Bayas-Rea, Rosa de los Ángeles; Félix, Fernando

2018-01-01

The common bottlenose dolphin, Tursiops truncatus, is widely distributed along the western coast of South America. In Ecuador, a resident population of bottlenose dolphins inhabits the inner estuarine area of the Gulf of Guayaquil located in the southwestern part of the country and is under threat from different human activities in the area. Only one genetic study on South American common bottlenose dolphins has been carried out to date, and understanding genetic variation of wildlife populations, especially species that are identified as threatened, is crucial for defining conservation units and developing appropriate conservation strategies. In order to evaluate the evolutionary link of this population, we assessed the phylogenetic relationships, phylogeographic patterns, and population structure using mitochondrial DNA (mtDNA). The sampling comprised: (i) 31 skin samples collected from free-ranging dolphins at three locations in the Gulf of Guayaquil inner estuary, (ii) 38 samples from stranded dolphins available at the collection of the “Museo de Ballenas de Salinas,” (iii) 549 mtDNA control region (mtDNA CR) sequences from GenBank, and (iv) 66 concatenated sequences from 7-mtDNA regions (12S rRNA, 16S rRNA, NADH dehydrogenase subunit I–II, cytochrome oxidase I and II, cytochrome b, and CR) obtained from mitogenomes available in GenBank. Our analyses indicated population structure between both inner and outer estuary dolphin populations as well as with distinct populations of T. truncatus using mtDNA CR. Moreover, the inner estuary bottlenose dolphin (estuarine bottlenose dolphin) population exhibited lower levels of genetic diversity than the outer estuary dolphin population according to the mtDNA CR. Finally, the estuarine bottlenose dolphin population was genetically distinct from other T. truncatus populations based on mtDNA CR and 7-mtDNA regions. From these results, we suggest that the estuarine bottlenose dolphin population should be considered a distinct lineage. This dolphin population faces a variety of anthropogenic threats in this area; thus, we highlight its fragility and urge authorities to issue prompt management and conservation measures. PMID:29707430

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Gang

Mid-latitude extreme weather events are responsible for a large part of climate-related damage. Yet large uncertainties remain in climate model projections of heat waves, droughts, and heavy rain/snow events on regional scales, limiting our ability to effectively use these projections for climate adaptation and mitigation. These uncertainties can be attributed to both the lack of spatial resolution in the models, and to the lack of a dynamical understanding of these extremes. The approach of this project is to relate the fine-scale features to the large scales in current climate simulations, seasonal re-forecasts, and climate change projections in a very widemore » range of models, including the atmospheric and coupled models of ECMWF over a range of horizontal resolutions (125 to 10 km), aqua-planet configuration of the Model for Prediction Across Scales and High Order Method Modeling Environments (resolutions ranging from 240 km – 7.5 km) with various physics suites, and selected CMIP5 model simulations. The large scale circulation will be quantified both on the basis of the well tested preferred circulation regime approach, and very recently developed measures, the finite amplitude Wave Activity (FAWA) and its spectrum. The fine scale structures related to extremes will be diagnosed following the latest approaches in the literature. The goal is to use the large scale measures as indicators of the probability of occurrence of the finer scale structures, and hence extreme events. These indicators will then be applied to the CMIP5 models and time-slice projections of a future climate.« less

Fine-mapping of lipid regions in global populations discovers ethnic-specific signals and refines previously identified lipid loci

PubMed Central

Zubair, Niha; Luis Ambite, Jose; Bush, William S.; Kichaev, Gleb; Lu, Yingchang; Manichaikul, Ani; Sheu, Wayne H-H.; Absher, Devin; Assimes, Themistocles L.; Bielinski, Suzette J.; Bottinger, Erwin P.; Buzkova, Petra; Chuang, Lee-Ming; Chung, Ren-Hua; Cochran, Barbara; Dumitrescu, Logan; Gottesman, Omri; Haessler, Jeffrey W.; Haiman, Christopher; Heiss, Gerardo; Hsiung, Chao A.; Hung, Yi-Jen; Hwu, Chii-Min; Juang, Jyh-Ming J.; Le Marchand, Loic; Lee, I-Te; Lee, Wen-Jane; Lin, Li-An; Lin, Danyu; Lin, Shih-Yi; Mackey, Rachel H.; Martin, Lisa W.; Pasaniuc, Bogdan; Peters, Ulrike; Predazzi, Irene; Quertermous, Thomas; Reiner, Alex P.; Robinson, Jennifer; Rotter, Jerome I.; Ryckman, Kelli K.; Schreiner, Pamela J.; Stahl, Eli; Tao, Ran; Tsai, Michael Y.; Waite, Lindsay L.; Wang, Tzung-Dau; Buyske, Steven; Ida Chen, Yii-Der; Cheng, Iona; Crawford, Dana C.; Loos, Ruth J.F.; Rich, Stephen S.; Fornage, Myriam; North, Kari E.; Kooperberg, Charles; Carty, Cara L.

2016-01-01

Abstract Genome-wide association studies have identified over 150 loci associated with lipid traits, however, no large-scale studies exist for Hispanics and other minority populations. Additionally, the genetic architecture of lipid-influencing loci remains largely unknown. We performed one of the most racially/ethnically diverse fine-mapping genetic studies of HDL-C, LDL-C, and triglycerides to-date using SNPs on the MetaboChip array on 54,119 individuals: 21,304 African Americans, 19,829 Hispanic Americans, 12,456 Asians, and 530 American Indians. The majority of signals found in these groups generalize to European Americans. While we uncovered signals unique to racial/ethnic populations, we also observed systematically consistent lipid associations across these groups. In African Americans, we identified three novel signals associated with HDL-C (LPL, APOA5, LCAT) and two associated with LDL-C (ABCG8, DHODH). In addition, using this population, we refined the location for 16 out of the 58 known MetaboChip lipid loci. These results can guide tailored screening efforts, reveal population-specific responses to lipid-lowering medications, and aid in the development of new targeted drug therapies. PMID:28426890

Natural Models for Autonomous Control of Spatial Navigation, Sensing, and Guidance. Part 1

DTIC Science & Technology

2012-02-13

ketocarotenoid pigment astaxanthin is deposited in the antennal scale of a stomatopod crustacean, Odontodactylus scyllarus. Positive correlation between...partial polarization and the presence of astaxanthin indicates that the antennal scale polarizes light with astaxanthin . Both the optical properties and...the fine structure of the polarizationally-active cuticle suggest that the dipole axes of the astaxanthin molecules are oriented nearly normal to the

Three sets of crystallographic sub-planar structures in quartz formed by tectonic deformation

NASA Astrophysics Data System (ADS)

Derez, Tine; Pennock, Gill; Drury, Martyn; Sintubin, Manuel

2016-05-01

In quartz, multiple sets of fine planar deformation microstructures that have specific crystallographic orientations parallel to planes with low Miller-Bravais indices are commonly considered as shock-induced planar deformation features (PDFs) diagnostic of shock metamorphism. Using polarized light microscopy, we demonstrate that up to three sets of tectonically induced sub-planar fine extinction bands (FEBs), sub-parallel to the basal, γ, ω, and π crystallographic planes, are common in vein quartz in low-grade tectonometamorphic settings. We conclude that the observation of multiple (2-3) sets of fine scale, closely spaced, crystallographically controlled, sub-planar microstructures is not sufficient to unambiguously distinguish PDFs from tectonic FEBs.

A FRAMEWORK FOR FINE-SCALE COMPUTATIONAL FLUID DYNAMICS AIR QUALITY MODELING AND ANALYSIS

EPA Science Inventory

Fine-scale Computational Fluid Dynamics (CFD) simulation of pollutant concentrations within roadway and building microenvironments is feasible using high performance computing. Unlike currently used regulatory air quality models, fine-scale CFD simulations are able to account rig...

Accommodating environmental variation in population models: metaphysiological biomass loss accounting.

PubMed

Owen-Smith, Norman

2011-07-01

1. There is a pressing need for population models that can reliably predict responses to changing environmental conditions and diagnose the causes of variation in abundance in space as well as through time. In this 'how to' article, it is outlined how standard population models can be modified to accommodate environmental variation in a heuristically conducive way. This approach is based on metaphysiological modelling concepts linking populations within food web contexts and underlying behaviour governing resource selection. Using population biomass as the currency, population changes can be considered at fine temporal scales taking into account seasonal variation. Density feedbacks are generated through the seasonal depression of resources even in the absence of interference competition. 2. Examples described include (i) metaphysiological modifications of Lotka-Volterra equations for coupled consumer-resource dynamics, accommodating seasonal variation in resource quality as well as availability, resource-dependent mortality and additive predation, (ii) spatial variation in habitat suitability evident from the population abundance attained, taking into account resource heterogeneity and consumer choice using empirical data, (iii) accommodating population structure through the variable sensitivity of life-history stages to resource deficiencies, affecting susceptibility to oscillatory dynamics and (iv) expansion of density-dependent equations to accommodate various biomass losses reducing population growth rate below its potential, including reductions in reproductive outputs. Supporting computational code and parameter values are provided. 3. The essential features of metaphysiological population models include (i) the biomass currency enabling within-year dynamics to be represented appropriately, (ii) distinguishing various processes reducing population growth below its potential, (iii) structural consistency in the representation of interacting populations and (iv) capacity to accommodate environmental variation in space as well as through time. Biomass dynamics provide a common currency linking behavioural, population and food web ecology. 4. Metaphysiological biomass loss accounting provides a conceptual framework more conducive for projecting and interpreting the population consequences of climatic shifts and human transformations of habitats than standard modelling approaches. © 2011 The Author. Journal of Animal Ecology © 2011 British Ecological Society.

Transverse bacterial migration induced by chemotaxis in a packed column with structured physical heterogeneity.

PubMed

Wang, Meng; Ford, Roseanne M

2009-08-01

The significance of chemotaxis in directing bacterial migration toward contaminants in natural porous media was investigated under groundwater flow conditions. A laboratory-scale column, with a coarse-grained sand core surrounded by a fine-grained annulus, was used to simulate natural aquifers with strata of different hydraulic conductivities. A chemoattractant source was placed along the central axis of the column to model contaminants trapped in the heterogeneous subsurface. Chemotactic bacterial strains, Escherichia coli HCB1 and Pseudomonas putida F1, introduced into the column by a pulse injection, were found to alter their transport behaviors under the influence of the attractant chemical emanating from the central source. For E. coil HCB1, approximately 18% more of the total population relative to the control without attractant exited the column from the coarse sand layer due to the chemotactic effects of alpha-methylaspartate under an average fluid velocity of 5.1 m/d. Although P. putida F1 demonstrated no observable changes in migration pathways with the model contaminant acetate under the same flow rate, when the flow rate was reduced to 1.9 m/d, approximately 6-10% of the population relative to the control migrated from the fine sand layer toward attractant into the coarse sand layer. Microbial transport properties were further quantified by a mathematical model to examine the significance of bacterial motility and chemotaxis under different hydrodynamic conditions, which suggested important considerations for strain selection and practical operation of bioremediation schemes.

Contributions to the understanding of large-scale coherent structures in developing free turbulent shear flows

NASA Technical Reports Server (NTRS)

Liu, J. T. C.

1986-01-01

Advances in the mechanics of boundary layer flow are reported. The physical problems of large scale coherent structures in real, developing free turbulent shear flows, from the nonlinear aspects of hydrodynamic stability are addressed. The presence of fine grained turbulence in the problem, and its absence, lacks a small parameter. The problem is presented on the basis of conservation principles, which are the dynamics of the problem directed towards extracting the most physical information, however, it is emphasized that it must also involve approximations.

Connecting Mobility to Infectious Diseases: The Promise and Limits of Mobile Phone Data.

PubMed

Wesolowski, Amy; Buckee, Caroline O; Engø-Monsen, Kenth; Metcalf, C J E

2016-12-01

Human travel can shape infectious disease dynamics by introducing pathogens into susceptible populations or by changing the frequency of contacts between infected and susceptible individuals. Quantifying infectious disease-relevant travel patterns on fine spatial and temporal scales has historically been limited by data availability. The recent emergence of mobile phone calling data and associated locational information means that we can now trace fine scale movement across large numbers of individuals. However, these data necessarily reflect a biased sample of individuals across communities and are generally aggregated for both ethical and pragmatic reasons that may further obscure the nuance of individual and spatial heterogeneities. Additionally, as a general rule, the mobile phone data are not linked to demographic or social identifiers, or to information about the disease status of individual subscribers (although these may be made available in smaller-scale specific cases). Combining data on human movement from mobile phone data-derived population fluxes with data on disease incidence requires approaches that can tackle varying spatial and temporal resolutions of each data source and generate inference about dynamics on scales relevant to both pathogen biology and human ecology. Here, we review the opportunities and challenges of these novel data streams, illustrating our examples with analyses of 2 different pathogens in Kenya, and conclude by outlining core directions for future research. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

Fine- and hyperfine-structure effects in molecular photoionization. II. Resonance-enhanced multiphoton ionization and hyperfine-selective generation of molecular cations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Germann, Matthias; Willitsch, Stefan, E-mail: stefan.willitsch@unibas.ch

2016-07-28

Resonance-enhanced multiphoton ionization (REMPI) is a widely used technique for studying molecular photoionization and producing molecular cations for spectroscopy and dynamics studies. Here, we present a model for describing hyperfine-structure effects in the REMPI process and for predicting hyperfine populations in molecular ions produced by this method. This model is a generalization of our model for fine- and hyperfine-structure effects in one-photon ionization of molecules presented in Paper I [M. Germann and S. Willitsch, J. Chem. Phys. 145, 044314 (2016)]. This generalization is achieved by covering two main aspects: (1) treatment of the neutral bound-bound transition including the hyperfine structuremore » that makes up the first step of the REMPI process and (2) modification of our ionization model to account for anisotropic populations resulting from this first excitation step. Our findings may be used for analyzing results from experiments with molecular ions produced by REMPI and may serve as a theoretical background for hyperfine-selective ionization experiments.« less

Direct Numerical Simulations of Small-Scale Gravity Wave Instability Dynamics in Variable Stratification and Shear

NASA Astrophysics Data System (ADS)

Mixa, T.; Fritts, D. C.; Laughman, B.; Wang, L.; Kantha, L. H.

2015-12-01

Multiple observations provide compelling evidence that gravity wave dissipation events often occur in multi-scale environments having highly-structured wind and stability profiles extending from the stable boundary layer into the mesosphere and lower thermosphere. Such events tend to be highly localized and thus yield local energy and momentum deposition and efficient secondary gravity wave generation expected to have strong influences at higher altitudes [e.g., Fritts et al., 2013; Baumgarten and Fritts, 2014]. Lidars, radars, and airglow imagers typically cannot achieve the spatial resolution needed to fully quantify these small-scale instability dynamics. Hence, we employ high-resolution modeling to explore these dynamics in representative environments. Specifically, we describe numerical studies of gravity wave packets impinging on a sheet of high stratification and shear and the resulting instabilities and impacts on the gravity wave amplitude and momentum flux for various flow and gravity wave parameters. References: Baumgarten, Gerd, and David C. Fritts (2014). Quantifying Kelvin-Helmholtz instability dynamics observed in noctilucent clouds: 1. Methods and observations. Journal of Geophysical Research: Atmospheres, 119.15, 9324-9337. Fritts, D. C., Wang, L., & Werne, J. A. (2013). Gravity wave-fine structure interactions. Part I: Influences of fine structure form and orientation on flow evolution and instability. Journal of the Atmospheric Sciences, 70(12), 3710-3734.

Genetic Diversity among Bacillus anthracis Soil Isolates at Fine Geographic Scales

PubMed Central

Bader, Douglas E.

2012-01-01

Environmental samples were collected from carcass sites during and after anthrax outbreaks in 2000 and 2001 in the bison (Bison bison) population within Wood Buffalo National Park and the Hook Lake Region north of Wood Buffalo National Park. Bacillus anthracis spores were isolated from these samples and confirmed using phenotypic characterization and real-time PCR. Confirmed B. anthracis isolates were typed using multiple-locus variable-number tandem repeat analysis (MLVA15) and single-nucleotide-repeat analysis (SNRA). B. anthracis isolates split into two clades based on MLVA15, while SNRA allowed some isolates between carcass sites to be distinguished from each other. SNRA polymorphisms were also present within a single carcass site. Some isolates from different carcass sites having the same SNRA type had divergent MLVA types; this finding leads to questions about hierarchical typing methods and the robustness of the fine-scale typing of Bacillus anthracis. PMID:22773624

Fine-scale topography in sensory systems: insights from Drosophila and vertebrates

PubMed Central

Kaneko, Takuya; Ye, Bing

2015-01-01

To encode the positions of sensory stimuli, sensory circuits form topographic maps in the central nervous system through specific point-to-point connections between pre- and post-synaptic neurons. In vertebrate visual systems, the establishment of topographic maps involves the formation of a coarse topography followed by that of fine-scale topography that distinguishes the axon terminals of neighboring neurons. It is known that intrinsic differences in the form of broad gradients of guidance molecules instruct coarse topography while neuronal activity is required for fine-scale topography. On the other hand, studies in the Drosophila visual system have shown that intrinsic differences in cell adhesion among the axon terminals of neighboring neurons instruct the fine-scale topography. Recent studies on activity-dependent topography in the Drosophila somatosensory system have revealed a role of neuronal activity in creating molecular differences among sensory neurons for establishing fine-scale topography, implicating a conserved principle. Here we review the findings in both Drosophila and vertebrates and propose an integrated model for fine-scale topography. PMID:26091779

Fine-scale topography in sensory systems: insights from Drosophila and vertebrates.

PubMed

Kaneko, Takuya; Ye, Bing

2015-09-01

To encode the positions of sensory stimuli, sensory circuits form topographic maps in the central nervous system through specific point-to-point connections between pre- and postsynaptic neurons. In vertebrate visual systems, the establishment of topographic maps involves the formation of a coarse topography followed by that of fine-scale topography that distinguishes the axon terminals of neighboring neurons. It is known that intrinsic differences in the form of broad gradients of guidance molecules instruct coarse topography while neuronal activity is required for fine-scale topography. On the other hand, studies in the Drosophila visual system have shown that intrinsic differences in cell adhesion among the axon terminals of neighboring neurons instruct the fine-scale topography. Recent studies on activity-dependent topography in the Drosophila somatosensory system have revealed a role of neuronal activity in creating molecular differences among sensory neurons for establishing fine-scale topography, implicating a conserved principle. Here we review the findings in both Drosophila and vertebrates and propose an integrated model for fine-scale topography.

Small Traditional Human Communities Sustain Genomic Diversity over Microgeographic Scales despite Linguistic Isolation

PubMed Central

Cox, Murray P.; Hudjashov, Georgi; Sim, Andre; Savina, Olga; Karafet, Tatiana M.; Sudoyo, Herawati; Lansing, J. Stephen

2016-01-01

At least since the Neolithic, humans have largely lived in networks of small, traditional communities. Often socially isolated, these groups evolved distinct languages and cultures over microgeographic scales of just tens of kilometers. Population genetic theory tells us that genetic drift should act quickly in such isolated groups, thus raising the question: do networks of small human communities maintain levels of genetic diversity over microgeographic scales? This question can no longer be asked in most parts of the world, which have been heavily impacted by historical events that make traditional society structures the exception. However, such studies remain possible in parts of Island Southeast Asia and Oceania, where traditional ways of life are still practiced. We captured genome-wide genetic data, together with linguistic records, for a case–study system—eight villages distributed across Sumba, a small, remote island in eastern Indonesia. More than 4,000 years after these communities were established during the Neolithic period, most speak different languages and can be distinguished genetically. Yet their nuclear diversity is not reduced, instead being comparable to other, even much larger, regional groups. Modeling reveals a separation of time scales: while languages and culture can evolve quickly, creating social barriers, sporadic migration averaged over many generations is sufficient to keep villages linked genetically. This loosely-connected network structure, once the global norm and still extant on Sumba today, provides a living proxy to explore fine-scale genome dynamics in the sort of small traditional communities within which the most recent episodes of human evolution occurred. PMID:27274003

Adaptive responses and disruptive effects: how major wildfire influences kinship-based social interactions in a forest marsupial.

PubMed

Banks, Sam C; Blyton, Michaela D J; Blair, David; McBurney, Lachlan; Lindenmayer, David B

2012-02-01

Environmental disturbance is predicted to play a key role in the evolution of animal social behaviour. This is because disturbance affects key factors underlying social systems, such as demography, resource availability and genetic structure. However, because natural disturbances are unpredictable there is little information on their effects on social behaviour in wild populations. Here, we investigated how a major wildfire affected cooperation (sharing of hollow trees) by a hollow-dependent marsupial. We based two alternative social predictions on the impacts of fire on population density, genetic structure and resources. We predicted an adaptive social response from previous work showing that kin selection in den-sharing develops as competition for den resources increases. Thus, kin selection should occur in burnt areas because the fire caused loss of the majority of hollow-bearing trees, but no detectable mortality. Alternatively, fire may have a disruptive social effect, whereby postfire home range-shifts 'neutralize' fine-scale genetic structure, thereby removing opportunities for kin selection between neighbours. Both predictions occurred: the disruptive social effect in burnt habitat and the adaptive social response in adjacent unburnt habitat. The latter followed a massive demographic influx to unburnt 'refuge' habitat that increased competition for dens, leading to a density-related kin selection response. Our results show remarkable short-term plasticity of animal social behaviour and demonstrate how the social effects of disturbance extend into undisturbed habitat owing to landscape-scale demographic shifts. We predicted long-term changes in kinship-based cooperative behaviour resulting from the genetic and resource impacts of forecast changes to fire regimes in these forests. © 2011 Blackwell Publishing Ltd.

Fluvial gravel stabilization by net-spinning Hydropsychid caddisflies: exploring the magnitude and geographic scope of ecosystem engineering effect and evaluating resistance to anthropogenic stresses

NASA Astrophysics Data System (ADS)

Daniels, M.; Albertson, L.; Sklar, L. S.; Tumolo, B.; Mclaughlin, M. K.

2017-12-01

Several studies have demonstrated the substantial effects that organisms can have on earth surface processes. Known as ecosystem engineers, in streams these organisms maintain, modify, or create physical habitat structure by influencing fluvial processes such as gravel movement, fine sediment deposition and bank erosion. However, the ecology of ecosystem engineers and the magnitude of ecosystem engineering effects in a world increasingly influence by anthropogenically-driven changes is not well understood. Here we present a synthesis of research findings on the potential gravel stabilization effects of Hydropsychid caddisflies, a globally distributed group of net-spinning insects that live in the benthic substrate of most freshwater streams. Hydropsychid caddisflies act as ecosystem engineers because these silk structures can fundamentally alter sediment transport conditions, including sediment stability and flow currents. The silk nets spun by these insects attach gravel grains to one another, increasing the shear stress required to initiate grain entrainment. In a series of independent laboratory experiments, we investigate the gravel size fractions most affected by these silk attachments. We also investigate the role of anthropogenic environmental stresses on ecosystem engineering potential by assessing the impact of two common stressors, high fine sediment loads and stream drying, on silk structures. Finally, an extensive field survey of grain size and Hydropsychid caddisfly population densities informs a watershed-scale network model of Hydropsychid caddisfly gravel stabilizing potential. Our findings provide some of the first evidence that caddisfly silk may be a biological structure that is resilient to various forms of human-mediated stress and that the effects of animal ecosystem engineers are underappreciated as an agent of resistance and recovery for aquatic communities experiencing changes in sediment loads and hydrologic regimes.

Joint the active source and passive source seismic to research the fine crustal structure of the Lushan area

NASA Astrophysics Data System (ADS)

Chen, Q.; Yu, C.

2017-12-01

On April 20, 2013, Ms7.0 strong earthquake (Lushan earthquake) occurred in Lanshan County Ya'an City, Sichuan Province. It is another earthquake that occurred in the Longmenshan fault zone after the Wenchuan earthquake. However, there is still no conclusive conclusion in relationship between the fine structure of the Lushan area and triggering seismic fault . In this study, the crustal structure, the shallow structure and the hidden faults and the focal mechanism of the Lushan earthquake were analyzed by using the deep seismic reflection profile and the broadband seismic array data. Combined with the surface geological information, the structure and fracture cause of the Lishan earthquake were discussed.We have synthetic analyzed the seismic precursors, fine locating, focal mechanism analysis and time-tomographic imaging of the broadband seismic data before and after the earthquake in Lushan earthquake, and obtained the seismic distribution, the focal mechanism and the crustal fine structure in the Lushan area. And we use these results to detailed interpreted the deep reflection seismic section of the Lushan earthquake zone.The results show that the crust of the Lushan area is characterized by a distinct structure of upper crust with thickness about 14.75km. The nature of the faults is inferred to be thrusting in the region due to the pushing of the crustal material of the Tibetan plateau into the southeast part of the rigid Sichuan basin. The shuangshi-Dachuan fault stretches from the surface to the deep crust at a low angle, and is dominated by thrusting in a form of imbricate structure with small-scale faults nearby. Whereas the Guangyuan-Dayi fault is a positive flower structure with a listric shape, consisting of six branches. Its movement is dominated by thrusting with gentle horizontal slip.

Fine-scale phylogenetic architecture of a complex bacterial community.

PubMed

Acinas, Silvia G; Klepac-Ceraj, Vanja; Hunt, Dana E; Pharino, Chanathip; Ceraj, Ivica; Distel, Daniel L; Polz, Martin F

2004-07-29

Although molecular data have revealed the vast scope of microbial diversity, two fundamental questions remain unanswered even for well-defined natural microbial communities: how many bacterial types co-exist, and are such types naturally organized into phylogenetically discrete units of potential ecological significance? It has been argued that without such information, the environmental function, population biology and biogeography of microorganisms cannot be rigorously explored. Here we address these questions by comprehensive sampling of two large 16S ribosomal RNA clone libraries from a coastal bacterioplankton community. We show that compensation for artefacts generated by common library construction techniques reveals fine-scale patterns of community composition. At least 516 ribotypes (unique rRNA sequences) were detected in the sample and, by statistical extrapolation, at least 1,633 co-existing ribotypes in the sampled population. More than 50% of the ribotypes fall into discrete clusters containing less than 1% sequence divergence. This pattern cannot be accounted for by interoperon variation, indicating a large predominance of closely related taxa in this community. We propose that such microdiverse clusters arise by selective sweeps and persist because competitive mechanisms are too weak to purge diversity from within them.

Micro- and nanostructures of iridescent wing scales in purple emperor butterflies (Lepidoptera: Apatura ilia and A. iris).

PubMed

Ćurčić, Srećko B; Pantelić, Dejan V; Ćurčić, Božidar P M; Savić-Šević, Svetlana N; Makarov, Slobodan E; Lačković, Vesna B; Labudović-Borović, Milica M; Ćurčić, Nina B; Stojanović, Dejan V

2012-07-01

Apatura ilia (Denis and Schiffermüller, 1775) and A. iris (Linnaeus, 1758) are fascinating butterflies found in the Palaearctic ecozone (excepting the north of Africa). The wings of these insects are covered with a great number of two types of scales positioned like roof tiles. Type I scales are on the surface, while type II scales are situated below them. The structural color of the type I scales is recognized only on the dorsal side of both the fore and hind wings of the males of the aforementioned species. Both types of scales are responsible for pigment color of the wings, but iridescence is observed only in the type I scales. The brilliant structural color is due to a multilayer structure. The features of the scales, their dimensions and fine structure were obtained using scanning electron microscopy. Cross sections of the scales were then analyzed by transmission electron microscopy. The scales of the "normal" and clytie forms of A. ilia have a different nanostructure, but are of the same type. A similar type of structure, but with a different morphology, was also noticed in A. iris. The scales of the analyzed species resemble the scales of tropical Morpho butterflies. Copyright © 2012 Wiley Periodicals, Inc.

Phenotypic and genetic differentiation among yellow monkeyflower populations from thermal and non-thermal soils in Yellowstone National Park.

PubMed

Lekberg, Ylva; Roskilly, Beth; Hendrick, Margaret F; Zabinski, Catherine A; Barr, Camille M; Fishman, Lila

2012-09-01

In flowering plants, soil heterogeneity can generate divergent natural selection over fine spatial scales, and thus promote local adaptation in the absence of geographic barriers to gene flow. Here, we investigate phenotypic and genetic differentiation in one of the few flowering plants that thrives in both geothermal and non-thermal soils in Yellowstone National Park (YNP). Yellow monkeyflowers (Mimulus guttatus) growing at two geothermal ("thermal") sites in YNP were distinct in growth form and phenology from paired populations growing nearby (<500 m distant) in non-thermal soils. In simulated thermal and non-thermal environments, thermal plants remained significantly divergent from non-thermal plants in vegetative, floral, mating system, and phenological traits. Plants from both thermal populations flowered closer to the ground, allocated relatively more to sexual reproduction, were more likely to initiate flowering under short daylengths, and made smaller flowers that could efficiently self-fertilize without pollinators. These shared differences are consistent with local adaptation to life in the ephemeral window for growth and reproduction created by winter and spring snowmelt on hot soils. In contrast, habitat type (thermal vs. non-thermal) explained little of the genetic variation at neutral markers. Instead, we found that one thermal population (Agrostis Headquarters; AHQ-T) was strongly differentiated from all other populations (all F (ST) > 0.34), which were only weakly differentiated from each other (all F (ST) < 0.07). Phenotypic differentiation of thermal M. guttatus, but little population genetic evidence of long-term ecotypic divergence, encourages further investigations of the potential for fine-scale adaptation and reproductive isolation across the geothermal gradient in Yellowstone.

Predicting habitat suitability for rare plants at local spatial scales using a species distribution model.

PubMed

Gogol-Prokurat, Melanie

2011-01-01

If species distribution models (SDMs) can rank habitat suitability at a local scale, they may be a valuable conservation planning tool for rare, patchily distributed species. This study assessed the ability of Maxent, an SDM reported to be appropriate for modeling rare species, to rank habitat suitability at a local scale for four edaphic endemic rare plants of gabbroic soils in El Dorado County, California, and examined the effects of grain size, spatial extent, and fine-grain environmental predictors on local-scale model accuracy. Models were developed using species occurrence data mapped on public lands and were evaluated using an independent data set of presence and absence locations on surrounding lands, mimicking a typical conservation-planning scenario that prioritizes potential habitat on unsurveyed lands surrounding known occurrences. Maxent produced models that were successful at discriminating between suitable and unsuitable habitat at the local scale for all four species, and predicted habitat suitability values were proportional to likelihood of occurrence or population abundance for three of four species. Unfortunately, models with the best discrimination (i.e., AUC) were not always the most useful for ranking habitat suitability. The use of independent test data showed metrics that were valuable for evaluating which variables and model choices (e.g., grain, extent) to use in guiding habitat prioritization for conservation of these species. A goodness-of-fit test was used to determine whether habitat suitability values ranked habitat suitability on a continuous scale. If they did not, a minimum acceptable error predicted area criterion was used to determine the threshold for classifying habitat as suitable or unsuitable. I found a trade-off between model extent and the use of fine-grain environmental variables: goodness of fit was improved at larger extents, and fine-grain environmental variables improved local-scale accuracy, but fine-grain variables were not available at large extents. No single model met all habitat prioritization criteria, and the best models were overlaid to identify consensus areas of high suitability. Although the four species modeled here co-occur and are treated together for conservation planning, model accuracy and predicted suitable areas varied among species.

Fine-scale variation of historical fire regimes in sagebrush-steppe and juniper woodland: An example from California, USA

Treesearch

Richard F. Miller; Emily K. Heyerdahl

2008-01-01

Coarse-scale estimates of fire intervals across the mountain big sagebrush (Artemisia tridentata spp. vaseyana (Rydb.) Beetle) alliance range from decades to centuries. However, soil depth and texture can affect the abundance and continuity of fine fuels and vary at fine spatial scales, suggesting fire regimes may vary at similar scales. We explored...

Transport out of the lower stratospheric Arctic vortex by Rossby wave breaking

NASA Technical Reports Server (NTRS)

Waugh, D. W.; Plumb, R. A.; Atkinson, R. J.; Schoeberl, M. R.; Lait, L. R.; Newman, P. A.; Loewenstein, M.; Toohey, D. W.; Avallone, L. M.; Webster, C. R.

1994-01-01

The fine-scale structure in lower stratospheric tracer transport during the period of the two Arctic Airborne Stratospheric Expeditions (January and February 1989; December 1991 to March 1992) is investigated using contour advection with surgery calculations. These calculations show that Rossby wave breaking is an ongoing occurrence during these periods and that air is ejected from the polar vortex in the form of long filamentary structures. There is good qualitative agreement between these filaments and measurements of chemical tracers taken aboard the NASA ER-2 aircraft. The ejected air generally remains filamentary and is stretched and mixed with midlatitude air as it is wrapped around the vortex. This process transfers vortex air into midlatitudes and also produces a narrow region of fine-scale filaments surrounding the polar vortex. Among other things, this makes it difficult to define a vortex edge. The calculations also show that strong stirring can occur inside as well as outside the vortex.

A Coarse-to-Fine Geometric Scale-Invariant Feature Transform for Large Size High Resolution Satellite Image Registration

PubMed Central

Chang, Xueli; Du, Siliang; Li, Yingying; Fang, Shenghui

2018-01-01

Large size high resolution (HR) satellite image matching is a challenging task due to local distortion, repetitive structures, intensity changes and low efficiency. In this paper, a novel matching approach is proposed for the large size HR satellite image registration, which is based on coarse-to-fine strategy and geometric scale-invariant feature transform (SIFT). In the coarse matching step, a robust matching method scale restrict (SR) SIFT is implemented at low resolution level. The matching results provide geometric constraints which are then used to guide block division and geometric SIFT in the fine matching step. The block matching method can overcome the memory problem. In geometric SIFT, with area constraints, it is beneficial for validating the candidate matches and decreasing searching complexity. To further improve the matching efficiency, the proposed matching method is parallelized using OpenMP. Finally, the sensing image is rectified to the coordinate of reference image via Triangulated Irregular Network (TIN) transformation. Experiments are designed to test the performance of the proposed matching method. The experimental results show that the proposed method can decrease the matching time and increase the number of matching points while maintaining high registration accuracy. PMID:29702589

Cellulose fibres, nanofibrils and microfibrils: The morphological sequence of MFC components from a plant physiology and fibre technology point of view

NASA Astrophysics Data System (ADS)

Chinga-Carrasco, Gary

2011-06-01

During the last decade, major efforts have been made to develop adequate and commercially viable processes for disintegrating cellulose fibres into their structural components. Homogenisation of cellulose fibres has been one of the principal applied procedures. Homogenisation has produced materials which may be inhomogeneous, containing fibres, fibres fragments, fibrillar fines and nanofibrils. The material has been denominated microfibrillated cellulose (MFC). In addition, terms relating to the nano-scale have been given to the MFC material. Several modern and high-tech nano-applications have been envisaged for MFC. However, is MFC a nano-structure? It is concluded that MFC materials may be composed of (1) nanofibrils, (2) fibrillar fines, (3) fibre fragments and (4) fibres. This implies that MFC is not necessarily synonymous with nanofibrils, microfibrils or any other cellulose nano-structure. However, properly produced MFC materials contain nano-structures as a main component, i.e. nanofibrils.

Comparison of Thaumarchaeotal populations from four deep sea basins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Techtman, Stephen M.; Mahmoudi, Nagissa; Whitt, Kendall T.

The nitrogen cycle in the marine environment is strongly affected by ammonia-oxidizing Thaumarchaeota. In some marine settings, Thaumarchaeotes can comprise a large percentage of the prokaryotic population. To better understand the biogeographic patterns of Thaumarchaeotes, we sought to investigate differences in their abundance and phylogenetic diversity between geographically distinct basins. Samples were collected from four marine basins (The Caspian Sea, the Great Australian Bight, and the Central and Eastern Mediterranean). The concentration of bacterial and archaeal 16S rRNA genes and archaeal amoA genes were assessed using qPCR. Minimum entropy decomposition was used to elucidate the fine-scale diversity of Thaumarchaeotes. Wemore » demonstrated that there were significant differences in the abundance and diversity of Thaumarchaeotes between these four basins. The diversity of Thaumarchaeotal oligotypes differed between basins with many oligotypes only present in one of the four basins, which suggests that their distribution showed biogeographic patterning. There were also significant differences in Thaumarchaeotal community structure between these basins. This would suggest that geographically distant, yet geochemically similar basins may house distinct Thaumarchaeaotal populations. In conclusion, these findings suggest that Thaumarchaeota are very diverse and that biogeography in part contributes in determining the diversity and distribution of Thaumarchaeotes.« less

Comparison of Thaumarchaeotal populations from four deep sea basins

DOE PAGES

Techtman, Stephen M.; Mahmoudi, Nagissa; Whitt, Kendall T.; ...

2017-10-03

The nitrogen cycle in the marine environment is strongly affected by ammonia-oxidizing Thaumarchaeota. In some marine settings, Thaumarchaeotes can comprise a large percentage of the prokaryotic population. To better understand the biogeographic patterns of Thaumarchaeotes, we sought to investigate differences in their abundance and phylogenetic diversity between geographically distinct basins. Samples were collected from four marine basins (The Caspian Sea, the Great Australian Bight, and the Central and Eastern Mediterranean). The concentration of bacterial and archaeal 16S rRNA genes and archaeal amoA genes were assessed using qPCR. Minimum entropy decomposition was used to elucidate the fine-scale diversity of Thaumarchaeotes. Wemore » demonstrated that there were significant differences in the abundance and diversity of Thaumarchaeotes between these four basins. The diversity of Thaumarchaeotal oligotypes differed between basins with many oligotypes only present in one of the four basins, which suggests that their distribution showed biogeographic patterning. There were also significant differences in Thaumarchaeotal community structure between these basins. This would suggest that geographically distant, yet geochemically similar basins may house distinct Thaumarchaeaotal populations. In conclusion, these findings suggest that Thaumarchaeota are very diverse and that biogeography in part contributes in determining the diversity and distribution of Thaumarchaeotes.« less

Spatial models reveal the microclimatic buffering capacity of old-growth forests

PubMed Central

Frey, Sarah J. K.; Hadley, Adam S.; Johnson, Sherri L.; Schulze, Mark; Jones, Julia A.; Betts, Matthew G.

2016-01-01

Climate change is predicted to cause widespread declines in biodiversity, but these predictions are derived from coarse-resolution climate models applied at global scales. Such models lack the capacity to incorporate microclimate variability, which is critical to biodiversity microrefugia. In forested montane regions, microclimate is thought to be influenced by combined effects of elevation, microtopography, and vegetation, but their relative effects at fine spatial scales are poorly known. We used boosted regression trees to model the spatial distribution of fine-scale, under-canopy air temperatures in mountainous terrain. Spatial models predicted observed independent test data well (r = 0.87). As expected, elevation strongly predicted temperatures, but vegetation and microtopography also exerted critical effects. Old-growth vegetation characteristics, measured using LiDAR (light detection and ranging), appeared to have an insulating effect; maximum spring monthly temperatures decreased by 2.5°C across the observed gradient in old-growth structure. These cooling effects across a gradient in forest structure are of similar magnitude to 50-year forecasts of the Intergovernmental Panel on Climate Change and therefore have the potential to mitigate climate warming at local scales. Management strategies to conserve old-growth characteristics and to curb current rates of primary forest loss could maintain microrefugia, enhancing biodiversity persistence in mountainous systems under climate warming. PMID:27152339

Spatial models reveal the microclimatic buffering capacity of old-growth forests.

PubMed

Frey, Sarah J K; Hadley, Adam S; Johnson, Sherri L; Schulze, Mark; Jones, Julia A; Betts, Matthew G

2016-04-01

Climate change is predicted to cause widespread declines in biodiversity, but these predictions are derived from coarse-resolution climate models applied at global scales. Such models lack the capacity to incorporate microclimate variability, which is critical to biodiversity microrefugia. In forested montane regions, microclimate is thought to be influenced by combined effects of elevation, microtopography, and vegetation, but their relative effects at fine spatial scales are poorly known. We used boosted regression trees to model the spatial distribution of fine-scale, under-canopy air temperatures in mountainous terrain. Spatial models predicted observed independent test data well (r = 0.87). As expected, elevation strongly predicted temperatures, but vegetation and microtopography also exerted critical effects. Old-growth vegetation characteristics, measured using LiDAR (light detection and ranging), appeared to have an insulating effect; maximum spring monthly temperatures decreased by 2.5°C across the observed gradient in old-growth structure. These cooling effects across a gradient in forest structure are of similar magnitude to 50-year forecasts of the Intergovernmental Panel on Climate Change and therefore have the potential to mitigate climate warming at local scales. Management strategies to conserve old-growth characteristics and to curb current rates of primary forest loss could maintain microrefugia, enhancing biodiversity persistence in mountainous systems under climate warming.

Complex Ancient Genetic Structure and Cultural Transitions in Southern African Populations.

PubMed

Montinaro, Francesco; Busby, George B J; Gonzalez-Santos, Miguel; Oosthuitzen, Ockie; Oosthuitzen, Erika; Anagnostou, Paolo; Destro-Bisol, Giovanni; Pascali, Vincenzo L; Capelli, Cristian

2017-01-01

The characterization of the structure of southern African populations has been the subject of numerous genetic, medical, linguistic, archaeological, and anthropological investigations. Current diversity in the subcontinent is the result of complex events of genetic admixture and cultural contact between early inhabitants and migrants that arrived in the region over the last 2000 years. Here, we analyze 1856 individuals from 91 populations, comprising novel and published genotype data, to characterize the genetic ancestry profiles of 631 individuals from 51 southern African populations. Combining both local ancestry and allele frequency based analyses, we identify a tripartite, ancient, Khoesan-related genetic structure. This structure correlates neither with linguistic affiliation nor subsistence strategy, but with geography, revealing the importance of isolation-by-distance dynamics in the area. Fine-mapping of these components in southern African populations reveals admixture and cultural reversion involving several Khoesan groups, and highlights that Bantu speakers and Coloured individuals have different mixtures of these ancient ancestries. Copyright © 2017 Montinaro et al.

Structure formation in organic thin films observed in real time by energy dispersive near-edge x-ray absorption fine-structure spectroscopy

NASA Astrophysics Data System (ADS)

Scholz, M.; Sauer, C.; Wiessner, M.; Nguyen, N.; Schöll, A.; Reinert, F.

2013-08-01

We study the structure formation of 1,4,5,8-naphthalene-tetracarboxylicacid-dianhydride (NTCDA) multilayer films on Ag(111) surfaces by energy dispersive near-edge x-ray absorption fine-structure spectroscopy (NEXAFS) and photoelectron spectroscopy. The time resolution of seconds of the method allows us to identify several sub-processes, which occur during the post-growth three-dimensional structural ordering, as well as their characteristic time scales. After deposition at low temperature the NTCDA molecules are preferentially flat lying and the films exhibit no long-range order. Upon annealing the molecules flip into an upright orientation followed by an aggregation in a transient phase which exists for several minutes. Finally, three-dimensional islands are established with bulk-crystalline structure involving substantial mass transport on the surface and morphological roughening. By applying the Kolmogorov-Johnson-Mehl-Avrami model the activation energies of the temperature-driven sub-processes can be derived from the time evolution of the NEXAFS signal.

The evolutionary origin of feathers.

PubMed

Regal, P J

1975-03-01

Previous theories relating the origin of feathers to flight or to heat conservation are considered to be inadequate. There is need for a model of feather evolution that gives attention to the function and adaptive advantage of intermediate structures. The present model attempts to reveal and to deal with, the spectrum of complex questions that must be considered. In several genera of modern lizards, scales are elongated in warm climates. It is argued that these scales act as small shields to solar radiation. Experiments are reported that tend to confirm this. Using lizards as a conceptual model, it is argued that feathers likewise arose as adaptations to intense solar radiation. Elongated scales are assumed to have subdivided into finely branched structures that produced a heat-shield, flexible as well as long and broad. Associated muscles had the function of allowing the organism fine control over rates of heat gain and loss: the specialized scales or early feathers could be moved to allow basking in cool weather or protection in hot weather. Subdivision of the scales also allowed a close fit between the elements of the insulative integument. There would have been mechanical and thermal advantages to having branches that interlocked into a pennaceous structure early in evolution, so the first feathers may have been pennaceous. A versatile insulation of movable, branched scales would have been a preadaptation for endothermy. As birds took to the air they faced cooling problems despite their insulative covering because of high convective heat loss. Short glides may have initially been advantageous in cooling an animal under heat stress, but at some point the problem may have shifted from one of heat exclusion to one of heat retention. Endothermy probably evolved in conjunction with flight. If so, it is an unnecessary assumption to postulate that the climate cooled and made endothermy advantageous. The development of feathers is complex and a model is proposed that gives attention to the fundamental problems of deriving a branched structure with a cylindrical base from an elongated scale.

Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils.

PubMed

VanInsberghe, David; Maas, Kendra R; Cardenas, Erick; Strachan, Cameron R; Hallam, Steven J; Mohn, William W

2015-11-01

The genus Bradyrhizobium has served as a model system for studying host-microbe symbiotic interactions and nitrogen fixation due to its importance in agricultural productivity and global nitrogen cycling. In this study, we identify a bacterial group affiliated with this genus that dominates the microbial communities of coniferous forest soils from six distinct ecozones across North America. Representative isolates from this group were obtained and characterized. Using quantitative population genomics, we show that forest soil populations of Bradyrhizobium represent ecotypes incapable of nodulating legume root hairs or fixing atmospheric nitrogen. Instead, these populations appear to be free living and have a greater potential for metabolizing aromatic carbon sources than their close symbiotic relatives. In addition, we identify fine-scaled differentiation between populations inhabiting neighboring soil layers that illustrate how diversity within Bradyrhizobium is structured by habitat similarity. These findings reconcile incongruent observations about this widely studied and important group of bacteria and highlight the value of ecological context to interpretations of microbial diversity and taxonomy. These results further suggest that the influence of this genus likely extends well beyond facilitating agriculture, especially as forest ecosystems are large and integral components of the biosphere. In addition, this study demonstrates how focusing research on economically important microorganisms can bias our understanding of the natural world.

Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils

PubMed Central

VanInsberghe, David; Maas, Kendra R; Cardenas, Erick; Strachan, Cameron R; Hallam, Steven J; Mohn, William W

2015-01-01

The genus Bradyrhizobium has served as a model system for studying host–microbe symbiotic interactions and nitrogen fixation due to its importance in agricultural productivity and global nitrogen cycling. In this study, we identify a bacterial group affiliated with this genus that dominates the microbial communities of coniferous forest soils from six distinct ecozones across North America. Representative isolates from this group were obtained and characterized. Using quantitative population genomics, we show that forest soil populations of Bradyrhizobium represent ecotypes incapable of nodulating legume root hairs or fixing atmospheric nitrogen. Instead, these populations appear to be free living and have a greater potential for metabolizing aromatic carbon sources than their close symbiotic relatives. In addition, we identify fine-scaled differentiation between populations inhabiting neighboring soil layers that illustrate how diversity within Bradyrhizobium is structured by habitat similarity. These findings reconcile incongruent observations about this widely studied and important group of bacteria and highlight the value of ecological context to interpretations of microbial diversity and taxonomy. These results further suggest that the influence of this genus likely extends well beyond facilitating agriculture, especially as forest ecosystems are large and integral components of the biosphere. In addition, this study demonstrates how focusing research on economically important microorganisms can bias our understanding of the natural world. PMID:25909973

Islands within an island: repeated adaptive divergence in a single population.

PubMed

Langin, Kathryn M; Sillett, T Scott; Funk, W Chris; Morrison, Scott A; Desrosiers, Michelle A; Ghalambor, Cameron K

2015-03-01

Physical barriers to gene flow were once viewed as prerequisites for adaptive evolutionary divergence. However, a growing body of theoretical and empirical work suggests that divergence can proceed within a single population. Here we document genetic structure and spatially replicated patterns of phenotypic divergence within a bird species endemic to 250 km(2) Santa Cruz Island, California, USA. Island scrub-jays (Aphelocoma insularis) in three separate stands of pine habitat had longer, shallower bills than jays in oak habitat, a pattern that mirrors adaptive differences between allopatric populations of the species' mainland congener. Variation in both bill measurements was heritable, and island scrub-jays mated nonrandomly with respect to bill morphology. The population was not panmictic; instead, we found a continuous pattern of isolation by distance across the east-west axis of the island, as well as a subtle genetic discontinuity across the boundary between the largest pine stand and adjacent oak habitat. The ecological factors that appear to have facilitated adaptive differentiation at such a fine scale--environmental heterogeneity and localized dispersal--are ubiquitous in nature. These findings support recent arguments that microgeographic patterns of adaptive divergence may be more common than currently appreciated, even in mobile taxonomic groups like birds. © 2015 The Author(s).

The phylogeographical history of the Iberian steppe plant Ferula loscosii (Apiaceae): a test of the abundant-centre hypothesis.

PubMed

Pérez-Collazos, E; Sanchez-Gómez, P; Jiménez, F; Catalán, P

2009-03-01

The geology and climate of the western Mediterranean area were strongly modified during the Late Tertiary and the Quaternary. These geological and climatic events are thought to have induced changes in the population histories of plants in the Iberian Peninsula. However, fine-scale genetic spatial architecture across western Mediterranean steppe plant refugia has rarely been investigated. A population genetic analysis of amplified fragment length polymorphism variation was conducted on present-day, relict populations of Ferula loscosii (Apiaceae). This species exhibits high individual/population numbers in the middle Ebro river valley and, according to the hypothesis of an abundant-centre distribution, these northern populations might represent a long-standing/ancestral distribution centre. However, our results suggest that the decimated southern and central Iberian populations are more variable and structured than the northeastern ones, representing the likely vestiges of an ancestral distribution centre of the species. Phylogeographical analysis suggests that F. loscosii likely originated in southern Spain and then migrated towards the central and northeastern ranges, further supporting a Late Miocene southern-bound Mediterranean migratory way for its oriental steppe ancestors. In addition, different glacial-induced conditions affected the southern and northern steppe Iberian refugia during the Quaternary. The contrasting genetic homogeneity of the Ebro valley range populations compared to the southern Iberian ones possibly reflects more severe bottlenecks and subsequent genetic drift experienced by populations of the northern Iberia refugium during the Pleistocene, followed by successful postglacial expansion from only a few founder plants.

Concurrent validity between instruments of assessment of motor development in infants exposed to HIV.

PubMed

Siegle, Cristhina Bonilha Huster; Dos Santos Cardoso de Sá, Cristina

2018-02-01

Exposure to HIV during pregnancy is a risks to development. Exposed child should have assessed its development since birth. Alberta Infant Motor Scale is a tool which assess gross motor skills, with easy application and low cost. Up to now, this scale had not proven its validity for the population exposed to HIV. It's necessary to compare its with a gold standard tool, Bayley scale, which assess gross and fine motor skills, has a high cost and longer application time required. Studies compare results of Alberta with Bayley's total motor score (gross + fine). However, it's also necessary to compare Alberta's result with only Bayley's gross motor result, because it's what both evaluate in common. to verify the concurrent validity of AIMS in infants exposed to HIV; to verify the correlation of AIMS and BSITD III for this population and to compare if these coefficients differ in the central age groups and extremities of the AIMS. 82 infants exposed to HIV evaluated in 1st, 2nd, 3rd, 4th, 8th, 12th, 15th, 16th, 17th and 18th months, with Alberta Infant Motor Scale and Bayley Scale (motor subscale). For analysis of concurrent validity, results of raw scores of the scales were compared with the correlation analysis. First analysis: Alberta's score with Bayley's total (gross + fine) motor score. Second analysis: Alberta's score with Bayley's gross motor score. In the first correlation analysis, results were: r = 0.62 in 1 st month, r = 0.64 in 2nd month, r = 0.08 in 3rd month, r = 0.45 in 4th month; r = 0.62 in 8th month, r = 0.60 in the 12th month. In the second correlation analysis, results were: r = 0.69 in 1 st month; r = 0.58 in 2nd month; r = 0.25 in 3rd month; r = 0.45 in the 4th month; r = 0.77 in 8th month; r = 0.73 in 12th month. Analyzes of the 15th, 16th, 17th and 18th months couldn't be performed because at these ages all the children had already reached the maximum score in the AIMS. Results were significant and indicate correlation between scales. Found results agree with other studies that found high correlations between the scales in premature and risk groups. However, these studies compare results of gross motor skills assessments with gross and fine motor skills assessments. Our results show that correlation only between the gross motor skills have higher coefficient values, and we believe this is the best way to compare the scales, with what both assessed in common. Alberta scale has correlation with Bayley scale in assessing of children exposed to HIV, and can be a substitute to Bayley in assessing of these children. Results are stronger when comparing only what both scales assess in common. Copyright © 2018 Elsevier Inc. All rights reserved.

Tree regeneration spatial patterns in ponderosa pine forests following stand-replacing fire: Influence of topography and neighbors

Treesearch

Justin P. Ziegler; Chad M. Hoffman; Paula J. Fornwalt; Carolyn H. Sieg; Michael A. Battaglia; Marin E. Chambers; Jose M. Iniguez

2017-01-01

Shifting fire regimes alter forest structure assembly in ponderosa pine forests and may produce structural heterogeneity following stand-replacing fire due, in part, to fine-scale variability in growing environments. We mapped tree regeneration in eighteen plots 11 to 15 years after stand-replacing fire in Colorado and South Dakota, USA. We used point pattern analyses...

Persistent fine-scale fault structures control rupture development in Parkfield, CA.

NASA Astrophysics Data System (ADS)

Perrin, C.; Waldhauser, F.; Scholz, C. H.

2016-12-01

We investigate the fine-scale geometry and structure of the San Andreas Fault (SAF) near Parkfield, CA, and their role in the development of the 1966 and 2004 M6 earthquakes. Both events broke the fault mainly unilaterally with similar length ( 30 km) but in opposite directions. Seismic slip occurred in a narrow zone between 5 and 10 km depth, as outlined by the concentration of aftershocks along the edge of the slip area. Across fault distribution of the 2004 aftershocks show a rapid decrease of event density away from the fault core. The damage zone is narrower in the Parkfield section (few 100 meters) than in the creeping section ( 1 km). We observe a similar but broader distribution during the interseismic periods. This implies that stress accumulates in a volume around the fault during interseismic periods, whereas coseismic deformation is more localized on the mature SAF. Large aftershocks are concentrated at both rupture tips, characterized by strong heterogeneities in the fault structure at the surface and at depth: i) in the south near Gold Hill-Cholame, a large releasing bend (>25°) separates the Parkfield section from the southern section of the SAF; ii) in the north at Middle Mountain, the surface fault trace goes through an ancient restraining step-over connecting the Parkfield and creeping sections. Fine-scale analysis of the 2004 aftershocks reveals a change in the fault dip and local variations of the fault strike (up to 25°) beneath Middle Mountain, in good agreement with focal mechanisms, which show oblique normal and reverse faulting. We observe these variations during the interseismic periods before and after the 2004 event, suggesting that the structural heterogeneities persisted through at least two earthquake cycles. These heterogeneities act as barriers to rupture propagation of moderate size earthquakes at Parkfield, but also as stress concentrations where rupture initiates.

Using Lidar and Radar measurements to constrain predictions of forest ecosystem structure and function.

PubMed

Antonarakis, Alexander S; Saatchi, Sassan S; Chazdon, Robin L; Moorcroft, Paul R

2011-06-01

Insights into vegetation and aboveground biomass dynamics within terrestrial ecosystems have come almost exclusively from ground-based forest inventories that are limited in their spatial extent. Lidar and synthetic-aperture Radar are promising remote-sensing-based techniques for obtaining comprehensive measurements of forest structure at regional to global scales. In this study we investigate how Lidar-derived forest heights and Radar-derived aboveground biomass can be used to constrain the dynamics of the ED2 terrestrial biosphere model. Four-year simulations initialized with Lidar and Radar structure variables were compared against simulations initialized from forest-inventory data and output from a long-term potential-vegtation simulation. Both height and biomass initializations from Lidar and Radar measurements significantly improved the representation of forest structure within the model, eliminating the bias of too many large trees that arose in the potential-vegtation-initialized simulation. The Lidar and Radar initializations decreased the proportion of larger trees estimated by the potential vegetation by approximately 20-30%, matching the forest inventory. This resulted in improved predictions of ecosystem-scale carbon fluxes and structural dynamics compared to predictions from the potential-vegtation simulation. The Radar initialization produced biomass values that were 75% closer to the forest inventory, with Lidar initializations producing canopy height values closest to the forest inventory. Net primary production values for the Radar and Lidar initializations were around 6-8% closer to the forest inventory. Correcting the Lidar and Radar initializations for forest composition resulted in improved biomass and basal-area dynamics as well as leaf-area index. Correcting the Lidar and Radar initializations for forest composition and fine-scale structure by combining the remote-sensing measurements with ground-based inventory data further improved predictions, suggesting that further improvements of structural and carbon-flux metrics will also depend on obtaining reliable estimates of forest composition and accurate representation of the fine-scale vertical and horizontal structure of plant canopies.

Population structure and inbreeding vary with successional stage in created Spartina alterniflora marshes

USGS Publications Warehouse

Travis, S.E.; Proffitt, C.E.; Ritland, K.

2004-01-01

Recruitment patterns in clonal plant populations are predicted to vary with seed dispersal capability and disturbance regime, such that species with small, widely dispersed seeds will become increasingly dominated by vegetative recruitment on disturbed areas following early colonization. Subsequent mortality due to competitive or stochastic effects is then predicted to cause a gradual decline in both clonal diversity and the ability of surviving clones to avoid geitonogamous mating and possible inbreeding depression. We tested predictions of these hypotheses by comparing four adjacent populations of the salt marsh plant, Spartina alterniflora, ranging in age from 2 to ???50 yr, by measuring fine-scale genetic structure at the level of both ramets and genets, and the rate of inbreeding. For this purpose, we sampled maternal tissue and seeds from discrete patches in the field and then genotyped both maternal and seedling tissue (germinated in a growth chamber) using standard molecular protocols. As predicted, we observed an increase in clonal diversity (measured as the complement of the Simpson Index corrected for finite sample sizes, 1-D) up to a maximum of 0.71 within 3-m2 patches at 16 yr, declining to 0.55 by ???50 yr. Local recruitment of seedlings was evident as genetic structure occurring at the level of patches, as measured by the fixation index, ??, which was inversely correlated with diversity (R2 > 0.90 at all patch scales). Outcrossing rates were positively associated with clonal diversity, with the highest level (89%) at an intermediate level of 1-D. The greatest selfing (32%) occurred in young (2-yr-old) patches with low diversity. Biparental inbreeding was minimal in all populations, never exceeding 1%. Inbreeding depression was inferred to be severe, as evidenced by near-zero adult inbreeding coefficients. These results suggest a possible fitness trade-off between clonal growth and the opportunity for outcrossing. We recommend that restoration plantings of clonal species with limited sexual recruitment capabilities should be designed to ensure adequate clonal diversity for the avoidance of inbreeding and the ability to adapt to subsequent environmental disturbances.

Similarity spectra analysis of high-performance jet aircraft noise.

PubMed

Neilsen, Tracianne B; Gee, Kent L; Wall, Alan T; James, Michael M

2013-04-01

Noise measured in the vicinity of an F-22A Raptor has been compared to similarity spectra found previously to represent mixing noise from large-scale and fine-scale turbulent structures in laboratory-scale jet plumes. Comparisons have been made for three engine conditions using ground-based sideline microphones, which covered a large angular aperture. Even though the nozzle geometry is complex and the jet is nonideally expanded, the similarity spectra do agree with large portions of the measured spectra. Toward the sideline, the fine-scale similarity spectrum is used, while the large-scale similarity spectrum provides a good fit to the area of maximum radiation. Combinations of the two similarity spectra are shown to match the data in between those regions. Surprisingly, a combination of the two is also shown to match the data at the farthest aft angle. However, at high frequencies the degree of congruity between the similarity and the measured spectra changes with engine condition and angle. At the higher engine conditions, there is a systematically shallower measured high-frequency slope, with the largest discrepancy occurring in the regions of maximum radiation.

Farms, pastures and woodlands: the fine-scale distribution of Palearctic Culicoides spp. biting midges along an agro-ecological gradient.

PubMed

Rigot, T; Drubbel, M Vercauteren; Delécolle, J-C; Gilbert, M

2013-03-01

The spatial epidemiology of Bluetongue virus (BTV) at the landscape level relates to the fine-scale distribution and dispersal capacities of its vectors, midges belonging to the genus Culicoides Latreille (Diptera: Ceratopogonidae). Although many previous researches have carried out Culicoides sampling on farms, little is known of the fine-scale distribution of Culicoides in the landscape immediately surrounding farms. The aim of this study was to gain a better understanding of Culicoides populations at increasing distances from typical dairy farms in north-west Europe, through the use of eight Onderstepoort-type black-light traps positioned along linear transects departing from farms, going through pastures and entering woodlands. A total of 16 902 Culicoides were collected in autumn 2008 and spring 2009. The majority were females, of which more than 97% were recognized as potential vectors. In pastures, we found decreasing numbers of female Culicoides as a function of the distance to the farm. This pattern was modelled by leptokurtic models, with parameters depending on season and species. By contrast, the low number of male Culicoides caught were homogeneously distributed along the transects. When transects entered woodlands, we found a higher abundance of Culicoides than expected considering the distance of the sampling sites to the farm, although this varied according to species. © 2012 The Authors. Medical and Veterinary Entomology © 2012 The Royal Entomological Society.

Spatial patterns of native freshwater mussels in the Upper Mississippi River

USGS Publications Warehouse

Ries, Patricia R.; DeJager, Nathan R.; Zigler, Steven J.; Newton, Teresa

2016-01-01

Multiple physical and biological factors structure freshwater mussel communities in large rivers, and their distributions have been described as clumped or patchy. However, few surveys of mussel populations have been conducted over areas large enough and at resolutions fine enough to quantify spatial patterns in their distribution. We used global and local indicators of spatial autocorrelation (i.e., Moran’s I) to quantify spatial patterns of adult and juvenile (≤5 y of age) freshwater mussels across multiple scales based on survey data from 4 reaches (navigation pools 3, 5, 6, and 18) of the Upper Mississippi River, USA. Native mussel densities were sampled at a resolution of ∼300 m and across distances ranging from 21 to 37 km, making these some of the most spatially extensive surveys conducted in a large river. Patch density and the degree and scale of patchiness varied by river reach, age group, and the scale of analysis. In all 4 pools, some patches of adults overlapped patches of juveniles, suggesting spatial and temporal persistence of adequate habitat. In pools 3 and 5, patches of juveniles were found where there were few adults, suggesting recent emergence of positive structuring mechanisms. Last, in pools 3, 5, and 6, some patches of adults were found where there were few juveniles, suggesting that negative structuring mechanisms may have replaced positive ones, leading to a lack of localized recruitment. Our results suggest that: 1) the detection of patches of freshwater mussels requires a multiscaled approach, 2) insights into the spatial and temporal dynamics of structuring mechanisms can be gained by conducting independent analyses of adults and juveniles, and 3) maps of patch distributions can be used to guide restoration and management actions and identify areas where mussels are most likely to influence ecosystem function.

Generation of intense high-order vortex harmonics.

PubMed

Zhang, Xiaomei; Shen, Baifei; Shi, Yin; Wang, Xiaofeng; Zhang, Lingang; Wang, Wenpeng; Xu, Jiancai; Yi, Longqiong; Xu, Zhizhan

2015-05-01

This Letter presents for the first time a scheme to generate intense high-order optical vortices that carry orbital angular momentum in the extreme ultraviolet region based on relativistic harmonics from the surface of a solid target. In the three-dimensional particle-in-cell simulation, the high-order harmonics of the high-order vortex mode is generated in both reflected and transmitted light beams when a linearly polarized Laguerre-Gaussian laser pulse impinges on a solid foil. The azimuthal mode of the harmonics scales with its order. The intensity of the high-order vortex harmonics is close to the relativistic region, with the pulse duration down to attosecond scale. The obtained intense vortex beam possesses the combined properties of fine transversal structure due to the high-order mode and the fine longitudinal structure due to the short wavelength of the high-order harmonics. In addition to the application in high-resolution detection in both spatial and temporal scales, it also presents new opportunities in the intense vortex required fields, such as the inner shell ionization process and high energy twisted photons generation by Thomson scattering of such an intense vortex beam off relativistic electrons.

FRB microstructure revealed by the real-time detection of FRB170827

NASA Astrophysics Data System (ADS)

Farah, W.; Flynn, C.; Bailes, M.; Jameson, A.; Bannister, K. W.; Barr, E. D.; Bateman, T.; Bhandari, S.; Caleb, M.; Campbell-Wilson, D.; Chang, S.-W.; Deller, A.; Green, A. J.; Hunstead, R.; Jankowski, F.; Keane, E.; Macquart, J.-P.; Möller, A.; Onken, C. A.; Osłowski, S.; Parthasarathy, A.; Plant, K.; Ravi, V.; Shannon, R.; Tucker, B. E.; Venkatraman Krishnan, V.; Wolf, C.

2018-05-01

We report a new Fast Radio Burst (FRB) discovered in real-time as part of the UTMOST project at the Molonglo Observatory Synthesis Radio Telescope (MOST). FRB170827 is the first detected with our low-latency (<24 s), machine-learning-based FRB detection system. The FRB discovery was accompanied by the capture of voltage data at the native time and frequency resolution of the observing system, enabling coherent dedispersion and detailed off-line analysis, which have unveiled fine temporal and frequency structure. The dispersion measure (DM) of 176.80 ± 0.04 pc cm-3, is the lowest of the FRB population. The Milky Way contribution along the line of sight is ˜ 40 pc cm-3, leaving an excess DM of ˜ 145 pc cm-3. The FRB has a fluence > 20 ± 7 Jy ms, and is narrow, with a width of ˜ 400 μs at 10% of its maximum amplitude. However, the burst shows three temporal components, the narrowest of which is ˜ 30 μs, and a scattering timescale of 4.1 ± 2.7 μs. The FRB shows spectral modulations on frequency scales of 1.5 MHz and 0.1 MHz. Both are prominent in the dynamic spectrum, which shows a very bright region of emission between 841 and 843 MHz, and weaker, patchy emission across the entire band. We show the fine spectral structure could arise in the FRB host galaxy, or its immediate vicinity.

Heterogeneity and anisotropy in the lithospheric mantle

NASA Astrophysics Data System (ADS)

Tommasi, Andréa; Vauchez, Alain

2015-10-01

The lithospheric mantle is intrinsically heterogeneous and anisotropic. These two properties govern the repartition of deformation, controlling intraplate strain localization and development of new plate boundaries. Geophysical and geological observations provide clues on the types, ranges, and characteristic length scales of heterogeneity and anisotropy in the lithospheric mantle. Seismic tomography points to variations in geothermal gradient and hence in rheological behavior at scales of hundreds of km. Seismic anisotropy data substantiate anisotropic physical properties consistent at scales of tens to hundreds of km. Receiver functions imply lateral and vertical heterogeneity at scales < 10 km, which might record gradients in composition or anisotropy. Observations on naturally deformed peridotites establish that compositional heterogeneity and Crystal Preferred Orientations (CPOs) are ubiquitous from the mm to the km scales. These data allow discussing the processes that produce/destroy heterogeneity and anisotropy and constraining the time scales over which they are active. This analysis highlights: (i) the role of deformation and reactive percolation of melts and fluids in producing compositional and structural heterogeneity and the feedbacks between these processes, (ii) the weak mechanical effect of mineralogical variations, and (iii) the low volumes of fine-grained microstructures and difficulty to preserve them. In contrast, olivine CPO and the resulting anisotropy of mechanical and thermal properties are only modified by deformation. Based on this analysis, we propose that strain localization at the plate scale is, at first order, controlled by large-scale variations in thermal structure and in CPO-induced anisotropy. In cold parts of the lithospheric mantle, grain size reduction may contribute to strain localization, but the low volume of fine-grained domains limits this effect.

Metabolism drives distribution and abundance in extremophile fish

PubMed Central

McHugh, Peter A.; Glover, Chris N.; McIntosh, Angus R.

2017-01-01

Differences in population density between species of varying size are frequently attributed to metabolic rates which are assumed to scale with body size with a slope of 0.75. This assumption is often criticised on the grounds that 0.75 scaling of metabolic rate with body size is not universal and can vary significantly depending on species and life-history. However, few studies have investigated how interspecific variation in metabolic scaling relationships affects population density in different sized species. Here we predict inter-specific differences in metabolism from niche requirements, thereby allowing metabolic predictions of species distribution and abundance at fine spatial scales. Due to the differences in energetic efficiency required along harsh-benign gradients, an extremophile fish (brown mudfish, Neochanna apoda) living in harsh environments had slower metabolism, and thus higher population densities, compared to a fish species (banded kōkopu, Galaxias fasciatus) in physiologically more benign habitats. Interspecific differences in the intercepts for the relationship between body and density disappeared when species mass-specific metabolic rates, rather than body sizes, were used to predict density, implying population energy use was equivalent between mudfish and kōkopu. Nevertheless, despite significant interspecific differences in the slope of the metabolic scaling relationships, mudfish and kōkopu had a common slope for the relationship between body size and population density. These results support underlying logic of energetic equivalence between different size species implicit in metabolic theory. However, the precise slope of metabolic scaling relationships, which is the subject of much debate, may not be a reliable indicator of population density as expected under metabolic theory. PMID:29176819

High resolution telescope and spectrograph observations of solar fine structure in the 1600 A region

NASA Technical Reports Server (NTRS)

Cook, J. W.; Brueckner, G. E.; Bartoe, J.-D. F.

1983-01-01

High spatial resolution spectroheliograms of the 1600 A region obtained during the HRTS rocket flight of 1978 February 13 are presented. The morphology, fine structure, and temporal behavior of emission bright points (BPs) in active and quiet regions are illustrated. In quiet regions, network elements persist as morphological units, although individual BPs may vary in intensity while usually lasting the flight duration. In cell centers, the BPs are highly variable on a 1 minute time scale. BPs in plages remain more constant in brightness over the observing sequence. BPs cover less than 4 percent of the quiet surface. The lifetime and degree of packing of BPs vary with the local strength of the magnetic field.

Development of piezoelectric composites for transducers

NASA Astrophysics Data System (ADS)

Safari, A.

1994-07-01

For the past decade and a half, many different types of piezoelectric ceramic-polymer composites have been developed intended for transducer applications. These diphasic composites are prepared from non-active polymer, such as epoxy, and piezoelectric ceramic, such as PZT, in the form of filler powders, elongated fibers, multilayer and more complex three-dimensional structures. For the last four years, most of the efforts have been given to producing large area and fine scale PZT fiber composites. In this paper, processing of piezoelectric ceramic-polymer composites with various connectivity patterns are reviewed. Development of fine scale piezoelectric composites by lost mold, injection molding and the relic method are described. Research activities of different groups for preparing large area piezocomposites for hydrophone and actuator applications are briefly reviewed. Initial development of electrostrictive ceramics and composites are also

Estimating fine-scale land use change dynamics using an expedient photointerpretation-based method

Treesearch

Tonya Lister; Andrew Lister; Eunice Alexander

2009-01-01

Population growth and urban expansion have resulted in the loss of forest land. With growing concerns about this loss and its implications for global processes and carbon budgets, there is a great need for detailed and reliable land use change data. Currently, the Northern Research Station uses an Annual Inventory design whereby all plots are revisited every 5 years...

Network analysis reveals multiscale controls on streamwater chemistry

USGS Publications Warehouse

McGuire, Kevin J.; Torgersen, Christian E.; Likens, Gene E.; Buso, Donald C.; Lowe, Winsor H.; Bailey, Scott W.

2014-01-01

By coupling synoptic data from a basin-wide assessment of streamwater chemistry with network-based geostatistical analysis, we show that spatial processes differentially affect biogeochemical condition and pattern across a headwater stream network. We analyzed a high-resolution dataset consisting of 664 water samples collected every 100 m throughout 32 tributaries in an entire fifth-order stream network. These samples were analyzed for an exhaustive suite of chemical constituents. The fine grain and broad extent of this study design allowed us to quantify spatial patterns over a range of scales by using empirical semivariograms that explicitly incorporated network topology. Here, we show that spatial structure, as determined by the characteristic shape of the semivariograms, differed both among chemical constituents and by spatial relationship (flow-connected, flow-unconnected, or Euclidean). Spatial structure was apparent at either a single scale or at multiple nested scales, suggesting separate processes operating simultaneously within the stream network and surrounding terrestrial landscape. Expected patterns of spatial dependence for flow-connected relationships (e.g., increasing homogeneity with downstream distance) occurred for some chemical constituents (e.g., dissolved organic carbon, sulfate, and aluminum) but not for others (e.g., nitrate, sodium). By comparing semivariograms for the different chemical constituents and spatial relationships, we were able to separate effects on streamwater chemistry of (i) fine-scale versus broad-scale processes and (ii) in-stream processes versus landscape controls. These findings provide insight on the hierarchical scaling of local, longitudinal, and landscape processes that drive biogeochemical patterns in stream networks.

Network analysis reveals multiscale controls on streamwater chemistry

PubMed Central

McGuire, Kevin J.; Torgersen, Christian E.; Likens, Gene E.; Buso, Donald C.; Lowe, Winsor H.; Bailey, Scott W.

2014-01-01

By coupling synoptic data from a basin-wide assessment of streamwater chemistry with network-based geostatistical analysis, we show that spatial processes differentially affect biogeochemical condition and pattern across a headwater stream network. We analyzed a high-resolution dataset consisting of 664 water samples collected every 100 m throughout 32 tributaries in an entire fifth-order stream network. These samples were analyzed for an exhaustive suite of chemical constituents. The fine grain and broad extent of this study design allowed us to quantify spatial patterns over a range of scales by using empirical semivariograms that explicitly incorporated network topology. Here, we show that spatial structure, as determined by the characteristic shape of the semivariograms, differed both among chemical constituents and by spatial relationship (flow-connected, flow-unconnected, or Euclidean). Spatial structure was apparent at either a single scale or at multiple nested scales, suggesting separate processes operating simultaneously within the stream network and surrounding terrestrial landscape. Expected patterns of spatial dependence for flow-connected relationships (e.g., increasing homogeneity with downstream distance) occurred for some chemical constituents (e.g., dissolved organic carbon, sulfate, and aluminum) but not for others (e.g., nitrate, sodium). By comparing semivariograms for the different chemical constituents and spatial relationships, we were able to separate effects on streamwater chemistry of (i) fine-scale versus broad-scale processes and (ii) in-stream processes versus landscape controls. These findings provide insight on the hierarchical scaling of local, longitudinal, and landscape processes that drive biogeochemical patterns in stream networks. PMID:24753575

Network analysis reveals multiscale controls on streamwater chemistry.

PubMed

McGuire, Kevin J; Torgersen, Christian E; Likens, Gene E; Buso, Donald C; Lowe, Winsor H; Bailey, Scott W

2014-05-13

By coupling synoptic data from a basin-wide assessment of streamwater chemistry with network-based geostatistical analysis, we show that spatial processes differentially affect biogeochemical condition and pattern across a headwater stream network. We analyzed a high-resolution dataset consisting of 664 water samples collected every 100 m throughout 32 tributaries in an entire fifth-order stream network. These samples were analyzed for an exhaustive suite of chemical constituents. The fine grain and broad extent of this study design allowed us to quantify spatial patterns over a range of scales by using empirical semivariograms that explicitly incorporated network topology. Here, we show that spatial structure, as determined by the characteristic shape of the semivariograms, differed both among chemical constituents and by spatial relationship (flow-connected, flow-unconnected, or Euclidean). Spatial structure was apparent at either a single scale or at multiple nested scales, suggesting separate processes operating simultaneously within the stream network and surrounding terrestrial landscape. Expected patterns of spatial dependence for flow-connected relationships (e.g., increasing homogeneity with downstream distance) occurred for some chemical constituents (e.g., dissolved organic carbon, sulfate, and aluminum) but not for others (e.g., nitrate, sodium). By comparing semivariograms for the different chemical constituents and spatial relationships, we were able to separate effects on streamwater chemistry of (i) fine-scale versus broad-scale processes and (ii) in-stream processes versus landscape controls. These findings provide insight on the hierarchical scaling of local, longitudinal, and landscape processes that drive biogeochemical patterns in stream networks.

Complex distribution patterns, ecology and coexistence of ploidy levels of Allium oleraceum (Alliaceae) in the Czech Republic

PubMed Central

Duchoslav, Martin; Šafářová, Lenka; Krahulec, František

2010-01-01

Background and Aims Despite extensive study of polyploidy, its origin, and ecogeographical differences between polyploids and their diploid progenitors, few studies have addressed ploidy-level structure and patterns of ecogeographical differentiation at various spatial scales using detailed sampling procedures. The pattern of coexistence of polyploids in the geophyte Allium oleraceum at the landscape and locality scale and their ecology were studied. Methods Flow cytometry and root-tip squashes were used to identify the ploidy level of 4347 plants from 325 populations sampled from the Czech Republic using a stratified random sampling procedure. Ecological differentiation among ploidy levels was tested by comparing sets of environmental variables recorded at each locality. Key Results Across the entire sampling area, pentaploids (2n = 5x = 40) predominated, while hexaploids (2n = 6x = 48) and tetraploids (2n = 4x = 32) were less frequent. The distribution of tetra- and hexaploids was partially sympatric (in the eastern part) to parapatric (in the western part of the Czech Republic) whereas pentaploids were sympatric with other cytotypes. Plants of different ploidy levels were found to be ecologically differentiated and the ruderal character of cytotypes increased in the direction 4x → 5x → 6x with the largest realized niche differences between tetra- and hexaploids. Most populations contained only one ploidy level (77 %), 22 % had two (all possible combinations) and 1 % were composed of three ploidy levels. The majority of 4x + 5x and 5x + 6x mixed populations occurred in sympatry with uniform populations of the participating cytotypes in sites with ecologically heterogeneous or marginal environment, suggesting secondary contact between cytotypes. Some mixed 4x + 6x populations dominated by tetraploids being sympatric and intermixed with uniform 4x populations might represent primary zones of cytotype contact. Almost no mixed accessions were observed on the fine spatial scale in mixed populations. Conclusions The results provide evidence for adaptive differences among ploidy levels, which may contribute to their complex distribution pattern. The prevalence of asexual reproduction, limited dispersal and equilibrium-disrupting processes may support local coexistence of cytotypes. PMID:20363760

Factors associated with the deposition of Cladophora on Lake Michigan beaches in 2012

USGS Publications Warehouse

Riley, Stephen C.; Tucker, Taaja R.; Adams, Jean V.; Fogarty, Lisa R.; Lafrancois, Brenda Moraska

2015-01-01

Deposition of the macroalgae Cladophora spp. was monitored on 18 beaches around Lake Michigan during 2012 at a high temporal frequency. We observed a high degree of spatial variability in Cladophora deposition among beaches on Lake Michigan, even within local regions, with no clear regional pattern in the intensity of Cladophora deposition. A strong seasonal pattern in Cladophora deposition was observed, with the heaviest deposition occurring during mid-summer. Several beaches exhibited high temporal variability in Cladophora deposition over short time scales, suggesting that drifting algal mats may be extremely dynamic in nearshore environments of the Great Lakes. Cladophora deposition on Lake Michigan beaches was primarily related to the presence of nearshore structures, local population density, and nearshore bathymetry. There was relatively little evidence that waves, winds, or currents were associated with Cladophora deposition on beaches, but this may be due to the relatively poor resolution of existing nearshore hydrodynamic data. Developing a predictive understanding of beach-cast Cladophora dynamics in Great Lakes environments may require both intensive Cladophora monitoring and fine-scale local hydrodynamic modeling efforts.

Genomic analyses of Northern snakehead (Channa argus) populations in North America

PubMed Central

Resh, Carlee A.; Galaska, Matthew P.

2018-01-01

Background The introduction of northern snakehead (Channa argus; Anabantiformes: Channidae) and their subsequent expansion is one of many problematic biological invasions in the United States. This harmful aquatic invasive species has become established in various parts of the eastern United States, including the Potomac River basin, and has recently become established in the Mississippi River basin in Arkansas. Effective management of C. argus and prevention of its further spread depends upon knowledge of current population structure in the United States. Methods Novel methods for invasive species using whole genomic scans provide unprecedented levels of data, which are able to investigate fine scale differences between and within populations of organisms. In this study, we utilize 2b-RAD genomic sequencing to recover 1,007 single-nucleotide polymorphism (SNP) loci from genomic DNA extracted from 165 C. argus individuals: 147 individuals sampled along the East Coast of the United States and 18 individuals sampled throughout Arkansas. Results Analysis of those SNP loci help to resolve existing population structure and recover five genetically distinct populations of C. argus in the United States. Additionally, information from the SNP loci enable us to begin to calculate the long-term effective population size ranges of this harmful aquatic invasive species. We estimate long-term Ne to be 1,840,000–18,400,000 for the Upper Hudson River basin, 4,537,500–45,375,000 for the Lower Hudson River basin, 3,422,500–34,225,000 for the Potomac River basin, 2,715,000–7,150,000 for Philadelphia, and 2,580,000–25,800,000 for Arkansas populations. Discussion and Conclusions This work provides evidence for the presence of more genetic populations than previously estimated and estimates population size, showing the invasive potential of C. argus in the United States. The valuable information gained from this study will allow effective management of the existing populations to avoid expansion and possibly enable future eradication efforts. PMID:29637024

Genomic analyses of Northern snakehead (Channa argus) populations in North America.

PubMed

Resh, Carlee A; Galaska, Matthew P; Mahon, Andrew R

2018-01-01

The introduction of northern snakehead ( Channa argus ; Anabantiformes: Channidae) and their subsequent expansion is one of many problematic biological invasions in the United States. This harmful aquatic invasive species has become established in various parts of the eastern United States, including the Potomac River basin, and has recently become established in the Mississippi River basin in Arkansas. Effective management of C. argus and prevention of its further spread depends upon knowledge of current population structure in the United States. Novel methods for invasive species using whole genomic scans provide unprecedented levels of data, which are able to investigate fine scale differences between and within populations of organisms. In this study, we utilize 2b-RAD genomic sequencing to recover 1,007 single-nucleotide polymorphism (SNP) loci from genomic DNA extracted from 165 C. argus individuals: 147 individuals sampled along the East Coast of the United States and 18 individuals sampled throughout Arkansas. Analysis of those SNP loci help to resolve existing population structure and recover five genetically distinct populations of C. argus in the United States. Additionally, information from the SNP loci enable us to begin to calculate the long-term effective population size ranges of this harmful aquatic invasive species. We estimate long-term N e to be 1,840,000-18,400,000 for the Upper Hudson River basin, 4,537,500-45,375,000 for the Lower Hudson River basin, 3,422,500-34,225,000 for the Potomac River basin, 2,715,000-7,150,000 for Philadelphia, and 2,580,000-25,800,000 for Arkansas populations. This work provides evidence for the presence of more genetic populations than previously estimated and estimates population size, showing the invasive potential of C. argus in the United States. The valuable information gained from this study will allow effective management of the existing populations to avoid expansion and possibly enable future eradication efforts.

The influence of hydrology and waterway distance on population structure of Chinook salmon Oncorhynchus tshawytscha in a large river.

PubMed

Olsen, J B; Beacham, T D; Wetklo, M; Seeb, L W; Smith, C T; Flannery, B G; Wenburg, J K

2010-04-01

Adult Chinook salmon Oncorhynchus tshawytscha navigate in river systems using olfactory cues that may be influenced by hydrologic factors such as flow and the number, size and spatial distribution of tributaries. Thus, river hydrology may influence both homing success and the level of straying (gene flow), which in turn influences population structure. In this study, two methods of multivariate analysis were used to examine the extent to which four indicators of hydrology and waterway distance explained population structure of O. tshawytscha in the Yukon River. A partial Mantel test showed that the indicators of hydrology were positively associated with broad-scale (Yukon basin) population structure, when controlling for the influence of waterway distance. Multivariate multiple regression showed that waterway distance, supplemented with the number and flow of major drainage basins, explained more variation in broad-scale population structure than any single indicator. At an intermediate spatial scale, indicators of hydrology did not appear to influence population structure after accounting for waterway distance. These results suggest that habitat changes in the Yukon River, which alter hydrology, may influence the basin-wide pattern of population structure in O. tshawytscha. Further research is warranted on the role of hydrology in concert with waterway distance in influencing population structure in Pacific salmon.

Admixture and gene flow from Russia in the recovering Northern European brown bear (Ursus arctos).

PubMed

Kopatz, Alexander; Eiken, Hans Geir; Aspi, Jouni; Kojola, Ilpo; Tobiassen, Camilla; Tirronen, Konstantin F; Danilov, Pjotr I; Hagen, Snorre B

2014-01-01

Large carnivores were persecuted to near extinction during the last centuries, but have now recovered in some countries. It has been proposed earlier that the recovery of the Northern European brown bear is supported by migration from Russia. We tested this hypothesis by obtaining for the first time continuous sampling of the whole Finnish bear population, which is located centrally between the Russian and Scandinavian bear populations. The Finnish population is assumed to experience high gene flow from Russian Karelia. If so, no or a low degree of genetic differentiation between Finnish and Russian bears could be expected. We have genotyped bears extensively from all over Finland using 12 validated microsatellite markers and compared their genetic composition to bears from Russian Karelia, Sweden, and Norway. Our fine masked investigation identified two overlapping genetic clusters structured by isolation-by-distance in Finland (pairwise FST = 0.025). One cluster included Russian bears, and migration analyses showed a high number of migrants from Russia into Finland, providing evidence of eastern gene flow as an important driver during recovery. In comparison, both clusters excluded bears from Sweden and Norway, and we found no migrants from Finland in either country, indicating that eastern gene flow was probably not important for the population recovery in Scandinavia. Our analyses on different spatial scales suggest a continuous bear population in Finland and Russian Karelia, separated from Scandinavia.

Admixture and Gene Flow from Russia in the Recovering Northern European Brown Bear (Ursus arctos)

PubMed Central

Kopatz, Alexander; Eiken, Hans Geir; Aspi, Jouni; Kojola, Ilpo; Tobiassen, Camilla; Tirronen, Konstantin F.; Danilov, Pjotr I.; Hagen, Snorre B.

2014-01-01

Large carnivores were persecuted to near extinction during the last centuries, but have now recovered in some countries. It has been proposed earlier that the recovery of the Northern European brown bear is supported by migration from Russia. We tested this hypothesis by obtaining for the first time continuous sampling of the whole Finnish bear population, which is located centrally between the Russian and Scandinavian bear populations. The Finnish population is assumed to experience high gene flow from Russian Karelia. If so, no or a low degree of genetic differentiation between Finnish and Russian bears could be expected. We have genotyped bears extensively from all over Finland using 12 validated microsatellite markers and compared their genetic composition to bears from Russian Karelia, Sweden, and Norway. Our fine masked investigation identified two overlapping genetic clusters structured by isolation-by-distance in Finland (pairwise FST = 0.025). One cluster included Russian bears, and migration analyses showed a high number of migrants from Russia into Finland, providing evidence of eastern gene flow as an important driver during recovery. In comparison, both clusters excluded bears from Sweden and Norway, and we found no migrants from Finland in either country, indicating that eastern gene flow was probably not important for the population recovery in Scandinavia. Our analyses on different spatial scales suggest a continuous bear population in Finland and Russian Karelia, separated from Scandinavia. PMID:24839968

Effects of Demographic History on the Detection of Recombination Hotspots from Linkage Disequilibrium

PubMed Central

Dapper, Amy L; Payseur, Bret A

2018-01-01

Abstract In some species, meiotic recombination is concentrated in small genomic regions. These “recombination hotspots” leave signatures in fine-scale patterns of linkage disequilibrium, raising the prospect that the genomic landscape of hotspots can be characterized from sequence variation. This approach has led to the inference that hotspots evolve rapidly in some species, but are conserved in others. Historic demographic events, such as population bottlenecks, are known to affect patterns of linkage disequilibrium across the genome, violating population genetic assumptions of this approach. Although such events are prevalent, demographic history is generally ignored when making inferences about the evolution of recombination hotspots. To determine the effect of demography on the detection of recombination hotspots, we use the coalescent to simulate haplotypes with a known recombination landscape. We measure the ability of popular linkage disequilibrium-based programs to detect hotspots across a range of demographic histories, including population bottlenecks, hidden population structure, population expansions, and population contractions. We find that demographic events have the potential to greatly reduce the power and increase the false positive rate of hotspot discovery. Neither the power nor the false positive rate of hotspot detection can be predicted without also knowing the demographic history of the sample. Our results suggest that ignoring demographic history likely overestimates the power to detect hotspots and therefore underestimates the degree of hotspot sharing between species. We suggest strategies for incorporating demographic history into population genetic inferences about recombination hotspots. PMID:29045724

Fine-mapping of lipid regions in global populations discovers ethnic-specific signals and refines previously identified lipid loci.

PubMed

Zubair, Niha; Graff, Mariaelisa; Luis Ambite, Jose; Bush, William S; Kichaev, Gleb; Lu, Yingchang; Manichaikul, Ani; Sheu, Wayne H-H; Absher, Devin; Assimes, Themistocles L; Bielinski, Suzette J; Bottinger, Erwin P; Buzkova, Petra; Chuang, Lee-Ming; Chung, Ren-Hua; Cochran, Barbara; Dumitrescu, Logan; Gottesman, Omri; Haessler, Jeffrey W; Haiman, Christopher; Heiss, Gerardo; Hsiung, Chao A; Hung, Yi-Jen; Hwu, Chii-Min; Juang, Jyh-Ming J; Le Marchand, Loic; Lee, I-Te; Lee, Wen-Jane; Lin, Li-An; Lin, Danyu; Lin, Shih-Yi; Mackey, Rachel H; Martin, Lisa W; Pasaniuc, Bogdan; Peters, Ulrike; Predazzi, Irene; Quertermous, Thomas; Reiner, Alex P; Robinson, Jennifer; Rotter, Jerome I; Ryckman, Kelli K; Schreiner, Pamela J; Stahl, Eli; Tao, Ran; Tsai, Michael Y; Waite, Lindsay L; Wang, Tzung-Dau; Buyske, Steven; Ida Chen, Yii-Der; Cheng, Iona; Crawford, Dana C; Loos, Ruth J F; Rich, Stephen S; Fornage, Myriam; North, Kari E; Kooperberg, Charles; Carty, Cara L

2016-12-15

Genome-wide association studies have identified over 150 loci associated with lipid traits, however, no large-scale studies exist for Hispanics and other minority populations. Additionally, the genetic architecture of lipid-influencing loci remains largely unknown. We performed one of the most racially/ethnically diverse fine-mapping genetic studies of HDL-C, LDL-C, and triglycerides to-date using SNPs on the MetaboChip array on 54,119 individuals: 21,304 African Americans, 19,829 Hispanic Americans, 12,456 Asians, and 530 American Indians. The majority of signals found in these groups generalize to European Americans. While we uncovered signals unique to racial/ethnic populations, we also observed systematically consistent lipid associations across these groups. In African Americans, we identified three novel signals associated with HDL-C (LPL, APOA5, LCAT) and two associated with LDL-C (ABCG8, DHODH). In addition, using this population, we refined the location for 16 out of the 58 known MetaboChip lipid loci. These results can guide tailored screening efforts, reveal population-specific responses to lipid-lowering medications, and aid in the development of new targeted drug therapies. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Recognition of strong seasonality and climatic cyclicity in an ancient, fluvially dominated, tidally influenced point bar: Middle McMurray Formation, Lower Steepbank River, north-eastern Alberta, Canada

NASA Astrophysics Data System (ADS)

Jablonski, Bryce V. J.; Dalrymple, Robert W.

2016-04-01

Inclined heterolithic stratification in the Lower Cretaceous McMurray Formation, exposed along the Steepbank River in north-eastern Alberta, Canada, accumulated on point bars of a 30 to 40 m deep continental-scale river in the fluvial-marine transition. This inclined heterolithic stratification consists of two alternating lithologies, sand and fine-grained beds. Sand beds were deposited rapidly by unidirectional currents and contain little or no bioturbation. Fine-grained beds contain rare tidal structures, and are intensely bioturbated by low-diversity ichnofossil assemblages. The alternations between the sand and fine-grained beds are probably caused by strong variations in fluvial discharge; that are believed to be seasonal (probably annual) in duration. The sand beds accumulated during river floods, under fluvially dominated conditions when the water was fresh, whereas the fine-grained beds accumulated during the late stages of the river flood and deposition continued under tidally influenced brackish-water conditions during times of low-river flow (i.e. the interflood periods). These changes reflect the annual migration in the positions of the tidal and salinity limits within the fluvial-marine transition that result from changes in river discharge. Sand and fine-grained beds are cyclically organized in the studied outcrops forming metre-scale cycles. A single metre-scale cycle is defined by a sharp base, an upward decrease in sand-bed thickness and upward increases in the preservation of fine-grained beds and the intensity of bioturbation. Metre-scale cycles are interpreted to be the product of a longer term (decadal) cyclicity in fluvial discharge, probably caused by fluctuations in ocean or solar dynamics. The volumetric dominance of river-flood deposits within the succession suggests that accumulation occurred in a relatively landward position within the fluvial-marine transition. This study shows that careful observation can reveal much about the interplay of processes within the fluvial-marine transition, which in turn provides a powerful tool for determining the palaeo-environmental location of a deposit within the fluvial-marine transition.

Quantifying apparent anisotropy in a chemically heterogeneous Earth's mantle

NASA Astrophysics Data System (ADS)

Faccenda, M.; Ferreira, A. M.; Lithgow-Bertelloni, C. R.; Stixrude, L. P.; Pennacchioni, G.

2017-12-01

The interpretation of seismic observations of anisotropy is not straightforward. For example, it is well established that a finely layered, purely isotropic medium is equivalent at large scale to a homogeneous anisotropic medium (Backus, 1962) and there is seismological evidence for fine layered media, such as quasi-laminated structures constrained from high-frequency scattered waves (e.g., Furumura and Kennett, 2005; Kennett and Furumura, 2008). Thus, when imaging fine layering with seismic wave data with wavelength larger than the layer's thickness may result in artificial (also called apparent) anisotropy. Recent studies identified families of stable fine scale models that are equivalent to long-wavelength, vertically transversely isotropic (VTI) models (Fichtner et al., 2013; Wang et al., 2013; Bodin et al., 2015), and efforts to consider more general media are currently under way (e.g., Capdeville et al., 2010a,b). However, it is not clear whether the equivalent fine scale models are compatible with the properties of Earth's mantle materials. In this contribution, we quantify apparent anisotropy arising from fine layering by considering a range of realistic Earth's compositions both at grain and rock scale. We show that significant apparent anisotropy can be formed in ideal conditions only in very narrow regions, while in most of the Earth's mantle apparent anisotropy will hardly be detectable. ReferencesBackus, G.E., 1962. J. Geophys. Res. 67, 4427-4440. Bodin, T., Capdeville, Y., Romanowicz, B. & Montagner, J.-P., 2015. In The Earth's Heterogeneous Mantle, pp. 105-144, eds Khan, A. & Deschamps, F., Springer. Capdeville, Y., Guillot, L., Marigo, J.J., 2010a. Geophys. J. Int. 182, 903-922. Capdeville, Y., Guillot, L., Marigo, J.J., 2010b. Geophys. J. Int. 181, 897-910. Fichtner, A., B. Kennett, and J. Trampert, 2013. Phys. Earth Planet. Inter., 219, 11-20. Furumura, T., Kennett, B.L.N., 2005. J. Geophys. Res. 110, 10.129/2004JB003486. Kennett, B.L.N., Furumura, T., 2008. Geophys. J. Int. 172, 363-382. Wang, N., Montagner J.-P., Fichtner, A., Capdeville, Y., 2013. Geophys. Res. Lett. 40, 4284-4288.

Integrated Monitoring of Mola mola Behaviour in Space and Time.

PubMed

Sousa, Lara L; López-Castejón, Francisco; Gilabert, Javier; Relvas, Paulo; Couto, Ana; Queiroz, Nuno; Caldas, Renato; Dias, Paulo Sousa; Dias, Hugo; Faria, Margarida; Ferreira, Filipe; Ferreira, António Sérgio; Fortuna, João; Gomes, Ricardo Joel; Loureiro, Bruno; Martins, Ricardo; Madureira, Luis; Neiva, Jorge; Oliveira, Marina; Pereira, João; Pinto, José; Py, Frederic; Queirós, Hugo; Silva, Daniel; Sujit, P B; Zolich, Artur; Johansen, Tor Arne; de Sousa, João Borges; Rajan, Kanna

2016-01-01

Over the last decade, ocean sunfish movements have been monitored worldwide using various satellite tracking methods. This study reports the near-real time monitoring of fine-scale (< 10 m) behaviour of sunfish. The study was conducted in southern Portugal in May 2014 and involved satellite tags and underwater and surface robotic vehicles to measure both the movements and the contextual environment of the fish. A total of four individuals were tracked using custom-made GPS satellite tags providing geolocation estimates of fine-scale resolution. These accurate positions further informed sunfish areas of restricted search (ARS), which were directly correlated to steep thermal frontal zones. Simultaneously, and for two different occasions, an Autonomous Underwater Vehicle (AUV) video-recorded the path of the tracked fish and detected buoyant particles in the water column. Importantly, the densities of these particles were also directly correlated to steep thermal gradients. Thus, both sunfish foraging behaviour (ARS) and possibly prey densities, were found to be influenced by analogous environmental conditions. In addition, the dynamic structure of the water transited by the tracked individuals was described by a Lagrangian modelling approach. The model informed the distribution of zooplankton in the region, both horizontally and in the water column, and the resultant simulated densities positively correlated with sunfish ARS behaviour estimator (rs = 0.184, p<0.001). The model also revealed that tracked fish opportunistically displace with respect to subsurface current flow. Thus, we show how physical forcing and current structure provide a rationale for a predator's fine-scale behaviour observed over a two weeks in May 2014.

Integrated Monitoring of Mola mola Behaviour in Space and Time

PubMed Central

Sousa, Lara L.; López-Castejón, Francisco; Gilabert, Javier; Relvas, Paulo; Couto, Ana; Queiroz, Nuno; Caldas, Renato; Dias, Paulo Sousa; Dias, Hugo; Faria, Margarida; Ferreira, Filipe; Ferreira, António Sérgio; Fortuna, João; Gomes, Ricardo Joel; Loureiro, Bruno; Martins, Ricardo; Madureira, Luis; Neiva, Jorge; Oliveira, Marina; Pereira, João; Pinto, José; Py, Frederic; Queirós, Hugo; Silva, Daniel; Sujit, P. B.; Zolich, Artur; Johansen, Tor Arne; de Sousa, João Borges; Rajan, Kanna

2016-01-01

Over the last decade, ocean sunfish movements have been monitored worldwide using various satellite tracking methods. This study reports the near-real time monitoring of fine-scale (< 10 m) behaviour of sunfish. The study was conducted in southern Portugal in May 2014 and involved satellite tags and underwater and surface robotic vehicles to measure both the movements and the contextual environment of the fish. A total of four individuals were tracked using custom-made GPS satellite tags providing geolocation estimates of fine-scale resolution. These accurate positions further informed sunfish areas of restricted search (ARS), which were directly correlated to steep thermal frontal zones. Simultaneously, and for two different occasions, an Autonomous Underwater Vehicle (AUV) video-recorded the path of the tracked fish and detected buoyant particles in the water column. Importantly, the densities of these particles were also directly correlated to steep thermal gradients. Thus, both sunfish foraging behaviour (ARS) and possibly prey densities, were found to be influenced by analogous environmental conditions. In addition, the dynamic structure of the water transited by the tracked individuals was described by a Lagrangian modelling approach. The model informed the distribution of zooplankton in the region, both horizontally and in the water column, and the resultant simulated densities positively correlated with sunfish ARS behaviour estimator (rs = 0.184, p<0.001). The model also revealed that tracked fish opportunistically displace with respect to subsurface current flow. Thus, we show how physical forcing and current structure provide a rationale for a predator’s fine-scale behaviour observed over a two weeks in May 2014. PMID:27494028

Examination of Cross-Scale Coupling During Auroral Events using RENU2 and ISINGLASS Sounding Rocket Data.

NASA Astrophysics Data System (ADS)

Kenward, D. R.; Lessard, M.; Lynch, K. A.; Hysell, D. L.; Hampton, D. L.; Michell, R.; Samara, M.; Varney, R. H.; Oksavik, K.; Clausen, L. B. N.; Hecht, J. H.; Clemmons, J. H.; Fritz, B.

2017-12-01

The RENU2 sounding rocket (launched from Andoya rocket range on December 13th, 2015) observed Poleward Moving Auroral Forms within the dayside cusp. The ISINGLASS rockets (launched from Poker Flat rocket range on February 22, 2017 and March 2, 2017) both observed aurora during a substorm event. Despite observing very different events, both campaigns witnessed a high degree of small scale structuring within the larger auroral boundary, including Alfvenic signatures. These observations suggest a method of coupling large-scale energy input to fine scale structures within aurorae. During RENU2, small (sub-km) scale drivers persist for long (10s of minutes) time scales and result in large scale ionospheric (thermal electron) and thermospheric response (neutral upwelling). ISINGLASS observations show small scale drivers, but with short (minute) time scales, with ionospheric response characterized by the flight's thermal electron instrument (ERPA). The comparison of the two flights provides an excellent opportunity to examine ionospheric and thermospheric response to small scale drivers over different integration times.

Varying Herbivore Population Structure Correlates with Lack of Local Adaptation in a Geographic Variable Plant-Herbivore Interaction

PubMed Central

Cogni, Rodrigo; Trigo, José R.; Futuyma, Douglas J.

2011-01-01

Local adaptation of parasites to their hosts due to coevolution is a central prediction of many theories in evolutionary biology. However, empirical studies looking for parasite local adaptation show great variation in outcomes, and the reasons for such variation are largely unknown. In a previous study, we showed adaptive differentiation in the arctiid moth Utetheisa ornatrix to its host plant, the pyrrolizidine alkaloid-bearing legume Crotalaria pallida, at the continental scale, but found no differentiation at the regional scale. In the present study, we sampled the same sites to investigate factors that may contribute to the lack of differentiation at the regional scale. We performed field observations that show that specialist and non-specialist polyphagous herbivore incidence varies among populations at both scales. With a series of common-garden experiments we show that some plant traits that may affect herbivory (pyrrolizidine alkaloids and extrafloral nectaries) vary at the regional scale, while other traits (trichomes and nitrogen content) just vary at the continental scale. These results, combined with our previous evidence for plant population differentiation based on larval performance on fresh fruits, suggest that U. ornatrix is subjected to divergent selection even at the regional scale. Finally, with a microsatellite study we investigated population structure of U. ornatrix. We found that population structure is not stable over time: we found population differentiation at the regional scale in the first year of sampling, but not in the second year. Unstable population structure of the herbivore is the most likely cause of the lack of regional adaptation. PMID:22220208

Spatial Modeling and Uncertainty Assessment of Fine Scale Surface Processes Based on Coarse Terrain Elevation Data

NASA Astrophysics Data System (ADS)

Rasera, L. G.; Mariethoz, G.; Lane, S. N.

2017-12-01

Frequent acquisition of high-resolution digital elevation models (HR-DEMs) over large areas is expensive and difficult. Satellite-derived low-resolution digital elevation models (LR-DEMs) provide extensive coverage of Earth's surface but at coarser spatial and temporal resolutions. Although useful for large scale problems, LR-DEMs are not suitable for modeling hydrologic and geomorphic processes at scales smaller than their spatial resolution. In this work, we present a multiple-point geostatistical approach for downscaling a target LR-DEM based on available high-resolution training data and recurrent high-resolution remote sensing images. The method aims at generating several equiprobable HR-DEMs conditioned to a given target LR-DEM by borrowing small scale topographic patterns from an analogue containing data at both coarse and fine scales. An application of the methodology is demonstrated by using an ensemble of simulated HR-DEMs as input to a flow-routing algorithm. The proposed framework enables a probabilistic assessment of the spatial structures generated by natural phenomena operating at scales finer than the available terrain elevation measurements. A case study in the Swiss Alps is provided to illustrate the methodology.

Subpicosecond X rotations of atomic clock states

NASA Astrophysics Data System (ADS)

Song, Yunheung; Lee, Han-gyeol; Kim, Hyosub; Jo, Hanlae; Ahn, Jaewook

2018-05-01

We demonstrate subpicosecond-timescale population transfer between the pair of hyperfine ground states of atomic rubidium using a single laser-pulse. Our scheme utilizes the geometric and dynamic phases induced during Rabi oscillation through the fine-structure excited state to construct an X rotation gate for the hyperfine-state qubit system. The experiment performed with a femtosecond laser and cold rubidium atoms, in a magnetooptical trap, shows over 98% maximal population transfer between the clock states.

Development of a Linear Ion Trap Mass Spectrometer (LITMS) Investigation for Future Planetary Surface Missions

NASA Technical Reports Server (NTRS)

Brinckerhoff, W.; Danell, R.; Van Ameron, F.; Pinnick, V.; Li, X.; Arevalo, R.; Glavin, D.; Getty, S.; Mahaffy, P.; Chu, P.;

Untangling the contribution of aspect, drainage position and elevation to the spatial variability of fine surface fuels in south east Australian forests

NASA Astrophysics Data System (ADS)

Sheridan, Gary; nyman, petter; Duff, Tom; Baillie, Craig; Bovill, William; Lane, Patrick; Tolhurst, Kevin

2015-04-01

The prediction of fuel moisture content is important for estimating the rate of spread of wildfires, the ignition probability of firebrands, and for the efficient scheduling of prescribed fire. The moisture content of fine surface fuels varies spatially at large scales (10's to 100's km) due to variation in meteorological variables (eg. temperature, relative humidity, precipitation). At smaller scales (100's of metres) in steep topography spatial variability is attributed to topographic influences that include differences in radiation due to aspect and slope, differences in precipitation, temperature and relative humidity due to elevation, and differences in soil moisture due to hillslope drainage position. Variable forest structure and canopy shading adds further to the spatial variability in surface fuel moisture. In this study we aim to combine daily 5km resolution gridded weather data with 20m resolution DEM and vegetation structure data to predict the spatial variability of fine surface fuels in steep topography. Microclimate stations were established in south east Australia to monitor surface fine fuel moisture continuously (every 15 minutes) using newly developed instrumented litter packs, in addition to temperature and relative humidity measurements inside the litter pack, and measurement of precipitation and energy inputs above and below the forest canopy. Microclimate stations were established across a gradient of aspect (5 stations), drainage position (7 stations), elevation (15 stations), and canopy cover conditions (6 stations). The data from this extensive network of microclimate stations across a broad spectrum of topographic conditions is being analysed to enable the downscaling of gridded weather data to spatial scales that are relevant to the connectivity of wildfire fuels and to the scheduling and outcome of prescribed fires. The initial results from the first year of this study are presented here.

Combined single crystal polarized XAFS and XRD at high pressure: probing the interplay between lattice distortions and electronic order at multiple length scales in high T c cuprates

DOE PAGES

Fabbris, G.; Hücker, M.; Gu, G. D.; ...

2016-07-14

Some of the most exotic material properties derive from electronic states with short correlation length (~10-500 Å), suggesting that the local structural symmetry may play a relevant role in their behavior. In this study, we discuss the combined use of polarized x-ray absorption fine structure and x-ray diffraction at high pressure as a powerful method to tune and probe structural and electronic orders at multiple length scales. Besides addressing some of the technical challenges associated with such experiments, we illustrate this approach with results obtained in the cuprate La 1.875Ba 0.125CuO 4, in which the response of electronic order tomore » pressure can only be understood by probing the structure at the relevant length scales.« less

CO-DARK Star Formation and Black Hole Activity in 3C 368 at Z = 1.131: Coeval Growth of Stellar and Supermassive Black Hole Masses

NASA Astrophysics Data System (ADS)

Lamarche, C.; Stacey, G.; Brisbin, D.; Ferkinhoff, C.; Hailey-Dunsheath, S.; Nikola, T.; Riechers, D.; Sharon, C. E.; Spoon, H.; Vishwas, A.

2017-02-01

We present the detection of four far-infrared fine-structure oxygen lines, as well as strong upper limits for the CO(2-1) and [N II] 205 μm lines, in 3C 368, a well-studied radio-loud galaxy at z = 1.131. These new oxygen lines, taken in conjunction with previously observed neon and carbon fine-structure lines, suggest a powerful active galactic nucleus (AGN), accompanied by vigorous and extended star formation. A starburst dominated by O8 stars, with an age of ˜6.5 Myr, provides a good fit to the fine-structure line data. This estimated age of the starburst makes it nearly concurrent with the latest episode of AGN activity, suggesting a link between the growth of the supermassive black hole and stellar population in this source. We do not detect the CO(2-1) line, down to a level twelve times lower than the expected value for star-forming galaxies. This lack of CO line emission is consistent with recent star formation activity if the star-forming molecular gas has low metallicity, is highly fractionated (such that CO is photodissociated throughout much of the clouds), or is chemically very young (such that CO has not yet had time to form). It is also possible, although we argue it is unlikely, that the ensemble of fine-structure lines is emitted from the region heated by the AGN.

A theoretically consistent stochastic cascade for temporal disaggregation of intermittent rainfall

NASA Astrophysics Data System (ADS)

Lombardo, F.; Volpi, E.; Koutsoyiannis, D.; Serinaldi, F.

2017-06-01

Generating fine-scale time series of intermittent rainfall that are fully consistent with any given coarse-scale totals is a key and open issue in many hydrological problems. We propose a stationary disaggregation method that simulates rainfall time series with given dependence structure, wet/dry probability, and marginal distribution at a target finer (lower-level) time scale, preserving full consistency with variables at a parent coarser (higher-level) time scale. We account for the intermittent character of rainfall at fine time scales by merging a discrete stochastic representation of intermittency and a continuous one of rainfall depths. This approach yields a unique and parsimonious mathematical framework providing general analytical formulations of mean, variance, and autocorrelation function (ACF) for a mixed-type stochastic process in terms of mean, variance, and ACFs of both continuous and discrete components, respectively. To achieve the full consistency between variables at finer and coarser time scales in terms of marginal distribution and coarse-scale totals, the generated lower-level series are adjusted according to a procedure that does not affect the stochastic structure implied by the original model. To assess model performance, we study rainfall process as intermittent with both independent and dependent occurrences, where dependence is quantified by the probability that two consecutive time intervals are dry. In either case, we provide analytical formulations of main statistics of our mixed-type disaggregation model and show their clear accordance with Monte Carlo simulations. An application to rainfall time series from real world is shown as a proof of concept.