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Sample records for abundance population structure

  1. Abundant mitochondrial DNA variation and world-wide population structure in humpback whales.

    PubMed Central

    Baker, C S; Perry, A; Bannister, J L; Weinrich, M T; Abernethy, R B; Calambokidis, J; Lien, J; Lambertsen, R H; Ramírez, J U; Vasquez, O

    1993-01-01

    Hunting during the last 200 years reduced many populations of mysticete whales to near extinction. To evaluate potential genetic bottlenecks in these exploited populations, we examined mitochondrial DNA control region sequences from 90 individual humpback whales (Megaptera novaeangliae) representing six subpopulations in three ocean basins. Comparisons of relative nucleotide and nucleotype diversity reveal an abundance of genetic variation in all but one of the oceanic subpopulations. Phylogenetic reconstruction of nucleotypes and analysis of maternal gene flow show that current genetic variation is not due to postexploitation migration between oceans but is a relic of past population variability. Calibration of the rate of control region evolution across three families of whales suggests that existing humpback whale lineages are of ancient origin. Preservation of preexploitation variation in humpback whales may be attributed to their long life-span and overlapping generations and to an effective, though perhaps not timely, international prohibition against hunting. PMID:8367488

  2. Distribution, Abundance and Population Structuring of Beaked Whales in the Great Bahama Canyon, Northern Bahamas

    DTIC Science & Technology

    2007-01-01

    whales, killer whales and oceanic bottlenose dolphins , as part of an effort to assess abundance, stock structure and diet. Sightings of sea turtles...Kogia breviceps) 3 1.0 1 – 2 4 Unknown Kogia species 3 2.0 1 – 2 5 Pan-tropical spotted dolphin (Stenella attenuata) 5...10.0 4 – 25 62 Atlantic spotted dolphin (Stenella frontalis) 2 13.0 12 – 14 26 Stenella sp. 1 1.0 1 – 1 1

  3. Artemia parthenogenetica (Branchiopoda: Anostraca) from the Large Aral Sea: Abundance, distribution, population structure and cyst production

    NASA Astrophysics Data System (ADS)

    Arashkevich, Elena G.; Sapozhnikov, P. V.; Soloviov, K. A.; Kudyshkin, T. V.; Zavialov, P. O.

    2009-03-01

    The brine shrimp Artemia parthenogenetica appeared in the Large Aral Sea (Central Asia) in 1998 when mineralization reached 63 ppt. Data on Artemia abundance and biomass, along with temperature and salinity measurements were collected in the western basin during 2002-2006, primarily in the autumn. During the study period, population density grew progressively, both in terms of number, from 250 to 1260 individuals per m 3, and in terms of biomass, from 0.3 to 1.3 g per m 3. In 2005, the population density and spatial distribution in the different parts of the sea (western and eastern basins and strait) was assessed. The horizontal distribution of the Artemia population was uniform in the deep central part of the western basin, although the distribution was quite patchy in the shallow coastal zone. Depth habitat of Artemia was restricted to the upper 20-25 m of depth, as the oxygen depletion and formation of anoxic layer prevented distribution of Artemia to the deeper waters. In autumn, all females reproduced oviparously, with an average clutch size of 30-35 eggs per female. The number of eggs in a clutch was positively correlated with female body length ( r2 = 0.36-0.44).

  4. Microgeographic population structure of green swordail fish: genetic differentiation despite abundant migration.

    PubMed

    Tatarenkov, A; Healey, C I M; Avise, J C

    2010-01-01

    Swordtails (Xiphophorus; Poeciliidae) have figured prominently in research on fish mating behaviours, sexual selection, and carcinogenesis, but their population structures and dispersal patterns have been relatively neglected. Using nine microsatellite loci, we estimated genetic differentiation in Xiphophorus helleri within and between adjacent streams in Belize. The genetic data were complemented by a tagging study of movement within one stream. In the absence of physical dispersal barriers (waterfalls), population structure followed an isolation by distance (IBD) pattern. Genetic differentiation (F(ST) up to 0.07) was significant between and within creeks, despite high dispersal in the latter as judged by the tagging data. Such heterogeneity apparently was a result of genetic drift in local demes, due to small population sizes and highly skewed paternity. The IBD pattern was interrupted by waterfalls, boosting F(ST) above 0.30 between adjacent samples across these barriers. Overall, our results are helpful in understanding the interplay of evolutionary forces and population dynamics in a small fish living in a changeable habitat.

  5. Abundance, population structure and production of macro-invertebrate shredders in a Mediterranean brackish lagoon, Lake Ichkeul, Tunisia

    NASA Astrophysics Data System (ADS)

    Casagranda, Caterina; Dridi, Mohamed Sadok; Boudouresque, Charles François

    2006-02-01

    Abundance, population structure and production of the macro-invertebrates belonging to the functional feeding group of the shredders were studied in the Ichkeul wetland, northern Tunisia, from July 1993 to April 1994. Mean above-ground macrophyte biomass was at a maximum in September followed by a complete breakdown of the Potamogeton pectinatus L. meadow from October onward due to high salinity following an exceptionally dry winter. Only the meadow of Ruppia cirrhosa (Petagna) Grande at Tinja remained in place. Abundance of Gammarus aequicauda (Martynov 1931), Idotea chelipes (Pallas 1766) and Sphaeroma hookeri Leach 1814 was significantly related to the R. cirrhosa biomass. Gammarus aequicauda presented two recruitment periods in spring and autumn, and S. hookeri a third one in winter. The population of I. chelipes was renewed during winter by continued reproduction without any spring generation. Recruitment of all three species was not very successful during the study period. Life span of all three species was between 12 and 15 months. Despite their relatively low biomass and production rate, the shredders have a key function in processing macrophyte matter to different trophic levels through fragmentation and accelerating the decomposition of macrophyte biomass accumulated at the end of the growth season in the Ichkeul lagoon.

  6. [Relative abundance, population structure, habitat preferences and activity patterns of Tapirus bairdii (Perissodactyla: Tapiridae), in Chimalapas forest, Oaxaca, Mexico].

    PubMed

    Lira-Torres, Iván; Briones-Salas, Miguel; Sánchez-Rojas, Gerardo

    2014-12-01

    Baird's tapir (Tapirus bairdii) is endangered primarily because of habitat loss and fragmentation, and overhunting throughout its distribution range. One of the priority land areas for the conservation of this species is the Northern part of its range in the Chimalapas forest, Oaxaca. The aim of this research was to determine the relative abundance, population struc- ture, habitat preferences and activity patterns of Baird's tapir (Tapirus bairdii) in the Chimalapas forest, Oaxaca, Mexico, through the non-invasive technique of camera-trap sampling. A total of five sampling sessions were undertaken among 2009-2013, and used a total of 30 camera-traps in each period. The determinant factor of the sampling design was the hunting between two study areas. A total sampling effort of 9000 trap-days allowed to estimate an index of relative abundance (IRA) of 6.77 tapir photographs/1,000 trap-days (n = 61). IRA varied significantly between sampling stations (Mann-Whitney, p < 0.01). The frequency of Baird's tapir photos was higher in the dry season in tropical rain forest without hunting (χ2, p < 0.5). In the rainy season, the tropical rain forest and secondary vegetation habitats showed higher photo frequency than expected from random (χ2, p < 0.5). Considering population structure, a 95.08% of adult animals was obtained in photographic records (n = 58). Three types of activity pattern were observed, with more nocturnal records (88.33%; Kruskal-Wallis, p < 0.05). The Chimalapas forest appears to be the second most important terrestrial priority ecoregion, just after the Mayan Forest (Campeche, Chiapas, Quintana Roo), for the conservation of tapir populations, not only for Mexico but also for Central America.

  7. Distribution, Abundance and Population Structuring of Beaked Whales in the Great Bahama Canyon, Northern Bahamas

    DTIC Science & Technology

    2009-09-30

    2001) Joint interim report Bahamas marine mammal stranding event of 15 – 16 March 2000. National Oceanographic and Atmospheric Administration. 59...Structuring of Beaked Whales in the Great Bahama Canyon, Northern Bahamas Diane Elaine Claridge Bahamas Marine Mammal Research Organisation P.O. Box AB...National Marine Mammal Laboratory 7600 Sand Point Way NE Seattle, WA 98115 phone: (206) 526-4539 fax: (206) 526-6615 email: John.Durban

  8. Distribution, Abundance and Population Structuring of Beaked Whales in the Great Bahama Canyon, Northern Bahamas

    DTIC Science & Technology

    2010-09-30

    central Aleutian Islands (Table 1) and in resident killer whales (Orcinus orca ) in the Gulf of Alaska. Table 1. Comparison of contaminant ...samples to contribute to the study of beaked whale diet (through fatty acid, stable isotope and contaminant analyses) and stock structure (using...small. Analysis of absolute lipid-normalized concentrations of POPs suggests only slight inter-species differences. The levels of contamination in the

  9. Distribution, Abundance and Population Structuring of Beaked Whales in the Great Bahama Canyon, Northern Bahamas

    DTIC Science & Technology

    2012-01-01

    killer whales (Orcinus orca ) in the Gulf of Alaska. Table 4. Comparison of contaminant concentration levels (ng/g lipid) between Blainville’s and...collect skin and blubber biopsy samples to investigate beaked whale diet through fatty acid, stable isotope and contaminant analyses; and stock structure...concentrations of POPs suggests only slight inter-species differences. The levels of contamination in the Bahamas whales were not inordinately high and for

  10. Effects of predation and habitat structure on the abundance and population structure of the rock shrimp Rhynchocinetes typus (Caridea) on temperate rocky reefs.

    PubMed

    Ory, Nicolas C; Dudgeon, D; Dumont, C P; Miranda, L; Thiel, M

    2012-01-01

    Human disturbances, such as overfishing, may disrupt predator-prey interactions and modify food webs. Underwater surveys were carried out at six shallow-water reef barrens in temperate waters of northern-central Chile from October to December 2010 to describe the effects of predation, habitat complexity (low, medium and high) and refuge availability on the abundance and population structure of the rock shrimp Rhynchocinetes typus (Rhynchocinetidae), an important mesoconsumer on subtidal hard substrata. Three sites were within managed (restricted access) areas for fishermen, and three were unmanaged (open-access). Field observations and tethering experiments were conducted to examine the relationship between fish and shrimp abundances, and the relative predation rates on shrimps. Direct effects of predation on R. typus body-size distribution were examined from shrimps collected in the field and fish stomachs. The presence and the abundance of R. typus increased with habitat reef complexity and refuge availability. Shrimp abundance was negatively related to fish abundance in managed areas, but not in open-access areas, where shrimp densities were the highest. Also, predation rates and body-size distribution of shrimps were unrelated, although fish consumed more large shrimps than should be expected from their distribution in the field. R. typus occurred most often in shelters with wide openings, offering limited protection against predators, but providing potential aggregation sites for shrimps. Overall, direct effects of predation on shrimp densities and population structure were weak, but indirect effects on shrimp distribution within reefs appear to have been mediated through behavioural responses. Our study highlights the need to assess both numerical and behavioural responses of prey to determine the effects of predator loss on mesoconsumer populations.

  11. Capella: Structure and Abundances

    NASA Technical Reports Server (NTRS)

    Brickhouse, Nancy S.

    1999-01-01

    This grant covers the analysis of EUVE spectra of the cool star binary system Capella. This project has also required the analysis of simultaneous Advanced Satellite for Cosmology and Astrophysics (ASCA) data. The ASCA spectrum of Capella could not be fit with standard models; by imposing models based on strong lines observed with EUVE, a problem wavelength region was identified. Correcting the problem required calculations of atomic collision strengths of higher principal quantum number than had ever been calculated. With these new models applied to the ASCA spectrum, better fits were obtained. Findings are that: (1) ASCA and EUVE spectra are both dominated by a region at 6 x 10(exp 6) K. (2) The high energy cut-off of the ASCA spectrum is consistent with emission from the highest ionization stages of EUVE, namely Fe XXIV. (3) EUVE requires a continuous emission measure distribution with more than two temperatures. (4) The ASCA spectra are of such high statistical significance that systematic uncertainties dominate, including atomic physics issues and calibration issues. (5) While the ASCA spectral fits achieve lower Chi(exp 2 with two-temperature fits, the EUVE-derived emission measure distribution models are also consistent with the spectra. (6) The Fe/H ratio obtained from the ASCA fit is within 20 % of the Fe/H abundance obtained from the summed spectra of Capella over 5 EUVE pointings, as well as the 1996 EUVE data. This result confirms our claims that quasi-continua composed of weak emission lines in the short wavelength spectrometer of EUVE are not major contributors to the measured Capella continuum. Other abundance ratios are also determined from the ASCA data, using models derived with EUVE. Si, Si, and Mg appear to be close to solar photospheric values, while the ratio of Ne/Fe is three to four times lower than solar photospheric values. Whether there is a general First Ionization Potential (FIP) effect or a specific neon anomaly cannot be determined

  12. Capella: Structure and Abundances

    NASA Technical Reports Server (NTRS)

    Brickhouse, Nancy S.

    1999-01-01

    This grant covers the analysis of ASCA spectra of the cool star binary system Capella. This project has also required the analysis of simultaneous EUVE data. The ASCA spectrum of Capella could not be fit with standard models; by imposing models based on strong lines observed with EUVE, a problem wavelength region was identified. Correcting the problem required calculations of atomic collision strengths of higher principal quantum number than had ever been calculated, resulting in a paper in process by Liedahl and Brickhouse. With these new models applied to the ASCA spectrum, better fits were obtained. While solar abundance ratios are generally consistent with the ASCA data, the ratio of Ne/Fe is three to four times lower than solar photospheric values. Whether there is a general First Ionization Potential (FIP) effect or a specific neon anomaly cannot be determined from these data. Detailed discussion has been provided to NASA in the most recent annual report (1997). Two poster presentations have been made regarding modeling requirements. A substantial paper is in the final revision form, following review by six co-authors. The results of this work have wide implications, since the newly calculated emission lines almost certainly contribute to other problems in fitting not only other stellar spectra, but also composite supernova remnants, galaxies, and cooling flow clusters of galaxies. Furthermore, Liedahl and Brickhouse have identified other species for which lines of a similar nature (high principal quantum number) will contribute significant flux. For moderate resolution X-ray spectra, lines left out of the models in relatively isolated bands, will be attributed to continuum flux by spectral fitting engines, causing errors in line-to-continuum ratios. Thus addressing the general theoretical problem is of crucial importance.

  13. Spatio-Temporal Variation in Age Structure and Abundance of the Endangered Snail Kite: Pooling across Regions Masks a Declining and Aging Population

    PubMed Central

    Kendall, William L.; Fletcher, Robert J.; Kitchens, Wiley M.

    2016-01-01

    While variation in age structure over time and space has long been considered important for population dynamics and conservation, reliable estimates of such spatio-temporal variation in age structure have been elusive for wild vertebrate populations. This limitation has arisen because of problems of imperfect detection, the potential for temporary emigration impacting assessments of age structure, and limited information on age. However, identifying patterns in age structure is important for making reliable predictions of both short- and long-term dynamics of populations of conservation concern. Using a multistate superpopulation estimator, we estimated region-specific abundance and age structure (the proportion of individuals within each age class) of a highly endangered population of snail kites for two separate regions in Florida over 17 years (1997–2013). We find that in the southern region of the snail kite—a region known to be critical for the long-term persistence of the species—the population has declined significantly since 1997, and during this time, it has increasingly become dominated by older snail kites (> 12 years old). In contrast, in the northern region—a region historically thought to serve primarily as drought refugia—the population has increased significantly since 2007 and age structure is more evenly distributed among age classes. Given that snail kites show senescence at approximately 13 years of age, where individuals suffer higher mortality rates and lower breeding rates, these results reveal an alarming trend for the southern region. Our work illustrates the importance of accounting for spatial structure when assessing changes in abundance and age distribution and the need for monitoring of age structure in imperiled species. PMID:27681854

  14. Spatio-temporal variation in age structure and abundance of the endangered snail kite: Pooling across regions masks a declining and aging population

    USGS Publications Warehouse

    Reichert, Brian E.; Kendall, William; Fletcher, Robert J.; Kitchens, Wiley M.

    2016-01-01

    While variation in age structure over time and space has long been considered important for population dynamics and conservation, reliable estimates of such spatio-temporal variation in age structure have been elusive for wild vertebrate populations. This limitation has arisen because of problems of imperfect detection, the potential for temporary emigration impacting assessments of age structure, and limited information on age. However, identifying patterns in age structure is important for making reliable predictions of both short- and long-term dynamics of populations of conservation concern. Using a multistate superpopulation estimator, we estimated region-specific abundance and age structure (the proportion of individuals within each age class) of a highly endangered population of snail kites for two separate regions in Florida over 17 years (1997–2013). We find that in the southern region of the snail kite—a region known to be critical for the long-term persistence of the species—the population has declined significantly since 1997, and during this time, it has increasingly become dominated by older snail kites (> 12 years old). In contrast, in the northern region—a region historically thought to serve primarily as drought refugia—the population has increased significantly since 2007 and age structure is more evenly distributed among age classes. Given that snail kites show senescence at approximately 13 years of age, where individuals suffer higher mortality rates and lower breeding rates, these results reveal an alarming trend for the southern region. Our work illustrates the importance of accounting for spatial structure when assessing changes in abundance and age distribution and the need for monitoring of age structure in imperiled species.

  15. Spatial and temporal variation in the abundance, distribution and population structure of epibenthic megafauna in Port Foster, Deception Island

    NASA Astrophysics Data System (ADS)

    Cranmer, T. L.; Ruhl, H. A.; Baldwin, R. J.; Kaufmann, R. S.

    2003-06-01

    Abundance and spatial distribution of epibenthic megafauna were examined at Port Foster, Deception Island, five times between March 1999 and November 2000. Camera sled surveys and bottom trawls were used to identify and collect specimens, and camera sled photographs also were used to determine abundances and spatial distributions for each species. The ophiuroid Ophionotus victoriae, the regular echinoid Sterechinus neumayeri, and one or more species of Porifera were the most abundant taxa during this sampling period. Abundances of O. victoriae varied throughout the annual cycle, peaking in June 2000, and were correlated positively with sedimentation rates. In contrast, abundances of S. neumayeri were consistent throughout the sampling period, except for a peak in June 2000, during austral winter. Peak abundances for both species coincided with a large number of small individuals, indicating apparent recruitment events for O. victoriae and S. neumayeri during this time period. Poriferans, as a group, had statistically similar abundances during each sampling period. Low-abundance species tended to be aggregated on both small and large spatial scales, their distributions probably influenced by reproductive method, gregarious settlement, and food availability. The spatial distribution of S. neumayeri in June 2000 and O. victoriae was random across multiple spatial scales, perhaps in response to food availability and broad environmental tolerances, respectively.

  16. Increased seawater temperature increases the abundance and alters the structure of natural Vibrio populations associated with the coral Pocillopora damicornis

    PubMed Central

    Tout, Jessica; Siboni, Nachshon; Messer, Lauren F.; Garren, Melissa; Stocker, Roman; Webster, Nicole S.; Ralph, Peter J.; Seymour, Justin R.

    2015-01-01

    Rising seawater temperature associated with global climate change is a significant threat to coral health and is linked to increasing coral disease and pathogen-related bleaching events. We performed heat stress experiments with the coral Pocillopora damicornis, where temperature was increased to 31°C, consistent with the 2–3°C predicted increase in summer sea surface maxima. 16S rRNA amplicon sequencing revealed a large shift in the composition of the bacterial community at 31°C, with a notable increase in Vibrio, including known coral pathogens. To investigate the dynamics of the naturally occurring Vibrio community, we performed quantitative PCR targeting (i) the whole Vibrio community and (ii) the coral pathogen Vibrio coralliilyticus. At 31°C, Vibrio abundance increased by 2–3 orders of magnitude and V. coralliilyticus abundance increased by four orders of magnitude. Using a Vibrio-specific amplicon sequencing assay, we further demonstrated that the community composition shifted dramatically as a consequence of heat stress, with significant increases in the relative abundance of known coral pathogens. Our findings provide quantitative evidence that the abundance of potential coral pathogens increases within natural communities of coral-associated microbes as a consequence of rising seawater temperature and highlight the potential negative impacts of anthropogenic climate change on coral reef ecosystems. PMID:26042096

  17. Abundance, distribution and population structure of the copepod Calanus finmarchicus in a springtime right whale feeding area in the southwestern Gulf of Maine

    NASA Astrophysics Data System (ADS)

    Wishner, Karen F.; Schoenherr, Jill R.; Beardsley, Robert; Chen, Changsheng

    Springtime aggregations of the planktivorous right whale ( Eubalaena glacialis) occur in the northern Great South Channel region of the southwestern Gulf of Maine, where they feed upon dense concentrations of the copepod Calanus finmarchicus. This association was studied during the multidisciplinary South Channel Ocean Productivity Experiment (SCOPEX) in 1988 and 1989. The spatial and temporal variability of the abundance, geographic distribution, and population structure of these copepods were analyzed using data from 99 vertically-stratified or horizontally-sequenced MOCNESS plankton tows. Higher water column abundances and higher relative proportion of older copepod lifestages occurred near feeding whales compared to sites without whales, but total water column copepod biomass and Calanus abundance did not always differ between these types of locations. This suggests that the whales seek out aggregations of older copepod lifestages rather than simply the most dense aggregations. Other factors (and perhaps an element of chance) may influence which specific patches, among all patches potentially suitable in terms of copepod abundance and age composition, the whales utilize at a particular time. The times and locations of the highest Calansus water column abundances varied between years, as did the presence of feeding whales, probably because of year-to-year differences in the springtime temperature cycle and current strength. A temporal progression of lifestages occurred within the region in both years during the roughly 3-week duration of each survey, indicative of a growing rather than a diapausing population, at least up to the copepodite 4 (C4) stage. Due in part to a delay in the springtime warming in 1989 compared to 1988, the copepod development cycle, which is largely driven by in situ temperature, was delayed about 1-2 weeks in 1989. Peak abundances of younger Calanus were found in the northwestern part of the region each year, whereas peak abundances of

  18. Population Structure, Abundance and Movement of Whale Sharks in the Arabian Gulf and the Gulf of Oman

    PubMed Central

    Robinson, David P.; Jaidah, Mohammed Y.; Bach, Steffen; Lee, Katie; Jabado, Rima W.; Rohner, Christoph A.; March, Abi; Caprodossi, Simone; Henderson, Aaron C.; Mair, James M.; Ormond, Rupert; Pierce, Simon J.

    2016-01-01

    Data on the occurrence of whale sharks, Rhincodon typus, in the Arabian Gulf and Gulf of Oman were collected by dedicated boat surveys and via a public-sightings scheme during the period from 2011 to 2014. A total of 422 individual whale sharks were photo-identified from the Arabian Gulf and the northern Gulf of Oman during that period. The majority of sharks (81%, n = 341) were encountered at the Al Shaheen area of Qatar, 90 km off the coast, with the Musandam region of Oman a secondary area of interest. At Al Shaheen, there were significantly more male sharks (n = 171) than females (n = 78; X2 = 17.52, P < 0.05). Mean estimated total length (TL) for sharks was 6.90 m ± 1.24 (median = 7 m; n = 296). Males (7.25 m ± 1.34; median = 8 m, n = 171) were larger than females (6.44 m ±1.09; median = 7 m, n = 78; Mann-Whitney U test, p < 0.01). Of the male sharks assessed for maturity 63% were mature (n = 81), with 50% attaining maturity by 7.29 m and 100% by 9.00 m. Two female sharks of >9 m individuals were visually assessed as pregnant. Connectivity among sharks sighted in Qatari, Omani and UAE waters was confirmed by individual spot pattern matches. A total of 13 identified sharks were re-sighted at locations other than that at which they were first sighted, including movements into and out of the Arabian Gulf through the Strait of Hormuz. Maximum likelihood techniques were used to model an estimated combined population for the Arabian Gulf and Gulf of Oman of 2837 sharks ± 1243.91 S.E. (95% C.I. 1720–6295). The Al Shaheen aggregation is thus the first site described as being dominated by mature males while the free-swimming pregnant females are the first reported from the Indian Ocean. PMID:27362839

  19. Population Structure, Abundance and Movement of Whale Sharks in the Arabian Gulf and the Gulf of Oman.

    PubMed

    Robinson, David P; Jaidah, Mohammed Y; Bach, Steffen; Lee, Katie; Jabado, Rima W; Rohner, Christoph A; March, Abi; Caprodossi, Simone; Henderson, Aaron C; Mair, James M; Ormond, Rupert; Pierce, Simon J

    2016-01-01

    Data on the occurrence of whale sharks, Rhincodon typus, in the Arabian Gulf and Gulf of Oman were collected by dedicated boat surveys and via a public-sightings scheme during the period from 2011 to 2014. A total of 422 individual whale sharks were photo-identified from the Arabian Gulf and the northern Gulf of Oman during that period. The majority of sharks (81%, n = 341) were encountered at the Al Shaheen area of Qatar, 90 km off the coast, with the Musandam region of Oman a secondary area of interest. At Al Shaheen, there were significantly more male sharks (n = 171) than females (n = 78; X2 = 17.52, P < 0.05). Mean estimated total length (TL) for sharks was 6.90 m ± 1.24 (median = 7 m; n = 296). Males (7.25 m ± 1.34; median = 8 m, n = 171) were larger than females (6.44 m ±1.09; median = 7 m, n = 78; Mann-Whitney U test, p < 0.01). Of the male sharks assessed for maturity 63% were mature (n = 81), with 50% attaining maturity by 7.29 m and 100% by 9.00 m. Two female sharks of >9 m individuals were visually assessed as pregnant. Connectivity among sharks sighted in Qatari, Omani and UAE waters was confirmed by individual spot pattern matches. A total of 13 identified sharks were re-sighted at locations other than that at which they were first sighted, including movements into and out of the Arabian Gulf through the Strait of Hormuz. Maximum likelihood techniques were used to model an estimated combined population for the Arabian Gulf and Gulf of Oman of 2837 sharks ± 1243.91 S.E. (95% C.I. 1720-6295). The Al Shaheen aggregation is thus the first site described as being dominated by mature males while the free-swimming pregnant females are the first reported from the Indian Ocean.

  20. Population Genetic Structure, Abundance, and Health Status of Two Dominant Benthic Species in the Saba Bank National Park, Caribbean Netherlands: Montastraea cavernosa and Xestospongia muta

    PubMed Central

    de Bakker, Didier M.; Meesters, Erik H. W. G.; van Bleijswijk, Judith D. L.; Luttikhuizen, Pieternella C.; Breeuwer, Hans J. A. J.; Becking, Leontine E.

    2016-01-01

    Saba Bank, a submerged atoll in the Caribbean Sea with an area of 2,200 km2, has attained international conservation status due to the rich diversity of species that reside on the bank. In order to assess the role of Saba Bank as a potential reservoir of diversity for the surrounding reefs, we examined the population genetic structure, abundance and health status of two prominent benthic species, the coral Montastraea cavernosa and the sponge Xestospongia muta. Sequence data were collected from 34 colonies of M. cavernosa (nDNA ITS1-5.8S-ITS2; 892 bp) and 68 X. muta sponges (mtDNA I3-M11 partition of COI; 544 bp) on Saba Bank and around Saba Island, and compared with published data across the wider Caribbean. Our data indicate that there is genetic connectivity between populations on Saba Bank and the nearby Saba Island as well as multiple locations in the wider Caribbean, ranging in distance from 100s–1000s km. The genetic diversity of Saba Bank populations of M. cavernosa (π = 0.055) and X. muta (π = 0.0010) was comparable to those in other regions in the western Atlantic. Densities and health status were determined along 11 transects of 50 m2 along the south-eastern rim of Saba Bank. The densities of M. cavernosa (0.27 ind. m-2, 95% CI: 0.12–0.52) were average, while the densities of X. muta (0.09 ind. m-2, 95% CI: 0.02–0.32) were generally higher with respect to other Caribbean locations. No disease or bleaching was present in any of the specimens of the coral M. cavernosa, however, we did observe partial tissue loss (77.9% of samples) as well as overgrowth (48.1%), predominantly by cyanobacteria. In contrast, the majority of observed X. muta (83.5%) showed signs of presumed bleaching. The combined results of apparent gene flow among populations on Saba Bank and surrounding reefs, the high abundance and unique genetic diversity, indicate that Saba Bank could function as an important buffer for the region. Either as a natural source of larvae to

  1. Population Genetic Structure, Abundance, and Health Status of Two Dominant Benthic Species in the Saba Bank National Park, Caribbean Netherlands: Montastraea cavernosa and Xestospongia muta.

    PubMed

    de Bakker, Didier M; Meesters, Erik H W G; van Bleijswijk, Judith D L; Luttikhuizen, Pieternella C; Breeuwer, Hans J A J; Becking, Leontine E

    2016-01-01

    Saba Bank, a submerged atoll in the Caribbean Sea with an area of 2,200 km2, has attained international conservation status due to the rich diversity of species that reside on the bank. In order to assess the role of Saba Bank as a potential reservoir of diversity for the surrounding reefs, we examined the population genetic structure, abundance and health status of two prominent benthic species, the coral Montastraea cavernosa and the sponge Xestospongia muta. Sequence data were collected from 34 colonies of M. cavernosa (nDNA ITS1-5.8S-ITS2; 892 bp) and 68 X. muta sponges (mtDNA I3-M11 partition of COI; 544 bp) on Saba Bank and around Saba Island, and compared with published data across the wider Caribbean. Our data indicate that there is genetic connectivity between populations on Saba Bank and the nearby Saba Island as well as multiple locations in the wider Caribbean, ranging in distance from 100s-1000s km. The genetic diversity of Saba Bank populations of M. cavernosa (π = 0.055) and X. muta (π = 0.0010) was comparable to those in other regions in the western Atlantic. Densities and health status were determined along 11 transects of 50 m2 along the south-eastern rim of Saba Bank. The densities of M. cavernosa (0.27 ind. m-2, 95% CI: 0.12-0.52) were average, while the densities of X. muta (0.09 ind. m-2, 95% CI: 0.02-0.32) were generally higher with respect to other Caribbean locations. No disease or bleaching was present in any of the specimens of the coral M. cavernosa, however, we did observe partial tissue loss (77.9% of samples) as well as overgrowth (48.1%), predominantly by cyanobacteria. In contrast, the majority of observed X. muta (83.5%) showed signs of presumed bleaching. The combined results of apparent gene flow among populations on Saba Bank and surrounding reefs, the high abundance and unique genetic diversity, indicate that Saba Bank could function as an important buffer for the region. Either as a natural source of larvae to replenish

  2. Effects of Fragment and Vegetation Structure on the Population Abundance of Ateles hybridus, Alouatta seniculus and Cebus albifrons in Magdalena Valley, Colombia.

    PubMed

    Marsh, Christopher; Link, Andres; King-Bailey, Gillian; Donati, Giuseppe

    2016-01-01

    Many primate species currently subsist in fragmented and anthropogenically disturbed habitats. Different threats arise depending on the species' life history strategy, dietary requirements and habitat preference. Additionally, anthropogenic disturbance is far from uniform and may affect individual forest fragments in a single landscape in differing ways. We studied the effects of fragmentation on three species of diurnal primate, Cebus albifrons, Alouatta seniculus and Ateles hybridus, in Magdalena Valley, Colombia. We tested the assumption that generalist species are more resilient than specialist species to habitat degradation by examining the fragments' vegetation and spatial structure and how these affected primate presence and abundance patterns. We found C. albifrons, a generalist, to be the most abundant species in 9 of 10 forest fragments, regardless of the level of habitat disturbance. A. hybridus, a large-bodied primate with a specialist diet, was either absent or low in abundance in fragments that had experienced recent disturbances and was found only in higher-quality fragments, regardless of the fragment size. A. seniculus, a species considered to have a highly flexible diet and the ability to survive in degraded habitat, was found in intermediate abundances between those of Cebus spp. and Ateles spp., and was more frequently found in high-quality fragments.

  3. Spatial scaling of avian population dynamics: population abundance, growth rate, and variability.

    PubMed

    Jones, Jason; Doran, Patrick J; Holmes, Richard T

    2007-10-01

    Synchrony in population fluctuations has been identified as an important component of population dynamics. In a previous study, we determined that local-scale (<15-km) spatial synchrony of bird populations in New England was correlated with synchronous fluctuations in lepidopteran larvae abundance and with the North Atlantic Oscillation. Here we address five questions that extend the scope of our earlier study using North American Breeding Bird Survey data. First, do bird populations in eastern North America exhibit spatial synchrony in abundances at scales beyond those we have documented previously? Second, does spatial synchrony depend on what population metric is analyzed (e.g., abundance, growth rate, or variability)? Third, is there geographic concordance in where species exhibit synchrony? Fourth, for those species that exhibit significant geographic concordance, are there landscape and habitat variables that contribute to the observed patterns? Fifth, is spatial synchrony affected by a species' life history traits? Significant spatial synchrony was common and its magnitude was dependent on the population metric analyzed. Twenty-four of 29 species examined exhibited significant synchrony in population abundance: mean local autocorrelation (rho)= 0.15; mean spatial extent (mean distance where rho=0) = 420.7 km. Five of the 29 species exhibited significant synchrony in annual population growth rate (mean local autocorrelation = 0.06, mean distance = 457.8 km). Ten of the 29 species exhibited significant synchrony in population abundance variability (mean local autocorrelation = 0.49, mean distance = 413.8 km). Analyses of landscape structure indicated that habitat variables were infrequent contributors to spatial synchrony. Likewise, we detected no effects of life history traits on synchrony in population abundance or growth rate. However, short-distance migrants exhibited more spatially extensive synchrony in population variability than either year

  4. "Capture" Me if You Can: Estimating Abundance of Dolphin Populations

    ERIC Educational Resources Information Center

    Thompson, Jessica; Curran, Mary Carla; Cox, Tara

    2016-01-01

    Animal populations are monitored over time to assess the effects of environmental disaster and disease, as well as the efficacy of laws designed to protect them. Determining the abundance of a species within a defined area is one method of monitoring a population. In "Capture" Me if You Can, middle school students will use data collected…

  5. Comparative abundance and population structure of sympatric Afrotropical tortoises in six rainforest areas: the differential effects of ``traditional veneration'' and of ``subsistence hunting'' by local people

    NASA Astrophysics Data System (ADS)

    Luiselli, Luca

    2003-07-01

    Hinge-back tortoises are actively hunted by human populations in sub-Saharan Africa, and are currently threatened in wide areas of their ranges. The wide wetlands and moist rainforests of the Niger Delta (southeastern Nigeria, west Africa) house three sympatric species of hinge-back tortoises: Kinixys erosa, K. homeana, and K. belliana nogueyi. These tortoises are subjected to strong hunting pressure for several reasons (mainly domestic consumption), but in a few places in Bayelsa and Rivers States (eastern axis of the Niger Delta), they are traditionally venerated as "holy animals" bringing happiness. These few places may represent ideal laboratories for monitoring the effects of hundreds of years of "traditional conservation" on the wild populations of a tropical reptile. Here, I compare the apparent abundance, sex ratio, body sizes, microhabitats, and seasonal occurrence of free-ranging Kinixys populations inhabiting three of these "traditional sanctuaries" with the same ecological aspects of conspecifics from three neighbouring areas where the tortoises are actively hunted. K. homeana was the most common species at all sites, followed by K. erosa, whereas K. belliana was extremely rare. Adult sex ratio did not depart significantly from equality both in K. erosa and in K. homeana, and was not influenced by locality or by type of "management" (veneration or harvesting). The frequency of juveniles of K. homeana was significantly higher in areas with traditional veneration than in areas of harvesting, but the same pattern was not observed in K. erosa. There was a significant decrease in terms of the number of observed specimens between areas of traditional protection and areas of usual harvesting in all species, and this trend was more obvious in K. homeana than in K. erosa. The ratio "number of observed erosa/number of observed homeana" was not dependent on the presence of traditional veneration. Mean body sizes were not different in harvest areas and in

  6. A revised DDO abundance calibration for population I red giants

    NASA Astrophysics Data System (ADS)

    Piatti, A. E.; Claria, J. J.; Minniti, D.

    1993-12-01

    Several arguments that justify establishing a revised abundance calibration for DDO photometry of population I red giants are presented. The components of the blanketing vector in the DDO C(45-48) vs C(42-45) diagram are determined for late-type dwarfs and giants. We have redefined the DDO cyanogen anomaly and calibrated it against metallicity. The sample of field giants now available with abundances derived from high dispersion spectroscopy is substantially larger than previously available, leading to a more accurate abundance calibration. Iso-abundance lines in the C(41-42) vs C(42-45) diagram have been determined for population IG and K giants and an iterative method for deriving abundances of these stars is described. We show that the new DDO abundances are in very good agreement with those derived from high dispersion spectroscopy. The new method improves by about 0.1 dex the DDO abundances derived for early G and/or late K giants, with respect to the delta(CN) method of Janes (1975).

  7. Herbivory: effects on plant abundance, distribution and population growth

    PubMed Central

    Maron, John L; Crone, Elizabeth

    2006-01-01

    Plants are attacked by many different consumers. A critical question is how often, and under what conditions, common reductions in growth, fecundity or even survival that occur due to herbivory translate to meaningful impacts on abundance, distribution or dynamics of plant populations. Here, we review population-level studies of the effects of consumers on plant dynamics and evaluate: (i) whether particular consumers have predictably more or less influence on plant abundance, (ii) whether particular plant life-history types are predictably more vulnerable to herbivory at the population level, (iii) whether the strength of plant–consumer interactions shifts predictably across environmental gradients and (iv) the role of consumers in influencing plant distributional limits. Existing studies demonstrate numerous examples of consumers limiting local plant abundance and distribution. We found larger effects of consumers on grassland than woodland forbs, stronger effects of herbivory in areas with high versus low disturbance, but no systematic or unambiguous differences in the impact of consumers based on plant life-history or herbivore feeding mode. However, our ability to evaluate these and other patterns is limited by the small (but growing) number of studies in this area. As an impetus for further study, we review strengths and challenges of population-level studies, such as interpreting net impacts of consumers in the presence of density dependence and seed bank dynamics. PMID:17002942

  8. Dielectrophoretic capture of low abundance cell population using thick electrodes

    PubMed Central

    Marchalot, Julien; Chateaux, Jean-François; Faivre, Magalie; Mertani, Hichem C.; Ferrigno, Rosaria; Deman, Anne-Laure

    2015-01-01

    Enrichment of rare cell populations such as Circulating Tumor Cells (CTCs) is a critical step before performing analysis. This paper presents a polymeric microfluidic device with integrated thick Carbon-PolyDimethylSiloxane composite (C-PDMS) electrodes designed to carry out dielectrophoretic (DEP) trapping of low abundance biological cells. Such conductive composite material presents advantages over metallic structures. Indeed, as it combines properties of both the matrix and doping particles, C-PDMS allows the easy and fast integration of conductive microstructures using a soft-lithography approach while preserving O2 plasma bonding properties of PDMS substrate and avoiding a cumbersome alignment procedure. Here, we first performed numerical simulations to demonstrate the advantage of such thick C-PDMS electrodes over a coplanar electrode configuration. It is well established that dielectrophoretic force (FDEP) decreases quickly as the distance from the electrode surface increases resulting in coplanar configuration to a low trapping efficiency at high flow rate. Here, we showed quantitatively that by using electrodes as thick as a microchannel height, it is possible to extend the DEP force influence in the whole volume of the channel compared to coplanar electrode configuration and maintaining high trapping efficiency while increasing the throughput. This model was then used to numerically optimize a thick C-PDMS electrode configuration in terms of trapping efficiency. Then, optimized microfluidic configurations were fabricated and tested at various flow rates for the trapping of MDA-MB-231 breast cancer cell line. We reached trapping efficiencies of 97% at 20 μl/h and 78.7% at 80 μl/h, for 100 μm thick electrodes. Finally, we applied our device to the separation and localized trapping of CTCs (MDA-MB-231) from a red blood cells sample (concentration ratio of 1:10). PMID:26392836

  9. Abundance trends and status of the Little Colorado River population of humpback chub

    USGS Publications Warehouse

    Coggins, L.G.; Pine, William E.; Walters, C.J.; Van Haverbeke, D. R.; Ward, D.; Johnstone, H.C.

    2006-01-01

    The abundance of the Little Colorado River population of federally listed humpback chub Gila cypha in Grand Canyon has been monitored since the late 1980s by means of catch rate indices and capture-recapture-based abundance estimators. Analyses of data from all sources using various methods are consistent and indicate that the adult population has declined since monitoring began. Intensive tagging led to a high proportion (>80%) of the adult population being marked by the mid-1990s. Analysis of these data using both closed and open abundance estimation models yields results that agree with catch rate indices about the extent of the decline. Survival rates for age-2 and older fish are age dependent but apparently not time dependent. Back-calculation of recruitment using the apparent 1990s population age structure implies periods of higher recruitment in the late 1970s to early 1980s than is now the case. Our analyses indicate that the U.S. Fish and Wildlife Service recovery criterion of stable abundance is not being met for this population. Also, there is a critical need to develop new abundance indexing and tagging methods so that early, reliable, and rapid estimates of humpback chub recruitment can be obtained to evaluate population responses to management actions designed to facilitate the restoration of Colorado River native fish communities. ?? Copyright by the American Fisheries Society 2006.

  10. Chemical abundances of multiple stellar populations in massive globular clusters

    NASA Astrophysics Data System (ADS)

    Marino, Anna F.

    2017-03-01

    Multiple stellar populations in the Milky Way globular clusters manifest themselves with a large variety. Although chemical abundance variations in light elements, including He, are ubiquitous, the amount of these variations is different in different globulars. Stellar populations with distinct Fe, C+N+O and slow-neutron capture elements have been now detected in some globular clusters, whose number will likely increase. All these chemical features correspond to specific photometric patterns. I review the chemical+photometric features of the multiple stellar populations in globular clusters and discuss how the interpretation of data is being more and more challenging. Very excitingly, the origin and evolution of globular clusters is being a complex puzzle to compose.

  11. Landscape context affects genetic diversity at a much larger spatial extent than population abundance.

    PubMed

    Jackson, Nathan D; Fahrig, Lenore

    2014-04-01

    Regional landscape context influences the fate of local populations, yet the spatial extent of this influence (called the "scale of effect") is difficult to predict. Thus, a major problem for conservation management is to understand the factors governing the scale of effect such that landscape structure surrounding a focal area is measured and managed at the biologically relevant spatial scale. One unresolved question is whether and how scale of effect may depend on the population response measured (e.g., abundance vs. presence/absence). If scales of effect differ across population outcomes of a given species, management based on one outcome may compromise another, further complicating conservation decision making. Here we used an individual-based simulation model to investigate how scales of effect of landscapes that vary in the amount and fragmentation of habitat differ among three population responses (local abundance, presence/absence, and genetic diversity). We also explored how the population response measured affects the relative importance of habitat amount and fragmentation in shaping local populations, and how dispersal distance mediates the magnitude and spatial scale of these effects. We found that the spatial scale most strongly influencing local populations depended on the outcome measured and was predicted to be small for abundance, medium-sized for presence/absence, and large for genetic diversity. Increasing spatial scales likely resulted from increasing temporal scales over which outcomes were regulated (with local genetic diversity being regulated over the largest number of generations). Thus, multiple generations of dispersal and gene flow linked local population patterns to regional population size. The effects of habitat amount dominated the effects of fragmentation for all three outcomes. Increased dispersal distance strongly reduced abundance, but not presence/absence or genetic diversity. Our results suggest that managing protected species

  12. A method for estimating abundance of mobile populations using telemetry and counts of unmarked animals

    USGS Publications Warehouse

    Clement, Matthew; O'Keefe, Joy M; Walters, Brianne

    2015-01-01

    While numerous methods exist for estimating abundance when detection is imperfect, these methods may not be appropriate due to logistical difficulties or unrealistic assumptions. In particular, if highly mobile taxa are frequently absent from survey locations, methods that estimate a probability of detection conditional on presence will generate biased abundance estimates. Here, we propose a new estimator for estimating abundance of mobile populations using telemetry and counts of unmarked animals. The estimator assumes that the target population conforms to a fission-fusion grouping pattern, in which the population is divided into groups that frequently change in size and composition. If assumptions are met, it is not necessary to locate all groups in the population to estimate abundance. We derive an estimator, perform a simulation study, conduct a power analysis, and apply the method to field data. The simulation study confirmed that our estimator is asymptotically unbiased with low bias, narrow confidence intervals, and good coverage, given a modest survey effort. The power analysis provided initial guidance on survey effort. When applied to small data sets obtained by radio-tracking Indiana bats, abundance estimates were reasonable, although imprecise. The proposed method has the potential to improve abundance estimates for mobile species that have a fission-fusion social structure, such as Indiana bats, because it does not condition detection on presence at survey locations and because it avoids certain restrictive assumptions.

  13. Negative binomial models for abundance estimation of multiple closed populations

    USGS Publications Warehouse

    Boyce, Mark S.; MacKenzie, Darry I.; Manly, Bryan F.J.; Haroldson, Mark A.; Moody, David W.

    2001-01-01

    Counts of uniquely identified individuals in a population offer opportunities to estimate abundance. However, for various reasons such counts may be burdened by heterogeneity in the probability of being detected. Theoretical arguments and empirical evidence demonstrate that the negative binomial distribution (NBD) is a useful characterization for counts from biological populations with heterogeneity. We propose a method that focuses on estimating multiple populations by simultaneously using a suite of models derived from the NBD. We used this approach to estimate the number of female grizzly bears (Ursus arctos) with cubs-of-the-year in the Yellowstone ecosystem, for each year, 1986-1998. Akaike's Information Criteria (AIC) indicated that a negative binomial model with a constant level of heterogeneity across all years was best for characterizing the sighting frequencies of female grizzly bears. A lack-of-fit test indicated the model adequately described the collected data. Bootstrap techniques were used to estimate standard errors and 95% confidence intervals. We provide a Monte Carlo technique, which confirms that the Yellowstone ecosystem grizzly bear population increased during the period 1986-1998.

  14. Beryllium and Boron abundances in population II stars

    NASA Technical Reports Server (NTRS)

    1995-01-01

    The scientific focus of this program was to undertake UV spectroscopic abundance analyses of extremely metal poor stars with attention to determining abundances of light elements such as beryllium and boron. The abundances are likely to reflect primordial abundances within the early galaxy and help to constrain models for early galactic nucleosynthesis. The general metal abundances of these stars are also important for understanding stellar evolution.

  15. Correlated variation and population differentiation in satellite DNA abundance among lines of Drosophila melanogaster.

    PubMed

    Wei, Kevin H-C; Grenier, Jennifer K; Barbash, Daniel A; Clark, Andrew G

    2014-12-30

    Tandemly repeating satellite DNA elements in heterochromatin occupy a substantial portion of many eukaryotic genomes. Although often characterized as genomic parasites deleterious to the host, they also can be crucial for essential processes such as chromosome segregation. Adding to their interest, satellite DNA elements evolve at high rates; among Drosophila, closely related species often differ drastically in both the types and abundances of satellite repeats. However, due to technical challenges, the evolutionary mechanisms driving this rapid turnover remain unclear. Here we characterize natural variation in simple-sequence repeats of 2-10 bp from inbred Drosophila melanogaster lines derived from multiple populations, using a method we developed called k-Seek that analyzes unassembled Illumina sequence reads. In addition to quantifying all previously described satellite repeats, we identified many novel repeats of low to medium abundance. Many of the repeats show population differentiation, including two that are present in only some populations. Interestingly, the population structure inferred from overall satellite quantities does not recapitulate the expected population relationships based on the demographic history of D. melanogaster. We also find that some satellites of similar sequence composition are correlated across lines, revealing concerted evolution. Moreover, correlated satellites tend to be interspersed with each other, further suggesting that concerted change is partially driven by higher order structure. Surprisingly, we identified negative correlations among some satellites, suggesting antagonistic interactions. Our study demonstrates that current genome assemblies vastly underestimate the complexity, abundance, and variation of highly repetitive satellite DNA and presents approaches to understand their rapid evolutionary divergence.

  16. [Abundance of Trans-Volga population of the great bustard (Otis tarda L.)].

    PubMed

    Oparin, M L; Kondratenkov, I A; Oparina, O S

    2003-01-01

    We studied the abundance, spatial structure, and democratic parameters of the Trans-Volga population of great bustard as well as this species connection to the habitats during premigratory movements. The data were obtained by monitoring a test area of 1,200,000 hectares in 1998-2000. Time-related changes in the structure of great bustard habitats in Saratov Trans-Volga Region during the 20th century are described and the mechanisms underlying the changes in this species connection to the habitats under the influence of anthropogenic factors are proposed.

  17. Colonial, more widely distributed and less abundant bird species undergo wider population fluctuations independent of their population trend

    PubMed Central

    Møller, Anders P.

    2017-01-01

    Understanding temporal variability in population size is important for conservation biology because wide population fluctuations increase the risk of extinction. Previous studies suggested that certain ecological, demographic, life-history and genetic characteristics of species might be related to the degree of their population fluctuations. We checked whether that was the case in a large sample of 231 European breeding bird species while taking a number of potentially confounding factors such as population trends or similarities among species due to common descent into account. When species-specific characteristics were analysed one by one, the magnitude of population fluctuations was positively related to coloniality, habitat, total breeding range, heterogeneity of breeding distribution and natal dispersal, and negatively related to urbanisation, abundance, relative number of subspecies, parasitism and proportion of polymorphic loci. However, when abundance (population size) was included in the analyses of the other parameters, only coloniality, habitat, total breeding range and abundance remained significantly related to population fluctuations. The analysis including all these predictors simultaneously showed that population size fluctuated more in colonial, less abundant species with larger breeding ranges. Other parameters seemed to be related to population fluctuations only because of their association with abundance or coloniality. The unexpected positive relationship between population fluctuations and total breeding range did not seem to be mediated by abundance. The link between population fluctuations and coloniality suggests a previously unrecognized cost of coloniality. The negative relationship between population size and population fluctuations might be explained by at least three types of non-mutually exclusive stochastic processes: demographic, environmental and genetic stochasticity. Measurement error in population indices, which was unknown, may

  18. Colonial, more widely distributed and less abundant bird species undergo wider population fluctuations independent of their population trend.

    PubMed

    Cuervo, José J; Møller, Anders P

    2017-01-01

    Understanding temporal variability in population size is important for conservation biology because wide population fluctuations increase the risk of extinction. Previous studies suggested that certain ecological, demographic, life-history and genetic characteristics of species might be related to the degree of their population fluctuations. We checked whether that was the case in a large sample of 231 European breeding bird species while taking a number of potentially confounding factors such as population trends or similarities among species due to common descent into account. When species-specific characteristics were analysed one by one, the magnitude of population fluctuations was positively related to coloniality, habitat, total breeding range, heterogeneity of breeding distribution and natal dispersal, and negatively related to urbanisation, abundance, relative number of subspecies, parasitism and proportion of polymorphic loci. However, when abundance (population size) was included in the analyses of the other parameters, only coloniality, habitat, total breeding range and abundance remained significantly related to population fluctuations. The analysis including all these predictors simultaneously showed that population size fluctuated more in colonial, less abundant species with larger breeding ranges. Other parameters seemed to be related to population fluctuations only because of their association with abundance or coloniality. The unexpected positive relationship between population fluctuations and total breeding range did not seem to be mediated by abundance. The link between population fluctuations and coloniality suggests a previously unrecognized cost of coloniality. The negative relationship between population size and population fluctuations might be explained by at least three types of non-mutually exclusive stochastic processes: demographic, environmental and genetic stochasticity. Measurement error in population indices, which was unknown, may

  19. Filling a void: abundance estimation of North American populations of arctic geese using hunter recoveries

    USGS Publications Warehouse

    Alisauskas, R.T.; Drake, K.L.; Nichols, J.D.; Thomson, David L.; Cooch, Evan G.; Conroy, Michael J.

    2009-01-01

    We consider use of recoveries of marked birds harvested by hunters, in conjunction with continental harvest estimates, for drawing inferences about continental abundance of a select number of goose species. We review assumptions of this method, a version of the Lincoln?Petersen approach, and consider its utility as a tool for making decisions about harvest management in comparison to current sources of information. Finally, we compare such estimates with existing count data, photographic estimates, or other abundance estimates. In most cases, Lincoln estimates are far higher than abundances assumed or perhaps accepted by many waterfowl biologists and managers. Nevertheless, depending on the geographic scope of inference, we suggest that this approach for abundance estimation of arctic geese may have usefulness for retrospective purposes or to assist with harvest management decisions for some species. Lincoln?s estimates may be as close or closer to truth than count, index, or photo data, and can be used with marking efforts currently in place for estimation of survival and harvest rates. Although there are bias issues associated with estimates of both harvest and harvest rate, some of the latter can be addressed with proper allocation of marks to spatially structured populations if subpopulations show heterogeneity in harvest rates.

  20. Estimating the abundance of mouse populations of known size: promises and pitfalls of new methods

    USGS Publications Warehouse

    Conn, P.B.; Arthur, A.D.; Bailey, L.L.; Singleton, G.R.

    2006-01-01

    Knowledge of animal abundance is fundamental to many ecological studies. Frequently, researchers cannot determine true abundance, and so must estimate it using a method such as mark-recapture or distance sampling. Recent advances in abundance estimation allow one to model heterogeneity with individual covariates or mixture distributions and to derive multimodel abundance estimators that explicitly address uncertainty about which model parameterization best represents truth. Further, it is possible to borrow information on detection probability across several populations when data are sparse. While promising, these methods have not been evaluated using mark?recapture data from populations of known abundance, and thus far have largely been overlooked by ecologists. In this paper, we explored the utility of newly developed mark?recapture methods for estimating the abundance of 12 captive populations of wild house mice (Mus musculus). We found that mark?recapture methods employing individual covariates yielded satisfactory abundance estimates for most populations. In contrast, model sets with heterogeneity formulations consisting solely of mixture distributions did not perform well for several of the populations. We show through simulation that a higher number of trapping occasions would have been necessary to achieve good estimator performance in this case. Finally, we show that simultaneous analysis of data from low abundance populations can yield viable abundance estimates.

  1. Population abundance and sex ratio in dioecious helminth parasites.

    PubMed

    Poulin, Robert

    1997-07-01

    Parasite populations are highly fragmented in space and time, and consist of aggregates of genetically similar individuals sharing the same host. To avoid inbreeding, theory predicts that female-biased sex ratios should be strongly favoured when either or both prevalence and intensity of infection are low. Other models indicate that if sex ratios are selected to increase the probability of mating, they should be less biased at a high intensity of infection in polygamous parasites, since at high intensities all females are mated. To test these predictions, the relationship between sex ratio and both the prevalence and intensity of infection was examined in comparative studies across 193 populations of nematode and acanthocephalan parasites. Sex ratios in these two dioecious, polygamous taxa are usually female biased. Among natural populations, no significant relationship was observed once the confounding effects of phylogeny had been removed. However, among experimental populations of nematodes, a negative relationship was found between intensity of infection and sex ratio, even after controlling for phylogeny. In other words, at high intensities, populations of nematodes are less female biased. This result must be treated with caution because of the unusually high numbers of worms per host in experimental infections. Nevertheless, combined with information on the proximate mechanisms regulating sex ratios in these parasites, it suggests a link between the characteristics of parasite populations and their sex ratio.

  2. Chemical abundances in LMC stellar populations. II. The bar sample

    NASA Astrophysics Data System (ADS)

    Van der Swaelmen, M.; Hill, V.; Primas, F.; Cole, A. A.

    2013-12-01

    Aims: This paper compares the chemical evolution of the Large Magellanic Cloud (LMC) to that of the Milky Way (MW) and investigates the relation between the bar and the inner disc of the LMC in the context of the formation of the bar. Methods: We obtained high-resolution and mid signal-to-noise ratio spectra with FLAMES/GIRAFFE at ESO/VLT and performed a detailed chemical analysis of 106 and 58 LMC field red giant stars (mostly older than 1 Gyr), located in the bar and the disc of the LMC respectively. To validate our stellar parameter determinations and abundance measurement procedures, we performed thorough tests using the well-known mildly metal-poor Milky-Way thick disc giant Arcturus (HD 124897, α Boo). We measured elemental abundances for O, Mg, Si, Ca, Ti (α-elements), Na (light odd element), Sc, V, Cr, Co, Ni, Cu (iron-peak elements), Y, Zr, Ba, La, and Eu (s- and r-elements). Results: We find that the α-element ratios [Mg/Fe] and [O/Fe] are lower in the LMC than in the MW while the LMC has similar [Si/Fe], [Ca/Fe], and [Ti/Fe] to the MW. As for the heavy elements, [Ba,La/Eu] exhibit a strong increase with increasing metallicity starting from [Fe/H] ≈ -0.8 dex, and the LMC has lower [Y + Zr/Ba + La] ratios than the MW. Cu is almost constant over all metallicities and about 0.5 dex lower in the LMC than in the MW. The LMC bar and inner disc exhibit differences in their [α/ Fe] (slightly larger scatter for the bar in the metallicity range [-1, -0.5]), their Eu (the bar trend is above the disc trend for [Fe/H] ≥ -0.5 dex), their Y and Zr, their Na and their V (offset between the bar and the disc distributions). Conclusions: Our results show that the chemical history of the LMC experienced a strong contribution from type Ia supernovae as well as a strong s-process enrichment from metal-poor AGB winds. Massive stars made a smaller contribution to the chemical enrichment compared to the MW. The observed differences between the bar and the disc speak in

  3. The existence and abundance of ghost ancestors in biparental populations.

    PubMed

    Gravel, Simon; Steel, Mike

    2015-05-01

    In a randomly-mating biparental population of size N there are, with high probability, individuals who are genealogical ancestors of every extant individual within approximately log2(N) generations into the past. We use this result of J. Chang to prove a curious corollary under standard models of recombination: there exist, with high probability, individuals within a constant multiple of log2(N) generations into the past who are simultaneously (i) genealogical ancestors of each of the individuals at the present, and (ii) genetic ancestors to none of the individuals at the present. Such ancestral individuals-ancestors of everyone today that left no genetic trace-represent 'ghost' ancestors in a strong sense. In this short note, we use simple analytical argument and simulations to estimate how many such individuals exist in finite Wright-Fisher populations.

  4. Distribution and abundance of zooplankton populations in Crater Lake, Oregon

    USGS Publications Warehouse

    Larson, G.L.; McIntire, C.D.; Buktenica, M.W.; Girdner, S.F.; Truitt, R.E.

    2007-01-01

    The zooplankton assemblages in Crater Lake exhibited consistency in species richness and general taxonomic composition, but varied in density and biomass during the period between 1988 and 2000. Collectively, the assemblages included 2 cladoceran taxa and 10 rotifer taxa (excluding rare taxa). Vertical habitat partitioning of the water column to a depth of 200 m was observed for most species with similar food habits and/or feeding mechanisms. No congeneric replacement was observed. The dominant species in the assemblages were variable, switching primarily between periods of dominance of Polyarthra-Keratella cochlearis and Daphnia. The unexpected occurrence and dominance of Asplanchna in 1991 and 1992 resulted in a major change in this typical temporal shift between Polyarthra-K. cochlearis and Daphnia. Following a collapse of the zooplankton biomass in 1993 that was probably caused by predation from Asplanchna, Kellicottia dominated the zooplankton assemblage biomass between 1994 and 1997. The decline in biomass of Kellicottia by 1998 coincided with a dramatic increase in Daphnia biomass. When Daphnia biomass declined by 2000, Keratella biomass increased again. Thus, by 1998 the assemblage returned to the typical shift between Keratella-Polyarthra and Daphnia. Although these observations provided considerable insight about the interannual variability of the zooplankton assemblages in Crater Lake, little was discovered about mechanisms behind the variability. When abundant, kokanee salmon may have played an important role in the disappearance of Daphnia in 1990 and 2000 either through predation, inducing diapause, or both. ?? 2007 Springer Science+Business Media B.V.

  5. Commonly rare and rarely common: comparing population abundance of invasive and native aquatic species.

    PubMed

    Hansen, Gretchen J A; Vander Zanden, M Jake; Blum, Michael J; Clayton, Murray K; Hain, Ernie F; Hauxwell, Jennifer; Izzo, Marit; Kornis, Matthew S; McIntyre, Peter B; Mikulyuk, Alison; Nilsson, Erika; Olden, Julian D; Papeş, Monica; Sharma, Sapna

    2013-01-01

    Invasive species are leading drivers of environmental change. Their impacts are often linked to their population size, but surprisingly little is known about how frequently they achieve high abundances. A nearly universal pattern in ecology is that species are rare in most locations and abundant in a few, generating right-skewed abundance distributions. Here, we use abundance data from over 24,000 populations of 17 invasive and 104 native aquatic species to test whether invasive species differ from native counterparts in statistical patterns of abundance across multiple sites. Invasive species on average reached significantly higher densities than native species and exhibited significantly higher variance. However, invasive and native species did not differ in terms of coefficient of variation, skewness, or kurtosis. Abundance distributions of all species were highly right skewed (skewness>0), meaning both invasive and native species occurred at low densities in most locations where they were present. The average abundance of invasive and native species was 6% and 2%, respectively, of the maximum abundance observed within a taxonomic group. The biological significance of the differences between invasive and native species depends on species-specific relationships between abundance and impact. Recognition of cross-site heterogeneity in population densities brings a new dimension to invasive species management, and may help to refine optimal prevention, containment, control, and eradication strategies.

  6. Seasonal temperature and precipitation regulate brook trout young-of-the-year abundance and population dynamics

    USGS Publications Warehouse

    Kanno, Yoichiro; Pregler, Kasey C.; Hitt, Nathaniel P.; Letcher, Benjamin H.; Hocking, Daniel; Wofford, John E.B.

    2015-01-01

    Our results indicate that YOY abundance is a key driver of brook trout population dynamics that is mediated by seasonal weather patterns. A reliable assessment of climate change impacts on brook trout needs to account for how alternations in seasonal weather patterns impact YOY abundance and how such relationships may differ across the range of brook trout distribution.

  7. Abundance and Source Population of Suprathermal Heavy Ions in Corotating Interaction Regions

    NASA Astrophysics Data System (ADS)

    Jensema, R. J.; Desai, M. I.; Broiles, T. W.; Dayeh, M. A.

    2015-12-01

    In this study we analyze the abundances of suprathermal heavy ions in 75 Corotating Interaction Region (CIR) events between January 1st 1995 and December 31st 2008. We correlate the heavy ion abundances in these CIRs with those measured in the solar wind and suprathermal populations upstream of these events. Our analysis reveals that the CIR suprathermal heavy ion abundances vary by nearly two orders of magnitude over the solar activity cycle, with higher abundances (e.g., Fe/O) occurring during solar maximum and depleted values occurring during solar minimum. The abundances are also energy dependent, with larger abundances at higher energies, particularly during solar maximum. Following the method used by Mason et al. 2008, we correlate the CIR abundances with the corresponding solar wind and suprathermal values measured during 6-hour intervals for upstream periods spanning 10 days prior to the start of each CIR event. This correlation reveals that suprathermal heavy ions are better correlated with upstream suprathermal abundances measured at the same energy compared with the solar wind heavy ion abundances. Using the 6-hour averaging method, we also identified timeframes of maximum correlation between the CIR and the upstream suprathermal abundances, and find that the time of maximum correlation depends on the energy of the suprathermal ions. We discuss the implications of these results in terms of previous studies of CIR and suprathermal particles, and CIR seed populations and acceleration mechanisms.

  8. Performance of Baited Underwater Video: Does It Underestimate Abundance at High Population Densities?

    PubMed Central

    Stobart, Ben; Díaz, David; Álvarez, Federico; Alonso, Cristina; Mallol, Sandra; Goñi, Raquel

    2015-01-01

    Video survey techniques are now commonly used to estimate animal abundance under the assumption that estimates relate to true abundance, a key property needed to make video a valid survey tool. Using the spiny lobster Palinurus elephas as our model organism, we evaluate the effectiveness of baited underwater video (BUV) for estimating abundance in areas with widely different population density. We test three BUV abundance metrics and compare the results with an independently obtained abundance index from trammel-net surveys (Trammel). Video metrics used to estimate relative abundance include a value for total number of individuals per recording (TotN), the traditional maximum number of fish observed in a single video frame (MaxN), and the recently suggested alternative, the average of the mean MaxN from 5-minute periods throughout the duration of the recording (MeanN). This is the first video study of a wild population to include an estimate for TotN. Comparison of TotN with the other two BUV relative abundance metrics demonstrates that both of the latter lack resolution at high population densities. In spite of this, the three BUV metrics tested, as well as the independent estimate Trammel, distinguished high density areas from low density areas. Thus they could all be used to identify areas of differing population density, but MaxN and MeanN would not be appropriate metrics for studies aimed at documenting increases in abundance, such as those conducted to assess marine protected area effectiveness, as they are prone to sampling saturation. We also demonstrate that time of first arrival (T1) is highly correlated with all of the abundance indices; suggesting T1 may be a potentially useful index of abundance. However, these relationships require further investigation as our data suggests T1 may not adequately represent lobster abundance in areas of high density. PMID:26010738

  9. Performance of baited underwater video: does it underestimate abundance at high population densities?

    PubMed

    Stobart, Ben; Díaz, David; Álvarez, Federico; Alonso, Cristina; Mallol, Sandra; Goñi, Raquel

    2015-01-01

    Video survey techniques are now commonly used to estimate animal abundance under the assumption that estimates relate to true abundance, a key property needed to make video a valid survey tool. Using the spiny lobster Palinurus elephas as our model organism, we evaluate the effectiveness of baited underwater video (BUV) for estimating abundance in areas with widely different population density. We test three BUV abundance metrics and compare the results with an independently obtained abundance index from trammel-net surveys (Trammel). Video metrics used to estimate relative abundance include a value for total number of individuals per recording (TotN), the traditional maximum number of fish observed in a single video frame (MaxN), and the recently suggested alternative, the average of the mean MaxN from 5-minute periods throughout the duration of the recording (MeanN). This is the first video study of a wild population to include an estimate for TotN. Comparison of TotN with the other two BUV relative abundance metrics demonstrates that both of the latter lack resolution at high population densities. In spite of this, the three BUV metrics tested, as well as the independent estimate Trammel, distinguished high density areas from low density areas. Thus they could all be used to identify areas of differing population density, but MaxN and MeanN would not be appropriate metrics for studies aimed at documenting increases in abundance, such as those conducted to assess marine protected area effectiveness, as they are prone to sampling saturation. We also demonstrate that time of first arrival (T1) is highly correlated with all of the abundance indices; suggesting T1 may be a potentially useful index of abundance. However, these relationships require further investigation as our data suggests T1 may not adequately represent lobster abundance in areas of high density.

  10. Functional genotypes are associated with commensal Escherichia coli strain abundance within-host individuals and populations.

    PubMed

    Blyton, Michaela D J; Banks, Sam C; Peakall, Rod; Gordon, David M

    2013-08-01

    The selective pressures that determine genotype abundance and distribution frequently vary between ecological levels. Thus, it is often unclear whether the same functional genotypes will become abundant at different levels and how selection acting at these different scales is linked. In this study, we examined whether particular functional genotypes, defined by the presence or absence of 34 genes, of commensal Escherichia coli strains were associated with within-host abundance and/or host population abundance in a wild population of 54 adult mountain brushtail possums (Trichosurus cunninghami). Our results revealed that there was a positive correlation between a strain's relative abundance within individuals and the strain's abundance in the host population. We also found that strain abundance at both ecological levels was predicted by the same group of functional genes (agn43, focH, micH47, iroN, ygiL, ompT, kspmT2 and K1) that had associated patterns of occurrence. We propose that direct selection on the same functional genes at both levels may in part be responsible for the observed correlation between the ecological levels. However, a potential link between abundance within the host and excretion rate may also contribute.

  11. Impact of warming on abundance and occurrence of flatfish populations in the Bay of Biscay (France)

    NASA Astrophysics Data System (ADS)

    Hermant, Marie; Lobry, Jeremy; Bonhommeau, Sylvain; Poulard, Jean-Charles; Le Pape, Olivier

    2010-07-01

    The aim of the present study was to analyse the influence of warming on flatfish populations in the Bay of Biscay. 17 autumn cruises conducted from 1987 to 2006 over the whole shelf of the Bay of Biscay provided data for the abundance and occurrence of adults for twenty flatfish species. Trends in flatfish abundance were analysed with regard to geographic range of populations and interannual fluctuations in abundance were related to seawater temperature. Results showed significant trends in abundance and occurrence for 55% of the flatfish species in the Bay of Biscay. The response to warming of seawater was correlated to geographic ranges of species. While the abundance of the northern temperate species decreased, that of southern ones increased. Moreover, for 40% of the species which densities have significantly changed, abundances were correlated to temperatures in their year of birth, positively for southern species and negatively for northern ones. Last, the abundance of flatfish adults over the Bay of Biscay was compared to previous data on juveniles in the Bay of Vilaine, one of the estuarine nursery ground in this area. For the northern species which have disappeared, the decline in juvenile abundances preceded that of adults by several years, indicating that the recruitment is the process affected. We concluded on a major impact of warming to explain changes in flatfish species abundances. Nevertheless, the impact of fishing interacts with that of climate change because the exploited species appeared to be the most negatively affected.

  12. Abundance, distribution and size structure of Diadema antillarum (Echinodermata: Diadematidae) in South Eastern Cuban coral reefs.

    PubMed

    Martín Blanco, F; González Sansón, G; Pina Amargós, F; Clero Alonso, L

    2010-06-01

    The 1983-1984 mass mortality event of Diadema antillarum affected more than 93% of the total Caribbean population. Although there are no records about the status of Diadema populations before and after die-off on Cuban reefs, anecdotal information suggests that populations were struck. We analyzed spatial variation in the abundance and size structure of D. antillarum in 22 reefs sites in Jardines de la Reina, from June 2004 to September 2005. Counts of Diadema were performed in five 30x2 m transects at each sampling site and sampling time, and test diameters were measured in September 2005 at the same fore reefs. Abundances were higher at reef crests (mean densities 0.08-2.18 ind./m2), while reef slope populations reached a maximum site level of 0.13 ind./m2 at only one site and showed values up to three orders of magnitude lower than those from reef crests. Highest abundance occurred at the west margin of major channels between keys where larval recruitment seems to be favored by local oceanographic features and facilitated by the abundance of Echinometra lucunter. The size frequency distribution of D. antillarum indicates that recruitment began to be noticeable three years before September 2005, suggesting these populations were depleted in the past and they are recovering now.

  13. Composite stellar populations and element by element abundances in the Milky Way bulge and elliptical galaxies

    NASA Astrophysics Data System (ADS)

    Tang, Baitian; Worthey, Guy; Davis, A. Bianca

    2014-12-01

    This paper explores the integrated-light characteristics of the Milky Way (MW) bulge and to what extent they match those of elliptical galaxies in the local Universe. We model composite stellar populations with realistic abundance distribution functions (ADFs), tracking the trends of individual elements as a function of overall heavy element abundance as actually observed in MW bulge stars. The resultant predictions for absorption feature strengths from the MW bulge mimic elliptical galaxies better than solar neighbourhood stars do, but the MW bulge does not match elliptical galaxies, either. Comparing bulge versus elliptical galaxies, Fe, Ti, and Mg trend about the same for both but C, Na, and Ca seem irreconcilably different. Exploring the behaviour of abundance compositeness leads to the concepts of `red lean' where a narrower ADF appears more metal rich than a wide one, and `red spread' where the spectral difference between wide and narrow ADFs increases as the ADF peak is moved to more metal-rich values. Tests on the systematics of recovering abundance, abundance pattern, and age from composite stellar populations using single stellar population models were performed. The chemical abundance pattern was recovered adequately, though a few minor systematic effects were uncovered. The prospects of measuring the width of the ADF of an old stellar population were investigated and seem bright using UV to IR photometry.

  14. Comparing growth patterns among field populations of cereal aphids reveals factors limiting their maximum abundance.

    PubMed

    Honek, A; Jarosik, V; Dixon, A F G

    2006-06-01

    Cereal stands in central Europe are commonly infested with three species of aphids that may become serious pests. With increasing abundance, the proportion of a particular species in the total aphid population may remain constant, suggesting a density-independent exponential growth, or the proportion can change, suggesting density-dependent constraints on growth. The constraints that affect particular species, and thus their relative abundance, were studied. The proportionality between maximum abundances of the cereal aphids was studied using a 10-year census of the numbers of aphids infesting 268 winter wheat plots. For two species their abundance on leaves and ears was compared. With increasing aphid density the maximum abundance of Rhopalosiphum padi (Linnaeus) remained proportional, but not that of Sitobion avenae (Fabricius), which was constrained by the smaller surface area of ears compared to leaves. There was no evidence of inter-specific competition. Maximum abundance of R. padi and Metopolophium dirhodum (Walker) on leaves did not change proportionally as the proportion of M. dirhodum decreased with increasing overall aphid density. This decrease was probably caused by the restricted distribution of M. dirhodum, which is confined to leaves, where space is limiting. No change in proportion between populations was detected when the average densities were below 0.54 aphids per leaf or ear. Non-proportional relationships between aphid populations appeared to be due to spatial constraints, acting upon the more abundant population. Detecting the limitation of population growth can help with the assessment of when density-independent exponential growth is limited by density-dependent factors. This information may help in the development of models of cereal aphid population dynamics.

  15. Host density drives macroparasite abundance across populations of a critically endangered megaherbivore.

    PubMed

    Stringer, A P; Linklater, W L

    2015-09-01

    What determines the abundance of parasites is a central question within epidemiology. Epidemiological models predict that density-dependent transmission has a principal influence on parasite abundance. However, this mechanism is seldom tested in macroparasites, perhaps because multiple, comparable populations of the same host-parasite relationship are rare. We test the influence of a range of factors on parasite abundance across 18 populations of black rhinoceros (Diceros bicornis) in South Africa. Here we show that host density strongly predicts parasite abundance at the population level for both directly and indirectly transmitted parasites. All other models were not supported. The surprising influence of a single key factor, host density, within a complex ecological system demonstrates the validity of simple epidemiological models. Establishing this previously assumed relationship between host density and parasite abundance has major implications for disease control and parasite ecology. For instance, it is central to the idea of population density thresholds for parasitism, below which a parasite would become extinct. Density-dependent transmission is also essential for calculations of the basic reproductive number, and the hypothesis that parasites may regulate host population size.

  16. Estimating the abundance of clustered animal population by using adaptive cluster sampling and negative binomial distribution

    NASA Astrophysics Data System (ADS)

    Bo, Yizhou; Shifa, Naima

    2013-09-01

    An estimator for finding the abundance of a rare, clustered and mobile population has been introduced. This model is based on adaptive cluster sampling (ACS) to identify the location of the population and negative binomial distribution to estimate the total in each site. To identify the location of the population we consider both sampling with replacement (WR) and sampling without replacement (WOR). Some mathematical properties of the model are also developed.

  17. Dose-structured population dynamics.

    PubMed

    Ginn, Timothy R; Loge, Frank J

    2007-07-01

    Applied population dynamics modeling is relied upon with increasing frequency to quantify how human activities affect human and non-human populations. Current techniques include variously the population's spatial transport, age, size, and physiology, but typically not the life-histories of exposure to other important things occurring in the ambient environment, such as chemicals, heat, or radiation. Consequently, the effects of such 'abiotic' aspects of an ecosystem on populations are only currently addressed through individual-based modeling approaches that despite broad utility are limited in their applicability to realistic ecosystems [V. Grimm, Ten years of individual-based modeling in ecology: what have we learned and what could we learn in the future? Ecol. Model. 115 (1999) 129-148][1]. We describe a new category of population dynamics modeling, wherein population dynamical states of the biotic phases are structured on dose, and apply this framework to demonstrate how chemical species or other ambient aspects can be included in population dynamics in three separate examples involving growth suppression in fish, inactivation of microorganisms with ultraviolet irradiation, and metabolic lag in population growth. Dose-structuring is based on a kinematic approach that is a simple generalization of age-structuring, views the ecosystem as a multi-component mixture with reacting biotic/abiotic components. The resulting model framework accommodates (a) different memories of exposure as in recovery from toxic ambient conditions, (b) differentiation between exogenous and endogenous sources of variation in population response, and (c) quantification of acute or sub-acute effects on populations arising from life-history exposures to abiotic species. Classical models do not easily address the very important fact that organisms differ and have different experiences over their life cycle. The dose structuring is one approach to incorporate some of these elements into the

  18. Climate change effects on soil microarthropod abundance and community structure

    SciTech Connect

    Kardol, Paul; Reynolds, W. Nicholas; Norby, Richard J; Classen, Aimee T

    2011-01-01

    Long-term ecosystem responses to climate change strongly depend on how the soil subsystem and its inhabitants respond to these perturbations. Using open-top chambers, we studied the response of soil microarthropods to single and combined effects of ambient and elevated atmospheric [CO{sub 2}], ambient and elevated temperatures and changes in precipitation in constructed old-fields in Tennessee, USA. Microarthropods were assessed five years after treatments were initiated and samples were collected in both November and June. Across treatments, mites and collembola were the most dominant microarthropod groups collected. We did not detect any treatment effects on microarthropod abundance. In November, but not in June, microarthropod richness, however, was affected by the climate change treatments. In November, total microarthropod richness was lower in dry than in wet treatments, and in ambient temperature treatments, richness was higher under elevated [CO{sub 2}] than under ambient [CO{sub 2}]. Differential responses of individual taxa to the climate change treatments resulted in shifts in community composition. In general, the precipitation and warming treatments explained most of the variation in community composition. Across treatments, we found that collembola abundance and richness were positively related to soil moisture content, and that negative relationships between collembola abundance and richness and soil temperature could be explained by temperature-related shifts in soil moisture content. Our data demonstrate how simultaneously acting climate change factors can affect the structure of soil microarthropod communities in old-field ecosystems. Overall, changes in soil moisture content, either as direct effect of changes in precipitation or as indirect effect of warming or elevated [CO{sub 2}], had a larger impact on microarthropod communities than did the direct effects of the warming and elevated [CO{sub 2}] treatments. Moisture-induced shifts in soil

  19. Population Abundance of the Endangered Galapagos Sea Lion Zalophus wollebaeki in the Southeastern Galapagos Archipelago.

    PubMed

    Riofrío-Lazo, Marjorie; Arreguín-Sánchez, Francisco; Páez-Rosas, Diego

    2017-01-01

    There is great concern regarding the population status of the endangered Galapagos sea lion (GSL) because it has drastically decreased over the last 30 years. We determined the population size and growth trend of the GSL in the Galapagos southeastern region (SER) at three population levels based on the available census data: 1) SER (2011-2015), including 13 rookeries on the four islands San Cristóbal (SC), Española, Floreana, and Santa Fe, comprising 58% of the archipelago's population; 2) SC (2011-2015), including five rookeries, comprising 52% of the SER population; and 3) El Malecón (2005-2015), the largest rookery on SC and in the SER (43% of the population on SC and 22% in the SER). We also analyzed the influence of environmental variability on pup abundance in these rookeries. The current GSL population size in the SER, after applying correction factors to the counts, is estimated at approximately 2300-4100 individuals and has declined at an average annual rate (ʎ) of 8.7% over the last five years. A similar trend was determined for SC but at ʎ = 1.4% during the same period. For El Malecón, a count-based population viability analysis using a diffusion approximation approach showed that the population increased from 2005 to 2015 at ʎ = 2%. The interannual variability in pup abundance was associated with anomalies in sea surface temperature linked to oceanographic-atmospheric events, which impact the abundance and availability of prey, and ultimately may determine the population's reproductive success. Since rookeries in the SER had different population trends, management actions should be implemented based on their specific conditions, giving priority to rookeries such as El Malecón, which, despite showing a slightly increasing population trend, still faces a high risk of extinction due to anthropogenic disturbances and environmental variability that may affect its growth and survival.

  20. Population Abundance of the Endangered Galapagos Sea Lion Zalophus wollebaeki in the Southeastern Galapagos Archipelago

    PubMed Central

    Riofrío-Lazo, Marjorie; Arreguín-Sánchez, Francisco; Páez-Rosas, Diego

    2017-01-01

    There is great concern regarding the population status of the endangered Galapagos sea lion (GSL) because it has drastically decreased over the last 30 years. We determined the population size and growth trend of the GSL in the Galapagos southeastern region (SER) at three population levels based on the available census data: 1) SER (2011–2015), including 13 rookeries on the four islands San Cristóbal (SC), Española, Floreana, and Santa Fe, comprising 58% of the archipelago’s population; 2) SC (2011–2015), including five rookeries, comprising 52% of the SER population; and 3) El Malecón (2005–2015), the largest rookery on SC and in the SER (43% of the population on SC and 22% in the SER). We also analyzed the influence of environmental variability on pup abundance in these rookeries. The current GSL population size in the SER, after applying correction factors to the counts, is estimated at approximately 2300–4100 individuals and has declined at an average annual rate (ʎ) of 8.7% over the last five years. A similar trend was determined for SC but at ʎ = 1.4% during the same period. For El Malecón, a count-based population viability analysis using a diffusion approximation approach showed that the population increased from 2005 to 2015 at ʎ = 2%. The interannual variability in pup abundance was associated with anomalies in sea surface temperature linked to oceanographic-atmospheric events, which impact the abundance and availability of prey, and ultimately may determine the population’s reproductive success. Since rookeries in the SER had different population trends, management actions should be implemented based on their specific conditions, giving priority to rookeries such as El Malecón, which, despite showing a slightly increasing population trend, still faces a high risk of extinction due to anthropogenic disturbances and environmental variability that may affect its growth and survival. PMID:28052081

  1. Efficient estimation of abundance for patchily distributed populations via two-phase, adaptive sampling.

    USGS Publications Warehouse

    Conroy, M.J.; Runge, J.P.; Barker, R.J.; Schofield, M.R.; Fonnesbeck, C.J.

    2008-01-01

    Many organisms are patchily distributed, with some patches occupied at high density, others at lower densities, and others not occupied. Estimation of overall abundance can be difficult and is inefficient via intensive approaches such as capture-mark-recapture (CMR) or distance sampling. We propose a two-phase sampling scheme and model in a Bayesian framework to estimate abundance for patchily distributed populations. In the first phase, occupancy is estimated by binomial detection samples taken on all selected sites, where selection may be of all sites available, or a random sample of sites. Detection can be by visual surveys, detection of sign, physical captures, or other approach. At the second phase, if a detection threshold is achieved, CMR or other intensive sampling is conducted via standard procedures (grids or webs) to estimate abundance. Detection and CMR data are then used in a joint likelihood to model probability of detection in the occupancy sample via an abundance-detection model. CMR modeling is used to estimate abundance for the abundance-detection relationship, which in turn is used to predict abundance at the remaining sites, where only detection data are collected. We present a full Bayesian modeling treatment of this problem, in which posterior inference on abundance and other parameters (detection, capture probability) is obtained under a variety of assumptions about spatial and individual sources of heterogeneity. We apply the approach to abundance estimation for two species of voles (Microtus spp.) in Montana, USA. We also use a simulation study to evaluate the frequentist properties of our procedure given known patterns in abundance and detection among sites as well as design criteria. For most population characteristics and designs considered, bias and mean-square error (MSE) were low, and coverage of true parameter values by Bayesian credibility intervals was near nominal. Our two-phase, adaptive approach allows efficient estimation of

  2. Motor abundance and control structure in the golf swing.

    PubMed

    Morrison, A; McGrath, D; Wallace, E S

    2016-04-01

    Variability and control structure are under-represented areas of golf swing research. This study investigated the use of the abundant degrees of freedom in the golf swing of high and intermediate skilled golfers using uncontrolled manifold (UCM) analysis. The variance parallel to (VUCM) and orthogonal to (VOrth) the UCM with respect to the orientation and location of the clubhead were calculated. The higher skilled golfers had proportionally higher values of VUCM than lower skilled players for all measured outcome variables. Motor synergy was found in the control of the orientation of the clubhead and the combined outcome variables but not for clubhead location. Clubhead location variance zeroed-in on impact as has been previously shown, whereas clubhead orientation variance increased near impact. Both skill levels increased their control over the clubhead location leading up to impact, with more control exerted over the clubhead orientation in the early downswing. The results suggest that to achieve higher skill levels in golf may not lie simply in optimal technique, but may lie more in developing control over the abundant degrees of freedom in the body.

  3. The consistency and stability of abundance-occupancy relationships in large-scale population dynamics.

    PubMed

    Zuckerberg, Benjamin; Porter, William F; Corwin, Kimberley

    2009-01-01

    1. Abundance-occupancy relationships comprise some of the most general and well-explored patterns in macro-ecology. The theory governing these relationships predicts that species will exhibit a positive interspecific and intraspecific relationship between regional occupancy and local abundance. Abundance-occupancy relationships have important implications in using distributional surveys, such as atlases, to understand and document large-scale population dynamics and the consequences of environmental change. A basic need for interpreting such data bases is a better understanding of whether changes in regional occupancy reflect changes in local abundance across species of varying life-history characteristics. 2. Our objective was to test the predictions of the abundance-occupancy rule using two independent data sets, the New York State Breeding Bird Atlas and the North American Breeding Bird Survey. The New York State Breeding Bird Atlas consists of 5332 25-km(2) survey blocks and is one of the first atlases in the USA to be completed for two time periods (1980-85 and 2000-05). The North American Breeding Survey is a large-scale annual survey intended to document the relative abundance and population change of songbirds throughout the USA. 3. We found that regional occupancy was positively correlated with relative abundance across 98 (beta = 0.60 +/- 0.11 SE, P < 0.001, R(2) = 0.60) and 85 species (beta = 0.67 +/- 0.06 SE, P < 0.001, R(2) = 0.57) in two separate time periods. This relationship proved stable over time and was notably consistent between breeding habitat groups and migratory guilds. 4. Between 1980 and 2005, changes in regional occupancy were highly correlated with long-term abundance trend estimates for 75 species (beta = 5.73 +/- 0.24 SE, P < 0.001, R(2) = 0.88). Over a 20-year period, woodland and resident birds showed an increase in occupancy while grassland species showed the greatest decline; these patterns were mirrored by changes in local

  4. The ornament-condition relationship varies with parasite abundance at population level in a female bird

    NASA Astrophysics Data System (ADS)

    Vergara, Pablo; Martínez-Padilla, Jesús; Redpath, Stephen M.; Mougeot, Francois

    2011-10-01

    Environmental heterogeneity is expected to create variation in the ornament-condition relationship. This topic has been studied in males with less attention being given to females. Here, we explore inter-population variation in the relationship between the size of a male-like trait, supra-orbital combs, and body mass in female red grouse Lagopus lagopus scoticus. We used the abundance of the nematode Trichostrongylus tenuis, a parasite with strong negative effects on this species, as a proxy of environmental conditions. We studied six populations over 5 years and showed that the comb size-body mass relationship varied with mean parasite abundance, with stronger ornament-condition relationships in populations with higher parasite infection levels. Our study supports the idea that environmental conditions, and in particular parasite infection levels, may affect the reliability of female ornaments as condition indicators.

  5. Effects of abundance on infection in natural populations: field voles and cowpox virus.

    PubMed

    Begon, Michael; Telfer, Sandra; Burthe, Sarah; Lambin, Xavier; Smith, Matthew J; Paterson, Steve

    2009-03-01

    Detailed results on the dynamics of cowpox virus infection in four natural populations of the field vole, Microtus agrestis, are presented. Populations were sampled every 4 weeks (8 weeks in mid-winter) for 6 years. The purpose was to examine the relationships between overall or susceptible host abundance (N, S) and both the number of infected hosts (I) and the prevalence of infection (I/N). Overall, both I and I/N increased with N. However, evidence for a threshold abundance, below which infection was not found, was at best equivocal in spite of the wide range of abundances sampled. Cross-correlation analyses reflected annual and multi-annual cycles in N, I, S and I/N, but whereas N was most strongly correlated with contemporary values of I and I/N, in the case of S, the strongest correlations were with values 1 to 2 months preceding the values of I and I/N. There was no evidence for a 'juvenile dilution effect' (prevalence decreasing with abundance as new susceptibles flush into the population) and only weak evidence of a time-delayed effect of abundance on the number infected. We argue that these effects may occur only in systems with characteristics that are not found here. Transfer function analyses, which have been neglected in epidemiology, were applied. These models, with ln(S) as the input parameter, in spite of their simplicity, could be linked closely to conventional formulations of the transmission process and were highly effective in predicting the number infected. By contrast, transfer function models with ln(N) as the input parameter were less successful in predicting the number infected and/or were more complex and more difficult to interpret. Nonetheless, overall, we contend that while monitoring numbers susceptible has most to offer, monitoring overall abundance may provide valuable insights into the dynamics of infection.

  6. Laplacian eigenfunctions learn population structure.

    PubMed

    Zhang, Jun; Niyogi, Partha; McPeek, Mary Sara

    2009-12-01

    Principal components analysis has been used for decades to summarize genetic variation across geographic regions and to infer population migration history. More recently, with the advent of genome-wide association studies of complex traits, it has become a commonly-used tool for detection and correction of confounding due to population structure. However, principal components are generally sensitive to outliers. Recently there has also been concern about its interpretation. Motivated from geometric learning, we describe a method based on spectral graph theory. Regarding each study subject as a node with suitably defined weights for its edges to close neighbors, one can form a weighted graph. We suggest using the spectrum of the associated graph Laplacian operator, namely, Laplacian eigenfunctions, to infer population structure. In simulations and real data on a ring species of birds, Laplacian eigenfunctions reveal more meaningful and less noisy structure of the underlying population, compared with principal components. The proposed approach is simple and computationally fast. It is expected to become a promising and basic method for population genetics and disease association studies.

  7. Optimal sampling design for estimating spatial distribution and abundance of a freshwater mussel population

    USGS Publications Warehouse

    Pooler, P.S.; Smith, D.R.

    2005-01-01

    We compared the ability of simple random sampling (SRS) and a variety of systematic sampling (SYS) designs to estimate abundance, quantify spatial clustering, and predict spatial distribution of freshwater mussels. Sampling simulations were conducted using data obtained from a census of freshwater mussels in a 40 X 33 m section of the Cacapon River near Capon Bridge, West Virginia, and from a simulated spatially random population generated to have the same abundance as the real population. Sampling units that were 0.25 m 2 gave more accurate and precise abundance estimates and generally better spatial predictions than 1-m2 sampling units. Systematic sampling with ???2 random starts was more efficient than SRS. Estimates of abundance based on SYS were more accurate when the distance between sampling units across the stream was less than or equal to the distance between sampling units along the stream. Three measures for quantifying spatial clustering were examined: Hopkins Statistic, the Clumping Index, and Morisita's Index. Morisita's Index was the most reliable, and the Hopkins Statistic was prone to false rejection of complete spatial randomness. SYS designs with units spaced equally across and up stream provided the most accurate predictions when estimating the spatial distribution by kriging. Our research indicates that SYS designs with sampling units equally spaced both across and along the stream would be appropriate for sampling freshwater mussels even if no information about the true underlying spatial distribution of the population were available to guide the design choice. ?? 2005 by The North American Benthological Society.

  8. Genealogical histories in structured populations.

    PubMed

    Kumagai, Seiji; Uyenoyama, Marcy K

    2015-06-01

    In genealogies of genes sampled from structured populations, lineages coalesce at rates dependent on the states of the lineages. For migration and coalescence events occurring on comparable time scales, for example, only lineages residing in the same deme of a geographically subdivided population can have descended from a common ancestor in the immediately preceding generation. Here, we explore aspects of genealogical structure in a population comprising two demes, between which migration may occur. We use generating functions to obtain exact densities and moments of coalescence time, number of mutations, total tree length, and age of the most recent common ancestor of the sample. We describe qualitative features of the distribution of gene genealogies, including factors that influence the geographical location of the most recent common ancestor and departures of the distribution of internode lengths from exponential.

  9. Variation in predation pressure as a mechanism underlying differences in numerical abundance between populations of the poeciliid fish Heterandria formosa

    USGS Publications Warehouse

    Richardson, J.M.L.; Gunzburger, M.S.; Travis, J.

    2006-01-01

    We explored whether a variation in predation and habitat complexity between conspecific populations can drive qualitatively different numerical dynamics in those populations. We considered two disjunct populations of the least killifish, Heterandria formosa, that exhibit long-term differences in density, top fish predator species, and dominant aquatic vegetation. Monthly censuses over a 3-year period found that in the higher density population, changes in H. formosa density exhibited a strong negative autocorrelation structure: increases (decreases) at one census tended to be followed by decreases (increases) at the next one. However, no such correlation was present in the lower density population. Monthly census data also revealed that predators, especially Lepomis sp., were considerably more abundant at the site with lower H. formosa densities. Experimental studies showed that the predation by Lepomis gulosus occurred at a much higher rate than predation by two other fish and two dragonfly species, although L. gulosus and L. punctatus had similar predation rates when the amount of vegetative cover was high. The most effective predator, L. gulosus, did not discriminate among life stages (males, females, and juveniles) of H. formosa. Increased predation rates by L. gulosus could keep H. formosa low in one population, thereby eliminating strong negative density-dependent regulation. In support of this, changes in H. formosa density were positively correlated with changes in vegetative cover for the population with a history of lower density, but not for the population with a history of higher density. Our results are consistent with the hypothesis that the observed differences among natural populations in numerical abundance and dynamics are caused in part by the differences in habitat complexity and the predator community. ?? Springer-Verlag 2005.

  10. Fish abundance and population stability in a reservoir tailwater and an unregulated headwater stream

    USGS Publications Warehouse

    Jacobs, K.E.; Swink, W.D.

    1983-01-01

    Fish abundance and population stability were compared in the tailwater and in an unregulated tributary of Barren River Lake, a flood control reservoir in south central Kentucky. Fish abundance was greater in the tailwater near the dam and was dominated by three species common in the reservoir: gizzard shad (Dorosoma cepedianum), bluegills (Lepomis macrochirus), and white crappies (Pomoxis annularis). Three riverine suckers were less abundant in the tailwater than in the unregulated stream: northern hog suckers (Hypentelium nigricans), black redhorse (Moxostoma duquesnei), and golden redhorse (Moxostoma erythrurum). The fish populations in the tailwater, particularly common carp (Cyprinus carpio), northern hog suckers, black redhorse, and golden redhorse, were less stable than those in the unregulated stream. Population stability is defined as the extent to which fish remain in a stream section. This study suggests that the occurrence of reservoir species in the tailwater was the result of fish passage from the reservoir during high discharges in fall and winter. Reservoir operations (altered flow, low summer water temperature, and poor summer water quality) probably were responsible for the unstable populations of common carp and riverine suckers in the tailwater.

  11. Lithium abundances in samples of dwarf stars of population II and very old population I

    NASA Astrophysics Data System (ADS)

    Beckman, J.; Rebolo, R.; Molaro, P.

    The CCD camera and Intermediate Dispersion Spectrograph of the 2.5 m Issaac Newton Telescope are used to obtain high quality spectra of the 6708-A Li-7 resonance doublet in 22 dwarfs with metallicities not greater than -0.7. A mean constant value of Log N(Li) = 2.07 (+ or - 0.1) is found for highly metal deficient dwarfs (Fe/H abundance ratios of not greater than 1.5) with atmospheric temperatures T(eff) greater than 5500 K, and a larger spread with values of Log N(Li) up to 2.4 for the warmer dwarfs with metallicities between -0.7 and -1.2. The results agree with previous findings by Spite et al. (1982, 1984) showing a highly uniform Li abundance near the inception of the galaxy. Li depletion appears to set in at higher temperatures for the moderately metal deficient stars than for the extremely metal deficient, consistent with metallicity-dependent depletion rates (low metals, low depletion).

  12. Comparing Population Patterns to Processes: Abundance and Survival of a Forest Salamander following Habitat Degradation

    PubMed Central

    Otto, Clint R. V.; Roloff, Gary J.; Thames, Rachael E.

    2014-01-01

    Habitat degradation resulting from anthropogenic activities poses immediate and prolonged threats to biodiversity, particularly among declining amphibians. Many studies infer amphibian response to habitat degradation by correlating patterns in species occupancy or abundance with environmental effects, often without regard to the demographic processes underlying these patterns. We evaluated how retention of vertical green trees (CANOPY) and coarse woody debris (CWD) influenced terrestrial salamander abundance and apparent survival in recently clearcut forests. Estimated abundance of unmarked salamanders was positively related to CANOPY (Canopy  = 0.21 (0.02–1.19; 95% CI), but not CWD (CWD  = 0.11 (−0.13–0.35) within 3,600 m2 sites, whereas estimated abundance of unmarked salamanders was not related to CANOPY (Canopy  = −0.01 (−0.21–0.18) or CWD (CWD  = −0.02 (−0.23–0.19) for 9 m2 enclosures. In contrast, apparent survival of marked salamanders within our enclosures over 1 month was positively influenced by both CANOPY and CWD retention (Canopy  = 0.73 (0.27–1.19; 95% CI) and CWD  = 1.01 (0.53–1.50). Our results indicate that environmental correlates to abundance are scale dependent reflecting habitat selection processes and organism movements after a habitat disturbance event. Our study also provides a cautionary example of how scientific inference is conditional on the response variable(s), and scale(s) of measure chosen by the investigator, which can have important implications for species conservation and management. Our research highlights the need for joint evaluation of population state variables, such as abundance, and population-level process, such as survival, when assessing anthropogenic impacts on forest biodiversity. PMID:24718498

  13. Comparing population patterns to processes: abundance and survival of a forest salamander following habitat degradation.

    PubMed

    Otto, Clint R V; Roloff, Gary J; Thames, Rachael E

    2014-01-01

    Habitat degradation resulting from anthropogenic activities poses immediate and prolonged threats to biodiversity, particularly among declining amphibians. Many studies infer amphibian response to habitat degradation by correlating patterns in species occupancy or abundance with environmental effects, often without regard to the demographic processes underlying these patterns. We evaluated how retention of vertical green trees (CANOPY) and coarse woody debris (CWD) influenced terrestrial salamander abundance and apparent survival in recently clearcut forests. Estimated abundance of unmarked salamanders was positively related to CANOPY (β Canopy  = 0.21 (0.02-1.19; 95% CI), but not CWD (β CWD  = 0.11 (-0.13-0.35) within 3,600 m2 sites, whereas estimated abundance of unmarked salamanders was not related to CANOPY (β Canopy  = -0.01 (-0.21-0.18) or CWD (β CWD  = -0.02 (-0.23-0.19) for 9 m2 enclosures. In contrast, apparent survival of marked salamanders within our enclosures over 1 month was positively influenced by both CANOPY and CWD retention (β Canopy  = 0.73 (0.27-1.19; 95% CI) and β CWD  = 1.01 (0.53-1.50). Our results indicate that environmental correlates to abundance are scale dependent reflecting habitat selection processes and organism movements after a habitat disturbance event. Our study also provides a cautionary example of how scientific inference is conditional on the response variable(s), and scale(s) of measure chosen by the investigator, which can have important implications for species conservation and management. Our research highlights the need for joint evaluation of population state variables, such as abundance, and population-level process, such as survival, when assessing anthropogenic impacts on forest biodiversity.

  14. Possible sources of the Population I lithium abundance and light-element evolution

    NASA Technical Reports Server (NTRS)

    Brown, Lawrence E.

    1992-01-01

    One-zone numerical models of Galactic chemical evolution of the light elements (lithium, beryllium, boron, and deuterium) with a broad sample of possible stellar lithium production sites and star formation histories, including the multiple merger model of Mathews and Schramm (1992), are examined. Models with high primordial lithium are constrained by observations of lithium and potassium in the interstellar medium of the LMC to have Li abundances close to the Population I value of about 10 exp -9. Li-7 production in intermediate- or high-mass stars (greater than 4 solar masses) is found to fit observations somewhat better than production in low-mass (1-5 solar masses) stars. Since elevated levels of lithium are commonly observed in intermediate-mass stars in the LMC, it is argued that this is indeed the major source of the Population I Li-7 abundance.

  15. A broad perspective on multiple abundance populations in the globular cluster NGC 1851

    NASA Astrophysics Data System (ADS)

    Simpson, Jeffrey D.; Martell, Sarah L.; Navin, Colin A.

    2017-02-01

    We present an analysis of the multiple stellar populations of the globular cluster NGC 1851. We used lower resolution spectra of giant stars to measure CN, CH, and calcium H & K spectral indices, and determine elemental abundances for carbon and nitrogen. The CN and CH indices were used to confirm that there are four populations of stars in the cluster. The primordial population of stars, with the lowest CN, was found to be generally chemically distinct in elemental abundances from the second-generation populations. As expected, [N/Fe] increases with increasing CN strength, but the only other element that correlated with CN was barium. The two largest populations of stars were found to have the same rate of carbon astration as the stars that ascend the giant branch. We were also able to confirm that four previously identified extratidal stars are chemically associated with the cluster. This work shows the benefit of considering the chemistry of globular clusters with both high- and low-resolution spectra.

  16. Microbial abundance and community structure in a melting alpine snowpack.

    PubMed

    Lazzaro, Anna; Wismer, Andrea; Schneebeli, Martin; Erny, Isolde; Zeyer, Josef

    2015-05-01

    Snowmelt is a crucial period for alpine soil ecosystems, as it is related to inputs of nutrients, particulate matter and microorganisms to the underlying soil. Although snow-inhabiting microbial communities represent an important inoculum for soils, they have thus far received little attention. The distribution and structure of these microorganisms in the snowpack may be linked to the physical properties of the snowpack at snowmelt. Snow samples were taken from snow profiles at four sites (1930-2519 m a.s.l.) in the catchment of the Tiefengletscher, Canton Uri, Switzerland. Microbial (Archaea, Bacteria and Fungi) communities were investigated through T-RFLP profiling of the 16S and 18S rRNA genes, respectively. In parallel, we assessed physical and chemical parameters relevant to the understanding of melting processes. Along the snow profiles, density increased with depth due to compaction, while other physico-chemical parameters, such as temperature and concentrations of DOC and soluble ions, remained in the same range (e.g. <2 mg DOC L(-1), 5-30 μg NH4 (+)-N L(-1)) in all samples at all sites. Along the snow profiles, no major change was observed either in cell abundance or in bacterial and fungal diversity. No Archaea could be detected in the snow. Microbial communities, however, differed significantly between sites. Our results show that meltwater rearranges soluble ions and microbial communities in the snowpack.

  17. [Composition, abundance and distribution of populations of commercially important gastropods in La Guajira, Colombian Caribbean].

    PubMed

    Nieto-Bernal, Ramón; Luis, Chasqui; Rodriguez, Angélica María; Castro, Erick; Gil-Agudelo, Diego L

    2013-06-01

    In the continental Colombian Caribbean the conch resource exploitation and the status of snails populations has been poorly studied, which are reflected in the lack of fisheries management. This study assesses composition, population density and distribution of the gastropods species that make conch resource in La Guajira region. Underwater visual censuses for snails were performed between September-November 2009 in 145100x4m (400m2) transects, spanning a total area of 56920m2 between Riohacha and Cabo de la Vela. The study was complemented with the evaluation of composition, abundance and size of gastropods conch found in the discarded-by-fishermen shell mounds in 13 beaches. In October 2010 another 40 transects were evaluated (16 000 m2) from the Southern of Riohacha to the Camarones village (La Guajira). We found a total of 9911 snails belonging to 12 species, the most abundant being Strombus pugilis with 8 912 individuals and an average density of 1 538.4 +/- 3 662.6 ind./ha, followed by Vasum muricatum with 374 individuals and an average density of 51.8 +/- 91.2 ind./ha. Calculating the importance value index (IVI) for both living organisms as the empty shells on beaches, shows that Turbinella angulata is the most used species by artisanal fishermen in the region. Cassis madagascariensis and Cassis tuberosa are also important snail resources in the region (as suggested by the number of empty shells found in beaches), but its densities were low. Strombus gigas, with only three living organisms found in the area, presented the lowest abundance ever found in the Colombian Caribbean (0.52 +/- 3.6 ind./ha), showing that queen conch population in La Guajira cannot support commercial exploitation. The abundance of discarded S. gigas shells on beaches suggests resource exploitation in the recent past. Results remarks the urgency of implementing management plans for snail fisheries in the region.

  18. Deer herbivory reduces web-building spider abundance by simplifying forest vegetation structure.

    PubMed

    Roberson, Elizabeth J; Chips, Michael J; Carson, Walter P; Rooney, Thomas P

    2016-01-01

    Indirect ecological effects are a common feature of ecological systems, arising when one species affects interactions among two or more other species. We examined how browsing by white-tailed deer (Odocoileus virginianus) indirectly affected the abundance and composition of a web-building spider guild through their effects on the structure of the ground and shrub layers of northern hardwood forests. We examined paired plots consisting of deer-free and control plots in the Allegheny Plateau region Pennsylvania and Northern Highlands region of Wisconsin. We recorded the abundance of seven types of webs, each corresponding to a family of web-building spiders. We quantified vegetation structure and habitat suitability for the spiders by computing a web scaffold availability index (WSAI) at 0.5 m and 1.0 m above the ground. At Northern Highlands sites, we recorded prey availability. Spider webs were twice as abundant in deer-free plots compared to control plots, while WSAI was 7-12 times greater in deerfree plots. Prey availability was lower in deer-free plots. With the exception of funnel web-builders, all spider web types were significantly more abundant in deer-free plots. Both deer exclusion and the geographic region of plots were significant predictors of spider community structure. In closed canopy forests with high browsing pressure, the low density of tree saplings and shrubs provides few locations for web-building spiders to anchor webs. Recruitment of these spiders may become coupled with forest disturbance events that increase tree and shrub recruitment. By modifying habitat structure, deer appear to indirectly modify arthropod food web interactions. As deer populations have increased in eastern North America over the past several decades, the effects of deer on web-building spiders may be widespread.

  19. Deer herbivory reduces web-building spider abundance by simplifying forest vegetation structure

    PubMed Central

    Chips, Michael J.; Carson, Walter P.

    2016-01-01

    Indirect ecological effects are a common feature of ecological systems, arising when one species affects interactions among two or more other species. We examined how browsing by white-tailed deer (Odocoileus virginianus) indirectly affected the abundance and composition of a web-building spider guild through their effects on the structure of the ground and shrub layers of northern hardwood forests. We examined paired plots consisting of deer-free and control plots in the Allegheny Plateau region Pennsylvania and Northern Highlands region of Wisconsin. We recorded the abundance of seven types of webs, each corresponding to a family of web-building spiders. We quantified vegetation structure and habitat suitability for the spiders by computing a web scaffold availability index (WSAI) at 0.5 m and 1.0 m above the ground. At Northern Highlands sites, we recorded prey availability. Spider webs were twice as abundant in deer-free plots compared to control plots, while WSAI was 7–12 times greater in deerfree plots. Prey availability was lower in deer-free plots. With the exception of funnel web-builders, all spider web types were significantly more abundant in deer-free plots. Both deer exclusion and the geographic region of plots were significant predictors of spider community structure. In closed canopy forests with high browsing pressure, the low density of tree saplings and shrubs provides few locations for web-building spiders to anchor webs. Recruitment of these spiders may become coupled with forest disturbance events that increase tree and shrub recruitment. By modifying habitat structure, deer appear to indirectly modify arthropod food web interactions. As deer populations have increased in eastern North America over the past several decades, the effects of deer on web-building spiders may be widespread. PMID:27703868

  20. Population Genetic Structure of Aedes fluviatilis (Diptera: Culicidae)

    PubMed Central

    Multini, Laura Cristina; Suesdek, Lincoln; Marrelli, Mauro Toledo

    2016-01-01

    Although Aedes fluviatilis is an anthropophilic mosquito found abundantly in urban environments, its biology, epidemiological potential and genetic characteristics are poorly understood. Climate change and urbanization processes that result in environmental modifications benefit certain anthropophilic mosquito species such as Ae. fluviatilis, greatly increasing their abundance in urban areas. To gain a better understanding of whether urbanization processes modulate the genetic structure of this species in the city of São Paulo, we used eight microsatellite loci to genetically characterize Ae. fluviatilis populations collected in nine urban parks in the city of São Paulo. Our results show that there is high gene flow among the populations of this species, heterozygosity deficiency and low genetic structure and that the species may have undergone a recent population expansion. There are two main hypotheses to explain these findings: (i) Ae. fluviatilis populations have undergone a population expansion as a result of urbanization; and (ii) as urbanization of the city of São Paulo occurred recently and was quite intense, the structuring of these populations cannot be observed yet, apart from in the populations of Ibirapuera and Piqueri parks, where the first signs of structuring have appeared. We believe that the expansion found in Ae. fluviatilis populations is probably correlated with the unplanned urbanization of the city of São Paulo, which transformed green areas into urbanized areas, as well as the increasing population density in the city. PMID:27598889

  1. Ecological niche structure and rangewide abundance patterns of species

    PubMed Central

    Martínez-Meyer, Enrique; Díaz-Porras, Daniel; Peterson, A. Townsend; Yáñez-Arenas, Carlos

    2013-01-01

    Spatial abundance patterns across species' ranges have attracted intense attention in macroecology and biogeography. One key hypothesis has been that abundance declines with geographical distance from the range centre, but tests of this idea have shown that the effect may occur indeed only in a minority of cases. We explore an alternative hypothesis: that species' abundances decline with distance from the centroid of the species' habitable conditions in environmental space (the ecological niche). We demonstrate consistent negative abundance–ecological distance relationships across all 11 species analysed (turtles to wolves), and that relationships in environmental space are consistently stronger than relationships in geographical space. PMID:23134784

  2. Population structure of Streptococcus oralis

    PubMed Central

    Do, Thuy; Jolley, Keith A.; Maiden, Martin C. J.; Gilbert, Steven C.; Clark, Douglas; Wade, William G.; Beighton, David

    2009-01-01

    Streptococcus oralis is a member of the normal human oral microbiota, capable of opportunistic pathogenicity; like related oral streptococci, it exhibits appreciable phenotypic and genetic variation. A multilocus sequence typing (MLST) scheme for S. oralis was developed and the resultant data analysed to examine the population structure of the species. Analysis of 113 isolates, confirmed as belonging to the S. oralis/mitis group by 16S rRNA gene sequencing, characterized the population as highly diverse and undergoing inter- and intra-species recombination with a probable clonal complex structure. ClonalFrame analysis of these S. oralis isolates along with examples of Streptococcus pneumoniae, Streptococcus mitis and Streptococcus pseudopneumoniae grouped the named species into distinct, coherent populations and did not support the clustering of S. pseudopneumoniae with S. mitis as reported previously using distance-based methods. Analysis of the individual loci suggested that this discrepancy was due to the possible hybrid nature of S. pseudopneumoniae. The data are available on the public MLST website (http://pubmlst.org/soralis/). PMID:19423627

  3. Estimating snow leopard population abundance using photography and capture-recapture techniques

    USGS Publications Warehouse

    Jackson, R.M.; Roe, J.D.; Wangchuk, R.; Hunter, D.O.

    2006-01-01

    Conservation and management of snow leopards (Uncia uncia) has largely relied on anecdotal evidence and presence-absence data due to their cryptic nature and the difficult terrain they inhabit. These methods generally lack the scientific rigor necessary to accurately estimate population size and monitor trends. We evaluated the use of photography in capture-mark-recapture (CMR) techniques for estimating snow leopard population abundance and density within Hemis National Park, Ladakh, India. We placed infrared camera traps along actively used travel paths, scent-sprayed rocks, and scrape sites within 16- to 30-km2 sampling grids in successive winters during January and March 2003-2004. We used head-on, oblique, and side-view camera configurations to obtain snow leopard photographs at varying body orientations. We calculated snow leopard abundance estimates using the program CAPTURE. We obtained a total of 66 and 49 snow leopard captures resulting in 8.91 and 5.63 individuals per 100 trap-nights during 2003 and 2004, respectively. We identified snow leopards based on the distinct pelage patterns located primarily on the forelimbs, flanks, and dorsal surface of the tail. Capture probabilities ranged from 0.33 to 0.67. Density estimates ranged from 8.49 (SE = 0.22; individuals per 100 km2 in 2003 to 4.45 (SE = 0.16) in 2004. We believe the density disparity between years is attributable to different trap density and placement rather than to an actual decline in population size. Our results suggest that photographic capture-mark-recapture sampling may be a useful tool for monitoring demographic patterns. However, we believe a larger sample size would be necessary for generating a statistically robust estimate of population density and abundance based on CMR models.

  4. Field population abundance of leafhopper (Homoptera: Cicadelidae) and planthopper (Homoptera: Delphacidae) as affected by rice growth stages

    NASA Astrophysics Data System (ADS)

    Hafizal, M. M.; Idris, A. B.

    2013-11-01

    The leafhopper (Homoptera: Delphacidae) and planthopper (Homoptera: Cicadelidae) are considered as important rice pest in Asia including Malaysia. As phloem-feeders, they can cause loss to rice growth development and their population abundance is thought to be influenced by rice growth stages. This study was conducted to examine the population of Delphacidae and Cicadelidae between different rice growth stages, i.e. before and after rice planting periods. Monthly sampling was conducted in three sites in Kuala Selangor at before planting, vegetative, reproductive, maturing stages and post-harvest period using sweeping net and light traps. Population abundance of Delphacidae and Cicadelidae were found to be significantly different and positively correlated with different rice growth stages (p<0.05). Delphacidae was most abundance during maturing stages, while the abundance of Cicadelidae peaked during reproductive stage of rice growth. Differences in temporal abundance of the population of these two homopterans indicated adaptive feeding strategy to reduce food competition.

  5. Genetics of single-cell protein abundance variation in large yeast populations

    NASA Astrophysics Data System (ADS)

    Albert, Frank W.; Treusch, Sebastian; Shockley, Arthur H.; Bloom, Joshua S.; Kruglyak, Leonid

    2014-02-01

    Variation among individuals arises in part from differences in DNA sequences, but the genetic basis for variation in most traits, including common diseases, remains only partly understood. Many DNA variants influence phenotypes by altering the expression level of one or several genes. The effects of such variants can be detected as expression quantitative trait loci (eQTL). Traditional eQTL mapping requires large-scale genotype and gene expression data for each individual in the study sample, which limits sample sizes to hundreds of individuals in both humans and model organisms and reduces statistical power. Consequently, many eQTL are probably missed, especially those with smaller effects. Furthermore, most studies use messenger RNA rather than protein abundance as the measure of gene expression. Studies that have used mass-spectrometry proteomics reported unexpected differences between eQTL and protein QTL (pQTL) for the same genes, but these studies have been even more limited in scope. Here we introduce a powerful method for identifying genetic loci that influence protein expression in the yeast Saccharomyces cerevisiae. We measure single-cell protein abundance through the use of green fluorescent protein tags in very large populations of genetically variable cells, and use pooled sequencing to compare allele frequencies across the genome in thousands of individuals with high versus low protein abundance. We applied this method to 160 genes and detected many more loci per gene than previous studies. We also observed closer correspondence between loci that influence protein abundance and loci that influence mRNA abundance of a given gene. Most loci that we detected were clustered in `hotspots' that influence multiple proteins, and some hotspots were found to influence more than half of the proteins that we examined. The variants that underlie these hotspots have profound effects on the gene regulatory network and provide insights into genetic variation in cell

  6. Environmental metabolomics links genotype to phenotype and predicts genotype abundance in wild plant populations.

    PubMed

    Field, Katie J; Lake, Janice A

    2011-08-01

    'The Holy Grail' of plant ecology is to uncover rules that associate species and traits with environmental constraints, community composition and subsequent ecosystem functioning. These aims have been crystallized in recent years within the context of global climate change and environmental pollution, increasing the urgency of the need to predict how vegetation will respond across spatial scales. We investigated whether genetic diversity is associated with the way in which phenotypic plasticity within plant populations is realized and whether this is related to genotype abundance. We used environmental metabolomics to demonstrate biochemical variation between co-occurring genotypes of Carex caryophyllea L. A novel combined metabolomic/functional trait analysis was used to test the functionality of this variation in governing plasticity to variation in edaphic conditions, with particular reference to metabolic pathways that play important roles in growth-related traits. We show that genetic diversity within a wild C. caryophyllea population relates to differences in metabolic composition and functional traits in response to soil nutrient variation, influencing genotype abundance within a community. Our findings highlight the vital role genetic diversity plays within a population in facilitating plant phenotypic plasticity and the potential usefulness of environmental metabolomics to future ecological studies.

  7. Modeling structured population dynamics using data from unmarked individuals

    USGS Publications Warehouse

    Grant, Evan H. Campbell; Zipkin, Elise; Thorson, James T.; See, Kevin; Lynch, Heather J.; Kanno, Yoichiro; Chandler, Richard; Letcher, Benjamin H.; Royle, J. Andrew

    2014-01-01

    The study of population dynamics requires unbiased, precise estimates of abundance and vital rates that account for the demographic structure inherent in all wildlife and plant populations. Traditionally, these estimates have only been available through approaches that rely on intensive mark–recapture data. We extended recently developed N-mixture models to demonstrate how demographic parameters and abundance can be estimated for structured populations using only stage-structured count data. Our modeling framework can be used to make reliable inferences on abundance as well as recruitment, immigration, stage-specific survival, and detection rates during sampling. We present a range of simulations to illustrate the data requirements, including the number of years and locations necessary for accurate and precise parameter estimates. We apply our modeling framework to a population of northern dusky salamanders (Desmognathus fuscus) in the mid-Atlantic region (USA) and find that the population is unexpectedly declining. Our approach represents a valuable advance in the estimation of population dynamics using multistate data from unmarked individuals and should additionally be useful in the development of integrated models that combine data from intensive (e.g., mark–recapture) and extensive (e.g., counts) data sources.

  8. Mountain goat abundance and population trends in the Olympic Mountains, northwestern Washington, 2016

    USGS Publications Warehouse

    Jenkins, Kurt J.; Happe, Patricia J.; Beirne, Katherine F.; Baccus, William T.

    2016-11-30

    Executive SummaryWe estimated abundance and trends of non-native mountain goats (Oreamnos americanus) in the Olympic Mountains of northwestern Washington, based on aerial surveys conducted during July 13–24, 2016. The surveys produced the seventh population estimate since the first formal aerial surveys were conducted in 1983. This was the second population estimate since we adjusted survey area boundaries and adopted new estimation procedures in 2011. Before 2011, surveys encompassed all areas free of glacial ice at elevations above 1,520 meters (m), but in 2011 we expanded survey unit boundaries to include suitable mountain goat habitats at elevations between 1,425 and 1,520 m. In 2011, we also began applying a sightability correction model allowing us to estimate undercounting bias associated with aerial surveys and to adjust survey results accordingly. The 2016 surveys were carried out by National Park Service (NPS) personnel in Olympic National Park and by Washington Department of Fish and Wildlife (WDFW) biologists in Olympic National Forest and in the southeastern part of Olympic National Park. We surveyed a total of 59 survey units, comprising 55 percent of the 60,218-hectare survey area. We estimated a mountain goat population of 623 ±43 (standard error, SE). Based on this level of estimation uncertainty, the 95-percent confidence interval ranged from 561 to 741 mountain goats at the time of the survey.We examined the rate of increase of the mountain goat population by comparing the current population estimate to previous estimates from 2004 and 2011. Because aerial survey boundaries changed between 2004 and 2016, we recomputed population estimates for 2011 and 2016 surveys based on the revised survey boundaries as well as the previously defined boundaries so that estimates were directly comparable across years. Additionally, because the Mount Washington survey unit was not surveyed in 2011, we used results from an independent survey of the Mount

  9. Links between Ammonia Oxidizer Community Structure, Abundance, and Nitrification Potential in Acidic Soils ▿ †

    PubMed Central

    Yao, Huaiying; Gao, Yangmei; Nicol, Graeme W.; Campbell, Colin D.; Prosser, James I.; Zhang, Limei; Han, Wenyan; Singh, Brajesh K.

    2011-01-01

    Ammonia oxidation is the first and rate-limiting step of nitrification and is performed by both ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the environmental drivers controlling the abundance, composition, and activity of AOA and AOB communities are not well characterized, and the relative importance of these two groups in soil nitrification is still debated. Chinese tea orchard soils provide an excellent system for investigating the long-term effects of low pH and nitrogen fertilization strategies. AOA and AOB abundance and community composition were therefore investigated in tea soils and adjacent pine forest soils, using quantitative PCR (qPCR), terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of respective ammonia monooxygenase (amoA) genes. There was strong evidence that soil pH was an important factor controlling AOB but not AOA abundance, and the ratio of AOA to AOB amoA gene abundance increased with decreasing soil pH in the tea orchard soils. In contrast, T-RFLP analysis suggested that soil pH was a key explanatory variable for both AOA and AOB community structure, but a significant relationship between community abundance and nitrification potential was observed only for AOA. High potential nitrification rates indicated that nitrification was mainly driven by AOA in these acidic soils. Dominant AOA amoA sequences in the highly acidic tea soils were all placed within a specific clade, and one AOA genotype appears to be well adapted to growth in highly acidic soils. Specific AOA and AOB populations dominated in soils at particular pH values and N content, suggesting adaptation to specific niches. PMID:21571885

  10. Abundance and phenology patterns of two pond-breeding salamanders determine species interactions in natural populations.

    PubMed

    Anderson, Thomas L; Hocking, Daniel J; Conner, Christopher A; Earl, Julia E; Harper, Elizabeth B; Osbourn, Michael S; Peterman, William E; Rittenhouse, Tracy A G; Semlitsch, Raymond D

    2015-03-01

    Phenology often determines the outcome of interspecific interactions, where early-arriving species often dominate interactions over those arriving later. The effects of phenology on species interactions are especially pronounced in aquatic systems, but the evidence is largely derived from experimental studies. We examined whether differences in breeding phenology between two pond-breeding salamanders (Ambystoma annulatum and A. maculatum) affected metamorph recruitment and demographic traits within natural populations, with the expectation that the fall-breeding A. annulatum would negatively affect the spring-breeding A. maculatum. We monitored populations of each species at five ponds over 4 years using drift fences. Metamorph abundance and survival of A. annulatum were affected by intra- and interspecific processes, whereas metamorph size and date of emigration were primarily influenced by intraspecific effects. Metamorph abundance, snout-vent length, date of emigration and survival for A. maculatum were all predicted by combinations of intra- and interspecific effects, but often showed negative relationships with A. annulatum metamorph traits and abundance. Size and date of metamorphosis were strongly correlated within each species, but in opposite patterns (negative for A. annulatum and positive for A. maculatum), suggesting that the two species use alternative strategies to enhance terrestrial survival and that these factors may influence their interactions. Our results match predictions from experimental studies that suggest recruitment is influenced by intra- and interspecific processes which are determined by phenological differences between species. Incorporating spatiotemporal variability when modeling population dynamics is necessary to understand the importance of phenology in species interactions, especially as shifts in phenology occur under climate change.

  11. Antifungal leaf-surface metabolites correlate with fungal abundance in sagebrush populations.

    PubMed

    Talley, Sharon M; Coley, Phyllis D; Kursar, Thomas A

    2002-11-01

    A central component in understanding plant-enemy interactions is to determine whether plant enemies, such as herbivores and pathogens, mediate the evolution of plant secondary metabolites. Using 26 populations of a broadly distributed plant species, sagebrush (Artemisia tridentata), we examined whether sagebrush populations in habitats with a greater prevalence of fungi contained antifungal secondary metabolites on leaf surfaces that were more active and diverse than sagebrush populations in habitats less favorable to fungi. Because moisture and temperature play a key role in the epidemiology of most plant-pathogen interactions, we also examined the relationship between the antifungal activity of secondary metabolites and the climate of a site. We evaluated the antifungal activity of sagebrush secondary metabolites against two fungi, a wild Penicillium sp. and a laboratory yeast, Saccharomyces cerevisiae, using a filter-paper disk assay and bioautography. Comparing the 26 sagebrush populations, we found that fungal abundance was a good predictor of both the activity (r2 = 0.36 for Saccharomyces, r2 = 0.37 for Penicillium) and number (r2 = 0.34 for Saccharomyces) of antifungal secondary metabolites. This suggests that selection imposed by fungal pathogens has led to more effective antifungal secondary metabolites. We found that the antifungal activity of sagebrush secondary metabolites was negatively related to average vapor pressure deficit of the habitat (r2 = 0.60 for Saccharomyces, r2 = 0.61 for Penicillium). Differences in antifungal activity among populations were not due to the amount of secondary metabolites, but rather to qualitative differences in the composition of antifungal compounds. Although all populations in habitats with high fungal prevalence had secondary metabolites with high antifungal activity, different suites of compounds were responsible for this activity, suggesting independent outcomes of selection on plants by fungal pathogens. The

  12. Pseudomonas aeruginosa Population Structure Revisited

    PubMed Central

    Pirnay, Jean-Paul; Bilocq, Florence; Pot, Bruno; Cornelis, Pierre; Zizi, Martin; Van Eldere, Johan; Deschaght, Pieter; Vaneechoutte, Mario; Jennes, Serge; Pitt, Tyrone; De Vos, Daniel

    2009-01-01

    At present there are strong indications that Pseudomonas aeruginosa exhibits an epidemic population structure; clinical isolates are indistinguishable from environmental isolates, and they do not exhibit a specific (disease) habitat selection. However, some important issues, such as the worldwide emergence of highly transmissible P. aeruginosa clones among cystic fibrosis (CF) patients and the spread and persistence of multidrug resistant (MDR) strains in hospital wards with high antibiotic pressure, remain contentious. To further investigate the population structure of P. aeruginosa, eight parameters were analyzed and combined for 328 unrelated isolates, collected over the last 125 years from 69 localities in 30 countries on five continents, from diverse clinical (human and animal) and environmental habitats. The analysed parameters were: i) O serotype, ii) Fluorescent Amplified-Fragment Length Polymorphism (FALFP) pattern, nucleotide sequences of outer membrane protein genes, iii) oprI, iv) oprL, v) oprD, vi) pyoverdine receptor gene profile (fpvA type and fpvB prevalence), and prevalence of vii) exoenzyme genes exoS and exoU and viii) group I pilin glycosyltransferase gene tfpO. These traits were combined and analysed using biological data analysis software and visualized in the form of a minimum spanning tree (MST). We revealed a network of relationships between all analyzed parameters and non-congruence between experiments. At the same time we observed several conserved clones, characterized by an almost identical data set. These observations confirm the nonclonal epidemic population structure of P. aeruginosa, a superficially clonal structure with frequent recombinations, in which occasionally highly successful epidemic clones arise. One of these clones is the renown and widespread MDR serotype O12 clone. On the other hand, we found no evidence for a widespread CF transmissible clone. All but one of the 43 analysed CF strains belonged to a ubiquitous P

  13. Does White Clover (Trifolium repens) Abundance in Temperate Pastures Determine Sitona obsoletus (Coleoptera: Curculionidae) Larval Populations?

    PubMed Central

    McNeill, Mark R.; van Koten, Chikako; Cave, Vanessa M.; Chapman, David; Hodgson, Hamish

    2016-01-01

    To determine if host plant abundance determined the size of clover root weevil (CRW) Sitona obsoletus larval populations, a study was conducted over 4 years in plots sown in ryegrass (Lolium perenne) (cv. Nui) sown at either 6 or 30 kg/ha and white clover (Trifolium repens) sown at a uniform rate of 8 kg/ha. This provided a range of % white clover content to investigate CRW population establishment and impacts on white clover survival. Larval sampling was carried out in spring (October) when larval densities are near their spring peak at Lincoln (Canterbury, New Zealand) with % clover measured in autumn (April) and spring (September) of each year. Overall, mean larval densities measured in spring 2012–2015 were 310, 38, 59, and 31 larvae m-2, respectively. There was a significant decline in larval populations between 2012 and 2013, but spring populations were relatively uniform thereafter. The mean % white clover measured in autumns of 2012 to 2015 was 17, 10, 3, and 11%, respectively. In comparison, mean spring % white clover from 2012 to 2015, averaged c. 5% each year. Analysis relating spring (October) larval populations to % white clover measured in each plot in autumn (April) found the 2012 larval population to be statistically significantly larger in the ryegrass 6 kg/ha plots than 30 kg/ha plots. Thereafter, sowing rate had no significant effect on larval populations. From 2013 to 2015, spring larval populations had a negative relationship with the previous autumn % white clover with the relationship highly significant for the 2014 data. When CRW larval populations in spring 2013 to 2015 were predicted from the 2013 to 2015 autumn % white clover, respectively, based on their positive relationship in 2012, the predicted densities were substantially larger than those observed. Conversely, when 2015 spring larval data and % clover was regressed against 2012–2014 larval populations, observed densities tended to be higher than predicted, but the numbers came

  14. Does White Clover (Trifolium repens) Abundance in Temperate Pastures Determine Sitona obsoletus (Coleoptera: Curculionidae) Larval Populations?

    PubMed

    McNeill, Mark R; van Koten, Chikako; Cave, Vanessa M; Chapman, David; Hodgson, Hamish

    2016-01-01

    To determine if host plant abundance determined the size of clover root weevil (CRW) Sitona obsoletus larval populations, a study was conducted over 4 years in plots sown in ryegrass (Lolium perenne) (cv. Nui) sown at either 6 or 30 kg/ha and white clover (Trifolium repens) sown at a uniform rate of 8 kg/ha. This provided a range of % white clover content to investigate CRW population establishment and impacts on white clover survival. Larval sampling was carried out in spring (October) when larval densities are near their spring peak at Lincoln (Canterbury, New Zealand) with % clover measured in autumn (April) and spring (September) of each year. Overall, mean larval densities measured in spring 2012-2015 were 310, 38, 59, and 31 larvae m(-2), respectively. There was a significant decline in larval populations between 2012 and 2013, but spring populations were relatively uniform thereafter. The mean % white clover measured in autumns of 2012 to 2015 was 17, 10, 3, and 11%, respectively. In comparison, mean spring % white clover from 2012 to 2015, averaged c. 5% each year. Analysis relating spring (October) larval populations to % white clover measured in each plot in autumn (April) found the 2012 larval population to be statistically significantly larger in the ryegrass 6 kg/ha plots than 30 kg/ha plots. Thereafter, sowing rate had no significant effect on larval populations. From 2013 to 2015, spring larval populations had a negative relationship with the previous autumn % white clover with the relationship highly significant for the 2014 data. When CRW larval populations in spring 2013 to 2015 were predicted from the 2013 to 2015 autumn % white clover, respectively, based on their positive relationship in 2012, the predicted densities were substantially larger than those observed. Conversely, when 2015 spring larval data and % clover was regressed against 2012-2014 larval populations, observed densities tended to be higher than predicted, but the numbers came

  15. Regional Distribution Shifts Help Explain Local Changes in Wintering Raptor Abundance: Implications for Interpreting Population Trends

    PubMed Central

    Paprocki, Neil; Heath, Julie A.; Novak, Stephen J.

    2014-01-01

    Studies of multiple taxa across broad-scales suggest that species distributions are shifting poleward in response to global climate change. Recognizing the influence of distribution shifts on population indices will be an important part of interpreting trends within management units because current practice often assumes that changes in local populations reflect local habitat conditions. However, the individual- and population-level processes that drive distribution shifts may occur across a large, regional scale and have little to do with the habitats within the management unit. We examined the latitudinal center of abundance for the winter distributions of six western North America raptor species using Christmas Bird Counts from 1975–2011. Also, we considered whether population indices within western North America Bird Conservation Regions (BCRs) were explained by distribution shifts. All six raptors had significant poleward shifts in their wintering distributions over time. Rough-legged Hawks (Buteo lagopus) and Golden Eagles (Aquila chrysaetos) showed the fastest rate of change, with 8.41 km yr−1 and 7.74 km yr−1 shifts, respectively. Raptors may be particularly responsive to warming winters because of variable migration tendencies, intraspecific competition for nesting sites that drives males to winter farther north, or both. Overall, 40% of BCR population trend models were improved by incorporating information about wintering distributions; however, support for the effect of distribution on BCR indices varied by species with Rough-legged Hawks showing the most evidence. These results emphasize the importance of understanding how regional distribution shifts influence local-scale population indices. If global climate change is altering distribution patterns, then trends within some management units may not reflect changes in local habitat conditions. The methods used to monitor and manage bird populations within local BCRs will fundamentally change as

  16. Regional distribution shifts help explain local changes in wintering raptor abundance: implications for interpreting population trends.

    PubMed

    Paprocki, Neil; Heath, Julie A; Novak, Stephen J

    2014-01-01

    Studies of multiple taxa across broad-scales suggest that species distributions are shifting poleward in response to global climate change. Recognizing the influence of distribution shifts on population indices will be an important part of interpreting trends within management units because current practice often assumes that changes in local populations reflect local habitat conditions. However, the individual- and population-level processes that drive distribution shifts may occur across a large, regional scale and have little to do with the habitats within the management unit. We examined the latitudinal center of abundance for the winter distributions of six western North America raptor species using Christmas Bird Counts from 1975-2011. Also, we considered whether population indices within western North America Bird Conservation Regions (BCRs) were explained by distribution shifts. All six raptors had significant poleward shifts in their wintering distributions over time. Rough-legged Hawks (Buteo lagopus) and Golden Eagles (Aquila chrysaetos) showed the fastest rate of change, with 8.41 km yr(-1) and 7.74 km yr(-1) shifts, respectively. Raptors may be particularly responsive to warming winters because of variable migration tendencies, intraspecific competition for nesting sites that drives males to winter farther north, or both. Overall, 40% of BCR population trend models were improved by incorporating information about wintering distributions; however, support for the effect of distribution on BCR indices varied by species with Rough-legged Hawks showing the most evidence. These results emphasize the importance of understanding how regional distribution shifts influence local-scale population indices. If global climate change is altering distribution patterns, then trends within some management units may not reflect changes in local habitat conditions. The methods used to monitor and manage bird populations within local BCRs will fundamentally change as

  17. Evaluating the performance of methods for estimating the abundance of rapidly declining coastal shark populations.

    PubMed

    McCauley, Douglas J; McLean, Kevin A; Bauer, John; Young, Hillary S; Micheli, Fiorenza

    2012-03-01

    Accurately surveying shark populations is critical to monitoring precipitous ongoing declines in shark abundance and interpreting the effects that these reductions are having on ecosystems. To evaluate the effectiveness of existing survey tools, we used field trials and computer simulations to critically examine the operation of four common methods for counting coastal sharks: stationary point counts, belt transects, video surveys, and mark and recapture abundance estimators. Empirical and theoretical results suggest that (1) survey method selection has a strong impact on the estimates of shark density that are produced, (2) standardizations by survey duration are needed to properly interpret and compare survey outputs, (3) increasing survey size does not necessarily increase survey precision, and (4) methods that yield the highest density estimates are not always the most accurate. These findings challenge some of the assumptions traditionally associated with surveying mobile marine animals. Of the methods we trialed, 8 x 50 m belt transects and a 20 m radius point count produced the most accurate estimates of shark density. These findings can help to improve the ways we monitor, manage, and understand the ecology of globally imperiled coastal shark populations.

  18. Assessing small mammal abundance with track-tube indices and mark-recapture population estimates

    USGS Publications Warehouse

    Wiewel, A.S.; Clark, W.R.; Sovada, M.A.

    2007-01-01

    We compared track-tube sampling with mark-recapture livetrapping and evaluated a track-tube index, defined as the number of track tubes with identifiable small mammal tracks during a 4-night period, as a predictor of small mammal abundance estimates in North Dakota grasslands. Meadow voles (Microtus pennsylvanicus) were the most commonly recorded species by both methods, but were underrepresented in track-tube sampling, whereas 13-lined ground squirrels (Spermophilus tridecemlineatus) and Franklin's ground squirrels (S. franklinii) were overrepresented in track-tube sampling. Estimates of average species richness were lower from track tubes than from livetrapping. Regression models revealed that the track-tube index was at best a moderately good predictor of small mammal population estimates because both the form (linear versus curvilinear) and slope of the relationship varied between years. In addition, 95% prediction intervals indicated low precision when predicting population estimates from new track-tube index observations. Track tubes required less time and expense than mark-recapture and eliminated handling of small mammals. Using track tubes along with mark-recapture in a double sampling for regression framework would have potential value when attempting to estimate abundance of small mammals over large areas. ?? 2007 American Society of Mammalogists.

  19. Direct reciprocity in structured populations

    PubMed Central

    van Veelen, Matthijs; García, Julián; Rand, David G.; Nowak, Martin A.

    2012-01-01

    Reciprocity and repeated games have been at the center of attention when studying the evolution of human cooperation. Direct reciprocity is considered to be a powerful mechanism for the evolution of cooperation, and it is generally assumed that it can lead to high levels of cooperation. Here we explore an open-ended, infinite strategy space, where every strategy that can be encoded by a finite state automaton is a possible mutant. Surprisingly, we find that direct reciprocity alone does not lead to high levels of cooperation. Instead we observe perpetual oscillations between cooperation and defection, with defection being substantially more frequent than cooperation. The reason for this is that “indirect invasions” remove equilibrium strategies: every strategy has neutral mutants, which in turn can be invaded by other strategies. However, reciprocity is not the only way to promote cooperation. Another mechanism for the evolution of cooperation, which has received as much attention, is assortment because of population structure. Here we develop a theory that allows us to study the synergistic interaction between direct reciprocity and assortment. This framework is particularly well suited for understanding human interactions, which are typically repeated and occur in relatively fluid but not unstructured populations. We show that if repeated games are combined with only a small amount of assortment, then natural selection favors the behavior typically observed among humans: high levels of cooperation implemented using conditional strategies. PMID:22665767

  20. Constraining the Galactic potential via action-based distribution functions for mono-abundance stellar populations

    NASA Astrophysics Data System (ADS)

    Ting, Yuan-Sen; Rix, Hans-Walter; Bovy, Jo; van de Ven, Glenn

    2013-09-01

    We present a rigorous and practical way of constraining the Galactic potential based on the phase-space information for many individual stars. Such an approach is needed to dynamically model the data from ongoing spectroscopic surveys of the Galaxy and in the future Gaia. This approach describes the orbit distribution of stars by a family of parametrized distribution function (DF) proposed by McMillan and Binney, which are based on actions. We find that these parametrized DFs are flexible enough to capture well the observed phase-space distributions of individual abundance-selected Galactic subpopulations of stars (`mono-abundance populations') for a disc-like gravitational potential, which enables independent dynamical constraints from each of the Galactic mono-abundance populations. We lay out a statistically rigorous way to constrain the Galactic potential parameters by constructing the joint likelihood of potential and DF parameters, and subsequently marginalizing over the DF parameters. This approach explicitly incorporates the spatial selection function inherent to all Galactic surveys, and can account for the uncertainties of the individual position-velocity observations. On that basis, we study the precision of the parameters of the Galactic potential that can be reached with various sample sizes and realistic spatial selection functions. By creating mock samples from the DF, we show that, even under a restrictive and realistic spatial selection function, given a two-parameter gravitational potential, one can recover the true potential parameters to a few per cent with sample sizes of a few thousands. The assumptions of axisymmetry, of DFs that are smooth in the actions and of no time variation remain important limitations in our current study.

  1. Constraining Stellar Population Models. I. Age, Metallicity and Abundance Pattern Compilation for Galactic Globular Clusters

    NASA Astrophysics Data System (ADS)

    Roediger, Joel C.; Courteau, Stéphane; Graves, Genevieve; Schiavon, Ricardo P.

    2014-01-01

    We present an extensive literature compilation of age, metallicity, and chemical abundance pattern information for the 41 Galactic globular clusters (GGCs) studied by Schiavon et al. Our compilation constitutes a notable improvement over previous similar work, particularly in terms of chemical abundances. Its primary purpose is to enable detailed evaluations of and refinements to stellar population synthesis models designed to recover the above information for unresolved stellar systems based on their integrated spectra. However, since the Schiavon sample spans a wide range of the known GGC parameter space, our compilation may also benefit investigations related to a variety of astrophysical endeavors, such as the early formation of the Milky Way, the chemical evolution of GGCs, and stellar evolution and nucleosynthesis. For instance, we confirm with our compiled data that the GGC system has a bimodal metallicity distribution and is uniformly enhanced in the α elements. When paired with the ages of our clusters, we find evidence that supports a scenario whereby the Milky Way obtained its globular clusters through two channels: in situ formation and accretion of satellite galaxies. The distributions of C, N, O, and Na abundances and the dispersions thereof per cluster corroborate the known fact that all GGCs studied so far with respect to multiple stellar populations have been found to harbor them. Finally, using data on individual stars, we verify that stellar atmospheres become progressively polluted by CN(O)-processed material after they leave the main sequence. We also uncover evidence which suggests that the α elements Mg and Ca may originate from more than one nucleosynthetic production site. We estimate that our compilation incorporates all relevant analyses from the literature up to mid-2012. As an aid to investigators in the fields named above, we provide detailed electronic tables of the data upon which our work is based at http

  2. INTERACTIONS BETWEEN BYTHOTREPHES CEDERSTROEMI AND LEPTODORA KINDTII INFERRED FROM SEASONAL POPULATION ABUNDANCE PATTERNS IN LAKE MICHIGAMME, MICHIGAN, USA

    EPA Science Inventory


    Bythotrephes cederstroemi is a non-indigenous predaceous zooplankter invading North American freshwater lakes in the Great Lakes region. We present seasonal population abundance values for both Bythotrephes and Leptodora kindtii from Lake Michigamme, Michigan for the years ...

  3. A Rainfall- and Temperature-Driven Abundance Model for Aedes albopictus Populations

    PubMed Central

    Tran, Annelise; L’Ambert, Grégory; Lacour, Guillaume; Benoît, Romain; Demarchi, Marie; Cros, Myriam; Cailly, Priscilla; Aubry-Kientz, Mélaine; Balenghien, Thomas; Ezanno, Pauline

    2013-01-01

    The mosquito Aedes (Stegomyia) albopictus (Skuse) (Diptera: Culicidae) is an invasive species which has colonized Southern Europe in the last two decades. As it is a competent vector for several arboviruses, its spread is of increasing public health concern, and there is a need for appropriate monitoring tools. In this paper, we have developed a modelling approach to predict mosquito abundance over time, and identify the main determinants of mosquito population dynamics. The model is temperature- and rainfall-driven, takes into account egg diapause during unfavourable periods, and was used to model the population dynamics of Ae. albopictus in the French Riviera since 2008. Entomological collections of egg stage from six locations in Nice conurbation were used for model validation. We performed a sensitivity analysis to identify the key parameters of the mosquito population dynamics. Results showed that the model correctly predicted entomological field data (Pearson r correlation coefficient values range from 0.73 to 0.93). The model’s main control points were related to adult’s mortality rates, the carrying capacity in pupae of the environment, and the beginning of the unfavourable period. The proposed model can be efficiently used as a tool to predict Ae. albopictus population dynamics, and to assess the efficiency of different control strategies. PMID:23624579

  4. Mountain goat abundance and population trends in the Olympic Mountains, Washington, 2011

    USGS Publications Warehouse

    Jenkins, Kurt; Happe, Patricia; Griffin, Paul C.; Beirne, Katherine; Hoffman, Roger; Baccus, William

    2011-01-01

    We conducted an aerial helicopter survey between July 18 and July 25, 2011, to estimate abundance and trends of introduced mountain goats (Oreamnos americanus) in the Olympic Mountains. The survey was the first since we developed a sightability correction model in 2008, which provided the means to estimate the number of mountain goats present in the surveyed areas and not seen during the aerial surveys, and to adjust for undercounting biases. Additionally, the count was the first since recent telemetry studies revealed that the previously defined survey zone, which was delineated at lower elevations by the 1,520-meter elevation contour, did not encompass all lands used by mountain goats during summer. We redefined the lower elevation boundary of survey units before conducting the 2011 surveys in an effort to more accurately estimate the entire mountain goat population. We surveyed 39 survey units, comprising 39 percent of the 59,615-hectare survey area. We estimated a mountain goat population of 344±44 (standard error, SE) in the expanded survey area. Based on this level of estimation uncertainty, the 95-percent confidence interval ranged from 258 to 430 mountain goats at the time of the survey. To permit comparisons of mountain goat populations between the 2004 and 2011 surveys, we recomputed population estimates derived from the 2004 survey using the newly developed bias correction methods, and we computed the 2004 and 2011 surveys based on comparable survey zone definitions (for example, using the boundaries of the 2004 survey). The recomputed estimates of mountain goat populations were 217±19 (SE) in 2004 and 303±41(SE) in 2011. The difference between the current 2011 population estimate (344±44[SE]) and the recomputed 2011 estimate (303±41[SE]) reflects the number of mountain goats counted in the expanded lower elevation portions of the survey zone added in 2011. We conclude that the population of mountain goats has increased in the Olympic Mountains at

  5. THE VERTICAL MOTIONS OF MONO-ABUNDANCE SUB-POPULATIONS IN THE MILKY WAY DISK

    SciTech Connect

    Bovy, Jo; Rix, Hans-Walter; Hogg, David W.; Zhang, Lan; Beers, Timothy C.; Lee, Young Sun

    2012-08-20

    We present the vertical kinematics of stars in the Milky Way's stellar disk inferred from Sloan Digital Sky Survey/Sloan Extension for Galactic Understanding and Exploration (SDSS/SEGUE) G-dwarf data, deriving the vertical velocity dispersion, {sigma}{sub z}, as a function of vertical height |z| and Galactocentric radius R for a set of 'mono-abundance' sub-populations of stars with very similar elemental abundances [{alpha}/Fe] and [Fe/H]. We find that all mono-abundance components exhibit nearly isothermal kinematics in |z|, and a slow outward decrease of the vertical velocity dispersion: {sigma}{sub z}(z, R | [{alpha}/Fe], [Fe/H]) Almost-Equal-To {sigma}{sub z}([{alpha}/Fe], [Fe/H]) Multiplication-Sign exp (- (R - R{sub 0})/7 kpc). The characteristic velocity dispersions of these components vary from {approx}15 km s{sup -1} for chemically young, metal-rich stars with solar [{alpha}/Fe], to {approx}> 50 km s{sup -1} for metal-poor stars that are strongly [{alpha}/Fe]-enhanced, and hence presumably very old. The mean {sigma}{sub z} gradient (d{sigma}{sub z}/dz) away from the mid-plane is only 0.3 {+-} 0.2 km s{sup -1} kpc{sup -1}. This kinematic simplicity of the mono-abundance components mirrors their geometric simplicity; we have recently found their density distribution to be simple exponentials in both the z- and R-directions. We find a continuum of vertical kinetic temperatures ({proportional_to}{sigma}{sup 2}{sub z}) as a function of ([{alpha}/Fe], [Fe/H]), which contribute to the total stellar surface-mass density approximately as {Sigma}{sub R{sub 0}}({sigma}{sup 2}{sub z}){proportional_to} exp(-{sigma}{sup 2}{sub z}). This and the existence of isothermal mono-abundance populations with intermediate dispersions (30-40 km s{sup -1}) reject the notion of a thin-thick-disk dichotomy. This continuum of disk components, ranging from old, 'hot', and centrally concentrated ones to younger, cooler, and radially extended ones, argues against models where the thicker

  6. Nitrogen abundances and multiple stellar populations in the globular clusters of the Fornax dSph

    SciTech Connect

    Larsen, Søren S.; Strader, Jay

    2014-12-10

    We use measurements of nitrogen abundances in red giants to search for multiple stellar populations in the four most metal-poor globular clusters (GCs) in the Fornax dwarf spheroidal galaxy (Fornax 1, 2, 3, and 5). New imaging in the F343N filter, obtained with the Wide Field Camera 3 on the Hubble Space Telescope, is combined with archival F555W and F814W observations to determine the strength of the NH band near 3370 Å. After accounting for observational errors, the spread in the F343N-F555W colors of red giants in the Fornax GCs is similar to that in M15 and corresponds to an abundance range of Δ[N/Fe] ∼ 2 dex, as observed also in several Galactic GCs. The spread in F555W-F814W is, instead, fully accounted for by observational errors. The stars with the reddest F343N-F555W colors (indicative of N-enhanced composition) have more centrally concentrated radial distributions in all four clusters, although the difference is not highly statistically significant within any individual cluster. From double-Gaussian fits to the color distributions, we find roughly equal numbers of 'N-normal' and 'N-enhanced' stars (formally ∼40% N-normal stars in Fornax 1, 3, and 5 and ∼60% in Fornax 2). We conclude that GC formation, in particular, regarding the processes responsible for the origin of multiple stellar populations, appears to have operated similarly in the Milky Way and in the Fornax dSph. Combined with the high ratio of metal-poor GCs to field stars in the Fornax dSph, this places an important constraint on scenarios for the origin of multiple stellar populations in GCs.

  7. The Abundance and Activity of Nitrate-Reducing Microbial Populations in Estuarine Sediments

    NASA Astrophysics Data System (ADS)

    Cardarelli, E.; Francis, C. A.

    2014-12-01

    Estuaries are productive ecosystems that ameliorate nutrient and metal contaminants from surficial water supplies. At the intersection of terrestrial and aquatic environments, estuarine sediments host major microbially-mediated geochemical transformations. These include denitrification (the conversion of nitrate to nitrous oxide and/or dinitrogen) and dissimilatory nitrate reduction to ammonium (DNRA). Denitrification has historically been seen as the predominant nitrate attenuation process and functions as an effective sink for nitrate. DNRA has previously been believed to be a minor nitrate reduction process and transforms nitrate within the ecosystem to ammonium, a more biologically available N species. Recent studies have compared the two processes in coastal environments and determined fluctuating environmental conditions may suppress denitrification, supporting an increased role for DNRA in the N cycle. Nitrate availability and salinity are factors thought to influence the membership of the microbial communities present, and the nitrate reduction process that predominates. The aim of this study is to investigate how nitrate concentration and salinity alter the transcript abundances of N cycling functional gene markers for denitrification (nirK, nirS) and DNRA (nrfA) in estuarine sediments at the mouth of the hypernutrified Old Salinas River, CA. Short-term whole core incubations amended with artificial freshwater/artificial seawater (2 psu, 35 psu) and with varying NO3- concentrations (200mM, 2000mM) were conducted to assess the activity as well as the abundance of the nitrate-reducing microbial populations present. Gene expression of nirK, nirS, and nrfA at the conclusion of the incubations was quantified using reverse transcription quantitative polymerase chain reaction (RT-qPCR). High abundances of nirK, nirS, and nrfA under particular conditions coupled with the resulting geochemical data ultimately provides insight onto how the aforementioned factors

  8. Tracing impacts of partner abundance in facultative pollination mutualisms: from individuals to populations.

    PubMed

    Geib, Jennifer C; Galen, Candace

    2012-07-01

    Partner abundance affects costs and benefits in obligate mutualisms, but its role in facultative partnerships is less clear. We address this gap in a pollination web consisting of two clovers (Trifolium) that differ in specialization on a bumble bee pollinator Bombus balteatus. We examine how pollination niche breadth affects plant responses to pollinator abundance, comparing early-flowering (specialized) and late-flowering (generalized) cohorts of T. parryi and early T. parryi to T. dasyphyllum, a pollination generalist. Co-pollinators disrupt the link between B. halteatus visitation and pollination rate for both clovers. Only for early-flowering T. parryi do visitation, pollination, and seed set increase with density of B. balteatus. Bumble bee density also alters timing of seed germination in T. parryi, with seeds from plants receiving augmented B. balteatus germinating sooner than seeds of open-pollinated counterparts. Benefits saturate at intermediate bumble bee densities. Despite strong effects of B. balteatus density on individual plant fitness components, population models suggest little impact of B. balteatus density on lamda in T. parryi or T. dasyphyllum. Findings show that functional redundancy in a pollinator guild mediates host-plant responses to partner density. Unexpected effects of pollinator density on life history schedule have implications for recruitment under pollinator decline.

  9. Patchy reaction-diffusion and population abundance: the relative importance of habitat amount and arrangement.

    PubMed

    Flather, Curtis H; Bevers, Michael

    2002-01-01

    A discrete reaction-diffusion model was used to estimate long-term equilibrium populations of a hypothetical species inhabiting patchy landscapes to examine the relative importance of habitat amount and arrangement in explaining population size. When examined over a broad range of habitat amounts and arrangements, population size was largely determined by a pure amount effect (proportion of habitat in the landscape accounted for >96% of the total variation compared to <1% for the arrangement main effect). However, population response deviated from a pure amount effect as coverage was reduced below 30%-50%. That deviation coincided with a persistence threshold as indicated by a rapid decline in the probability of landscapes supporting viable populations. When we partitioned experimental landscapes into sets of "above" and "below" persistence threshold, habitat arrangement became an important factor in explaining population size below threshold conditions. Regression analysis on below-threshold landscapes using explicit measures of landscape structure (after removing the covariation with habitat amount) indicated that arrangement variables accounted for 33%-39% of the variation in population size, compared to 27%-49% for habitat amount. Thus, habitat arrangement effects became important when species persistence became uncertain due to dispersal mortality.

  10. Ordering structured populations in multiplayer cooperation games

    PubMed Central

    Peña, Jorge; Wu, Bin; Traulsen, Arne

    2016-01-01

    Spatial structure greatly affects the evolution of cooperation. While in two-player games the condition for cooperation to evolve depends on a single structure coefficient, in multiplayer games the condition might depend on several structure coefficients, making it difficult to compare different population structures. We propose a solution to this issue by introducing two simple ways of ordering population structures: the containment order and the volume order. If population structure is greater than population structure in the containment or the volume order, then can be considered a stronger promoter of cooperation. We provide conditions for establishing the containment order, give general results on the volume order, and illustrate our theory by comparing different models of spatial games and associated update rules. Our results hold for a large class of population structures and can be easily applied to specific cases once the structure coefficients have been calculated or estimated. PMID:26819335

  11. Population Structure of Atlantic Mackerel (Scomber scombrus)

    PubMed Central

    Jansen, Teunis; Gislason, Henrik

    2013-01-01

    Atlantic mackerel (Scomber scombrus) occurs on both sides of the north Atlantic and has traditionally been grouped into 5 spawning components, some of which were thought to be isolated natal homing stocks. Previous studies have provided no evidence for cross Atlantic migration and no or weak support for isolated spawning components within either side of the North Atlantic. We question the de-facto accepted hypothesis of isolation between spawning components on the basis of spawning and age distribution data. The spawning intensities, proxied by larval abundances, are negatively correlated between the North Sea and Celtic Sea, which indicates that the two spawning components may be connected by straying individuals. This finding is based on unique larvae samples collected before the collapse of North Sea component, thus showing that the exchange is not a recent phenomenon due to the collapse. The analyses of old as well as more recent age distributions show that strong year classes spread into other areas where they spawn as adults (“twinning”). Our findings are in accordance with the lack of solid evidence for stock separation from previous analyses of tagging data, genetics, ectoparasite infections, otolith shapes, and blood phenotypes. Because no method has been able to identify the origin of spawning mackerel unequivocally from any of the traditional spawning components, and in the light of our results, we conclude that straying outweighs spatial segregation. We propose a new model where the population structure of mackerel is described as a dynamic cline, rather than as connected contingents. Temporal changes in hydrography and mackerel behavior may affect the steepness of the cline at various locations. The new interpretation of the population structure of Atlantic mackerel has important implications for research, assessment and management. PMID:23741381

  12. Population structure of Atlantic mackerel (Scomber scombrus).

    PubMed

    Jansen, Teunis; Gislason, Henrik

    2013-01-01

    Atlantic mackerel (Scomber scombrus) occurs on both sides of the north Atlantic and has traditionally been grouped into 5 spawning components, some of which were thought to be isolated natal homing stocks. Previous studies have provided no evidence for cross Atlantic migration and no or weak support for isolated spawning components within either side of the North Atlantic. We question the de-facto accepted hypothesis of isolation between spawning components on the basis of spawning and age distribution data. The spawning intensities, proxied by larval abundances, are negatively correlated between the North Sea and Celtic Sea, which indicates that the two spawning components may be connected by straying individuals. This finding is based on unique larvae samples collected before the collapse of North Sea component, thus showing that the exchange is not a recent phenomenon due to the collapse. The analyses of old as well as more recent age distributions show that strong year classes spread into other areas where they spawn as adults ("twinning"). Our findings are in accordance with the lack of solid evidence for stock separation from previous analyses of tagging data, genetics, ectoparasite infections, otolith shapes, and blood phenotypes. Because no method has been able to identify the origin of spawning mackerel unequivocally from any of the traditional spawning components, and in the light of our results, we conclude that straying outweighs spatial segregation. We propose a new model where the population structure of mackerel is described as a dynamic cline, rather than as connected contingents. Temporal changes in hydrography and mackerel behavior may affect the steepness of the cline at various locations. The new interpretation of the population structure of Atlantic mackerel has important implications for research, assessment and management.

  13. Abundance Trends and Status of the Little Colorado River Population of Humpback Chub: An Update Considering 1989-2006 Data

    USGS Publications Warehouse

    Coggins,, Lewis G.

    2008-01-01

    EXECUTIVE SUMMARY In 1967, the humpback chub (Gila cypha) (HBC) was added to the federal list of endangered species and is today protected under the Endangered Species Act of 1973. Only six populations of humpback chub are currently known to exist, five in the Colorado River Basin above Lees Ferry, Arizona, and one in Grand Canyon, Arizona. The majority of Grand Canyon humpback chub are found in the Little Colorado River (LCR)-the largest tributary to the Colorado River in Grand Canyon-and the Colorado River near its confluence with the Little Colorado River. Monitoring and research of the Grand Canyon humpback chub population is overseen by the U.S. Geological Survey's (USGS) Grand Canyon Monitoring and Research Center (GCMRC) under the auspices of the Glen Canyon Dam Adaptive Management Program (GCDAMP), a Federal initiative to protect and improve resources downstream of Glen Canyon Dam. This report provides updated information on the status and trends of the LCR population in light of new information and refined assessment methodology. An earlier assessment of the LCR population (Coggins and others, 2006a) used data collected during 1989?2002; the assessment provided here includes that data and additional data collected through 2006. Catch-rate indices, closed population mark-recapture model abundance estimates, results from the original age-structured mark recapture (ASMR) model (Coggins and others, 2006b), and a newly refined ASMR model are presented. This report also seeks to (1) formally evaluate alternative stock assessment models using Pearson residual analyses and information theoretic procedures, (2) use mark-recapture data to estimate the relationship between HBC age and length, (3) translate uncertainty in the assignment of individual fish age to resulting estimates of recruitment and abundance from the ASMR model, and (4) evaluate past and present stock assessments considering the available data sources and analyses, recognizing the limitations

  14. Isonymy structure of USA population.

    PubMed

    Barrai, I; Rodriguez-Larralde, A; Mamolini, E; Manni, F; Scapoli, C

    2001-02-01

    The isonymy structure of the 48 states of the continental United States of America was studied using the surname distributions of 18 million telephone users, distributed in 247 towns. The shortest linear distance between nearest neighbor towns included in the sample was 12.0 km. The largest distance was 4,577 km. The number of different surnames found in the whole analysis was 899,585. Lasker's distance was found to be significantly but weakly correlated with the geographic distance, with r = 0.21 +/- 0.01. A dendrogram of the 48 states was built from the matrix of isonymy distances: it divides the US into several clusters, in general correlated with geography. A notable exception is California and New Jersey, which cluster together. Wisconsin is separated from all other states. An important cluster is formed by Texas, Colorado, New Mexico, Nevada, and Arizona, together with Illinois and Florida. It was observed that Hispanic surnames are among the most frequent in Illinois, as they are in New Jersey and California. No main distinction among the states clearly attributable to surnames of French origin was detected; however, New Hampshire, Vermont, and Maine which have a considerable number of these surnames belong to the same northeastern cluster. From the present analysis, the great mobility of the US population emerges clearly, and it seems relevant that the practical absence of isolation by distance is seen also considering only small towns. It appears that groups of different origin are well-mixed over the whole area of the United States. The values of isonymy indicate that the south-central area of the USA has the highest level of inbreeding. In fact, the heterogeneity in surname composition is greater in the coastal areas, particularly on the East Coast, than anywhere else in the USA.

  15. Calibrating abundance indices with population size estimators of red back salamanders (Plethodon cinereus) in a New England forest

    PubMed Central

    Ellison, Aaron M.; Jackson, Scott

    2015-01-01

    Herpetologists and conservation biologists frequently use convenient and cost-effective, but less accurate, abundance indices (e.g., number of individuals collected under artificial cover boards or during natural objects surveys) in lieu of more accurate, but costly and destructive, population size estimators to detect and monitor size, state, and trends of amphibian populations. Although there are advantages and disadvantages to each approach, reliable use of abundance indices requires that they be calibrated with accurate population estimators. Such calibrations, however, are rare. The red back salamander, Plethodon cinereus, is an ecologically useful indicator species of forest dynamics, and accurate calibration of indices of salamander abundance could increase the reliability of abundance indices used in monitoring programs. We calibrated abundance indices derived from surveys of P. cinereus under artificial cover boards or natural objects with a more accurate estimator of their population size in a New England forest. Average densities/m2 and capture probabilities of P. cinereus under natural objects or cover boards in independent, replicate sites at the Harvard Forest (Petersham, Massachusetts, USA) were similar in stands dominated by Tsuga canadensis (eastern hemlock) and deciduous hardwood species (predominantly Quercus rubra [red oak] and Acer rubrum [red maple]). The abundance index based on salamanders surveyed under natural objects was significantly associated with density estimates of P. cinereus derived from depletion (removal) surveys, but underestimated true density by 50%. In contrast, the abundance index based on cover-board surveys overestimated true density by a factor of 8 and the association between the cover-board index and the density estimates was not statistically significant. We conclude that when calibrated and used appropriately, some abundance indices may provide cost-effective and reliable measures of P. cinereus abundance that could

  16. Calibrating abundance indices with population size estimators of red back salamanders (Plethodon cinereus) in a New England forest.

    PubMed

    Siddig, Ahmed A; Ellison, Aaron M; Jackson, Scott

    2015-01-01

    Herpetologists and conservation biologists frequently use convenient and cost-effective, but less accurate, abundance indices (e.g., number of individuals collected under artificial cover boards or during natural objects surveys) in lieu of more accurate, but costly and destructive, population size estimators to detect and monitor size, state, and trends of amphibian populations. Although there are advantages and disadvantages to each approach, reliable use of abundance indices requires that they be calibrated with accurate population estimators. Such calibrations, however, are rare. The red back salamander, Plethodon cinereus, is an ecologically useful indicator species of forest dynamics, and accurate calibration of indices of salamander abundance could increase the reliability of abundance indices used in monitoring programs. We calibrated abundance indices derived from surveys of P. cinereus under artificial cover boards or natural objects with a more accurate estimator of their population size in a New England forest. Average densities/m(2) and capture probabilities of P. cinereus under natural objects or cover boards in independent, replicate sites at the Harvard Forest (Petersham, Massachusetts, USA) were similar in stands dominated by Tsuga canadensis (eastern hemlock) and deciduous hardwood species (predominantly Quercus rubra [red oak] and Acer rubrum [red maple]). The abundance index based on salamanders surveyed under natural objects was significantly associated with density estimates of P. cinereus derived from depletion (removal) surveys, but underestimated true density by 50%. In contrast, the abundance index based on cover-board surveys overestimated true density by a factor of 8 and the association between the cover-board index and the density estimates was not statistically significant. We conclude that when calibrated and used appropriately, some abundance indices may provide cost-effective and reliable measures of P. cinereus abundance that

  17. Differences in ecological structure, function, and native species abundance between native and invaded Hawaiian streams.

    PubMed

    Holitzki, Tara M; MacKenzie, Richard A; Wiegner, Tracy N; McDermid, Karla J

    2013-09-01

    Poeciliids, one of the most invasive species worldwide, are found on almost every continent and have been identified as an "invasive species of concern" in the United States, New Zealand, and Australia. Despite their global prevalence, few studies have quantified their impacts on tropical stream ecosystem structure, function, and biodiversity. Utilizing Hawaiian streams as model ecosystems, we documented how ecological structure, function, and native species abundance differed between poeciliid-free and poeciliid-invaded tropical streams. Stream nutrient yields, benthic biofilm biomass, densities of macroinvertebrates and fish, and community structures of benthic algae, macroinvertebrates, and fish were compared between streams with and without established poeciliid populations on the island of Hawai'i, Hawaii, USA. Sum nitrate (sigmaNO3(-) = NO3(-) + NO2(-)), total nitrogen, and total organic carbon yields were eight times, six times, and five times higher, respectively, in poeciliid streams than in poeciliid-free streams. Benthic biofilm ash-free dry mass was 1.5x higher in poeciliid streams than in poeciliid-free streams. Percentage contributions of chironomids and hydroptilid caddisflies to macroinvertebrate densities were lower in poeciliid streams compared to poeciliid-free streams, while percentage contributions of Cheumatopsyche analis caddisflies, Dugesia sp. flatworms, and oligochaetes were higher. Additionally, mean densities of native gobies were two times lower in poeciliid streams than in poeciliid-free ones, with poeciliid densities being approximately eight times higher than native fish densities. Our results, coupled with the wide distribution of invasive poeciliids across Hawaii and elsewhere in the tropics, suggest that poeciliids may negatively impact the ecosystem structure, function, and native species abundance of tropical streams they invade. This underscores the need for increased public awareness to prevent future introductions and for

  18. Challenges of ecological monitoring: estimating population abundance from sparse trap counts

    PubMed Central

    Petrovskaya, Natalia; Petrovskii, Sergei; Murchie, Archie K.

    2012-01-01

    Ecological monitoring aims to provide estimates of pest species abundance—this information being then used for making decisions about means of control. For invertebrate species, population size estimates are often based on trap counts which provide the value of the population density at the traps' location. However, the use of traps in large numbers is problematic as it is costly and may also be disruptive to agricultural procedures. Therefore, the challenge is to obtain a reliable population size estimate from sparse spatial data. The approach we develop in this paper is based on the ideas of numerical integration on a coarse grid. We investigate several methods of numerical integration in order to understand how badly the lack of spatial data can affect the accuracy of results. We first test our approach on simulation data mimicking spatial population distributions of different complexity. We show that, rather counterintuitively, a robust estimate of the population size can be obtained from just a few traps, even when the population distribution has a highly complicated spatial structure. We obtain an estimate of the minimum number of traps required to calculate the population size with good accuracy. We then apply our approach to field data to confirm that the number of trap/sampling locations can be much fewer than has been used in many monitoring programmes. We also show that the accuracy of our approach is greater that that of the statistical method commonly used in field studies. Finally, we discuss the implications of our findings for ecological monitoring practice and show that the use of trap numbers ‘smaller than minimum’ may still be possible but it would result in a paradigm shift: the population size estimates should be treated probabilistically and the arising uncertainty may introduce additional risk in decision-making. PMID:21831888

  19. Spatial structuring within a reservoir fish population: implications for management

    USGS Publications Warehouse

    Stewart, David R.; Long, James M.; Shoup, Daniel E.

    2014-01-01

    Spatial structuring in reservoir fish populations can exist because of environmental gradients, species-specific behaviour, or even localised fishing effort. The present study investigated whether white crappie exhibited evidence of improved population structure where the northern more productive half of a lake is closed to fishing to provide waterfowl hunting opportunities. Population response to angling was modelled for each substock of white crappie (north (protected) and south (unprotected) areas), the entire lake (single-stock model) and by combining simulations of the two independent substock models (additive model). White crappie in the protected area were more abundant, consisting of larger, older individuals, and exhibited a lower total annual mortality rate than in the unprotected area. Population modelling found that fishing mortality rates between 0.1 and 0.3 resulted in sustainable populations (spawning potential ratios (SPR) >0.30). The population in the unprotected area appeared to be more resilient (SPR > 0.30) at the higher fishing intensities (0.35–0.55). Considered additively, the whole-lake fishery appeared more resilient than when modelled as a single-panmictic stock. These results provided evidence of spatial structuring in reservoir fish populations, and we recommend model assessments used to guide management decisions should consider those spatial differences in other populations where they exist.

  20. Consensus of population systems with community structures.

    PubMed

    Wang, Jing; Wu, Bin; Wang, Long; Fu, Feng

    2008-11-01

    Multicommunity population systems may reach a consensus state where the fractions of each species in different communities agree on a common value. In this paper, by analyzing the evolutionary dynamics based on an extended replicator equation incorporating community effects, the consensus problem of population systems with n communities is studied. In particular, the simple case of two communities is investigated in detail. In general, for n communities, a sufficient and necessary condition for population systems to reach a consensus of coexistent state is provided. Regarding the population dynamics for the four different types of games, whether the population systems can achieve consensus is determined. The dynamics of community-structured populations shows richer features than nonstructured populations, and some nontrivial phenomena arising from different community-structured population systems are illustrated with concrete numerical examples.

  1. Endoparasites in a Norwegian moose (Alces alces) population - Faunal diversity, abundance and body condition.

    PubMed

    Davidson, Rebecca K; Ličina, Tina; Gorini, Lucrezia; Milner, Jos M

    2015-04-01

    Many health surveillance programs for wild cervids do not include routine parasite screening despite evidence that gastrointestinal parasites can affect wildlife population dynamics by influencing host fecundity and survival. Slaughter weights of moose in some regions of Norway have been decreasing over recent decades but any role of parasites has not yet been considered. We investigated parasite faunal diversity of moose in Hedmark, SE Norway, by faecal analysis and identification of adult abomasal and caecal nematodes during the autumn hunting season. We related parasite prevalence and abundance to estimates of body condition, gender and age. We identified 11 parasite groups. Moose had high abomasal gastrointestinal nematode (GIN) burdens and all individuals were infected. Ostertagia antipini and Spiculopteragia alcis were the most prevalent abomasal GINs identified. O. leptospicularis and Telodorsagia circumcincta were also identified in the abomasa while a range of other GIN and Moniezia sp. eggs, and coccidia, Dictyocaulus sp. and Protostrongylid larvae were found in faeces. Female moose had higher mean abomasal nematode counts than males, particularly among adults. However, adult males had higher faecal egg counts than adult females which may reflect reduction in faecal volume with concentration of eggs among males during the rut. We found no strong evidence for the development of acquired immunity to abomasal nematodes with age, although there was a higher Protostrongylid and Moniezia infection prevalence in younger animals. High burdens of several parasites were associated with poor body condition in terms of slaughter weight relative to skeletal size but unrelated to visually evaluated fat reserves. Given findings from earlier experimental studies, our results imply sub-clinical effects of GI parasite infection on host condition. Managers should be aware that autumn faecal egg counts and field assessments of fat reserves may not be reliable indicators of

  2. The Relationship between Mono-abundance and Mono-age Stellar Populations in the Milky Way Disk

    NASA Astrophysics Data System (ADS)

    Minchev, I.; Steinmetz, M.; Chiappini, C.; Martig, M.; Anders, F.; Matijevic, G.; de Jong, R. S.

    2017-01-01

    Studying the Milky Way disk structure using stars in narrow bins of [Fe/H] and [α/Fe] has recently been proposed as a powerful method to understand the Galactic thick and thin disk formation. It has been assumed so far that these mono-abundance populations (MAPs) are also coeval, or mono-age, populations. Here we study this relationship for a Milky Way chemodynamical model and show that equivalence between MAPs and mono-age populations exists only for the high-[α/Fe] tail, where the chemical evolution curves of different Galactic radii are far apart. At lower [α/Fe]-values an MAP is composed of stars with a range in ages, even for small observational uncertainties and a small MAP bin size. Due to the disk inside-out formation, for these MAPs younger stars are typically located at larger radii, which results in negative radial age gradients that can be as large as 2 Gyr kpc‑1. Positive radial age gradients can result for MAPs at the lowest [α/Fe] and highest [Fe/H] end. Such variations with age prevent the simple interpretation of observations for which accurate ages are not available. Studying the variation with radius of the stellar surface density and scale height in our model, we find good agreement to recent analyses of the APOGEE red-clump (RC) sample when 1–4 Gyr old stars dominate (as expected for the RC). Our results suggest that the APOGEE data are consistent with a Milky Way model for which mono-age populations flare for all ages. We propose observational tests for the validity of our predictions and argue that using accurate age measurements, such as from asteroseismology, is crucial for putting constraints on Galactic formation and evolution.

  3. STRUCTURE AND FEEDBACK IN 30 DORADUS. II. STRUCTURE AND CHEMICAL ABUNDANCES

    SciTech Connect

    Pellegrini, E. W.; Baldwin, J. A.; Ferland, G. J.

    2011-09-01

    We use our new optical-imaging and spectrophotometric survey of key diagnostic emission lines in 30 Doradus, together with CLOUDY photoionization models, to study the physical conditions and ionization mechanisms along over 4000 individual lines of sight at points spread across the face of the extended nebula, out to a projected radius 75 pc from R136 at the center of the ionizing cluster NGC 2070. We focus on the physical conditions, geometry, and importance of radiation pressure on a point-by-point basis, with the aim of setting observational constraints on important feedback processes. We find that the dynamics and large-scale structure of 30 Dor are set by a confined system of X-ray bubbles in rough pressure equilibrium with each other and with the confining molecular gas. Although the warm (10,000 K) gas is photoionized by the massive young stars in NGC 2070, the radiation pressure does not currently play a major role in shaping the overall structure. The completeness of our survey also allows us to create a composite spectrum of 30 Doradus, simulating the observable spectrum of a spatially unresolved, distant giant extragalactic H II region. We find that the highly simplified models used in the 'strong line' abundance technique do in fact reproduce our observed line strengths and deduced chemical abundances, in spite of the more than one order of magnitude range in the ionization parameter and density of the actual gas in 30 Dor.

  4. Dietary supplementation with lactose or artificial sweetener enhances swine gut Lactobacillus population abundance.

    PubMed

    Daly, Kristian; Darby, Alistair C; Hall, Neil; Nau, Alexandra; Bravo, David; Shirazi-Beechey, Soraya P

    2014-06-01

    The commensal bacteria Lactobacillus are widely used as probiotic organisms conferring a heath benefit on the host. They have been implicated in promoting gut health via the stimulation of host immunity and anti-inflammatory responses, as well as protecting the intestinalmucosa against pathogen invasion. Lactobacilli grow by fermenting sugars and starches and produce lactic acid as their primary metabolic product. For efficient utilisation of varied carbohydrates, lactobacilli have evolved diverse sugar transport and metabolic systems, which are specifically induced by their own substrates. Many bacteria are also capable of sensing and responding to changes in their environment. These sensory responses are often independent of transport or metabolism and are mediated through membrane-spanning receptor proteins. We employed DNA-based pyrosequencing technology to investigate the changes in the intestinal microbiota of piglets weaned to a diet supplemented with either a natural sugar, lactose or an artificial sweetener (SUCRAM®, consisting of saccharin and neohesperidin dihydrochalcone (NHDC); Pancosma SA). The addition of either lactose or saccharin/NHDC to the piglets' feed dramatically increased the caecal population abundance of Lactobacillus, with concomitant increases in intraluminal lactic acid concentrations. This is the first report of the prebiotic-like effects of saccharin/NHDC, an artificial sweetener, being able to influence the commensal gut microbiota. The identification of the underlying mechanism(s) will assist in designing nutritional strategies for enhancing gut immunity and maintaining gut health.

  5. Spectra of late type dwarf stars of known abundance for stellar population models

    NASA Technical Reports Server (NTRS)

    Oconnell, R. W.

    1990-01-01

    The project consisted of two parts. The first was to obtain new low-dispersion, long-wavelength, high S/N IUE spectra of F-G-K dwarf stars with previously determined abundances, temperatures, and gravities. To insure high quality, the spectra are either trailed, or multiple exposures are taken within the large aperture. Second, the spectra are assembled into a library which combines the new data with existing IUE Archive data to yield mean spectral energy distributions for each important type of star. My principal responsibility is the construction and maintenance of this UV spectral library. It covers the spectral range 1200-3200A and is maintained in two parts: a version including complete wavelength coverage at the full spectral resolution of the Low Resolution cameras; and a selected bandpass version, consisting of the mean flux in pre-selected 20A bands. These bands are centered on spectral features or continuum regions of special utility - e.g. the C IV lambda 1550 or Mg II lambda 2800 feature. In the middle-UV region, special emphasis is given to those features (including continuum 'breaks') which are most useful in the study of F-G-K star spectra in the integrated light of old stellar populations.

  6. Forecasting spatially structured populations: the role of dispersal and scale.

    PubMed

    Xu, Cailin; Boyce, Mark S; Gadgil, Madhav; Nanjundiah, Vidyanand

    2005-03-21

    We forecasted spatially structured population models with complex dynamics, focusing on the effect of dispersal and spatial scale on the predictive capability of nonlinear forecasting (NLF). Dispersal influences NLF ability by its influence on population dynamics. For simple 2-cell models, when dispersal is small, our ability to predict abundance in subpopulations decreased and then increased with increasing dispersal. Spatial heterogeneity, dispersal manner, and environmental noise did not qualitatively change this result. But results are not clear for complex spatial configurations because of complicated dispersal interactions across subpopulations. Populations undergoing periodic fluctuations could be forecasted perfectly for all deterministic cases that we studied, but less reliably when environmental noise was incorporated. More importantly, for all models that we have examined, NLF was much worse at larger spatial scales as a consequence of the asynchronous dynamics of subpopulations when the dispersal rate was below some critical value. The only difference among models was the critical value of dispersal rate, which varied with growth rate, carrying capacity, mode of dispersal, and spatial configuration. These results were robust even when environmental noise was incorporated. Intermittency, common in the dynamics of spatially structured populations, lowered the predictive capability of NLF. Forecasting population behaviour is of obvious value in resource exploitation and conservation. We suggest that forecasting at local scales holds promise, whereas forecasting abundance at regional scales may yield poor results. Improved understanding of dispersal can enhance the management and conservation of natural resources, and may help us to understand resource-exploitation strategies employed by local indigenous humans.

  7. Consideraciones para la estimacion de abundancia de poblaciones de mamiferos. [Considerations for the estimation of abundance of mammal populations.

    USGS Publications Warehouse

    Walker, R.S.; Novare, A.J.; Nichols, J.D.

    2000-01-01

    Estimation of abundance of mammal populations is essential for monitoring programs and for many ecological investigations. The first step for any study of variation in mammal abundance over space or time is to define the objectives of the study and how and why abundance data are to be used. The data used to estimate abundance are count statistics in the form of counts of animals or their signs. There are two major sources of uncertainty that must be considered in the design of the study: spatial variation and the relationship between abundance and the count statistic. Spatial variation in the distribution of animals or signs may be taken into account with appropriate spatial sampling. Count statistics may be viewed as random variables, with the expected value of the count statistic equal to the true abundance of the population multiplied by a coefficient p. With direct counts, p represents the probability of detection or capture of individuals, and with indirect counts it represents the rate of production of the signs as well as their probability of detection. Comparisons of abundance using count statistics from different times or places assume that the p are the same for all times or places being compared (p= pi). In spite of considerable evidence that this assumption rarely holds true, it is commonly made in studies of mammal abundance, as when the minimum number alive or indices based on sign counts are used to compare abundance in different habitats or times. Alternatives to relying on this assumption are to calibrate the index used by testing the assumption of p= pi, or to incorporate the estimation of p into the study design.

  8. Refined phylogenetic structure of an abundant East Asian Y-chromosomal haplogroup O*-M134

    PubMed Central

    Ning, Chao; Yan, Shi; Hu, Kang; Cui, Yin-Qiu; Jin, Li

    2016-01-01

    The human Y-chromosome haplogroup O-M134 is one of the most abundant paternal lineages in East Asian populations, comprising ~13% of Han Chinese males, and also common in Kazakh, Korean, Japanese, Thai and so on. Despite its considerable prevalence, its current substructure is poorly resolved with only one downstream marker (M117) previously investigated. Here we address this deficiency by investigating some single-nucleotide polymorphisms (SNPs) previously reported being potentially associated with O-M134 based on high-throughput DNA-sequencing data. Using a panel of 1301 Chinese males we first identified 154 haplogroup O-M134 subjects. We then investigated the phylogenetic structure within this haplogroup using 10 SNPs (F444, F629, F3451, F46, F48, F209, F2887, F3386, F1739 and F152). Two major branches were identified, O-M117 and O-F444 and the latter was further divided into two main subclades, O-F629 and O-F3451, accounting for 10.84 and 0.92% of the Han Chinese, respectively. This update of O-M134 diversification permits better resolution of male lineages in population studies of East Asia. PMID:26306641

  9. Evolution of cooperation in spatially structured populations

    PubMed

    Brauchli; Killingback; Doebeli

    1999-10-21

    Using a spatial lattice model of the Iterated Prisoner's Dilemma we studied the evolution of cooperation within the strategy space of all stochastic strategies with a memory of one round. Comparing the spatial model with a randomly mixed model showed that (1) there is more cooperative behaviour in a spatially structured population, (2) PAVLOV and generous variants of it are very successful strategies in the spatial context and (3) in spatially structured populations evolution is much less chaotic than in unstructured populations. In spatially structured populations, generous variants of PAVLOV are found to be very successful strategies in playing the Iterated Prisoner's Dilemma. The main weakness of PAVLOV is that it is exploitable by defective strategies. In a spatial context this disadvantage is much less important than the good error correction of PAVLOV, and especially of generous PAVLOV, because in a spatially structured population successful strategies always build clusters. Copyright 1999 Academic Press.

  10. Asexual endophytes and associated alkaloids alter arthropod community structure and increase herbivore abundances on a native grass.

    PubMed

    Jani, Andrea J; Faeth, Stanley H; Gardner, Dale

    2010-01-01

    Despite their minute biomass, microbial symbionts of plants potentially alter herbivory, diversity and community structure. Infection of grasses by asexual endophytic fungi often decreases herbivore loads and alters arthropod diversity. However, most studies to date have involved agronomic grasses and often consider only infection status (infected vs. uninfected), without explicitly measuring endophyte-produced alkaloids, which vary among endophyte isolates and may impact consumers. We combined field experiments and population surveys to investigate how endophyte infection and associated alkaloids influence abundances, species richness, evenness and guild structure of arthropod communities on a native grass, Achnatherum robustum (sleepygrass). Surprisingly, we found that endophyte-produced alkaloids were associated with increased herbivore abundances and species richness. Our results suggest that, unlike what has been found in agronomic grass systems, high alkaloid levels in native grasses may not protect host grasses from arthropod herbivores, and may instead more negatively affect natural enemies of herbivores.

  11. A Long-Term Comparison of Yellowstone Cutthroat Trout Abundance and Size Structure in Their Historical Range in Idaho.

    SciTech Connect

    Meyer, Kevin A.; Schill, Daniel J.; Elle, F. Steven

    2002-05-23

    We compared estimates of population abundance and size structure for Yellowstone cutthroat trout Oncorhynchus clarki bouvieri obtained by electrofishing 77 stream segments across southeastern Idaho in the 1980s and again in 1999-2000 to test whether populations of Yellowstone cutthroat trout had changed. Sites sampled in the 1980s were relocated in 1999-2000 by using maps and photographs or by finding original site-boundary stakes, so that the same reach of stream was sampled during both periods. Abundance of Yellowstone cutthroat trout longer than 10 cm did not change, averaging 41 fish/100 m of stream during both the 1980s and 1999-2000. The proportion of the total catch of trout composed of Yellowstone cutthroat trout also did not change, averaging 82% in the 1980s and 78% in 1999-2000. At the 48 sites where size structure could be estimated for both periods, the proportion of Yellowstone cutthroat trout that were 10-20 cm long declined slightly (74% versus 66%), but the change was due entirely to the shift in size structure at the Teton River sites. The number of sites that contained rainbow trout O. mykiss or cutthroat trout 3 rainbow trout hybrids rose from 23 to 37, but the average proportion of the catch composed of rainbow trout and hybrids did not increase (7% in both the 1980s and 1999-2000). Although the distribution and abundance of Yellowstone cutthroat trout have been substantially reduced in Idaho over the last century, our results indicate that Yellowstone cutthroat trout abundance and size structure in Idaho have remained relatively stable at a large number of locations for the last 10-20 years. The expanding distribution of rainbow trout and hybrids in portions of the upper Snake River basin, however, calls for additional monitoring and active management actions.

  12. Improving removal-based estimates of abundance by sampling a population of spatially distinct subpopulations

    USGS Publications Warehouse

    Dorazio, R.M.; Jelks, H.L.; Jordan, F.

    2005-01-01

     A statistical modeling framework is described for estimating the abundances of spatially distinct subpopulations of animals surveyed using removal sampling. To illustrate this framework, hierarchical models are developed using the Poisson and negative-binomial distributions to model variation in abundance among subpopulations and using the beta distribution to model variation in capture probabilities. These models are fitted to the removal counts observed in a survey of a federally endangered fish species. The resulting estimates of abundance have similar or better precision than those computed using the conventional approach of analyzing the removal counts of each subpopulation separately. Extension of the hierarchical models to include spatial covariates of abundance is straightforward and may be used to identify important features of an animal's habitat or to predict the abundance of animals at unsampled locations.

  13. (Genetic structure of natural populations)

    SciTech Connect

    Not Available

    1988-01-01

    Our efforts in the first eight months were concentrated in obtaining a genomic clone of the copper-zinc superoxide dismutase (SOD) in Drosophila melanogaster and other Drosophila species. This we have now successfully accomplished. We seek to understand the role of SOD in radioresistance; how genetic variation in this enzyme is maintained in populations; and relevant aspects of its evolution that may contribute to these goals as well as to an understanding of molecular evolution in general. To accomplish these goals we are undertaking the following experiments: cloning and sequencing of (at least) one F allele, one S allele, and the null allele for SOD; cloning and sequencing SOD from species related to D. melanogaster; and cloning and sequencing the SOD gene from several independently sampled S and F alleles in D. melanogaster. We are also preparing to test the radioprotective effects of SOD. 67 refs.

  14. Population Structure in Nontypeable Haemophilus influenzae

    PubMed Central

    LaCross, Nathan C.; Marrs, Carl F.; Gilsdorf, Janet R.

    2013-01-01

    Nontypeable Haemophilus influenzae (NTHi) frequently colonize the human pharynx asymptomatically, and are an important cause of otitis media in children. Past studies have identified typeable H. influenzae as being clonal, but the population structure of NTHi has not been extensively characterized. The research presented here investigated the diversity and population structure in a well-characterized collection of NTHi isolated from the middle ears of children with otitis media or the pharynges of healthy children in three disparate geographic regions. Multilocus sequence typing identified 109 unique sequence types among 170 commensal and otitis media-associated NTHi isolates from Finland, Israel, and the US. The largest clonal complex contained only five sequence types, indicating a high level of genetic diversity. The eBURST v3, ClonalFrame 1.1, and structure 2.3.3 programs were used to further characterize diversity and population structure from the sequence typing data. Little clustering was apparent by either disease state (otitis media or commensalism) or geography in the ClonalFrame phylogeny. Population structure was clearly evident, with support for eight populations when all 170 isolates were analyzed. Interestingly, one population contained only commensal isolates, while two others consisted solely of otitis media isolates, suggesting associations between population structure and disease. PMID:23266487

  15. Comparative population structure of cavity-nesting sea ducks

    USGS Publications Warehouse

    Pearce, John M.; Eadie, John M.; Savard, Jean-Pierre L.; Christensen, Thomas K.; Berdeen, James; Taylor, Eric J.; Boyd, Sean; Einarsson, Árni

    2014-01-01

    A growing collection of mtDNA genetic information from waterfowl species across North America suggests that larger-bodied cavity-nesting species exhibit greater levels of population differentiation than smaller-bodied congeners. Although little is known about nest-cavity availability for these species, one hypothesis to explain differences in population structure is reduced dispersal tendency of larger-bodied cavity-nesting species due to limited abundance of large cavities. To investigate this hypothesis, we examined population structure of three cavity-nesting waterfowl species distributed across much of North America: Barrow's Goldeneye (Bucephala islandica), Common Goldeneye (B. clangula), and Bufflehead (B. albeola). We compared patterns of population structure using both variation in mtDNA control-region sequences and band-recovery data for the same species and geographic regions. Results were highly congruent between data types, showing structured population patterns for Barrow's and Common Goldeneye but not for Bufflehead. Consistent with our prediction, the smallest cavity-nesting species, the Bufflehead, exhibited the lowest level of population differentiation due to increased dispersal and gene flow. Results provide evidence for discrete Old and New World populations of Common Goldeneye and for differentiation of regional groups of both goldeneye species in Alaska, the Pacific Northwest, and the eastern coast of North America. Results presented here will aid management objectives that require an understanding of population delineation and migratory connectivity between breeding and wintering areas. Comparative studies such as this one highlight factors that may drive patterns of genetic diversity and population trends.

  16. Inter-annual variability in spring abundance of adult Calanus finmarchicus from the overwintering population in the southeastern Norwegian Sea

    NASA Astrophysics Data System (ADS)

    Dupont, Nicolas; Bagøien, Espen; Melle, Webjørn

    2017-03-01

    Calanus finmarchicus is the dominant copepod species in the Norwegian Sea, where it plays a key role in the ecosystem by transferring energy from primary producers to higher trophic levels. This paper analyses a 17-year time series, 1996-2012, on C. finmarchicus collected within the Atlantic Water mass along the Svinøy transect in the southeastern Norwegian Sea. We use the spring abundance of adult as a proxy for the size of C. finmarchicus' overwintered population. The inter-annual trend in spring abundance of adult C. finmarchicus in the 200-0 m depth-stratum is assessed while accounting for spring population development to the adult stage represented by day of year for sampling, inter-annual changes in timing of population development, and spatial differences. For the most oceanic stations, a significant inter-annual trend in spring abundance of adult C. finmarchicus was revealed using generalized additive models (GAM). This trend primarily consists in an increase prior to year 2000 and a decrease between years 2000 and ca. 2011. For the stations closer to the coast, the identified inter-annual trend is a decrease during a longer period from the late 90s until ca. 2011. From 2000 to 2011, our estimates suggest a 50% decrease for the most oceanic stations, and as much as an 81% decrease for the stations closer to the coast. In addition the results suggest a consistent change in phenology over the years and the stations. The predicted spring peak of overwintered adult population abundance is suggested to become shorter by 3 days, and the predicted maximum of abundance to take place 4 days earlier over the 17 years of the time-series. The results highlight significant changes in intensity and timing of the overwintered population of a key zooplankton species in the Norwegian Sea that may have important implications on the scale of an entire ecosystem.

  17. Population genetic structure in Lahontan cutthroat trout

    USGS Publications Warehouse

    Nielsen, Jennifer L.; Sage, George K.

    2002-01-01

    We used 10 microsatellite loci to examine the genetic population structure of cutthroat trout Oncorhynchus clarki within the Lahontan Basin complex. Genetic diversity was analyzed for trout from Nevada, California, and Utah representing three putative subspecies: Lahontan O. c. henshawi, Paiute O. c. seleniris, and Humboldt (an unnamed subspecies) cutthroat trout. We found significant differences in microsatellite diversity among the three putative subspecies found in this area. Analysis of molecular variance partitioned microsatellite variation as 9.8% among subspecies, 27.7% among populations, and 62.5% within populations of Lahontan Basin cutthroat trout. Genetic distance analyses (Cavalli-Sforza-Edwards and F st) supported unique population structure in cutthroat trout from the Humboldt and Pilot Peak drainages. Pairwise F st values for Lahontan cutthroat trout were not significantly correlated with geographic distance between population pairs (r 2 = 0.008; P < 0.0001), suggesting that they are extremely isolated populations with small effective sizes that are vulnerable to extinction. Two extant hatchery strains of Lahontan cutthroat trout showed genetic associations with different geographic source populations. The Pyramid Lake hatchery strain was most closely associated genetically with fish from Summit Lake. The Pilot Peak hatchery strain was associated genetically with Pilot Peak wild trout (Utah) and Macklin Creek trout (California). The phylogeographic diversity depicted in this study supports unique population structure and suggests important evolutionary relationships needed to evaluate transplanted populations and hatchery supplementation within the basin.

  18. Structured populations with diffusion and Feller conditions.

    PubMed

    Bartomiejczyk, Agnieszka; Leszczynski, Henryk

    2016-04-01

    We prove a weak maximum principle for structured population models with dynamic boundary conditions. We establish existence and positivity of solutions of these models and investigate the asymptotic behaviour of solutions. In particular, we analyse so called size profile.

  19. Effects of harvesting flowers from shrubs on the persistence and abundance of wild shrub populations at multiple spatial extents.

    PubMed

    Cabral, Juliano Sarmento; Bond, William J; Midgley, Guy F; Rebelo, Anthony G; Thuiller, Wilfried; Schurr, Frank M

    2011-02-01

    Wildflower harvesting is an economically important activity of which the ecological effects are poorly understood. We assessed how harvesting of flowers affects shrub persistence and abundance at multiple spatial extents. To this end, we built a process-based model to examine the mean persistence and abundance of wild shrubs whose flowers are subject to harvest (serotinous Proteaceae in the South African Cape Floristic Region). First, we conducted a general sensitivity analysis of how harvesting affects persistence and abundance at nested spatial extents. For most spatial extents and combinations of demographic parameters, persistence and abundance of flowering shrubs decreased abruptly once harvesting rate exceeded a certain threshold. At larger extents, metapopulations supported higher harvesting rates before their persistence and abundance decreased, but persistence and abundance also decreased more abruptly due to harvesting than at smaller extents. This threshold rate of harvest varied with species' dispersal ability, maximum reproductive rate, adult mortality, probability of extirpation or local extinction, strength of Allee effects, and carrying capacity. Moreover, spatial extent interacted with Allee effects and probability of extirpation because both these demographic properties affected the response of local populations to harvesting more strongly than they affected the response of metapopulations. Subsequently, we simulated the effects of harvesting on three Cape Floristic Region Proteaceae species and found that these species reacted differently to harvesting, but their persistence and abundance decreased at low rates of harvest. Our estimates of harvesting rates at maximum sustainable yield differed from those of previous investigations, perhaps because researchers used different estimates of demographic parameters, models of population dynamics, and spatial extent than we did. Good demographic knowledge and careful identification of the spatial extent

  20. The Distribution and Abundance of an Island Population of Koalas (Phascolarctos cinereus) in the Far North of Their Geographic Range

    PubMed Central

    McGregor, Denise C.; Kerr, Sarah E.; Krockenberger, Andrew K.

    2013-01-01

    Koalas are an iconic species of charismatic megafauna, of substantial social and conservation significance. They are widely distributed, often at low densities, and individuals can be difficult to detect, making population surveys challenging and costly. Consequently, koala population estimates have been limited and the results inconsistent. The aims of this study were to estimate the distribution, relative abundance and population size of the koalas on Magnetic Island, far north Queensland. Population densities were estimated in 18 different vegetation types present on the island using a Fecal Standing Crop Method. Koala density ranged from 0.404 ha−1, recorded in forest red gum and bloodwood woodland, to absence from eight of the vegetation types surveyed. The second highest density of 0.297 koalas ha−1 was recorded in mixed eucalypt woodland, which covers 45% of the island. The total abundance of koalas on Magnetic Island, not including those present in urban areas, was estimated at 825±175 (SEM). The large variation in koala density across vegetation types reinforces the need for sampling stratification when calculating abundance over large areas, as uniformity of habitat quality cannot be assumed. In this context, koala populations also occur in low densities in areas generally regarded as poor quality koala habitat. These results highlight the importance of protecting vegetation communities not traditionally considered to have high conservation value to koalas, as these habitats may be essential for maintaining viable, widespread, low-density populations. The results from this study provide a baseline to assess future trends in koala distribution, density and abundance on Magnetic Island. PMID:23527258

  1. Fingerprints of anomalous primordial Universe on the abundance of large scale structures

    NASA Astrophysics Data System (ADS)

    Baghram, Shant; Akbar Abolhasani, Ali; Firouzjahi, Hassan; Namjoo, Mohammad Hossein

    2014-12-01

    We study the predictions of anomalous inflationary models on the abundance of structures in large scale structure observations. The anomalous features encoded in primordial curvature perturbation power spectrum are (a): localized feature in momentum space, (b): hemispherical asymmetry and (c): statistical anisotropies. We present a model-independent expression relating the number density of structures to the changes in the matter density variance. Models with localized feature can alleviate the tension between observations and numerical simulations of cold dark matter structures on galactic scales as a possible solution to the missing satellite problem. In models with hemispherical asymmetry we show that the abundance of structures becomes asymmetric depending on the direction of observation to sky. In addition, we study the effects of scale-dependent dipole amplitude on the abundance of structures. Using the quasars data and adopting the power-law scaling knA-1 for the amplitude of dipole we find the upper bound nA < 0.6 for the spectral index of the dipole asymmetry. In all cases there is a critical mass scale Mc in which for M Mc) the enhancement in variance induced from anomalous feature decreases (increases) the abundance of dark matter structures in Universe.

  2. Fingerprints of anomalous primordial Universe on the abundance of large scale structures

    SciTech Connect

    Baghram, Shant; Abolhasani, Ali Akbar; Firouzjahi, Hassan; Namjoo, Mohammad Hossein E-mail: abolhasani@ipm.ir E-mail: MohammadHossein.Namjoo@utdallas.edu

    2014-12-01

    We study the predictions of anomalous inflationary models on the abundance of structures in large scale structure observations. The anomalous features encoded in primordial curvature perturbation power spectrum are (a): localized feature in momentum space, (b): hemispherical asymmetry and (c): statistical anisotropies. We present a model-independent expression relating the number density of structures to the changes in the matter density variance. Models with localized feature can alleviate the tension between observations and numerical simulations of cold dark matter structures on galactic scales as a possible solution to the missing satellite problem. In models with hemispherical asymmetry we show that the abundance of structures becomes asymmetric depending on the direction of observation to sky. In addition, we study the effects of scale-dependent dipole amplitude on the abundance of structures. Using the quasars data and adopting the power-law scaling k{sup n{sub A}-1} for the amplitude of dipole we find the upper bound n{sub A} < 0.6 for the spectral index of the dipole asymmetry. In all cases there is a critical mass scale M{sub c} in which for M M{sub c}) the enhancement in variance induced from anomalous feature decreases (increases) the abundance of dark matter structures in Universe.

  3. Genetic Structure of the Spanish Population

    PubMed Central

    2010-01-01

    Background Genetic admixture is a common caveat for genetic association analysis. Therefore, it is important to characterize the genetic structure of the population under study to control for this kind of potential bias. Results In this study we have sampled over 800 unrelated individuals from the population of Spain, and have genotyped them with a genome-wide coverage. We have carried out linkage disequilibrium, haplotype, population structure and copy-number variation (CNV) analyses, and have compared these estimates of the Spanish population with existing data from similar efforts. Conclusions In general, the Spanish population is similar to the Western and Northern Europeans, but has a more diverse haplotypic structure. Moreover, the Spanish population is also largely homogeneous within itself, although patterns of micro-structure may be able to predict locations of origin from distant regions. Finally, we also present the first characterization of a CNV map of the Spanish population. These results and original data are made available to the scientific community. PMID:20500880

  4. Genetic structure of the world's polar bear populations

    USGS Publications Warehouse

    Paetkau, David; Amstrup, Steven C.; Born, E.W.; Calvert, W.; Derocher, A.E.; Garner, G.W.; Messier, F.; Stirling, I.; Taylor, M.K.; Wiig, O.; Strobeck, C.

    1999-01-01

    We studied genetic structure in polar bear (Ursus maritimus) populations by typing a sample of 473 individuals spanning the species distribution at 16 highly variable microsatellite loci. No genetic discontinuities were found that would be consistent with evolutionarily significant periods of isolation between groups. Direct comparison of movement data and genetic data from the Canadian Arctic revealed a highly significant correlation. Genetic data generally supported existing population (management unit) designations, although there were two cases where genetic data failed to differentiate between pairs of populations previously resolved by movement data. A sharp contrast was found between the minimal genetic structure observed among populations surrounding the polar basin and the presence of several marked genetic discontinuities in the Canadian Arctic. The discontinuities in the Canadian Arctic caused the appearance of four genetic clusters of polar bear populations. These clusters vary in total estimated population size from 100 to over 10 000, and the smallest may merit a relatively conservative management strategy in consideration of its apparent isolation. We suggest that the observed pattern of genetic discontinuities has developed in response to differences in the seasonal distribution and pattern of sea ice habitat and the effects of these differences on the distribution and abundance of seals.

  5. Distinguishing Recent Admixture from Ancestral Population Structure

    PubMed Central

    Slatkin, Montgomery

    2017-01-01

    We develop and test two methods for distinguishing between recent admixture and ancestral population structure as explanations for greater similarity of one of two populations to an outgroup population. This problem arose when Neanderthals were found to be slightly more similar to nonAfrican than to African populations. The excess similarity is consistent with both recent admixture from Neanderthals into the ancestors of nonAfricans and subdivision in the ancestral population. Although later studies showed that there had been recent admixture, distinguishing between these two classes of models will be important in other situations, particularly when high-coverage genomes cannot be obtained for all populations. One of our two methods is based on the properties of the doubly conditioned frequency spectrum combined with the unconditional frequency spectrum. This method does not require a linkage map and can be used when there is relatively low coverage. The second method uses the extent of linkage disequilibrium among closely linked markers. PMID:28186554

  6. Ages of 70 Dwarfs of Three Populations in the Solar Neighborhood: Considering O and C Abundances in Stellar Models

    NASA Astrophysics Data System (ADS)

    Ge, Z. S.; Bi, S. L.; Chen, Y. Q.; Li, T. D.; Zhao, J. K.; Liu, K.; Ferguson, J. W.; Wu, Y. Q.

    2016-12-01

    Oxygen and carbon are important elements in stellar populations. Their behavior refers to the formation history of the stellar populations. C and O abundances would also obviously influence stellar opacities and the overall metal abundance Z. With observed high-quality spectroscopic properties, we construct stellar models with C and O elements to give more accurate ages for 70 metal-poor dwarfs, which have been determined to be high-α halo, low-α halo, and thick-disk stars. Our results show that high-α halo stars are somewhat older than low-α halo stars by around 2.0 Gyr. The thick-disk population has an age range in between the two halo populations. The age distribution profiles indicate that high-α halo and low-α halo stars match the in situ accretion simulation by Zolotov et al., and the thick-disk stars might be formed in a relatively quiescent and long-lasting process. We also note that stellar ages are very sensitive to O abundance, since the ages clearly increase with increasing [O/Fe] values. Additionally, we obtain several stars with peculiar ages, including 2 young thick-disk stars and 12 stars older than the universe age.

  7. Genetic structure among Fijian island populations.

    PubMed

    Shipley, Gerhard P; Taylor, Diana A; Tyagi, Anand; Tiwari, Geetanjali; Redd, Alan J

    2015-02-01

    We examined nine Y chromosome short tandem repeats (Y-STRs) and the mitochondrial DNA (mtDNA) hypervariable segment 1 region in the Fijian island populations of Viti Levu, Vanua Levu, Kadavu, the Lau islands and Rotuma. We found significant genetic structure among these populations for the Y-STRs, both with and without the Rotumans, but not for the mtDNA. We also found that all five populations exhibited the sex-biased admixture associated with areas settled by Austronesian-speaking people, with paternal lineages more strongly associated with Melanesian populations and maternal lineages more strongly associated with Polynesian populations. We also found that the Rotumans in the north and the Lau Islanders in the east were genetically more similar to Polynesian populations than were the other Fijians, but only for the mtDNA. For the Y-STRs, the Rotumans and the Lau Islanders were genetically as similar to Melanesian populations as were the other three populations. Of the five populations, the Rotumans were the most different in almost every regard. Although past genetic studies treated the Fijians as being genetically homogenous despite known geographic, phenotypic, cultural and linguistic variation, our findings show significant genetic variation and a need for a closer examination of individual island populations within Fiji, particularly the Rotumans, in order to better understand the process of the peopling of Fiji and of the surrounding regions.

  8. Estimating grizzly and black bear population abundance and trend in Banff National Park using noninvasive genetic sampling.

    PubMed

    Sawaya, Michael A; Stetz, Jeffrey B; Clevenger, Anthony P; Gibeau, Michael L; Kalinowski, Steven T

    2012-01-01

    We evaluated the potential of two noninvasive genetic sampling methods, hair traps and bear rub surveys, to estimate population abundance and trend of grizzly (Ursus arctos) and black bear (U. americanus) populations in Banff National Park, Alberta, Canada. Using Huggins closed population mark-recapture models, we obtained the first precise abundance estimates for grizzly bears (N= 73.5, 95% CI = 64-94 in 2006; N= 50.4, 95% CI = 49-59 in 2008) and black bears (N= 62.6, 95% CI = 51-89 in 2006; N= 81.8, 95% CI = 72-102 in 2008) in the Bow Valley. Hair traps had high detection rates for female grizzlies, and male and female black bears, but extremely low detection rates for male grizzlies. Conversely, bear rubs had high detection rates for male and female grizzlies, but low rates for black bears. We estimated realized population growth rates, lambda, for grizzly bear males (λ= 0.93, 95% CI = 0.74-1.17) and females (λ= 0.90, 95% CI = 0.67-1.20) using Pradel open population models with three years of bear rub data. Lambda estimates are supported by abundance estimates from combined hair trap/bear rub closed population models and are consistent with a system that is likely driven by high levels of human-caused mortality. Our results suggest that bear rub surveys would provide an efficient and powerful means to inventory and monitor grizzly bear populations in the Central Canadian Rocky Mountains.

  9. Population structure of the Classic period Maya.

    PubMed

    Scherer, Andrew K

    2007-03-01

    This study examines the population structure of Classic period (A.D. 250-900) Maya populations through analysis of odontometric variation of 827 skeletons from 12 archaeological sites in Mexico, Guatemala, Belize, and Honduras. The hypothesis that isolation by distance characterized Classic period Maya population structure is tested using Relethford and Blangero's (Hum Biol 62 (1990) 5-25) approach to R matrix analysis for quantitative traits. These results provide important biological data for understanding ancient Maya population history, particularly the effects of the competing Tikal and Calakmul hegemonies on patterns of lowland Maya site interaction. An overall F(ST) of 0.018 is found for the Maya area, indicating little among-group variation for the Classic Maya sites tested. Principal coordinates plots derived from the R matrix analysis show little regional patterning in the data, though the geographic outliers of Kaminaljuyu and a pooled Pacific Coast sample did not cluster with the lowland Maya sites. Mantel tests comparing the biological distance matrix to a geographic distance matrix found no association between genetic and geographic distance. In the Relethford-Blangero analysis, most sites possess negative or near-zero residuals, indicating minimal extraregional gene flow. The exceptions were Barton Ramie, Kaminaljuyu, and Seibal. A scaled R matrix analysis clarifies that genetic drift is a consideration for understanding Classic Maya population structure. All results indicate that isolation by distance does not describe Classic period Maya population structure.

  10. Hierarchical distance-sampling models to estimate population size and habitat-specific abundance of an island endemic.

    PubMed

    Sillett, T Scott; Chandler, Richard B; Royle, J Andrew; Kery, Marc; Morrison, Scott A

    2012-10-01

    Population size and habitat-specific abundance estimates are essential for conservation management. A major impediment to obtaining such estimates is that few statistical models are able to simultaneously account for both spatial variation in abundance and heterogeneity in detection probability, and still be amenable to large-scale applications. The hierarchical distance-sampling model of J. A. Royle, D. K. Dawson, and S. Bates provides a practical solution. Here, we extend this model to estimate habitat-specific abundance and rangewide population size of a bird species of management concern, the Island Scrub-Jay (Aphelocoma insularis), which occurs solely on Santa Cruz Island, California, USA. We surveyed 307 randomly selected, 300 m diameter, point locations throughout the 250-km2 island during October 2008 and April 2009. Population size was estimated to be 2267 (95% CI 1613-3007) and 1705 (1212-2369) during the fall and spring respectively, considerably lower than a previously published but statistically problematic estimate of 12 500. This large discrepancy emphasizes the importance of proper survey design and analysis for obtaining reliable information for management decisions. Jays were most abundant in low-elevation chaparral habitat; the detection function depended primarily on the percent cover of chaparral and forest within count circles. Vegetation change on the island has been dramatic in recent decades, due to release from herbivory following the eradication of feral sheep (Ovis aries) from the majority of the island in the mid-1980s. We applied best-fit fall and spring models of habitat-specific jay abundance to a vegetation map from 1985, and estimated the population size of A. insularis was 1400-1500 at that time. The 20-30% increase in the jay population suggests that the species has benefited from the recovery of native vegetation since sheep removal. Nevertheless, this jay's tiny range and small population size make it vulnerable to natural

  11. Hierarchical distance-sampling models to estimate population size and habitat-specific abundance of an island endemic

    USGS Publications Warehouse

    Sillett, Scott T.; Chandler, Richard B.; Royle, J. Andrew; Kéry, Marc; Morrison, Scott A.

    2012-01-01

    Population size and habitat-specific abundance estimates are essential for conservation management. A major impediment to obtaining such estimates is that few statistical models are able to simultaneously account for both spatial variation in abundance and heterogeneity in detection probability, and still be amenable to large-scale applications. The hierarchical distance-sampling model of J. A. Royle, D. K. Dawson, and S. Bates provides a practical solution. Here, we extend this model to estimate habitat-specific abundance and rangewide population size of a bird species of management concern, the Island Scrub-Jay (Aphelocoma insularis), which occurs solely on Santa Cruz Island, California, USA. We surveyed 307 randomly selected, 300 m diameter, point locations throughout the 250-km2 island during October 2008 and April 2009. Population size was estimated to be 2267 (95% CI 1613-3007) and 1705 (1212-2369) during the fall and spring respectively, considerably lower than a previously published but statistically problematic estimate of 12 500. This large discrepancy emphasizes the importance of proper survey design and analysis for obtaining reliable information for management decisions. Jays were most abundant in low-elevation chaparral habitat; the detection function depended primarily on the percent cover of chaparral and forest within count circles. Vegetation change on the island has been dramatic in recent decades, due to release from herbivory following the eradication of feral sheep (Ovis aries) from the majority of the island in the mid-1980s. We applied best-fit fall and spring models of habitat-specific jay abundance to a vegetation map from 1985, and estimated the population size of A. insularis was 1400-1500 at that time. The 20-30% increase in the jay population suggests that the species has benefited from the recovery of native vegetation since sheep removal. Nevertheless, this jay's tiny range and small population size make it vulnerable to natural

  12. Multiple Populations in NGC 1851: Abundance Variations and UV Photometric Synthesis in the Washington and HST/WFC3 Systems

    NASA Astrophysics Data System (ADS)

    Cummings, Jeffrey D.; Geisler, D.; Villanova, S.

    2017-04-01

    The analysis of multiple populations (MPs) in globular clusters (GCs), both spectroscopically and photometrically, is key in understanding their formation and evolution. The relatively narrow Johnson U, F336W, and Stromgren and Sloan u filters have been crucial in exhibiting these MPs photometrically, but in Paper I we showed that the broader Washington C filter can more efficiently detect MPs in the test case GC NGC 1851. Additionally, In Paper I we detected a double main sequence (MS) that has not been detected in previous observations of NGC 1851. We now match this photometry to NGC 1851's published RGB abundances and find that the two RGB branches observed in C generally exhibit different abundance characteristics in a variety of elements (e.g., Ba, Na, and O) and in CN band strengths, but no single element can define the two RGB branches. However, simultaneously considering [Ba/Fe] or CN strength with either [Na/Fe], [O/Fe], or CN strength can separate the two photometric RGB branches into two distinct abundance groups. Matches of NGC 1851's published SGB and HB abundances to the Washington photometry shows consistent characterizations of the MPs, which can be defined as an O-rich/N-normal population and an O-poor/N-rich population. Photometric synthesis for both the Washington C filter and the F336W filter finds that these abundance characteristics, with appropriate variations in He, can reproduce for both filters the photometric observations in both the RGB and the MS. This photometric synthesis also confirms the throughput advantages that the C filter has in detecting MPs.

  13. Population structure of ice-breeding seals.

    PubMed

    Davis, Corey S; Stirling, Ian; Strobeck, Curtis; Coltman, David W

    2008-07-01

    The development of population genetic structure in ice-breeding seal species is likely to be shaped by a combination of breeding habitat and life-history characteristics. Species that return to breed on predictable fast-ice locations are more likely to exhibit natal fidelity than pack-ice-breeding species, which in turn facilitates the development of genetic differentiation between subpopulations. Other aspects of life history such as geographically distinct vocalizations, female gregariousness, and the potential for polygynous breeding may also facilitate population structure. Based on these factors, we predicted that fast-ice-breeding seal species (the Weddell and ringed seal) would show elevated genetic differentiation compared to pack-ice-breeding species (the leopard, Ross, crabeater and bearded seals). We tested this prediction using microsatellite analysis to examine population structure of these six ice-breeding species. Our results did not support this prediction. While none of the Antarctic pack-ice species showed statistically significant population structure, the bearded seal of the Arctic pack ice showed strong differentiation between subpopulations. Again in contrast, the fast-ice-breeding Weddell seal of the Antarctic showed clear evidence for genetic differentiation while the ringed seal, breeding in similar habitat in the Arctic, did not. These results suggest that the development of population structure in ice-breeding phocid seals is a more complex outcome of the interplay of phylogenetic and ecological factors than can be predicted on the basis of breeding substrate and life-history characteristics.

  14. Abundance inhomogeneities and atmospheric structure in CN-bimodal globular cluster giants

    NASA Technical Reports Server (NTRS)

    Drake, Jeremy J.; Plez, Bertrand; Smith, Verne V.

    1993-01-01

    It has been suggested by several authors that the sodium and aluminum abundance variations correlating with CN-band strength, frequently observed in CN-bimodal globular cluster giants, could be spurious manifestations of different temperature structures in the 'CN-strong' and 'CN-weak' stars, caused by different molecular line blanketing related to the C, N, and O trio. For stellar parameters generally appropriate to giants in the intermediate metallicity CN-bimodal cluster M4, we demonstrate through new model atmosphere calculations, employing opacity sampling and spherical geometry, that the observed abundance anomalies cannot be the result of atmospheric temperature structure. Our results using spherical geometry are compared to identical calculations performed with plane-parallel geometry: the effects of atmospheric extension on derived abundances for all lines considered amount to less than 0.1 dex.

  15. Grain-rich diets differently alter ruminal and colonic abundance of microbial populations and lipopolysaccharide in goats.

    PubMed

    Metzler-Zebeli, Barbara U; Schmitz-Esser, Stephan; Klevenhusen, Fenja; Podstatzky-Lichtenstein, Leopold; Wagner, Martin; Zebeli, Qendrim

    2013-04-01

    High grain feeding has been associated with ruminal pH depression and microbial dysbiosis in cattle. Yet, the impact of high grain feeding on the caprine rumen and hindgut microbial community and lipopolysaccharide (LPS) release is largely unknown. Therefore, the objective was to investigate the effect of increasing dietary levels of barley grain on the microbial composition and LPS concentrations in the rumen and colon of goats. Effects were compared with respect to the responses of ruminal and colonic pH and short-chain fatty acid (SCFA) generation. Growing goats (n = 5-6) were fed diets containing 0, 30, or 60% coarsely ground barley grain for 6 weeks. Ruminal ciliate protozoa were counted with Bürker counting chamber, and quantitative PCR was used to compare bacterial populations. Increasing dietary grain level linearly increased (P < 0.05) ruminal numbers of entodiniomorphids. With the 60% grain diet, there was a reduction in ruminal abundance of the genus Prevotella and Fibrobacter succinogenes, whereas the ruminal abundance of Lactobacillus spp. increased compared to the 0 and 30% grain diets (P < 0.05). In the colon, abundance of the genus Prevotella and F. succinogenes increased (P < 0.05) in goats fed the 60% grain diet compared to those fed the other diets. Colonic abundance of Clostridium cluster I was related to the presence of grain in the diet. Ruminal LPS concentration decreased (P < 0.05) in response to the 60% grain diet, whereas its colonic concentration increased in response to the same diet (P < 0.05). Present results provide first insight on the adaptive response of rumen protozoa and rumen and colonic bacterial populations to increasing dietary levels of grain in goats. Although luminal pH largely affects microbial populations, fermentable substrate flow to the caprine hindgut may have played a greater role for colonic bacterial populations in the present study.

  16. Long-term prairie falcon population changes in relation to prey abundance, weather, land uses, and habitat conditions

    USGS Publications Warehouse

    Steenhof, Karen; Kochert, Michael N.; Carpenter, L.B.; Lehman, Robert N.

    1999-01-01

    We studied a nesting population of Prairie Falcons( Falco mexicanus) in the Snake River Birds of Prey National Conservation Area (NCA) from 1974-1997 to identify factors that influence abundance and reproduction. Our sampling period included two major droughts and associated crashes in Townsenda??s ground squirrel (Spermophilus townsendii) populations. The number of Prairie Falcon pairs found on long-term survey segments declined significantly from 1976-1997. Early declines were most severe at the eastern end of the NCA, where fires and agriculture have changed native shrubsteppe habitat. More recent declines occurred in the portion of canyon near the Orchard Training Area (OTA), where the Idaho Army National Guard conducts artillery firing and tank maneuvers. Overall Prairie Falcon reproductive rates were tied closely to annual indexes of ground squirrel abundance, but precipitation before and during the breeding season was related inversely to some measures of reproduction. Most reproductive parameters showed no significant trends over time, but during the 199Os, nesting success and productivity were lower in the stretch of canyon near the OTA than in adjacent areas. Extensive shrub loss, by itself, did not explain the pattern of declines in abundance and reproduction that we observed. Recent military training activities likely have interacted with fire and livestock grazing to create less than favorable foraging opportunities for Prairie Falcons in a large part of the NCA. To maintain Prairie Falcon populations in the NCA, managers should suppress wildfires, restore native plant communities, and regulate potentially incompatible land uses.

  17. Long-term Prairie Falcon population changes in relation to prey abundance, weather, land uses, and habitat conditions

    USGS Publications Warehouse

    Steenhof, K.; Kochert, M.N.; Carpenter, L.B.; Lehman, R.N.

    1999-01-01

    We studied a nesting population of Prairie Falcons (Falco mexicanus) in the Snake River Birds of Prey National Conservation Area (NCA) from 1974-1997 to identify factors that influence abundance and reproduction. Our sampling period included two major droughts and associated crashes in Townsend's ground squirrel (Spermophilus townsendii) populations. The number of Prairie Falcon pairs found on long-term survey segments declined significantly from 1976-1997. Early declines were most severe at the eastern end of the NCA, where fires and agriculture have changed native shrubsteppe habitat. More recent declines occurred in the portion of canyon near the Orchard Training Area (OTA), where the Idaho Army National Guard conducts artillery firing and tank maneuvers. Overall Prairie Falcon reproductive rates were tied closely to annual indexes of ground squirrel abundance, but precipitation before and during the breeding season was related inversely to some measures of reproduction. Most reproductive parameters showed no significant trends over time, but during the 1990s, nesting success and productivity were lower in the stretch of canyon near the OTA than in adjacent areas. Extensive shrub loss, by itself, did not explain the pattern of declines in abundance and reproduction that we observed. Recent military training activities likely have interacted with fire and livestock grazing to create less than favorable foraging opportunities for Prairie Falcons in a large part of the NCA. To maintain Prairie Falcon populations in the NCA, managers should suppress wildfires, restore native plant communities, and regulate potentially incompatible land uses.

  18. Abundance Trends and Status of the Little Colorado River Population of Humpback Chub: An Update Considering Data From 1989-2008

    USGS Publications Warehouse

    Coggins,, Lewis G.; Walters, Carl J.

    2009-01-01

    Mark-recapture methods have been used for the past two decades to assess trends in adult abundance and recruitment of the Little Colorado River (LCR) population of humpback chub. These methods indicate that the adult population declined through the 1980s and early 1990s but has been increasing for the past decade. Recruitment appears also to have increased, particularly in the 2003-4 period. Considering a range of assumed natural mortality-rates and magnitude of ageing error, it is unlikely that there are currently less than 6,000 adults or more than 10,000 adults. Our best estimate of the current adult (age 4 years or more) population is approximately 7,650 fish. Recent humpback chub assessments using the Age-Structured Mark-Recapture model (ASMR) and reported in 2006 (Melis and others, 2006) and 2008 (Coggins, 2008a,b) have provided abundance and recruitment trend estimates that have changed progressively over time as more data are considered by the model. The general pattern of change implies a less severe decline in adult abundance during the late 1980s through early 1990s, with attendant changes in recruitment supporting this demographic pattern. We have been concerned that these changes are not indicative of the true population and may be associated with a 'retrospective' bias as additional data are included in the ASMR model. To investigate this possibility, we developed a realistic individual-based simulation model (IBM) to generate replicate artificial data sets with similar characteristics to the true humpback chub data. The artificial data have known abundance trends and we analyzed these data with ASMR. On the basis of these simulations, we believe that errors in assigning age (and therefore brood-year) to fish based on their length are likely to have caused the retrospective bias pattern seen in the assessments and to have caused both less severe trends in the adult abundance estimates and progressively more severe downward bias in estimates of adult

  19. Ocean currents help explain population genetic structure

    PubMed Central

    White, Crow; Selkoe, Kimberly A.; Watson, James; Siegel, David A.; Zacherl, Danielle C.; Toonen, Robert J.

    2010-01-01

    Management and conservation can be greatly informed by considering explicitly how environmental factors influence population genetic structure. Using simulated larval dispersal estimates based on ocean current observations, we demonstrate how explicit consideration of frequency of exchange of larvae among sites via ocean advection can fundamentally change the interpretation of empirical population genetic structuring as compared with conventional spatial genetic analyses. Both frequency of larval exchange and empirical genetic difference were uncorrelated with Euclidean distance between sites. When transformed into relative oceanographic distances and integrated into a genetic isolation-by-distance framework, however, the frequency of larval exchange explained nearly 50 per cent of the variance in empirical genetic differences among sites over scales of tens of kilometres. Explanatory power was strongest when we considered effects of multiple generations of larval dispersal via intermediary locations on the long-term probability of exchange between sites. Our results uncover meaningful spatial patterning to population genetic structuring that corresponds with ocean circulation. This study advances our ability to interpret population structure from complex genetic data characteristic of high gene flow species, validates recent advances in oceanographic approaches for assessing larval dispersal and represents a novel approach to characterize population connectivity at small spatial scales germane to conservation and fisheries management. PMID:20133354

  20. Ocean currents help explain population genetic structure.

    PubMed

    White, Crow; Selkoe, Kimberly A; Watson, James; Siegel, David A; Zacherl, Danielle C; Toonen, Robert J

    2010-06-07

    Management and conservation can be greatly informed by considering explicitly how environmental factors influence population genetic structure. Using simulated larval dispersal estimates based on ocean current observations, we demonstrate how explicit consideration of frequency of exchange of larvae among sites via ocean advection can fundamentally change the interpretation of empirical population genetic structuring as compared with conventional spatial genetic analyses. Both frequency of larval exchange and empirical genetic difference were uncorrelated with Euclidean distance between sites. When transformed into relative oceanographic distances and integrated into a genetic isolation-by-distance framework, however, the frequency of larval exchange explained nearly 50 per cent of the variance in empirical genetic differences among sites over scales of tens of kilometres. Explanatory power was strongest when we considered effects of multiple generations of larval dispersal via intermediary locations on the long-term probability of exchange between sites. Our results uncover meaningful spatial patterning to population genetic structuring that corresponds with ocean circulation. This study advances our ability to interpret population structure from complex genetic data characteristic of high gene flow species, validates recent advances in oceanographic approaches for assessing larval dispersal and represents a novel approach to characterize population connectivity at small spatial scales germane to conservation and fisheries management.

  1. Distribution and abundance of marine bird and pinniped populations within Port Foster, Deception Island, Antarctica

    NASA Astrophysics Data System (ADS)

    Kendall, Katrina A.; Ruhl, Henry A.; Wilson, Robert C.

    2003-06-01

    Seabirds and pinnipeds were surveyed during four cruises from March 1999 to November 2000 at Port Foster, Deception Island, Antarctica. Abundances and distributions of three species of pinnipeds, Arctocephalus gazella (Antarctic fur seals), Leptonychotes weddelli (Weddell seals), and Lobodon carcinophagus (crabeater seals), and 11 species of marine birds were documented within Port Foster. A. gazella was the dominant pinniped within Port Foster; its abundance has increased since the 1986/87 austral summer season. A. gazella were concentrated at the entrance to Port Foster. More pinnipeds were observed during the austral summer than during the spring. The most dominant seabird, Pygoscelis antarctica (chinstrap penguin), was concentrated along the rocky cliffs behind the beaches where A. gazella hauled out. Larus dominicanus (kelp gull) and Daption capense (cape petrel) were the most dominant flying seabirds. All other seabird species were more widely distributed around Port Foster than P. antarctica. There was no clear trend in abundances of seabirds over the study period. It is possible that the protected area of Port Foster provides refuge for vagrants of colonies along the outer periphery of the island and as a stopover point for migrating species.

  2. The Abundance and Pollen Foraging Behaviour of Bumble Bees in Relation to Population Size of Whortleberry (Vaccinium uliginosum)

    PubMed Central

    Mayer, Carolin; Michez, Denis; Chyzy, Alban; Brédat, Elise; Jacquemart, Anne-Laure

    2012-01-01

    Habitat fragmentation can have severe effects on plant pollinator interactions, for example changing the foraging behaviour of pollinators. To date, the impact of plant population size on pollen collection by pollinators has not yet been investigated. From 2008 to 2010, we monitored nine bumble bee species (Bombus campestris, Bombus hortorum s.l., Bombus hypnorum, Bombus lapidarius, Bombus pascuorum, Bombus pratorum, Bombus soroensis, Bombus terrestris s.l., Bombus vestalis s.l.) on Vaccinium uliginosum (Ericaceae) in up to nine populations in Belgium ranging in size from 80 m2 to over 3.1 ha. Bumble bee abundance declined with decreasing plant population size, and especially the proportion of individuals of large bumble bee species diminished in smaller populations. The most remarkable and novel observation was that bumble bees seemed to switch foraging behaviour according to population size: while they collected both pollen and nectar in large populations, they largely neglected pollen collection in small populations. This pattern was due to large bumble bee species, which seem thus to be more likely to suffer from pollen shortages in smaller habitat fragments. Comparing pollen loads of bumble bees we found that fidelity to V. uliginosum pollen did not depend on plant population size but rather on the extent shrub cover and/or openness of the site. Bumble bees collected pollen only from three plant species (V. uliginosum, Sorbus aucuparia and Cytisus scoparius). We also did not discover any pollination limitation of V. uliginosum in small populations. We conclude that habitat fragmentation might not immediately threaten the pollination of V. uliginosum, nevertheless, it provides important nectar and pollen resources for bumble bees and declining populations of this plant could have negative effects for its pollinators. The finding that large bumble bee species abandon pollen collection when plant populations become small is of interest when considering plant and

  3. The abundance and pollen foraging behaviour of bumble bees in relation to population size of whortleberry (Vaccinium uliginosum).

    PubMed

    Mayer, Carolin; Michez, Denis; Chyzy, Alban; Brédat, Elise; Jacquemart, Anne-Laure

    2012-01-01

    Habitat fragmentation can have severe effects on plant pollinator interactions, for example changing the foraging behaviour of pollinators. To date, the impact of plant population size on pollen collection by pollinators has not yet been investigated. From 2008 to 2010, we monitored nine bumble bee species (Bombus campestris, Bombus hortorum s.l., Bombus hypnorum, Bombus lapidarius, Bombus pascuorum, Bombus pratorum, Bombus soroensis, Bombus terrestris s.l., Bombus vestalis s.l.) on Vaccinium uliginosum (Ericaceae) in up to nine populations in Belgium ranging in size from 80 m(2) to over 3.1 ha. Bumble bee abundance declined with decreasing plant population size, and especially the proportion of individuals of large bumble bee species diminished in smaller populations. The most remarkable and novel observation was that bumble bees seemed to switch foraging behaviour according to population size: while they collected both pollen and nectar in large populations, they largely neglected pollen collection in small populations. This pattern was due to large bumble bee species, which seem thus to be more likely to suffer from pollen shortages in smaller habitat fragments. Comparing pollen loads of bumble bees we found that fidelity to V. uliginosum pollen did not depend on plant population size but rather on the extent shrub cover and/or openness of the site. Bumble bees collected pollen only from three plant species (V.uliginosum, Sorbus aucuparia and Cytisus scoparius). We also did not discover any pollination limitation of V. uliginosum in small populations. We conclude that habitat fragmentation might not immediately threaten the pollination of V. uliginosum, nevertheless, it provides important nectar and pollen resources for bumble bees and declining populations of this plant could have negative effects for its pollinators. The finding that large bumble bee species abandon pollen collection when plant populations become small is of interest when considering plant and

  4. Abundant mitochondrial genome diversity, population differentiation and convergent evolution in pines.

    PubMed Central

    Wu, J; Krutovskii, K V; Strauss, S H

    1998-01-01

    We examined mitochondrial DNA polymorphisms via the analysis of restriction fragment length polymorphisms in three closely related species of pines from western North America: knobcone (Pinus attenuata Lemm.), Monterey (P. radiata D. Don), and bishop (P. muricata D. Don). A total of 343 trees derived from 13 populations were analyzed using 13 homologous mitochondrial gene probes amplified from three species by polymerase chain reaction. Twenty-eight distinct mitochondrial DNA haplotypes were detected and no common haplotypes were found among the species. All three species showed limited variability within populations, but strong differentiation among populations. Based on haplotype frequencies, genetic diversity within populations (HS) averaged 0.22, and population differentiation (GST and theta) exceeded 0.78. Analysis of molecular variance also revealed that >90% of the variation resided among populations. For the purposes of genetic conservation and breeding programs, species and populations could be readily distinguished by unique haplotypes, often using the combination of only a few probes. Neighbor-joining phenograms, however, strongly disagreed with those based on allozymes, chloroplast DNA, and morphological traits. Thus, despite its diagnostic haplotypes, the genome appears to evolve via the rearrangement of multiple, convergent subgenomic domains. PMID:9832536

  5. Osprey distribution, abundance, and status in western North America: II. The Oregon population

    USGS Publications Warehouse

    Henny, C.J.; Collins, J.A.; Deibert, W.J.

    1978-01-01

    An estimated 308 ? 23 pairs of Ospreys nested in the survey area in Oregon in 1976. Major concentration centers include Crane Prairie Reservoir and the adjacent Deschutes National Forest, the coastal lakes and reservoirs between Florence and North Bend, the Rogue River, the Lane County reservoirs, and the Umpqua River. An estimated 47 percent of the Oregon population is nesting at reservoirs. Limited information is available concerning the long-term status of the Oregon population; however, the ability of the species to pioneer newly created reservoirs emphasizes that the population is utilizing new habitats.

  6. Estimating population abundance and mapping distribution of wintering sea ducks in coastal waters of the mid-Atlantic

    USGS Publications Warehouse

    Koneff, M.D.; Royle, J. Andrew; Forsell, D.J.; Wortham, J.S.; Boomer, G.S.; Perry, M.C.

    2005-01-01

    Survey design for wintering scoters (Melanitta sp.) and other sea ducks that occur in offshore waters is challenging because these species have large ranges, are subject to distributional shifts among years and within a season, and can occur in aggregations. Interest in winter sea duck population abundance surveys has grown in recent years. This interest stems from concern over the population status of some sea ducks, limitations of extant breeding waterfowl survey programs in North America and logistical challenges and costs of conducting surveys in northern breeding regions, high winter area philopatry in some species and potential conservation implications, and increasing concern over offshore development and other threats to sea duck wintering habitats. The efficiency and practicality of statistically-rigorous monitoring strategies for mobile, aggregated wintering sea duck populations have not been sufficiently investigated. This study evaluated a 2-phase adaptive stratified strip transect sampling plan to estimate wintering population size of scoters, long-tailed ducks (Clangua hyemalis), and other sea ducks and provide information on distribution. The sampling plan results in an optimal allocation of a fixed sampling effort among offshore strata in the U.S. mid-Atlantic coast region. Phase I transect selection probabilities were based on historic distribution and abundance data, while Phase 2 selection probabilities were based on observations made during Phase 1 flights. Distance sampling methods were used to estimate detection rates. Environmental variables thought to affect detection rates were recorded during the survey and post-stratification and covariate modeling were investigated to reduce the effect of heterogeneity on detection estimation. We assessed cost-precision tradeoffs under a number of fixed-cost sampling scenarios using Monte Carlo simulation. We discuss advantages and limitations of this sampling design for estimating wintering sea duck

  7. ESTIMATING AVIAN POPULATION TRENDS USING A DETECTION-CORRECTED ABUNDANCE MODEL

    EPA Science Inventory

    Paper presents a new model for controlling detection heterogeneity in temporally stratified bird counts. The method will allow researchers to control for variation in observer ability in large-scale studies of avian population trends.

  8. Departures from LTE Populations Versus Anomalous Abundances: the Effects of Heating

    NASA Technical Reports Server (NTRS)

    Underhill, A. B.

    1985-01-01

    The deposit of nonradiative heat and momentum in the mantle of a hot star affects the interpretation of the stellar spectrum in two ways. First, a superheated and moving plasma should be considered when doing the analysis, and second, a model atom which is appropriate for the physical state of the line forming regions. Some examples are presented for H and He showing how the changes in the electron temperature affect the solution of the equations of statistical equilibrium. The observed spectra of the Wolf-Raynet stars HD 191765, HD 192103, and HD 192163 are compatible with a normal H/He abundance ratio.

  9. Coronal Thermal Structure and Abundance of Super-Metal-Rich Late-Type Stars

    NASA Technical Reports Server (NTRS)

    Brickhouse, Nancy; Mushotzky, Richard F. (Technical Monitor)

    2002-01-01

    This report covers the NASA grant NAG5-9943 for Cycle 1 XMM Guest Observer Program. The project is entitled 'Coronal Thermal Structure and Abundances of Super-Metal-Rich Late-Type Stars.' This observation is for grating spectroscopy of 30 Ari, a late-type star with very high metallicity (about twice solar). The goal is to use extreme cases to help understand how abundances change from the photosphere to the corona. The target was obtained by XMM-Newton on 2001 January 16 for 28000 sec. Data processing could not proceed until last fall because the SAS RGS software did not work. A poster was presented at the conference 'New Visions of the X-ray Universe in the XMM-Newton and Chandra Era,' held in Noordwijk 26-30 November 2001. The paper was entitled,'Coronal Abundances and Thermal Structure of the Super-Metal-Rich Star 30 Ari,'. The poster presented analysis of EPIC and RGS data to determine the individual abundances from the star and the emission measure distribution as a function of temperature. Results were compared with previous results on this star by our team using ASCA data.

  10. Experimentally reducing species abundance indirectly affects food web structure and robustness.

    PubMed

    Barbosa, Milton; Fernandes, G Wilson; Lewis, Owen T; Morris, Rebecca J

    2017-03-01

    Studies on the robustness of ecological communities suggest that the loss or reduction in abundance of individual species can lead to secondary and cascading extinctions. However, most such studies have been simulation-based analyses of the effect of primary extinction on food web structure. In a field experiment we tested the direct and indirect effects of reducing the abundance of a common species, focusing on the diverse and self-contained assemblage of arthropods associated with an abundant Brazilian shrub, Baccharis dracunculifolia D.C. (Asteraceae). Over a 5-month period we experimentally reduced the abundance of Baccharopelma dracunculifoliae (Sternorrhyncha: Psyllidae), the commonest galling species associated with B. dracunculifolia, in 15 replicate plots paired with 15 control plots. We investigated direct effects of the manipulation on parasitoids attacking B. dracunculifoliae, as well as indirect effects (mediated via a third species or through the environment) on 10 other galler species and 50 associated parasitoid species. The experimental manipulation significantly increased parasitism on B. dracunculifoliae in the treatment plots, but did not significantly alter either the species richness or abundance of other galler species. Compared to control plots, food webs in manipulated plots had significantly lower values of weighted connectance, interaction evenness and robustness (measured as simulated tolerance to secondary extinction), even when B. dracunculifoliae was excluded from calculations. Parasitoid species were almost entirely specialized to individual galler species, so the observed effects of the manipulation on food web structure could not have propagated via the documented trophic links. Instead, they must have spread either through trophic links not included in the webs (e.g. shared predators) or non-trophically (e.g. through changes in habitat availability). Our results highlight that the inclusion of both trophic and non

  11. Familial identification: population structure and relationship distinguishability.

    PubMed

    Rohlfs, Rori V; Fullerton, Stephanie Malia; Weir, Bruce S

    2012-02-01

    With the expansion of offender/arrestee DNA profile databases, genetic forensic identification has become commonplace in the United States criminal justice system. Implementation of familial searching has been proposed to extend forensic identification to family members of individuals with profiles in offender/arrestee DNA databases. In familial searching, a partial genetic profile match between a database entrant and a crime scene sample is used to implicate genetic relatives of the database entrant as potential sources of the crime scene sample. In addition to concerns regarding civil liberties, familial searching poses unanswered statistical questions. In this study, we define confidence intervals on estimated likelihood ratios for familial identification. Using these confidence intervals, we consider familial searching in a structured population. We show that relatives and unrelated individuals from population samples with lower gene diversity over the loci considered are less distinguishable. We also consider cases where the most appropriate population sample for individuals considered is unknown. We find that as a less appropriate population sample, and thus allele frequency distribution, is assumed, relatives and unrelated individuals become more difficult to distinguish. In addition, we show that relationship distinguishability increases with the number of markers considered, but decreases for more distant genetic familial relationships. All of these results indicate that caution is warranted in the application of familial searching in structured populations, such as in the United States.

  12. Familial Identification: Population Structure and Relationship Distinguishability

    PubMed Central

    Rohlfs, Rori V.; Fullerton, Stephanie Malia; Weir, Bruce S.

    2012-01-01

    With the expansion of offender/arrestee DNA profile databases, genetic forensic identification has become commonplace in the United States criminal justice system. Implementation of familial searching has been proposed to extend forensic identification to family members of individuals with profiles in offender/arrestee DNA databases. In familial searching, a partial genetic profile match between a database entrant and a crime scene sample is used to implicate genetic relatives of the database entrant as potential sources of the crime scene sample. In addition to concerns regarding civil liberties, familial searching poses unanswered statistical questions. In this study, we define confidence intervals on estimated likelihood ratios for familial identification. Using these confidence intervals, we consider familial searching in a structured population. We show that relatives and unrelated individuals from population samples with lower gene diversity over the loci considered are less distinguishable. We also consider cases where the most appropriate population sample for individuals considered is unknown. We find that as a less appropriate population sample, and thus allele frequency distribution, is assumed, relatives and unrelated individuals become more difficult to distinguish. In addition, we show that relationship distinguishability increases with the number of markers considered, but decreases for more distant genetic familial relationships. All of these results indicate that caution is warranted in the application of familial searching in structured populations, such as in the United States. PMID:22346758

  13. Spatial population structure of Yellowstone bison

    USGS Publications Warehouse

    Olexa, E.M.; Gogan, P.J.P.

    2007-01-01

    Increases in Yellowstone National Park, USA, bison (Bison bison) numbers and shifts in seasonal distribution have resulted in more frequent movements of bison beyond park boundaries and development of an interagency management plan for the Yellowstone bison population. Implementation of the plan under the adaptive management paradigm requires an understanding of the spatial and temporal structure of the population. We used polythetic agglomerative hierarchical cluster analysis of radiolocations obtained from free-ranging bison to investigate seasonal movements and aggregations. We classified radiolocations into 4 periods: annual, peak rut (15 Jul-15 Sep), extended rut (1 Jun-31 Oct), and winter (1 Nov-31 May). We documented spatial separation of Yellowstone bison into 2 segments, the northern and central herds, during all periods. The estimated year-round exchange rate (4.85-5.83%) of instrumented bison varied with the fusion strategy employed. We did not observe exchange between the 2 segments during the peak rut and it varied during the extended rut (2.15-3.23%). We estimated a winter exchange of 4.85-7.77%. The outcome and effectiveness of management actions directed at Yellowstone bison may be affected by spatial segregation and herd affinity within the population. Reductions based on total population size, but not applied to the entire population, may adversely affect one herd while having little effect on the other. Similarly, management actions targeting a segment of the population may benefit from the spatial segregation exhibited.

  14. Reef-scale trends in Florida Acropora spp. abundance and the effects of population enhancement

    PubMed Central

    Kerr, Katryna; Williams, Dana E.

    2016-01-01

    Since the listing of Acropora palmata and A. cervicornis under the US Endangered Species Act in 2006, increasing investments have been made in propagation of listed corals (primarily A. cervicornis, A. palmata to a much lesser extent) in offshore coral nurseries and outplanting cultured fragments to reef habitats. This investment is superimposed over a spatiotemporal patchwork of ongoing disturbances (especially storms, thermal bleaching, and disease) as well as the potential for natural population recovery. In 2014 and 2015, we repeated broad scale (>50 ha), low precision Acropora spp. censuses (i.e., direct observation by snorkelers documented via handheld GPS) originally conducted in appropriate reef habitats during 2005–2007 to evaluate the trajectory of local populations and the effect of population enhancement. Over the decade-long study, A. palmata showed a cumulative proportional decline of 0.4 –0.7x in colony density across all sites, despite very low levels of outplanting at some sites. A. cervicornis showed similar proportional declines at sites without outplanting. In contrast, sites that received A. cervicornis outplants showed a dramatic increase in density (over 13x). Indeed, change in A. cervicornis colony density was significantly positively correlated with cumulative numbers of outplants across sites. This study documents a substantive reef-scale benefit of Acropora spp. population enhancement in the Florida Keys, when performed at adequate levels, against a backdrop of ongoing population decline. PMID:27703862

  15. Supportive breeding boosts natural population abundance with minimal negative impacts on fitness of a wild population of Chinook salmon

    PubMed Central

    Hess, Maureen A; Rabe, Craig D; Vogel, Jason L; Stephenson, Jeff J; Nelson, Doug D; Narum, Shawn R

    2012-01-01

    While supportive breeding programmes strive to minimize negative genetic impacts to populations, case studies have found evidence for reduced fitness of artificially produced individuals when they reproduce in the wild. Pedigrees of two complete generations were tracked with molecular markers to investigate differences in reproductive success (RS) of wild and hatchery-reared Chinook salmon spawning in the natural environment to address questions regarding the demographic and genetic impacts of supplementation to a natural population. Results show a demographic boost to the population from supplementation. On average, fish taken into the hatchery produced 4.7 times more adult offspring, and 1.3 times more adult grand-offspring than naturally reproducing fish. Of the wild and hatchery fish that successfully reproduced, we found no significant differences in RS between any comparisons, but hatchery-reared males typically had lower RS values than wild males. Mean relative reproductive success (RRS) for hatchery F1 females and males was 1.11 (P = 0.84) and 0.89 (P = 0.56), respectively. RRS of hatchery-reared fish (H) that mated in the wild with either hatchery or wild-origin (W) fish was generally equivalent to W × W matings. Mean RRS of H × W and H × H matings was 1.07 (P = 0.92) and 0.94 (P = 0.95), respectively. We conclude that fish chosen for hatchery rearing did not have a detectable negative impact on the fitness of wild fish by mating with them for a single generation. Results suggest that supplementation following similar management practices (e.g. 100% local, wild-origin brood stock) can successfully boost population size with minimal impacts on the fitness of salmon in the wild. PMID:23025818

  16. Global Patterns of Abundance, Diversity and Community Structure of the Aminicenantes (Candidate Phylum OP8)

    PubMed Central

    Farag, Ibrahim F.; Davis, James P.; Youssef, Noha H.; Elshahed, Mostafa S.

    2014-01-01

    We investigated the global patterns of abundance, diversity, and community structure of members of the Aminicenantes (candidate phylum OP8). Our aim was to identify the putative ecological role(s) played by members of this poorly characterized bacterial lineages in various ecosystems. Analysis of near full-length 16S rRNA genes identified four classes and eight orders within the Aminicenantes. Within 3,134 datasets comprising ∼1.8 billion high throughput-generated partial 16S rRNA genes, 47,351 Aminicenantes-affiliated sequences were identified in 913 datasets. The Aminicenantes exhibited the highest relative abundance in hydrocarbon-impacted environments, followed by marine habitats (especially hydrothermal vents and coral-associated microbiome samples), and aquatic, non-marine habitats (especially in terrestrial springs and groundwater samples). While the overall abundance of the Aminicenantes was higher in low oxygen tension as well as non-saline and low salinity habitats, it was encountered in a wide range of oxygen tension, salinities, and temperatures. Analysis of the community structure of the Aminicenantes showed distinct patterns across various datasets that appear to be, mostly, driven by habitat variations rather than prevalent environmental parameters. We argue that the detection of the Aminicenantes across environmental extremes and the observed distinct community structure patterns reflect a high level of intraphylum metabolic diversity and adaptive capabilities that enable its survival and growth in a wide range of habitats and environmental conditions. PMID:24637619

  17. Community structure, abundance, and activity of methanotrophs in the Zoige wetland of the Tibetan Plateau.

    PubMed

    Yun, Juanli; Zhuang, Guoqiang; Ma, Anzhou; Guo, Hongguang; Wang, Yanfen; Zhang, Hongxun

    2012-05-01

    The Zoige wetland of the Tibetan Plateau is a high-altitude tundra wetland and one of the biggest methane emission centers in China. In this study, methanotrophs with respect to community structure, abundance, and activity were investigated in peat soils collected in the vicinity of different marshland plants that dominate different regions of the wetland, including Polygonum amphibium, Carex muliensis, and Eleocharis valleculosa (EV). 16S rRNA gene and particulate methane monooxygenase gene (pmoA) clone library sequence data indicated the presence of methanotrophs with two genera, Methylobacter and Methylocystis. Methylococcus, like pmoA gene sequences, were also retrieved and showed low similarity to those from Methylococcus spp. and thus indicates the existence of novel methanotrophs in the Zoige wetland. Quantitative polymerase chain reaction (qPCR) assays were used to measure the abundance of methantrophs and detected 10(7) to 10(8) of total pmoA gene copies per gram dry weight of soil in the three marshes. Group-specific qPCR and reverse transcriptase qPCR results found that the Methylobacter genus dominates the wetland, and Methylocystis methanotrophs were less abundant, although this group of methanotrophs was estimated to be more active according to mRNA/DNA ratio. Furthermore, EV marsh demonstrated the highest methanotrophs abundance and activity among the three marshes investigated. Our study suggests that both type I and type II methanotrophs contribute to the methane oxidation in the Zoige wetland.

  18. Natural selection and age-structured populations.

    PubMed

    Demetrius, L

    1975-03-01

    This paper studies the properties of a new class of demographic parameters for age-structured populations and analyzes the effect of natural selection on these parameters. Two new demographic variables are introduced: the entropy of a population and the reproductive potential. The entropy of a population measures the variability of the contribution of the different age classes to the stationary population. The reproductive potential measures the mean of the contribution of the different age classes to the Malthusian parameter. The Malthusian parameter is precisely the difference between the entropy and the reproductive potential. The effect of these demographic variables on changes in gene frequency is discussed. The concept of entropy of a genotype is introduced and it is shown that in a random mating population in Hardy-Weinberg equilibrium and under slow selection, the rate of change of entropy is equal to the genetic variance in entropy minus the covariance in entropy and reproductive potential. This result is an information theoretic analog of Fisher's fundamental theorem of natural selection.

  19. Resource competition in stage-structured populations.

    PubMed

    Revilla, T A

    2000-05-21

    Two models are made to account for the dynamics of a consumer-resource system in which the consumers are divided into juveniles and adults. The resource grows logistically and a type II functional response is assumed for consumers. Resource levels determine fecundity and maturation rates in one model, and mortality rates in the other. The analysis of the models shows that the condition for establishment of consumers is that the product of per capita fecundity rate and maturation rates is higher than the product of juvenile and adult per capita decay rates at a resource level equal to its carrying capacity. This result imposes a minimal abundance of resource able to maintain the consumers. A second result shows an equilibrium stage structure, with a small instability when juveniles and adults mean saturation constants are different. The implications of these results for community dynamics are discussed.

  20. Linking CAI abundance to polarimetric response in a population of ancient asteroids

    NASA Astrophysics Data System (ADS)

    Devogele, Maxime; Tanga, Paolo; Bendjoya, Philippe; Rivet, Jean-Pierre; Surdej, Jean; Bus, Schelte J.; Sunshine, Jessica M.; Cellino, Alberto; Campins, Humberto; Licandro, Javier; Pinilla-Alonso, Noemi; Carry, Benoit

    2016-10-01

    Polarimetry constitutes one of the fundamental tools for characterizing the surface texture and composition of airless Solar System bodies. In 2006, polarimetric observations led to the discovery of a new type of asteroids, which displays a peculiar polarimetric response. These asteroids are collectively known as "Barbarians", from (234) Barbara the first discovered one.The most commonly accepted explanation for this perculiar polarization response seems to be the presence of a high percentage of fluffy-type Calcium Aluminium-rich Inclusions (CAIs), whose optical properties could produce the observed polarization. Their reflectance spectra also exibit an absorption feature in the near-infrared around 2.1-2.2 microns, that is characteristic of this peculiar group.Based on these results, we organized a systematic polarimetric and near-infrared observational campaign of known Barbarians or candidate asteroids. These campaigns include members of the family of 1040 Klumpkea, 2085 Henan and 729 Watsonia, which are known to contain Barbarian and/or L-type asteroids also suspected to have such a polarimetric behaviour. We have made use of the ToPo polarimeter at the 1m telescope of the Centre pédagogique Planète et Univers (C2PU, Observatoire de la Côte d'Azur, France). The spectroscopic observations in the near-infrared were obtained with the SpeX instrument at the NASA's InfraRed Telescope Facility (IRTF).By combining polarimetry and spectroscopy we find a correlation between the abundance of CAIs and the inversion angle of the phase-polarization curve of Barbarian asteroids. This is the first time that a direct link has been established between a specific polarimetric response and the surface composition of asteroids. In addition, we find a considerable variety of CAI abundance from one object to the other, consistent with a wide range of possible albedos. Since these asteroids constitute a reservoir of primitive Solar System material, understanding their origin can

  1. Behavior and population structure of Anopheles darlingi in Colombia.

    PubMed

    Naranjo-Díaz, Nelson; Conn, Jan E; Correa, Margarita M

    2016-04-01

    Anopheles darlingi is a widely distributed and important malaria vector in Colombia. Biogeographical and ecological heterogeneity across the Colombian distribution led to the hypothesis of behavioral and genetic differentiation among A. darlingi populations. A total of 2017 A. darlingi specimens were collected during 222 h of sampling. This vector was the most abundant anopheline species in most of the localities sampled. Subdivision between samples collected west and east of the Andes was indicated by 1) mitochondrial COI and nuclear CAD sequences from NW-W and CE-S populations (COI ΦST=0.48761-0.81974, CAD FST=0.11319-0.21321), 2) a COI haplotype network, and 3) SAMOVA. Endo- and exophagy were detected in populations west of the Andes, whereas exophagy was evident in PTG, a locality east of the Andes. Isolation by resistance was significant for COI and explained 26% of the genetic differentiation. We suggest that at a macrogeographic scale, the Andes influence the differentiation of A. darlingi in Colombia and may drive divergence, and, at a microgeographic scale, ecological differences have a significant impact on structure. These data could constitute a baseline for the design of effective vector interventions, locality-specific for the east and similar for panmictic populations west of the Andes.

  2. Distribution and abundance of fish populations in Harike wetland--a Ramsar site in India.

    PubMed

    Dua, Anish; Parkash, Chander

    2009-03-01

    Harike wetland was declared a Ramsar site in 1990. It is located at the confluence of two major rivers of Indus rivers system, the Beas and the Sutlej, but was never explored extensively for its existing fish biodiversity. Earlier only 27 fish species of commercial value were reported from the wetland. Acknowledging its importance for rich diversity fish assemblages in seven different reaches of Harike wetland were studied to determine their abundance and distribution. 61 fish species of 35 genera were recorded from Harike wetland during the present study. Cirrihinus mrigala and Cyprinus carpio belonging to family Cyprinidae were the dominant fish species. Lake and Riyasat having many microhabitats supported highest diversity of fishes (60 and 56 respectively) followed by Beas (20) Sutlej (14), Confluence (12), Reservoir (9) and Downstream (8). Among the IUCN designated threatened species, 1 Critically Endangered, 4 Endangered and 13 Vulnerable fish species of India are found in Harike wetland. Species diversity index, dominance, evenness and catch per unit effort were calculated to ascertain the fish distribution in Harike wetland.

  3. Chemical Abundances in the Stellar Populations of the Leo I and Leo II dSph Galaxies

    NASA Astrophysics Data System (ADS)

    Bosler, T. L.; Smecker-Hane, T. A.; Stetson, P. B.

    2002-05-01

    Our goal is to map the chemical abundance distribution of the stellar populations of the Leo I and Leo II dwarf spheroidal (dSph) galaxies to constrain the physical processes that regulate their evolution. The dSphs are particularly interesting galaxies because their star formation histories (SFHs) appear to be much more complicated than theory would predict for such low mass, low luminosity, low surface-brightness galaxies. Color-magnitude diagrams (CMDs) of these dSphs have shown that they formed stars over many Gyr. In order to understand the true spread in stellar ages and chemical abundances we need more precise abundance indicators than can be inferred from CMD analysis: abundances based upon the broad-band colors of red giants are subject to large systematic errors because of limitations in convection theory, and poorly determined color--effective temperature relations produce sizable uncertainties in the derived shapes of theoretical red giant branches. Therefore we are measuring the abundance distribution of the Leo I and Leo II dSphs from spectroscopy of individual red giant stars using the Ca II absorption lines in the near infrared (8498, 8542, and 8662 Å). Our observations are made on the Keck I 10-meter Telescope using the Low Resolution Imaging Spectrometer. One night of successful observations yielded spectra of approximately 40 stars in each dSph from which abundances with random uncertainties of ≈ 0.1 dex will be derived. Calibration of the Ca II strengths to [Fe/H] has been done by Rutledge, et al. (1997, PASP, 109, 907) using Galactic globular clusters. We are also deriving a new calibration for [Ca/H]. This new calibration will remove the dependence on SFH built into the Rutledge, et al. calibration, i.e., the assumptions of a unique age for the system and a Galactic [Ca/Fe]--[Fe/H] relationship. Financial support for this project was provided by NSF grant AST-0070985 to TSH, and an ARCS Foundation fellowship to TB.

  4. Biotic Stress Shifted Structure and Abundance of Enterobacteriaceae in the Lettuce Microbiome

    PubMed Central

    Erlacher, Armin; Cardinale, Massimiliano; Grube, Martin; Berg, Gabriele

    2015-01-01

    Lettuce cultivars are not only amongst the most popular vegetables eaten raw, they are also involved in severe pathogen outbreaks world-wide. While outbreaks caused by Enterobacteriaceae species are well-studied, less is known about their occurrence in natural environments as well as the impact of biotic stress. Here, we studied the ecology of the human health-relevant bacterial family Enterobacteriaceae and assessed the impact of biotic disturbances by a soil-borne phytopathogenic fungus and Gastropoda on their structure and abundance in mesocosm and pot experiments. Using a polyphasic approach including network analyses of 16S rRNA gene amplicon libraries, quantitative PCR and complementary fluorescence in situ hybridization (FISH) microscopy we found substantial yet divergent Enterobacteriaceae communities. A similar spectrum of 14 genera was identified from rhizo- and phyllospheres but the abundance of Enterobacteriaceae was on average 3fold higher in phyllosphere samples. Both stress factors shifted the bacterial community of the leaf habitat, characterized by increases of species abundance and diversity. For the rhizosphere, we observed significant structural shifts of Enterobacteriaceae communities but also a high degree of resilience. These results could be confirmed by FISH microscopy but it was difficult to visualize phyllosphere communities. Additional inoculation experiments with Escherichia coli as model revealed their presence below the wax layer as well as in the endosphere of leaves. The observed presence influenced by stress factors and the endophytic life style of Enterobacteriaceae on lettuce can be an important aspect in relation to human health. PMID:25714833

  5. Physiological tolerances account for range limits and abundance structure in an invasive slug

    PubMed Central

    Lee, Jennifer E.; Janion, Charlene; Marais, Elrike; Jansen van Vuuren, Bettine; Chown, Steven L.

    2009-01-01

    Despite the importance of understanding the mechanisms underlying range limits and abundance structure, few studies have sought to do so. Here we use a terrestrial slug species, Deroceras panormitanum, that has invaded a remote, largely predator-free, Southern Ocean island as a model system to do so. Across Marion Island, slug density does not conform to an abundant centre distribution. Rather, abundance structure is characterized by patches and gaps. These are associated with this desiccation-sensitive species' preference for biotic and drainage line habitats that share few characteristics except for their high humidity below the vegetation surface. The coastal range margin has a threshold form, rapidly rising from zero to high density. Slugs do not occur where soil-exchangeable Na values are higher than 3000 mg kg−1, and in laboratory experiments, survival is high below this value but negligible above it. Upper elevation range margins are a function of the inability of this species to survive temperatures below an absolute limit of −6.4°C, which is regularly exceeded at 200 m altitude, above which slug density declines to zero. However, the linear decline in density from the coastal peak is probably also a function of a decline in performance or time available for activity. This is probably associated with an altitudinal decline in mean annual soil temperature. These findings support previous predictions made regarding the form of density change when substrate or climatic factors set range limits. PMID:19324817

  6. Population Dynamics of Aphthona whitfieldi (Coleoptera: Chrysomelidae), Pest of Jatropha curcas, and Environmental Factors Favoring Its Abundance in Burkina Faso

    PubMed Central

    Sawadogo, Alizèta; Nagalo, Estérer; Nacro, Souleymane; Rouamba, Mathurin; Kenis, Marc

    2015-01-01

    The flea beetle Aphthona whitfieldi Bryant (Coleoptera: Chrysomelidae) is the main pest of the bioenergy crop Jatropha curcas L. (Euphorbiaceae) in Burkina Faso and several other West African countries. Adults severely defoliate plants, resulting in seedling mortality, poor growth, and low yields. To study the population dynamics of the pest in the Sissili Province of Burkina Faso, 12 sites were monitored weekly during a year and 31 sites were inspected for damage at the peak period of insect abundance. The effect of cropping systems (hedge, intercropping, and monoculture) and surrounding vegetation on population densities of A. whitfieldi was assessed. Beetles were rarely found in the dry season and peaked in the second half of the rainy season. The cropping system did not significantly influence the abundance and attack level. In contrast, the close vicinity of fallow lands seems to increase damage levels. Many aspects of the biology and ecology of A. whitfieldi remain to be investigated before sustainable control methods can be developed. However, this study already allows us to propose recommendations for further research on management. PMID:26206896

  7. Responses of infaunal populations to benthoscape structure and the potential importance of transition zones

    USGS Publications Warehouse

    Zajac, R.N.; Lewis, R.S.; Poppe, L.J.; Twichell, D.C.; Vozarik, J.; DiGiacomo-Cohen, M. L.

    2003-01-01

    Relationships between population abundance and seafloor landscape, or benthoscape, structure were examined for 16 infaunal taxa in eastern Long Island Sound. Based on analyses of a side-scan sonar mosaic, the 19.4-km2 study area was comprised of six distinct large-scale (> km2) benthoscape elements, with varying levels of mesoscale (km2-m2) and small-scale (2) physical and biological habitat heterogeneity. Transition zones among elements varied from ~50 to 200 m in width, comprised ~32% of the benthoscape, and added to overall benthoscape heterogeneity. Population abundances of nine taxa varied significantly among the large-scale elements. Most species were found at high abundances only in one benthoscape element, but three had several foci of elevated abundances. Analyses of population responses to habitat heterogeneity at different spatial scales indicated that abundances of eight taxa varied significantly among spatial scales, but the significant scales were mixed among these species. Relatively large residual variations suggest significant amounts of mesoscale spatial variation were unaccounted for, varying from ~1 km2 to several m2. Responses to transition zones were mixed as well. Abundances of nine taxa varied significantly among transition zones and interiors of benthoscape elements, most with elevated abundances in transition zones. Our results show that infaunal populations exhibit complex and spatially varying patterns of abundance in relation to benthoscape structure and suggest that mesoscale variation may be particularly critical in this regard. Also, transition zones among benthoscape features add considerably to this variation and may be ecological important areas in seafloor environments.

  8. Verrucomicrobial community structure and abundance as indicators for changes in chemical factors linked to soil fertility.

    PubMed

    Navarrete, Acacio Aparecido; Soares, Tielle; Rossetto, Raffaella; van Veen, Johannes Antonie; Tsai, Siu Mui; Kuramae, Eiko Eurya

    2015-09-01

    Here we show that verrucomicrobial community structure and abundance are extremely sensitive to changes in chemical factors linked to soil fertility. Terminal restriction fragment length polymorphism fingerprint and real-time quantitative PCR assay were used to analyze changes in verrucomicrobial communities associated with contrasting soil nutrient conditions in tropical regions. In case study Model I ("Slash-and-burn deforestation") the verrucomicrobial community structures revealed disparate patterns in nutrient-enriched soils after slash-and-burn deforestation and natural nutrient-poor soils under an adjacent primary forest in the Amazonia (R = 0.819, P = 0.002). The relative proportion of Verrucomicrobia declined in response to increased soil fertility after slash-and-burn deforestation, accounting on average, for 4 and 2 % of the total bacterial signal, in natural nutrient-poor forest soils and nutrient-enriched deforested soils, respectively. In case study Model II ("Management practices for sugarcane") disparate patterns were revealed in sugarcane rhizosphere sampled on optimal and deficient soil fertility for sugarcane (R = 0.786, P = 0.002). Verrucomicrobial community abundance in sugarcane rhizosphere was negatively correlated with soil fertility, accounting for 2 and 5 % of the total bacterial signal, under optimal and deficient soil fertility conditions for sugarcane, respectively. In nutrient-enriched soils, verrucomicrobial community structures were related to soil factors linked to soil fertility, such as total nitrogen, phosphorus, potassium and sum of bases, i.e., the sum of calcium, magnesium and potassium contents. We conclude that community structure and abundance represent important ecological aspects in soil verrucomicrobial communities for tracking the changes in chemical factors linked to soil fertility under tropical environmental conditions.

  9. Exoplanet population inference and the abundance of Earth analogs from noisy, incomplete catalogs

    SciTech Connect

    Foreman-Mackey, Daniel; Hogg, David W.; Morton, Timothy D.

    2014-11-01

    No true extrasolar Earth analog is known. Hundreds of planets have been found around Sun-like stars that are either Earth-sized but on shorter periods, or else on year-long orbits but somewhat larger. Under strong assumptions, exoplanet catalogs have been used to make an extrapolated estimate of the rate at which Sun-like stars host Earth analogs. These studies are complicated by the fact that every catalog is censored by non-trivial selection effects and detection efficiencies, and every property (period, radius, etc.) is measured noisily. Here we present a general hierarchical probabilistic framework for making justified inferences about the population of exoplanets, taking into account survey completeness and, for the first time, observational uncertainties. We are able to make fewer assumptions about the distribution than previous studies; we only require that the occurrence rate density be a smooth function of period and radius (employing a Gaussian process). By applying our method to synthetic catalogs, we demonstrate that it produces more accurate estimates of the whole population than standard procedures based on weighting by inverse detection efficiency. We apply the method to an existing catalog of small planet candidates around G dwarf stars. We confirm a previous result that the radius distribution changes slope near Earth's radius. We find that the rate density of Earth analogs is about 0.02 (per star per natural logarithmic bin in period and radius) with large uncertainty. This number is much smaller than previous estimates made with the same data but stronger assumptions.

  10. Being abundant is not enough: a decrease in effective population size over eight generations in a Norwegian population of the seaweed, Fucus serratus.

    PubMed

    Coyer, James A; Hoarau, Galice; Sjøtun, Kjersti; Olsen, Jeanine L

    2008-12-23

    The brown alga Fucus serratus is a key foundation species on rocky intertidal shores of northern Europe. We sampled the same population off the coast of southern Norway in 2000 and 2008, and using 26 microsatellite loci, we estimated the changes in genetic diversity and effective population size (Ne). The unexpectedly low Ne (73-386) and Ne/N ratio (10-3-10-4), in combination with a significant decrease (14%) in allelic richness over the 8-year period, suggests an increased local extinction risk. If small Ne proves to be a common feature of F. serratus, then being abundant may not be enough for the species to weather future environmental changes.

  11. Magnetic Doppler imaging considering atmospheric structure modifications due to local abundances: a luxury or a necessity?

    NASA Astrophysics Data System (ADS)

    Kochukhov, O.; Wade, G. A.; Shulyak, D.

    2012-04-01

    Magnetic Doppler imaging is currently the most powerful method of interpreting high-resolution spectropolarimetric observations of stars. This technique has provided the very first maps of stellar magnetic field topologies reconstructed from time series of full Stokes vector spectra, revealing the presence of small-scale magnetic fields on the surfaces of Ap stars. These studies were recently criticised by Stift et al., who claimed that magnetic inversions are not robust and are seriously undermined by neglecting a feedback on the Stokes line profiles from the local atmospheric structure in the regions of enhanced metal abundance. We show that Stift et al. misinterpreted published magnetic Doppler imaging results and consistently neglected some of the most fundamental principles behind magnetic mapping. Using state-of-the-art opacity sampling model atmosphere and polarized radiative transfer codes, we demonstrate that the variation of atmospheric structure across the surface of a star with chemical spots affects the local continuum intensity but is negligible for the normalized local Stokes profiles except for the rare situation of a very strong line in an extremely Fe-rich atmosphere. For the disc-integrated spectra of an Ap star with extreme abundance variations, we find that the assumption of a mean model atmosphere leads to moderate errors in Stokes I but is negligible for the circular and linear polarization spectra. Employing a new magnetic inversion code, which incorporates the horizontal variation of atmospheric structure induced by chemical spots, we reconstructed new maps of magnetic field and Fe abundance for the bright Ap star α2 CVn. The resulting distribution of chemical spots changes insignificantly compared to the previous modelling based on a single model atmosphere, while the magnetic field geometry does not change at all. This shows that the assertions by Stift et al. are exaggerated as a consequence of unreasonable assumptions and

  12. Effects of ocean acidification on population dynamics and community structure of crustose coralline algae.

    PubMed

    Ordoñez, Alexandra; Doropoulos, Christopher; Diaz-Pulido, Guillermo

    2014-06-01

    Calcification and growth of crustose coralline algae (CCA) are affected by elevated seawater pCO2 and associated changes in carbonate chemistry. However, the effects of ocean acidification (OA) on population and community-level responses of CCA have barely been investigated. We explored changes in community structure and population dynamics (size structure and reproduction) of CCA in response to OA. Recruited from an experimental flow-through system, CCA settled onto the walls of plastic aquaria and developed under exposure to one of three pCO2 treatments (control [present day, 389±6 ppm CO2], medium [753±11 ppm], and high [1267±19 ppm]). Elevated pCO2 reduced total CCA abundance and affected community structure, in particular the density of the dominant species Pneophyllum sp. and Porolithon onkodes. Meanwhile, the relative abundance of P. onkodes declined from 24% under control CO2 to 8.3% in high CO2 (65% change), while the relative abundance of Pneophyllum sp. remained constant. Population size structure of P. onkodes differed significantly across treatments, with fewer larger individuals under high CO2. In contrast, the population size structure and number of reproductive structures (conceptacles) per crust of Pneophyllum sp. was similar across treatments. The difference in the magnitude of the response of species abundance and population size structure between species may have the potential to induce species composition changes in the future. These results demonstrate that the impacts of OA on key coral reef builders go beyond declines in calcification and growth, and suggest important changes to aspects of population dynamics and community ecology.

  13. Elemental abundance and spectral variations of the suprathermal heavy ion populations in interplanetary space

    NASA Astrophysics Data System (ADS)

    Al Dayeh, Maher Abdul Hamid

    Solar energetic particles (SEPs) associated with coronal mass ejections (CMEs) are usually accompanied by large particle intensities and magnetic clouds that often cause terrestrial geomagnetic storms. These storms present a danger to many aspects on earth, from satellites and communications, to power and pipelines, in addition to forming a danger to astronauts in space. The scientific objectives for studying SEPs in this dissertation are twofold. First is to improve our understanding of SEP sources, acceleration, and propagation in interplanetary (IP) space. The second is to improve our capabilities in space weather prediction. This dissertation investigates the source material of SEPs through detailed analysis of the temporal, compositional, and spectral variations of heavy ion species (mass > 4 nucleons) at the energy range ~0.045 MeV/nuc -10 MeV/nuc from December 1995 to December 2006, thus covering all of solar cycle 23. Data used in this dissertation are mainly from ULEIS and STEP time-of-flight mass spectrometers onboard the ACE (launched 08/1997) and Wind (launched 11/1994) spacecraft respectively. Observations reported in this work show that daily variations of low-energy heavy ions (~0.12 MeV/nucleon) in IP space are correlated with the solar cycle. Such dependence is not seen in a set of gradual SEP events. However, these events show large event-to-event fluctuations. This suggests that there exist multiple scenarios by which the seed material is injected into accelerating IP shocks, these are: (i) remnant material from previous flares that remain in IP space or get continuously replenished by frequent flare activity; (ii) direct contributions from accompanying flares, i.e., particles that escape from the flare through open field lines could encounter the CME shock, get re- accelerated and cause an enhancement in the heavy-ion abundances; (iii) the same or nearby active regions on the Sun produce suprathermal particles with flare-like composition that

  14. Time-dependent effect of graphene on the structure, abundance, and function of the soil bacterial community.

    PubMed

    Ren, Wenjie; Ren, Gaidi; Teng, Ying; Li, Zhengao; Li, Lina

    2015-10-30

    The increased application of graphene raises concerns about its environmental impact, but little information is available on the effect of graphene on the soil microbial community. This study evaluated the impact of graphene on the structure, abundance and function of the soil bacterial community based on quantitative real-time polymerase chain reaction (qPCR), pyrosequencing and soil enzyme activities. The results show that the enzyme activities of dehydrogenase and fluorescein diacetate (FDA) esterase and the biomass of the bacterial populations were transiently promoted by the presence of graphene after 4 days of exposure, but these parameters recovered completely after 21 days. Pyrosequencing analysis suggested a significant shift in some bacterial populations after 4 days, and the shift became weaker or disappeared as the exposure time increased to 60 days. During the entire exposure process, the majority of bacterial phylotypes remained unaffected. Some bacterial populations involved in nitrogen biogeochemical cycles and the degradation of organic compounds can be affected by the presence of graphene.

  15. Hungaria Asteroid Region Telescopic Spectral Survey (HARTSS): Stony Asteroids Abundant in the Background and Family Populations

    NASA Astrophysics Data System (ADS)

    Lucas, Michael P.; Emery, Joshua P.; Pinilla-Alonso, Noemi; Lindsay, Sean S.; Lorenzi, Vania

    2016-10-01

    The Hungaria region represents a "purgatory" for the closest, preserved samples of the material from which the terrestrial planets accreted. The Hungaria region harbors a collisional family of Xe-type asteroids, which are situated among a background of predominantly S-complex asteroids. Deciphering their surface composition may provide constraints on the nature of the primordial building blocks of the terrestrial planets. We hypothesize that planetesimals in the inner part of the primordial asteroid belt experienced partial- to full-melting and differentiation, the Hungaria region should retain any petrologically-evolved material that formed there.We have undertaken an observational campaign entitled the Hungaria Asteroid Region Telescopic Spectral Survey (HARTSS) to record near-infrared (NIR) spectra to characterize taxonomy, surface mineralogy, and potential meteorite analogs. We used NIR instruments at two ground-based facilities (NASA IRTF; TNG). Our data set includes spectra of 82 Hungaria asteroids (61 background; 21 family), 65 were observed during HARTSS. We compare S-complex background asteroids to calibrations developed via laboratory analyses of ordinary chondrites, and to our analyses (EPMA, XRD, VIS+NIR spectra) of 11 primitive achondrite (acapulcoite-lodranite clan) meteorites.We find that stony S-complex asteroids dominate the Hungaria background population (~80%). Background objects exhibit considerable spectral diversity, when quantified by spectral band parameter measurements, translates to a variety of surface compositions. Two main meteorite groups are represented within the Hungaria background: unmelted, nebular L chondrites (and/or L chondrites), and partially-melted primitive achondrites. H-chondrite mineralogies appear to be absent from the Hungaria background. Xe-type Hungaria family members exhibit spectral homogeneity, consistent with the hypothesis that the family was derived from the disruption of a parent body analogous to an enstatite

  16. Divergent patterns of abundance and age-class structure of headwater stream tadpoles in burned and unburned watersheds

    USGS Publications Warehouse

    Hossack, B.R.; Corn, P.S.; Fagre, D.B.

    2006-01-01

    Wildfire is a potential threat to many species with narrow environmental tolerances like the Rocky Mountain tailed frog (Ascaphus montanus Mittleman and Myers, 1949), which inhabits a region where the frequency and intensity of wildfires are expected to increase. We compared pre- and post-fire counts of tadpoles in eight streams in northwestern Montana to determine the effects of wildfire on A. montanus. All streams were initially sampled in 2001, 2 years before four of them burned in a large wildfire, and were resampled during the 2 years following the fire. Counts of tadpoles were similar in the two groups of streams before the fire. After the fire, tadpoles were almost twice as abundant in unburned streams than in burned streams. The fire seemed to have the greatest negative effect on abundance of age-1 tadpoles, which was reflected in the greater variation in same-stream age-class structure compared with those in unburned streams. Despite the apparent effect on tadpoles, we do not expect the wildfire to be an extirpation threat to populations in the streams that we sampled. Studies spanning a chronosequence of fires, as well as in other areas, are needed to assess the effects of fires on streams with A. montanus and to determine the severity and persistence of these effects.

  17. Linking genetic diversity and temporal fluctuations in population abundance of the introduced feral cat (Felis silvestris catus) on the Kerguelen archipelago.

    PubMed

    Devillard, S; Santin-Janin, H; Say, L; Pontier, D

    2011-12-01

    Linking temporal variations of genetic diversity, including allelic richness and heterozygosity, and spatio-temporal fluctuations in population abundance has emerged as an important tool for understanding demographic and evolutionary processes in natural populations. This so-called genetic monitoring was conducted across 12 consecutive years (1996-2007) at three sites for the feral cat, introduced onto the Kerguelen archipelago fifty years ago. Temporal changes in allelic richness and heterozygosity at 18 microsatellite DNA loci were compared with temporal changes in the adult population abundance index, obtained by typical demographic monitoring. No association was found at the island spatial scale, but we observed an association between genetic diversity and adult population indices from year to year within each study site. More particularly, the magnitude of successive increases or decreases in the adult population abundance index appeared to be the major factor linking the trajectories of genetic diversity and adult population abundance indices. Natal dispersal and/or local recruitment, both facilitated by high juvenile survival when the adult population size is small, is proposed as the major demographic processes contributing to such an observed pattern. Finally, we suggested avoiding the use of the harmonic mean as an estimator of long-term population size to study the relationships between demographic fluctuations and heterozygosity in populations characterized by strong multiannual density fluctuations.

  18. The Gaia-ESO Spectroscopic Survey: CNO abundances in giants of the multiple-population globular cluster NGC 1851

    NASA Astrophysics Data System (ADS)

    Tautvaisiene, Grazina; Drazdauskas, Arnas; Lardo, Carmela; Martell, Sarah; Pancino, Elena; Stonkute, Edita

    2015-08-01

    It has been suspected already more than thirty year ago that NGC 1851 is not chemically homogeneous. By now, it is clear that NGC 1851 has two distinct subgiant branches, however explanations of their origin so far lack consensus. Some authors explain them by two generations of stars, the first being primordial, while the second one being born from the ejecta of a fraction of the stars of the earlier one. There are suggestions that NGC 1851 might be the result of a merger of two globular clusters, or originated as the nucleus of a dwarf galaxy that was captured by the Milky Way. In this presentation, we provide a crucial missing information on CNO abundances determined in a homogeneous way for a large sample of NGC 1851 giants. High-resolution spectra were obtained with the VLT UVES spectrograph in a framework of the Gaia-ESO Survey. From the investigated stars we clearly see that the two NGC 1851 populations have by about 0.2 dex difference in metallicity, the sums of C+O+N differ by about 0.1 dex, the mean C/N ratio values differ by about 0.5 dex, chemical elements that are insensitive to internal stellar mixing show normal Galactic abundances of the corresponding metallicities. This leads us to the conclusion that NGC 1851 is a binary cluster. We provide interpretations of these and other results of the study.

  19. An evaluation of the effectiveness of a commercial mechanical trap to reduce abundance of adult nuisance mosquito populations.

    PubMed

    Jackson, Michael J; Gow, Jennifer L; Evelyn, Michelle J; McMahon, T J Scott; Howay, Tim J; Campbell, Harlan; Blancard, Jennifer; Thielman, Aynsley

    2012-12-01

    In this study, we explore the potential of a commercially available mechanical mosquito control device, the Liberty Plus Mosquito Magnet (hereafter referred to as Mosquito Magnet), to reduce the abundance of adult nuisance mosquito populations in public recreational areas. Mosquitoes were trapped on 2 replicate sites close to a campground at Brae Island Regional Park near Fort Langley, British Columbia, Canada. Each site comprised a treatment (Mosquito Magnets used) and control subsection (Mosquito Magnets not used). Mosquito numbers were assessed before and after the treatment period in both subsections at each site with Centers for Disease Control and Prevention (CDC) black light traps. Although nearly 200,000 mosquitoes from 14 different species were collected over 366 trap-nights from May 31 to July 31, 2008, the majority of those identified were Aedes sticticus (68%) and Ae. vexans (22%)-2 of the most notorious nuisance mosquito species in British Columbia. The number of mosquitoes captured by CDC black light traps increased overall during the study period due to natural seasonal variation. Nevertheless, a significant treatment effect (P = 0.0389) was associated with an average decrease of about 32% in the average number of adult mosquitoes collected per day. These results strongly suggest that Mosquito Magnets can reduce the abundance of nuisance mosquitoes, potentially reducing the biting pressure on the public, and providing another tool in mosquito control operations.

  20. Mesh size effects on assessments of planktonic hydrozoan abundance and assemblage structure

    NASA Astrophysics Data System (ADS)

    Nogueira Júnior, Miodeli; Pukanski, Luis Eduardo de M.; Souza-Conceição, José M.

    2015-04-01

    The choice of appropriate mesh-size is paramount to accurately quantify planktonic assemblages, however there is no such information available for hydrozoans. Here planktonic hydrozoan abundance and assemblage structure were compared using 200 and 500 μm meshes at Babitonga estuary (S Brazil), throughout a year cycle. Species richness and Shannon-Wiener diversity were higher in the 200 μm mesh, while evenness was typically higher in the 500 μm. Assemblage structure was significantly different between meshes (PERMANOVA, P < 0.05; n = 72 pairs of samples) both regarding taxa and size composition. These discrepancies are due to significant underestimation of small hydromedusae by the coarse mesh, like Obelia spp., young Liriope tetraphylla, Podocoryna loyola and others. Yet, larger taxa like Eucheilota maculata and adult L. tetraphylla were more abundant in the coarse mesh on some occasions and others such as Blackfordia virginica and Muggiaea kochi were similarly represented in both meshes. Overall collection efficiency of the coarse mesh (CE500) was 14.4%, with monthly averages between 1.6% and 43.0%, in July (winter) and January (summer) respectively. Differences between the meshes were size-dependent; CE500 was ~ 0.3% for hydrozoans sizing < 0.5 mm, ~ 21% for those between 1 and 2 mm, ~ 56% for those between 2 and 4 mm, and nearly 100% for larger ones, reaching up to 312% for hydrozoans > 8 mm in October. These results suggest that both meshes have their drawbacks and the best choice would depend on the objectives of each study. Nevertheless species richness, total abundances and most taxa were better represented by the 200 μm mesh, suggesting that it is more appropriate to quantitatively sample planktonic hydrozoan assemblages.

  1. Chemical Tagging Can Work: Identification of Stellar Phase-space Structures Purely by Chemical-abundance Similarity

    NASA Astrophysics Data System (ADS)

    Hogg, David W.; Casey, Andrew R.; Ness, Melissa; Rix, Hans-Walter; Foreman-Mackey, Daniel; Hasselquist, Sten; Ho, Anna Y. Q.; Holtzman, Jon A.; Majewski, Steven R.; Martell, Sarah L.; Mészáros, Szabolcs; Nidever, David L.; Shetrone, Matthew

    2016-12-01

    Chemical tagging promises to use detailed abundance measurements to identify spatially separated stars that were, in fact, born together (in the same molecular cloud) long ago. This idea has not yielded much practical success, presumably because of the noise and incompleteness in chemical-abundance measurements. We have succeeded in substantially improving spectroscopic measurements with The Cannon, which has now delivered 15 individual abundances for ∼ {10}5 stars observed as part of the APOGEE spectroscopic survey, with precisions around 0.04 dex. We test the chemical-tagging hypothesis by looking at clusters in abundance space and confirming that they are clustered in phase space. We identify (by the k-means algorithm) overdensities of stars in the 15-dimensional chemical-abundance space delivered by The Cannon, and plot the associated stars in phase space. We use only abundance-space information (no positional information) to identify stellar groups. We find that clusters in abundance space are indeed clusters in phase space, and we recover some known phase-space clusters and find other interesting structures. This is the first-ever project to identify phase-space structures at the survey-scale by blind search purely in abundance space; it verifies the precision of the abundance measurements delivered by The Cannon the prospects for future data sets appear very good.

  2. Effect of altitude and season on microbial activity, abundance and community structure in Alpine forest soils.

    PubMed

    Siles, José A; Cajthaml, Tomas; Minerbi, Stefano; Margesin, Rosa

    2016-03-01

    In the current context of climate change, the study of microbial communities along altitudinal gradients is especially useful. Only few studies considered altitude and season at the same time. We characterized four forest sites located in the Italian Alps, along an altitude gradient (545-2000 m a.s.l.), to evaluate the effect of altitude in spring and autumn on soil microbial properties. Each site in each season was characterized with regard to soil temperature, physicochemical properties, microbial activities (respiration, enzymes), community level physiological profiles (CLPP), microbial abundance and community structure (PLFA). Increased levels of soil organic matter (SOM) and nutrients were found at higher altitudes and in autumn, resulting in a significant increase of (soil dry-mass related) microbial activities and abundance at higher altitudes. Significant site- and season-specific effects were found for enzyme production. The significant interaction of the factors site and incubation temperature for soil microbial activities indicated differences in microbial communities and their responses to temperature among sites. CLPP revealed site-specific effects. Microbial community structure was influenced by altitudinal, seasonal and/or site-specific effects. Correlations demonstrated that altitude, and not season, was the main factor determining the changes in abiotic and biotic characteristics at the sites investigated.

  3. Community structure, population structure and topographical specialisation of Gyrodactylus (monogenea) ectoparasites living on sympatric stickleback species.

    PubMed

    Raeymaekers, Joost A M; Huyse, Tine; Maelfait, Hannelore; Hellemans, Bart; Volckaert, Filip A M

    2008-09-01

    In order to disentangle the contribution of host and parasite biology to host specificity, we compared the structure and population dynamics of the Gyrodactylus (von Nordmann, 1832) flatworm community living on sympatric three-spined Gasterosteus aculeatus L. and nine-spined Pungitius pungitius (L.) stickleback. Between April 2002 and March 2003, a small lowland creek was sampled monthly. Species identity of about 75% of the worms per host was determined with a genetic nuclear marker (ITS1). Each stickleback species hosted a characteristic gill- and fin-parasitic Gyrodactylus: G. arcuatus Bychowsky, 1933 and G. gasterostei Gläser, 1974 respectively infecting the three-spined stickleback, with G. rarus Wegener, 1910 and G. pungitii Malmberg, 1964 infecting the nine-spined stickleback. Host size and seasonal dynamics were strong determinants of parasite abundance. A strong interaction between host and parasite species determined infection levels and affected three levels of parasite organisation: community structure, population structure and topographical specialisation. Community and population structure were shaped by asymmetric cross-infections, resulting in a net transmission of the Gyro-dactylus species typical of the nine-spined stickleback towards the three-spined stickleback. Host density was not a major determinant of parasite exchange. Aggregation and topographical specialisation of the Gyrodactylus species of the three-spined stickleback were more pronounced than that of the nine-spined stickleback.

  4. Current land bird distribution and trends in population abundance between 1982 and 2012 on Rota, Mariana Islands

    USGS Publications Warehouse

    Camp, Richard J.; Brinck, Kevin W.; Gorresen, P. Marcos; Amidon, Fred A.; Radley, Paul M.; Berkowitz, S. Paul; Banko, Paul C.

    2015-01-01

    The western Pacific island of Rota is the fourth largest human-inhabited island in the Mariana archipelago and designated an Endemic Bird Area. Between 1982 and 2012, 12 point-transect distance-sampling surveys were conducted to assess bird population status. Surveys did not consistently sample the entire island; thus, we used a ratio estimator to estimate bird abundances in strata not sampled during every survey. Trends in population size were reliably estimated for 11 of 13 bird species, and 7 species declined over the 30-y time series, including the island collared-dove Streptopelia bitorquata, white-throated ground-dove Gallicolumba xanthonura, Mariana fruit-dove Ptilinopus roseicapilla, collared kingfisher Todiramphus chloris orii, Micronesian myzomela Myzomela rubratra, black drongo Dicrurus macrocercus, and Mariana crow Corvus kubaryi. The endangered Mariana crow (x̄  =  81 birds, 95% CI 30–202) declined sharply to fewer than 200 individuals in 2012, down from 1,491 birds in 1982 (95% CI  =  815–3,115). Trends increased for white tern Gygis alba, rufous fantail Rhipidura rufifrons mariae, and Micronesian starling Aplonis opaca. Numbers of the endangered Rota white-eye Zosterops rotensis declined from 1982 to the late 1990s but returned to 1980s levels by 2012, resulting in an overall stable trend. Trends for the yellow bittern Ixobrychus sinensis were inconclusive. Eurasian tree sparrow Passer montanus trends were not assessed; however, their numbers in 1982 and 2012 were similar. Occupancy models of the 2012 survey data revealed general patterns of land cover use and detectability among 12 species that could be reliably modeled. Occupancy was not assessed for the Eurasian tree sparrow because of insufficient detections. Based on the 2012 survey, bird distribution and abundance across Rota revealed three general patterns: 1) range restriction, including Mariana crow, Rota white-eye, and Eurasian tree sparrow; 2) widespread distribution, low

  5. Genetic structure of populations of Legionella pneumophila.

    PubMed Central

    Selander, R K; McKinney, R M; Whittam, T S; Bibb, W F; Brenner, D J; Nolte, F S; Pattison, P E

    1985-01-01

    The genetic structure of populations of Legionella pneumophila was defined by an analysis of electrophoretically demonstrable allelic variation at structural genes encoding 22 enzymes in 292 isolates from clinical and environmental sources. Nineteen of the loci were polymorphic, and 62 distinctive electrophoretic types (ETs), representing multilocus genotypes, were identified. Principal coordinates and clustering analyses demonstrated that isolates received as L. pneumophila were a heterogeneous array of genotypes that included two previously undescribed species. For 50 ETs of L. pneumophila (strict sense), mean genetic diversity per locus was 0.312, and diversity was equivalent in ETs represented by isolates recovered from clinical sources and those collected from environmental sources. Cluster analysis revealed four major groups or lineages of ETs in L. pneumophila. Genetic diversity among ETs of the same serotype was, on average, 93% of that in the total sample of ETs. Isolates marked by particular patterns of reactivity to a panel of nine monoclonal antibodies were also genetically heterogeneous, mean diversity within patterns being about 75% of the total. Both Pontiac fever and the pneumonic form of legionellosis may be caused by isolates of the same ET. The genetic structure of L. pneumophila is clonal, and many clones apparently are worldwide in distribution. The fact that L. pneumophila is only 60% as variable as Escherichia coli raises the possibility that isolates recovered from clinical cases and man-made environments are a restricted subset of all clones in the species as a whole. PMID:4030689

  6. Modeling wetland blackbird populations as a function of waterfowl abundance in the prairie pothole region of the United States and Canada

    USGS Publications Warehouse

    Forcey, G.M.; Linz, G.M.; Thogmartin, W.E.; Bleier, W.J.

    2008-01-01

    Blackbirds share wetland habitat with many waterfowl species in Bird Conservation Region 11 (BCR 11), the prairie potholes. Because of similar habitat preferences, there may be associations between blackbird populations and populations of one or more species of waterfowl in BCR11. This study models populations of red-winged blackbirds and yellow-headed blackbirds as a function of multiple waterfowl species using data from the North American Breeding Bird Survey within BCR11. For each blackbird species, we created a global model with blackbird abundance modeled as a function of 11 waterfowl species; nuisance effects (year, route, and observer) also were included in the model. Hierarchical Poisson regression models were fit using Markov chain Monte Carlo methods in WinBUGS 1.4.1. Waterfowl abundances were weakly associated with blackbird numbers, and no single waterfowl species showed a strong correlation with any blackbird species. These findings suggest waterfowl abundance from a single species is not likely a good bioindicator of blackbird abundance; however, a global model provided good fit for predicting red-winged blackbird abundance. Increased model complexity may be required for accurate predictions of blackbird abundance; the amount of data required to construct appropriate models may limit this approach for predicting blackbird abundance in the prairie potholes. Copyright ?? Taylor & Francis Group, LLC.

  7. Population inertia and its sensitivity to changes in vital rates and population structure

    USGS Publications Warehouse

    Koons, D.N.; Holmes, R.R.; Grand, J.B.

    2007-01-01

    Because the (st)age structure of a population may rarely be stable, studies of transient population dynamics and population momentum are becoming ever more popular. Yet, studies of "population momentum" are restricted in the sense that they describe the inertia of population size resulting from a demographic transition to the stationary population growth rate. Although rarely mentioned, inertia in population size is a general phenomenon and can be produced by any demographic transition or perturbation. Because population size is of central importance in demography, conservation, and management, formulas relating the sensitivity of population inertia to changes in underlying vital rates and population structure could provide much-needed insight into the dynamics of populations with unstable (st)age structure. Here, we derive such formulas, which are readily computable, and provide examples of their potential use in studies of life history and applied arenas of population study. ?? 2007 by the Ecological Society of America.

  8. Types of provincial structure and population health.

    PubMed

    Young, Frank W; Rodriguez, Eunice

    2005-01-01

    This paper explores the potential of using large administrative units for studies of population health within a country. The objective is to illustrate a new way of defining structural dimensions and to use them in examining variation in life expectancy rates. We use data from the 50 provinces of Spain as a case study. A factor analysis of organizational items such as schools, hotels and medical personnel is employed to define and generate "collective" measures for well-known provincial types, in this case: urban, commercial, industrial and tourist provinces. The scores derived from the factor analysis are then used in a regression model to predict life expectancy. The City-centered and Commercial provinces showed positive correlations with life expectancy while those for the Tourist provinces were negative. The industrial type was nonsignificant. Explanations of these correlations are proposed and the advantages and disadvantages of this exploratory technique are reviewed. The use of this technique for generating an overview of social organization and population health is discussed.

  9. Competing pressures on populations: long-term dynamics of food availability, food quality, disease, stress and animal abundance.

    PubMed

    Chapman, Colin A; Schoof, Valérie A M; Bonnell, Tyler R; Gogarten, Jan F; Calmé, Sophie

    2015-05-26

    Despite strong links between sociality and fitness that ultimately affect the size of animal populations, the particular social and ecological factors that lead to endangerment are not well understood. Here, we synthesize approximately 25 years of data and present new analyses that highlight dynamics in forest composition, food availability, the nutritional quality of food, disease, physiological stress and population size of endangered folivorous red colobus monkeys (Procolobus rufomitratus). There is a decline in the quality of leaves 15 and 30 years following two previous studies in an undisturbed area of forest. The consumption of a low-quality diet in one month was associated with higher glucocorticoid levels in the subsequent month and stress levels in groups living in degraded forest fragments where diet was poor was more than twice those in forest groups. In contrast, forest composition has changed and when red colobus food availability was weighted by the protein-to-fibre ratio, which we have shown positively predicts folivore biomass, there was an increase in the availability of high-quality trees. Despite these changing social and ecological factors, the abundance of red colobus has remained stable, possibly through a combination of increasing group size and behavioural flexibility.

  10. Competing pressures on populations: long-term dynamics of food availability, food quality, disease, stress and animal abundance

    PubMed Central

    Chapman, Colin A.; Schoof, Valérie A. M.; Bonnell, Tyler R.; Gogarten, Jan F.; Calmé, Sophie

    2015-01-01

    Despite strong links between sociality and fitness that ultimately affect the size of animal populations, the particular social and ecological factors that lead to endangerment are not well understood. Here, we synthesize approximately 25 years of data and present new analyses that highlight dynamics in forest composition, food availability, the nutritional quality of food, disease, physiological stress and population size of endangered folivorous red colobus monkeys (Procolobus rufomitratus). There is a decline in the quality of leaves 15 and 30 years following two previous studies in an undisturbed area of forest. The consumption of a low-quality diet in one month was associated with higher glucocorticoid levels in the subsequent month and stress levels in groups living in degraded forest fragments where diet was poor was more than twice those in forest groups. In contrast, forest composition has changed and when red colobus food availability was weighted by the protein-to-fibre ratio, which we have shown positively predicts folivore biomass, there was an increase in the availability of high-quality trees. Despite these changing social and ecological factors, the abundance of red colobus has remained stable, possibly through a combination of increasing group size and behavioural flexibility. PMID:25870398

  11. Chemical abundances of M giants in the Galactic centre: A single metal-rich population with low [α/Fe

    NASA Astrophysics Data System (ADS)

    Ryde, N.; Schultheis, M.

    2015-01-01

    Context. The formation and evolution of the Milky Way bulge is still largely an unanswered question. Some of the most essential observations needed for its modelling are the metallicity distribution and the trends of the α elements, as measured in stars. While bulge regions beyond R ≳ 50 pc of the centre have been targeted in several surveys, the central part has escaped a detailed study due to the extreme extinction and crowding. The abundance gradients from the centre are, however, of large diagnostic value. Aims: We aim at investigating the Galactic centre environment by probing M giants in the field by avoiding supergiants and cluster members. Methods: For nine field M-giants in the Galactic centre region, we have obtained high- and low-resolution spectra observed simultaneously with CRIRES and ISAAC on UT1 and UT3 of the VLT. The low-resolution spectra provide a means of determining the effective temperatures, and the high-resolution spectra provide detailed abundances of Fe, Mg, Si, and Ca. Results: We find a metal-rich population at [ Fe / H ] = + 0.11 ± 0.15 and a lack of the metal-poor population, which is found further out in the bulge, corroborating earlier studies. Our [α/Fe] element trends, however, show low values, by following the outer bulge trends. A possible exception of the [Ca/Fe] trend is found and needs further investigation. Conclusions: The results of the analysed field M-giants in the Galactic centre region exclude a scenario with rapid formation, in which SNIIe played a dominated role in the chemical enrichment of the gas. The high metallicities with low α-enhancement seems to indicate a bar-like population that is, perhaps, related to the nuclear bar. Based on observations collected at the European Southern Observatory, Chile, program number 089.B-0312(A)/VM/CRIRES and 089.B-0312(B)/VM/ISAAC.Figures 8 and 9 are available in electronic form at http://www.aanda.org

  12. Effects of coconut and fish oils on ruminal methanogenesis, fermentation, and abundance and diversity of microbial populations in vitro.

    PubMed

    Patra, A K; Yu, Z

    2013-03-01

    Coconut (CO) and fish (FO) oils were previously shown to inhibit rumen methanogenesis and biohydrogenation, which mitigates methane emission and helps improve beneficial fatty acids in meat and milk. This study aimed at investigating the comparative effects of CO and FO on the methanogenesis, fermentation, and microbial abundances and diversity in vitro rumen cultures containing different doses (0, 3.1, and 6.2 mL/L) of each oil and 400mg feed substrate using rumen fluid from lactating dairy cows as inocula. Increasing doses of CO and FO quadratically decreased concentrations of methane, but hydrogen concentrations were only increased quadratically by CO. Both oils linearly decreased dry matter and neutral detergent fiber digestibility of feeds but did not affect the concentration of total volatile fatty acids. However, CO reduced acetate percentage and acetate to propionate ratio and increased the percentages of propionate and butyrate to a greater extent than FO. Ammonia concentration was greater for CO than FO. As determined by quantitative real-time PCR, FO had greater inhibition to methanogens than CO, but the opposite was true for protozoal, Ruminococcus flavefaciens, and Fibrobacter succinogenes. Ruminococcus albus was not affected by either oil. Denaturing gradient gel electrophoresis (DGGE) profiles revealed that bacterial and archaeal community composition were changed differently by oil type. Based on Pareto-Lorenz evenness curve analysis of the DGGE profiles, CO noticeably changed the functional organization of archaea compared with FO. In conclusion, although both CO and FO decreased methane concentrations to a similar extent, the mode of reduction and the effect on abundances and diversity of archaeal and bacterial populations differed between the oils. Thus, the use of combination of CO and FO at a low dose may additively lower methanogenesis in the rumen while having little adverse effect on rumen fermentation.

  13. An assessment of techniques for monitoring San Joaquin kit fox population abundance on Naval Petroleum Reserve No. 1, Kern County, California

    SciTech Connect

    Harris, C.E.

    1987-04-01

    The monitoring of San Joaquin kit fox (Vulpes macrotis mutica) population abundance on Naval Petroleum Reserve No. 1 (NPR-1) by the US Department of Energy (DOE) is one aspect of compliance with the Endangered Species Act of 1973. Monitoring of the kit fox population is essential to determine the need for specific management programs, to assess the impacts of development activities, to evaluate the results of specific management programs, and to gather information on kit fox biology and ecology as they relate to other aspects of the NPR-1 environment. Several techniques are available to monitor population abundance, but the choice of methods used is dependent upon the specific objectives of the monitoring program. The inherent problem with most available techniques is the lack of uniformity of procedures and statistical repeatability, and the need for validation of indices and population estimates against known populations. If sufficient numbers of foxes can be captured, closed population models using capture-recapture data provide reasonable estimates of population size. Capture data can also be used to determine the minimum trappable population, and the minimum population size during those sessions when fewer than 40 foxes are trapped. The scent-station survey is the best method available for estimating relative kit fox abundance.

  14. Biogeography of avian blood parasites (Leucocytozoon spp.) in two resident hosts across Europe: phylogeographic structuring or the abundance-occupancy relationship?

    PubMed

    Jenkins, Tania; Owens, Ian P F

    2011-09-01

    Relationships between hosts and parasites represent complex co-evolving systems that can vary both temporally and spatially. This variation may result in different phylogeographic outcomes, ranging from highly geographically structured parasite populations comprised of specialist lineages that are locally abundant but have restricted global occupancy to geographically unstructured parasite populations consisting of widespread parasites. Here, we present results from a large biogeographic study of the Leucocytozoon blood parasites of two nonmigrant bird species, conducted at nine sites across Europe. The aim was to determine whether the parasite lineages of the two hosts were phylogeographically structured across Europe. Employing molecular methods, we found a large diversity of parasites, and although overall prevalence varied greatly, the parasites were not genetically structured. Several measures of local parasite abundance were associated with the number of sites that the lineage occurred in, which is consistent with the macroecological phenomenon of the abundance-occupancy relationship. Taken together, our results show that parasite dispersal is somewhat uncoupled to that of the host in this system: we suggest that broad host and/or vector preference may play an important role in determining the distribution of these parasites and in affecting host-parasite coevolution in this system.

  15. Hunting or habitat? Drivers of waterbird abundance and community structure in agricultural wetlands of southern India.

    PubMed

    Ramachandran, Ramesh; Kumar, Ajith; Gopi Sundar, Kolla S; Bhalla, Ravinder Singh

    2017-02-28

    The relative impacts of hunting and habitat on waterbird community were studied in agricultural wetlands of southern India. We surveyed wetlands to document waterbird community, and interviewed hunters to document hunting intensity, targeted species, and the motivations for hunting. Our results show that hunting leads to drastic declines in waterbird diversity and numbers, and skew the community towards smaller species. Hunting intensity, water spread, and vegetation cover were the three most important determinants of waterbird abundance and community structure. Species richness, density of piscivorous species, and medium-sized species (31-65 cm) were most affected by hunting. Out of 53 species recorded, 47 were hunted, with a preference for larger birds. Although illegal, hunting has increased in recent years and is driven by market demand. This challenges the widely held belief that waterbird hunting in India is a low intensity, subsistence activity, and undermines the importance of agricultural wetlands in waterbird conservation.

  16. Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes

    PubMed Central

    Saeedghalati, Mohammadkarim; Farahpour, Farnoush; Lange, Anja; Westendorf, Astrid M.; Seifert, Marc; Küppers, Ralf

    2017-01-01

    The community, the assemblage of organisms co-existing in a given space and time, has the potential to become one of the unifying concepts of biology, especially with the advent of high-throughput sequencing experiments that reveal genetic diversity exhaustively. In this spirit we show that a tool from community ecology, the Rank Abundance Distribution (RAD), can be turned by the new MaxRank normalization method into a generic, expressive descriptor for quantitative comparison of communities in many areas of biology. To illustrate the versatility of the method, we analyze RADs from various generalized communities, i.e. assemblages of genetically diverse cells or organisms, including human B cells, gut microbiomes under antibiotic treatment and of different ages and countries of origin, and other human and environmental microbial communities. We show that normalized RADs enable novel quantitative approaches that help to understand structures and dynamics of complex generalized communities. PMID:28114391

  17. Camera Traps on Wildlife Crossing Structures as a Tool in Gray Wolf (Canis lupus) Management - Five-Years Monitoring of Wolf Abundance Trends in Croatia

    PubMed Central

    Križan, Josip; Gužvica, Goran

    2016-01-01

    The conservation of gray wolf (Canis lupus) and its coexistence with humans presents a challenge and requires continuous monitoring and management efforts. One of the non-invasive methods that produces high-quality wolf monitoring datasets is camera trapping. We present a novel monitoring approach where camera traps are positioned on wildlife crossing structures that channel the animals, thereby increasing trapping success and increasing the cost-efficiency of the method. In this way we have followed abundance trends of five wolf packs whose home ranges are intersected by a motorway which spans throughout the wolf distribution range in Croatia. During the five-year monitoring of six green bridges we have recorded 28 250 camera-events, 132 with wolves. Four viaducts were monitored for two years, recording 4914 camera-events, 185 with wolves. We have detected a negative abundance trend of the monitored Croatian wolf packs since 2011, especially severe in the northern part of the study area. Further, we have pinpointed the legal cull as probable major negative influence on the wolf pack abundance trends (linear regression, r2 > 0.75, P < 0.05). Using the same approach we did not find evidence for a negative impact of wolves on the prey populations, both wild ungulates and livestock. We encourage strict protection of wolf in Croatia until there is more data proving population stability. In conclusion, quantitative methods, such as the one presented here, should be used as much as possible when assessing wolf abundance trends. PMID:27327498

  18. Camera Traps on Wildlife Crossing Structures as a Tool in Gray Wolf (Canis lupus) Management - Five-Years Monitoring of Wolf Abundance Trends in Croatia.

    PubMed

    Šver, Lidija; Bielen, Ana; Križan, Josip; Gužvica, Goran

    2016-01-01

    The conservation of gray wolf (Canis lupus) and its coexistence with humans presents a challenge and requires continuous monitoring and management efforts. One of the non-invasive methods that produces high-quality wolf monitoring datasets is camera trapping. We present a novel monitoring approach where camera traps are positioned on wildlife crossing structures that channel the animals, thereby increasing trapping success and increasing the cost-efficiency of the method. In this way we have followed abundance trends of five wolf packs whose home ranges are intersected by a motorway which spans throughout the wolf distribution range in Croatia. During the five-year monitoring of six green bridges we have recorded 28 250 camera-events, 132 with wolves. Four viaducts were monitored for two years, recording 4914 camera-events, 185 with wolves. We have detected a negative abundance trend of the monitored Croatian wolf packs since 2011, especially severe in the northern part of the study area. Further, we have pinpointed the legal cull as probable major negative influence on the wolf pack abundance trends (linear regression, r2 > 0.75, P < 0.05). Using the same approach we did not find evidence for a negative impact of wolves on the prey populations, both wild ungulates and livestock. We encourage strict protection of wolf in Croatia until there is more data proving population stability. In conclusion, quantitative methods, such as the one presented here, should be used as much as possible when assessing wolf abundance trends.

  19. Developing STR databases on structured populations: the native South Siberian population versus the Russian population.

    PubMed

    Zhivotovsky, Lev A; Malyarchuk, Boris A; Derenko, Miroslava V; Wozniak, Marcin; Grzybowski, Tomasz

    2009-09-01

    Developing a forensic DNA database on a population that consists of local ethnic groups separated by physical and cultural barriers is questionable as it can be genetically subdivided. On the other side, small sizes of ethnic groups, especially in alpine regions where they are sub-structured further into small villages, prevent collecting a large sample from each ethnic group. For such situations, we suggest to obtain both a total population database on allele frequencies across ethnic groups and a list of theta-values between the groups and the total data. We have genotyped 558 individuals from the native population of South Siberia, consisting of nine ethnic groups, at 17 autosomal STR loci of the kit packages AmpFlSTR SGM Plus i, Cyrillic AmpFlSTR Profiler Plus. The groups differentiate from each other with average theta-values of around 1.1%, and some reach up to three to four percent at certain loci. There exists between-village differentiation as well. Therefore, a database for the population of South Siberia is composed of data on allele frequencies in the pool of ethnic groups and data on theta-values that indicate variation in allele frequencies across the groups. Comparison to additional data on northeastern Asia (the Chukchi and Koryak) shows that differentiation in allele frequencies among small groups that are separated by large geographic distance can be even greater. In contrast, populations of Russians that live in large cities of the European part of Russia are homogeneous in allele frequencies, despite large geographic distance between them, and thus can be described by a database on allele frequencies alone, without any specific information on theta-values.

  20. Understanding cooperative behavior in structurally disordered populations

    NASA Astrophysics Data System (ADS)

    Xu, C.; Zhang, W.; Du, P.; Choi, C. W.; Hui, P. M.

    2016-06-01

    The effects of an inhomogeneous competing environment on the extent of cooperation are studied within the context of a site-diluted evolutionary snowdrift game on a square lattice, with the occupied sites representing the players, both numerically and analytically. The frequency of cooperation ℱ C generally shows a non-monotonic dependence on the fraction of occupied sites ρ, for different values of the payoff parameter r. Slightly diluting a lattice leads to a lower cooperation for small and high values of r. For a range of r, however, dilution leads to an enhanced cooperation. An analytic treatment is developed for ℱC I + ℱC II, with ℱC I emphasizing the importance of the small clusters of players especially for ℱC II from the other players is shown to be inadequate. A local configuration approximation (LCA) that treats the local competing configurations as the variables and amounts to include spatial correlation up to the neighborhood of a player's neighbors is developed. Results of ℱ C ( ρ) and the number of different local configurations from LCA are in good agreement with simulation results. A transparent physical picture of the dynamics stemming from LCA is also presented. The theoretical approach provides a framework that can be readily applied to competing agent-based models in structurally ordered and disordered populations.

  1. Fish passage and abundance around grade control structures on incised streams

    USGS Publications Warehouse

    Thomas, J.T.; Papanicolaou, A.N.; Pierce, C.L.; Dermisis, D.C.; Litvan, M.E.; Larson, C.J.

    2009-01-01

    This paper summarizes research from separate studies of fish passage over weirs (Larson et al., 2004; Litvan, 2006; Litvan, et al., 2008a-c) and weir hydraulics (Papanicolaou and Dermisis, 2006; Papanicolaou and Dermisis, in press). Channel incision in the deep loess region of western Iowa has caused decreased biodiversity because streams have high sediment loads, altered flow regimes, lost habitat, and lost lateral connectivity with their former floodplains. In-stream grade control structures (GCS) are built to prevent further erosion, protect infrastructure, and reduce sediment loads. However, GCS can have a detrimental impact on fisheries abundance and migration, biodiversity, and longitudinal connectivity. Fish mark-recapture studies were performed on stretches of streams with and without GCS. GCS with vertical or 1:4 (rise/run) downstream slopes did not allow fish migration, but GCS with slopes ??? 1:15 did. GCS sites were characterized by greater proportions of pool habitat, maximum depths, fish biomass, slightly higher index of biotic integrity (IBI) scores, and greater macroinvertebrate abundance and diversity than non-GCS sites. After modification of three GCS, IBI scores increased and fish species exhibiting truncated distributions before were found throughout the study area. Another study examined the hydraulic performance of GCS to facilitate unimpeded fish passage by determining the mean and turbulent flow characteristics in the vicinity of the GCS via detailed, non-intrusive field tests. Mean flow depth (Y) and velocity (V) atop the GCS were critical for evaluating GCS performance. Turbulent flow measurements illustrated that certain GCS designs cause sudden constrictions which form eddies large enough to disorient fish. GCS with slopes ??? 1:15 best met the minimum requirements to allow catfish passage of a flow depth of ??? 0.31 m and a mean flow velocity of ??? 1.22 m/s. ?? 2009 ASCE.

  2. Osprey distribution, abundance, and status in western North America: III. The Baja California and Gulf of California population

    USGS Publications Warehouse

    Henny, C.J.; Anderson, D.W.

    1979-01-01

    -An estimated 810 ? 55 pairs (minimum estimate) of ospreys (Pandion haliaetus) were nesting in the study area during our survey (24 March-l April 1977). Approximately 174 pairs nested along the Pacific side of Baja California, 255 pairs along the gulf side, 187 pairs on the Midriff Islands, and 194 pairs in coastal Sonora and Sinaloa. Most nested on cliffs adjacent to the sea (59%); some nested on cactus in flat terrain (26%). Seven per cent nested on the ground, three percent nested in mangroves and other trees in the southern portion of the study area,.and four percent nested on man-made structures. The extreme northwestern Baja California population that was extirpated early in this century has not recovered. However, several populations immediately to the south along the Pacific Coast now appear stationary. Pesticide residues in osprey eggs from Mexico were among the lowest reported for the species in North America.

  3. Detecting declines in the abundance of a bull trout (Salvelinus confluentus) population: Understanding the accuracy, precision, and costs of our efforts

    USGS Publications Warehouse

    Al-Chokhachy, R.; Budy, P.; Conner, M.

    2009-01-01

    Using empirical field data for bull trout (Salvelinus confluentus), we evaluated the trade-off between power and sampling effort-cost using Monte Carlo simulations of commonly collected mark-recapture-resight and count data, and we estimated the power to detect changes in abundance across different time intervals. We also evaluated the effects of monitoring different components of a population and stratification methods on the precision of each method. Our results illustrate substantial variability in the relative precision, cost, and information gained from each approach. While grouping estimates by age or stage class substantially increased the precision of estimates, spatial stratification of sampling units resulted in limited increases in precision. Although mark-resight methods allowed for estimates of abundance versus indices of abundance, our results suggest snorkel surveys may be a more affordable monitoring approach across large spatial scales. Detecting a 25% decline in abundance after 5 years was not possible, regardless of technique (power = 0.80), without high sampling effort (48% of study site). Detecting a 25% decline was possible after 15 years, but still required high sampling efforts. Our results suggest detecting moderate changes in abundance of freshwater salmonids requires considerable resource and temporal commitments and highlight the difficulties of using abundance measures for monitoring bull trout populations.

  4. The influence of food abundance, food dispersion and habitat structure on territory selection and size of an Afrotropical terrestrial insectivore

    USGS Publications Warehouse

    Stanley, Thomas R.; Newmark, William D.

    2015-01-01

    Most tropical insectivorous birds, unlike their temperate counterparts, hold and defend a feeding and breeding territory year-around. However, our understanding of ecological factors influencing territory selection and size in tropical insectivores is limited. Here we examine three prominent hypotheses relating food abundance, food dispersion (spatial arrangement of food items), and habitat structure to territoriality in the Usambara Thrush Turdus roehli. We first compared leaf-litter macro-invertebrate abundance and dispersion, and habitat structure between territories and random sites. We then examined the relation between these same ecological factors and territory size. Invertebrate abundance and dispersion were sparsely and evenly distributed across our study system and did not vary between territories and random sites. In contrast, habitat structure did vary between territories and random sites indicating the Usambara Thrush selects territories with open understorey and closed overstorey habitat. Invertebrate abundance and dispersion within territories of the Usambara Thrush were not associated with habitat structure. We believe the most likely explanation for the Usambara Thrush’s preference for open understorey and closed overstorey habitat relates to foraging behavior. Using information-theoretic model selection we found that invertebrate abundance was the highest-ranked predictor of territory size and was inversely related, consistent with food value theory of territoriality.

  5. High Concentrations of the Antibiotic Spiramycin in Wastewater Lead to High Abundance of Ammonia-Oxidizing Archaea in Nitrifying Populations.

    PubMed

    Zhang, Yu; Tian, Zhe; Liu, Miaomiao; Shi, Zhou Jason; Hale, Lauren; Zhou, Jizhong; Yang, Min

    2015-08-04

    To evaluate the potential effects of antibiotics on ammonia-oxidizing microbes, multiple tools including quantitative PCR (qPCR), 454-pyrosequencing, and a high-throughput functional gene array (GeoChip) were used to reveal the distribution of ammonia-oxidizing archaea (AOA) and archaeal amoA (Arch-amoA) genes in three wastewater treatment systems receiving spiramycin or oxytetracycline production wastewaters. The qPCR results revealed that the copy number ratios of Arch-amoA to ammonia-oxidizing bacteria (AOB) amoA genes were the highest in the spiramycin full-scale (5.30) and pilot-scale systems (1.49 × 10(-1)), followed by the oxytetracycline system (4.90 × 10(-4)), with no Arch-amoA genes detected in the control systems treating sewage or inosine production wastewater. The pyrosequencing result showed that the relative abundance of AOA affiliated with Thaumarchaeota accounted for 78.5-99.6% of total archaea in the two spiramycin systems, which was in accordance with the qPCR results. Mantel test based on GeoChip data showed that Arch-amoA gene signal intensity correlated with the presence of spiramycin (P < 0.05). Antibiotics explained 25.8% of variations in amoA functional gene structures by variance partitioning analysis. This study revealed the selection of AOA in the presence of high concentrations of spiramycin in activated sludge systems.

  6. Age structure and abundance levels in the entomological evaluation of an insecticide used in the control of Anopheles albimanus in southern Mexico.

    PubMed

    Bown, D N; Rodríguez, M H; Arredondo-Jiménez, J I; Loyola, E G; Rodríguez, M C

    1991-06-01

    Applications of bendiocarb produced a high insecticidal residual effect lasting up to 3 months on the most common indoor house surfaces. No significant decreases in mosquito man-biting rate levels were observed between treated and untreated villages. It was shown that almost equal proportions of intra- and peridomicillary mosquitoes came into contact with the insecticide, indicating that mosquitoes commonly enter houses, rest on treated surfaces and return to bite both indoors and outdoors. Although the insecticide was found to have a significant effect on the percentage parity (interpreted as abundance of older individuals) of intra- and peridomicillary Anopheles albimanus mosquitoes, parity recovered and continued a normal cyclic pattern that appeared to be dependent on relative abundance. The proximity of a treated village to an untreated village (1.2 km) can affect the age structure of mosquito populations through shared common resting and breeding sites.

  7. Towards a landscape scale management of pesticides: ERA using changes in modelled occupancy and abundance to assess long-term population impacts of pesticides.

    PubMed

    Topping, Chris J; Craig, Peter S; de Jong, Frank; Klein, Michael; Laskowski, Ryszard; Manachini, Barbara; Pieper, Silvia; Smith, Rob; Sousa, José Paulo; Streissl, Franz; Swarowsky, Klaus; Tiktak, Aaldrik; van der Linden, Ton

    2015-12-15

    Pesticides are regulated in Europe and this process includes an environmental risk assessment (ERA) for non-target arthropods (NTA). Traditionally a non-spatial or field trial assessment is used. In this study we exemplify the introduction of a spatial context to the ERA as well as suggest a way in which the results of complex models, necessary for proper inclusion of spatial aspects in the ERA, can be presented and evaluated easily using abundance and occupancy ratios (AOR). We used an agent-based simulation system and an existing model for a widespread carabid beetle (Bembidion lampros), to evaluate the impact of a fictitious highly-toxic pesticide on population density and the distribution of beetles in time and space. Landscape structure and field margin management were evaluated by comparing scenario-based ERAs for the beetle. Source-sink dynamics led to an off-crop impact even when no pesticide was present off-crop. In addition, the impacts increased with multi-year application of the pesticide whereas current ERA considers only maximally one year. These results further indicated a complex interaction between landscape structure and pesticide effect in time, both in-crop and off-crop, indicating the need for NTA ERA to be conducted at landscape- and multi-season temporal-scales. Use of AOR indices to compare ERA outputs facilitated easy comparison of scenarios, allowing simultaneous evaluation of impacts and planning of mitigation measures. The landscape and population ERA approach also demonstrates that there is a potential to change from regulation of a pesticide in isolation, towards the consideration of pesticide management at landscape scales and provision of biodiversity benefits via inclusion and testing of mitigation measures in authorisation procedures.

  8. Population II Li-6 as a probe of nucleosynthesis and stellar structure and evolution

    NASA Technical Reports Server (NTRS)

    Steigman, Gary; Fields, Brian D.; Olive, Keith A.; Schramm, David N.; Walker, Terry P.

    1993-01-01

    We discuss the importance of Population II Li-6 as a diagnostic for models of primordial nucleosynthesis, cosmic-ray nucleosyntheses in the early Galaxy, and the structure and evolution of metal-poor solar-type stars. The observation of Li-6 in the subdwarf HD 84937 is shown to be consistent with the existing Population II LiBeB data within the context of a simple three-component model: (1) standard big bang nucleosynthesis, (2) Population II cosmic-ray nucleosynthesis, (3) standard (nonrotating) stellar LiBeB depletion. If this interpretation is correct, we predict a potentially detectable boron abundance for this star: about 2 x 10 exp -12. Subsequent Population II LiBeB observations, and in particular further observations of Population II Li-6, are shown to be crucial to our understanding of the primordial and early galactic creation and destruction mechanisms for light elements.

  9. Population structure with localized haplotype clusters.

    PubMed

    Browning, Sharon R; Weir, Bruce S

    2010-08-01

    We propose a multilocus version of F(ST) and a measure of haplotype diversity using localized haplotype clusters. Specifically, we use haplotype clusters identified with BEAGLE, which is a program implementing a hidden Markov model for localized haplotype clustering and performing several functions including inference of haplotype phase. We apply this methodology to HapMap phase 3 data. With this haplotype-cluster approach, African populations have highest diversity and lowest divergence from the ancestral population, East Asian populations have lowest diversity and highest divergence, and other populations (European, Indian, and Mexican) have intermediate levels of diversity and divergence. These relationships accord with expectation based on other studies and accepted models of human history. In contrast, the population-specific F(ST) estimates obtained directly from single-nucleotide polymorphisms (SNPs) do not reflect such expected relationships. We show that ascertainment bias of SNPs has less impact on the proposed haplotype-cluster-based F(ST) than on the SNP-based version, which provides a potential explanation for these results. Thus, these new measures of F(ST) and haplotype-cluster diversity provide an important new tool for population genetic analysis of high-density SNP data.

  10. The abundant symmetry structure of hierarchies of nonlinear equations obtained by reciprocal links

    NASA Astrophysics Data System (ADS)

    Carillo, Sandra; Fuchssteiner, Benno

    1989-07-01

    Explicit computation for a Kawamoto-type equation shows that there is a rich associated symmetry structure for four separate hierarchies of nonlinear integrodifferential equations. Contrary to the general belief that symmetry groups for nonlinear evolution equations in 1+1 dimensions have to be Abelian, it is shown that, in this case, the symmetry group is noncommutative. Its semisimple part is isomorphic to the affine Lie algebra A(1)1 associated to sl(2,C). In two of the additional hierarchies that were found, an explicit dependence of the independent variable occurs. Surprisingly, the generic invariance for the Kawamoto-type equation obtained in Rogers and Carillo [Phys. Scr. 36, 865 (1987)] via a reciprocal link to the Möbius invariance of the singularity equation of the Kaup-Kupershmidt (KK) equation only holds for one of the additional hierarchies of symmetry groups. Thus the generic invariance is not a universal property for the complete symmetry group of equations obtained by reciprocal links. In addition to these results, the bi-Hamiltonian formulation of the hierarchy is given. A direct Bäcklund transformation between the (KK) hierarchy and the hierarchy of singularity equation for the Caudrey-Dodd-Gibbon-Sawada-Kotera equation is exhibited: This shows that the abundant symmetry structure found for the Kawamoto equation must exist for all fifth-order equations, which are known to be completely integrable since these equations are connected either by Bäcklund transformations or reciprocal links. It is shown that similar results must hold for all hierarchies emerging out of singularity hierarchies via reciprocal links. Furthermore, general aspects of the results are discussed.

  11. Geometrical Structures of Chemically Decomposed Thick and Thin Disk Populations

    NASA Astrophysics Data System (ADS)

    Kawata, D.; Brook, C. B.; Rahimi, A.; Gibson, B. K.

    2016-10-01

    We summarize the thick and thin disk formation commonly seen in cosmological N-body simulations. As suggested in Brook et al. (2004), a hierarchical clustering scenario causes multiple minor gas-rich mergers, and leads to the formation of a kinematically hot disk, thick disk population, at a high redshift. Once the mergers become less significant at a later epoch, the thin disk population starts building up. Because in this scenario the thick disk population forms intensively at high redshift through multiple gas-rich mergers, the thick disk population is compact and has systematically higher [α/Fe] abundance than the thin disk population. We discuss that the thick disk population would be affected by the formation of the thin disk and suffer from the radial migration, which helps the thick disk population to be observed in the solar neighborhood. In addition, we show that the current cosmological simulations also naturally predict that the thin disk population is flaring at the outer region. As shown in Rahimi et al. (2014), at high vertical height from the disk plane, the compact thick disk population (low metallicity and high [α/Fe]) is dominant in the inner region and the flaring thin disk population (high metallicity and low [α/Fe]) contributes more in the outer region. This helps to explain the positive radial metallicity gradient and negative radial [α/Fe] gradient observed at high vertical height in the Milky Way stellar disk.

  12. Genetic structure of Tribolium castaneum (Coleptera: Tenebrionidae) populations in mills

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The red flour beetle, Tribolium castaneum, is primarily found associated with human structures such as wheat and rice mills, which are spatially isolated resource patches with apparently limited immigration that could produce genetically structured populations. We investigated genetic diversity and...

  13. Population structure and genetic diversity of moose in Alaska.

    PubMed

    Schmidt, Jennifer I; Hundertmark, Kris J; Bowyer, R Terry; McCracken, Kevin G

    2009-01-01

    Moose (Alces alces) are highly mobile mammals that occur across arboreal regions of North America, Europe, and Asia. Alaskan moose (Alces alces gigas) range across much of Alaska and are primary herbivore consumers, exerting a prominent influence on ecosystem structure and functioning. Increased knowledge gained from population genetics provides insights into their population dynamics, history, and dispersal of these unique large herbivores and can aid in conservation efforts. We examined the genetic diversity and population structure of moose (n = 141) with 8 polymorphic microsatellites from 6 regions spanning much of Alaska. Expected heterozygosity was moderate (H(E) = 0.483-0.612), and private alleles ranged from 0 to 6. Both F(ST) and R(ST) indicated significant population structure (P < 0.001) with F(ST) < 0.109 and R(ST) < 0.125. Results of analyses from STRUCTURE indicated 2 prominent population groups, a mix of moose from the Yakutat and Tetlin regions versus all other moose, with slight substructure observed among the second population. Estimates of dispersal differed between analytical approaches, indicating a high level of historical or current gene flow. Mantel tests indicated that isolation-by-distance partially explained observed structure among moose populations (R(2) = 0.45, P < 0.01). Finally, there was no evidence of bottlenecks either at the population level or overall. We conclude that weak population structure occurs among moose in Alaska with population expansion from interior Alaska westward toward the coast.

  14. Genetic diversity, population structure, effective population size and demographic history of the Finnish wolf population.

    PubMed

    Aspi, J; Roininen, E; Ruokonen, M; Kojola, I; Vilà, C

    2006-05-01

    The Finnish wolf population (Canis lupus) was sampled during three different periods (1996-1998, 1999-2001 and 2002-2004), and 118 individuals were genotyped with 10 microsatellite markers. Large genetic variation was found in the population despite a recent demographic bottleneck. No spatial population subdivision was found even though a significant negative relationship between genetic relatedness and geographic distance suggested isolation by distance. Very few individuals did not belong to the local wolf population as determined by assignment analyses, suggesting a low level of immigration in the population. We used the temporal approach and several statistical methods to estimate the variance effective size of the population. All methods gave similar estimates of effective population size, approximately 40 wolves. These estimates were slightly larger than the estimated census size of breeding individuals. A Bayesian model based on Markov chain Monte Carlo simulations indicated strong evidence for a long-term population decline. These results suggest that the contemporary wolf population size is roughly 8% of its historical size, and that the population decline dates back to late 19th century or early 20th century. Despite an increase of over 50% in the census size of the population during the whole study period, there was only weak evidence that the effective population size during the last period was higher than during the first. This may be caused by increased inbreeding, diminished dispersal within the population, and decreased immigration to the population during the last study period.

  15. Ecology and Population Structure of Vibrionaceae in the Coastal Ocean

    DTIC Science & Technology

    2010-02-01

    determines the allele frequency within the patch. Gut microbiota are a unique assembly of 21 populations (Eckburg et al., 2005; Gao et al., 2007; Pei et al...et al., 2006). Microbiota of Animals Bacteria are attached to nearly all animal surfaces that are exposed to the environment and play important roles...in the health of the organism. Bacteria are particularly abundant in the gut , where nutrients are concentrated and conditions are fairly stable

  16. A spatial age-structured model for describing sea lamprey (Petromyzon marinus) population dynamics

    USGS Publications Warehouse

    Robinson, Jason M.; Wilberg, Michael J.; Adams, Jean V.; Jones, Michael L.

    2013-01-01

    The control of invasive sea lampreys (Petromyzon marinus) presents large scale management challenges in the Laurentian Great Lakes. No modeling approach has been developed that describes spatial dynamics of lamprey populations. We developed and validated a spatial and age-structured model and applied it to a sea lamprey population in a large river in the Great Lakes basin. We considered 75 discrete spatial areas, included a stock-recruitment function, spatial recruitment patterns, natural mortality, chemical treatment mortality, and larval metamorphosis. Recruitment was variable, and an upstream shift in recruitment location was observed over time. From 1993–2011 recruitment, larval abundance, and the abundance of metamorphosing individuals decreased by 80, 84, and 86%, respectively. The model successfully identified areas of high larval abundance and showed that areas of low larval density contribute significantly to the population. Estimated treatment mortality was less than expected but had a large population-level impact. The results and general approach of this work have applications for sea lamprey control throughout the Great Lakes and for the restoration and conservation of native lamprey species globally.

  17. Evolutionary dynamics of general group interactions in structured populations

    NASA Astrophysics Data System (ADS)

    Li, Aming; Broom, Mark; Du, Jinming; Wang, Long

    2016-02-01

    The evolution of populations is influenced by many factors, and the simple classical models have been developed in a number of important ways. Both population structure and multiplayer interactions have been shown to significantly affect the evolution of important properties, such as the level of cooperation or of aggressive behavior. Here we combine these two key factors and develop the evolutionary dynamics of general group interactions in structured populations represented by regular graphs. The traditional linear and threshold public goods games are adopted as models to address the dynamics. We show that for linear group interactions, population structure can favor the evolution of cooperation compared to the well-mixed case, and we see that the more neighbors there are, the harder it is for cooperators to persist in structured populations. We further show that threshold group interactions could lead to the emergence of cooperation even in well-mixed populations. Here population structure sometimes inhibits cooperation for the threshold public goods game, where depending on the benefit to cost ratio, the outcomes are bistability or a monomorphic population of defectors or cooperators. Our results suggest, counterintuitively, that structured populations are not always beneficial for the evolution of cooperation for nonlinear group interactions.

  18. Demographic connectivity for ursid populations at wildlife crossing structures in Banff National Park.

    PubMed

    Sawaya, Michael A; Clevenger, Anthony P; Kalinowski, Steven T

    2013-08-01

    Wildlife crossing structures are one solution to mitigating the fragmentation of wildlife populations caused by roads, but their effectiveness in providing connectivity has only been superficially evaluated. Hundreds of grizzly (Ursus arctos) and black bear (Ursus americanus) passages through under and overpasses have been recorded in Banff National Park, Alberta, Canada. However, the ability of crossing structures to allow individual and population-level movements across road networks remains unknown. In April 2006, we initiated a 3-year investigation into whether crossing structures provide demographic connectivity for grizzly and black bears in Banff National Park. We collected hair with multiple noninvasive methods to obtain genetic samples from grizzly and black bears around the Bow Valley. Our objectives were to determine the number of male and female grizzly and black bears that use crossing structures; examine spatial and temporal patterns of crossings; and estimate the proportions of grizzly and black bear populations in the Bow Valley that use crossing structures. Fifteen grizzly (7 female, 8 male) and 17 black bears (8 female, 9 male) used wildlife crossing structures. The number of individuals detected at wildlife crossing structures was highly correlated with the number of passages in space and time. Grizzly bears used open crossing structures (e.g., overpasses) more often than constricted crossings (e.g., culverts). Peak use of crossing structures for both bear species occurred in July, when high rates of foraging activity coincide with mating season. We compared the number of bears that used crossings with estimates of population abundance from a related study and determined that substantial percentages of grizzly (15.0% in 2006, 19.8% in 2008) and black bear (17.6% in 2006, 11.0% in 2008) populations used crossing structures. On the basis of our results, we concluded wildlife crossing structures provide demographic connectivity for bear populations

  19. Habitat-independent spatial structure in populations of some forest birds in eastern North America.

    PubMed

    Ricklefs, Robert E

    2013-01-01

    The extent to which populations fill available ecological space is critical to evaluating niche-based theories of community assembly, but habitat suitability for populations is difficult to assess. The absence of a species from areas of otherwise suitable habitat might indicate localized species-specific influences, including biological interactions with competitors, consumers or pathogens, on local population persistence. I used Bray-Curtis ordination axis scores, based on the distributions of forest birds across census plots in eastern North America, as proxies of general features of habitat suitability to predict local abundances of each species of small land bird. I then applied spatial analysis to identify significant spatial structure (Moran's I) in residuals (positive or negative) from predicted local densities, which would indicate localized species-specific influences on population size. Fifty-eight of 79 species exhibited no significant spatial structure in residual abundances, indicating that the ordination axes reflect most of the spatial variation in environmental conditions and habitat characteristics that influence population distribution and density or that samples were too small to detect significant spatial variation. Twenty-one species exhibited significant habitat-independent spatial structure of residuals within distances of 100 km. Aggregations of residuals for these species were independently located, for the most part, and thus probably unrelated to general features of the environment that affect many species. Among factors considered as potential causes of spatial anomalies, positive density dependence (Allee effects), intraspecific social aggregation and area sensitivity in response to forest fragmentation find little support in this analysis. Because of the species-specific nature of these clustered residuals, specialized pathogens are potential candidates to drive spatial anomalies in host abundance.

  20. Selection of Cooperation in Spatially Structured Populations

    NASA Astrophysics Data System (ADS)

    Yang, Hyunmo; Ghim, Cheol-Min

    The social dilemma games give rise to an emergence of cooperation in which altruistic individuals survive the natural selection at higher rate than random chance. We try to extend our understanding of this spatial reciprocity by including the impact of degree-degree correlation on the propensity toward prosocial behaviour in an otherwise well-mixed population. In a stochastic death-birth process with weak selection, we find that the disassortative degree mixing, or negative correlation between the degrees of neighbouring nodes significantly promotes the fixation of cooperators whereas the assortative mixing acts to suppress it. This is consistent with the fact that the spatial heterogeneity weakens the average tendency of a population to cooperate, which we describe in a unified scheme of the effective isothermality in coarse-grained networks. We also discuss the individual-level incentives that indirectly foster restructuring the social networks toward the more cooperative topologies.

  1. Accounting for subgroup structure in line-transect abundance estimates of false killer whales (Pseudorca crassidens) in Hawaiian waters.

    PubMed

    Bradford, Amanda L; Forney, Karin A; Oleson, Erin M; Barlow, Jay

    2014-01-01

    For biological populations that form aggregations (or clusters) of individuals, cluster size is an important parameter in line-transect abundance estimation and should be accurately measured. Cluster size in cetaceans has traditionally been represented as the total number of individuals in a group, but group size may be underestimated if group members are spatially diffuse. Groups of false killer whales (Pseudorca crassidens) can comprise numerous subgroups that are dispersed over tens of kilometers, leading to a spatial mismatch between a detected group and the theoretical framework of line-transect analysis. Three stocks of false killer whales are found within the U.S. Exclusive Economic Zone of the Hawaiian Islands (Hawaiian EEZ): an insular main Hawaiian Islands stock, a pelagic stock, and a Northwestern Hawaiian Islands (NWHI) stock. A ship-based line-transect survey of the Hawaiian EEZ was conducted in the summer and fall of 2010, resulting in six systematic-effort visual sightings of pelagic (n = 5) and NWHI (n = 1) false killer whale groups. The maximum number and spatial extent of subgroups per sighting was 18 subgroups and 35 km, respectively. These sightings were combined with data from similar previous surveys and analyzed within the conventional line-transect estimation framework. The detection function, mean cluster size, and encounter rate were estimated separately to appropriately incorporate data collected using different methods. Unlike previous line-transect analyses of cetaceans, subgroups were treated as the analytical cluster instead of groups because subgroups better conform to the specifications of line-transect theory. Bootstrap values (n = 5,000) of the line-transect parameters were randomly combined to estimate the variance of stock-specific abundance estimates. Hawai'i pelagic and NWHI false killer whales were estimated to number 1,552 (CV = 0.66; 95% CI = 479-5,030) and 552 (CV = 1.09; 95% CI = 97

  2. Hierarchical spatial structure of genetically variable nucleopolyhedroviruses infecting cyclic populations of western tent caterpillars.

    PubMed

    Cooper, Dawn; Cory, Jenny S; Myers, Judith H

    2003-04-01

    The cyclic population dynamics of western tent caterpillars, Malacosoma californicum pluviale, are associated with epizootics of a nucleopolyhedrovirus, McplNPV. Given the dynamic fluctuations in host abundance and levels of viral infection, host resistance and virus virulence might be expected to change during different phases of the cycle. As a first step in determining if McplNPV virulence and population structure change with host density, we used restriction fragment length polymorphism (RFLP) analysis to examine the genetic diversity of McplNPV infecting western tent caterpillar populations at different spatial scales. Thirteen dominant genetic variants were identified in 39 virus isolates (individual larvae) collected from field populations during one year of low host density, and another distinct variant was discovered among nine additional isolates in two subsequent years of declining host density. The distribution of these genetic variants was not random and indicated that the McplNPV population was structured at several spatial levels. A high proportion of the variation could be explained by family grouping, which suggested that isolates collected within a family were more likely to be the same than isolates compared among populations. Additionally, virus variants from within populations (sites) were more likely to be the same than isolates collected from tent caterpillar populations on different islands. This may indicate that there is limited mixing of virus among tent caterpillar families and populations when host population density is low. Thus there is potential for the virus to become locally adapted to western tent caterpillar populations in different sites. However, no dominant genotype was observed at any site. Whether and how selection acts on the genetically diverse nucleopolyhedrovirus populations as host density changes will be investigated over the next cycle of tent caterpillar populations.

  3. Spatial Genetic Structure of the Abundant and Widespread Peatmoss Sphagnum magellanicum Brid.

    PubMed Central

    Kyrkjeeide, Magni Olsen; Hassel, Kristian; Flatberg, Kjell Ivar; Shaw, A. Jonathan; Yousefi, Narjes; Stenøien, Hans K.

    2016-01-01

    Spore-producing organisms have small dispersal units enabling them to become widespread across continents. However, barriers to gene flow and cryptic speciation may exist. The common, haploid peatmoss Sphagnum magellanicum occurs in both the Northern and Southern hemisphere, and is commonly used as a model in studies of peatland ecology and peatmoss physiology. Even though it will likely act as a rich source in functional genomics studies in years to come, surprisingly little is known about levels of genetic variability and structuring in this species. Here, we assess for the first time how genetic variation in S. magellanicum is spatially structured across its full distribution range (Northern Hemisphere and South America). The morphologically similar species S. alaskense was included for comparison. In total, 195 plants were genotyped at 15 microsatellite loci. Sequences from two plastid loci (trnG and trnL) were obtained from 30 samples. Our results show that S. alaskense and almost all plants of S. magellanicum in the northern Pacific area are diploids and share the same gene pool. Haploid plants occur in South America, Europe, eastern North America, western North America, and southern Asia, and five genetically differentiated groups with different distribution ranges were found. Our results indicate that S. magellanicum consists of several distinct genetic groups, seemingly with little or no gene flow among them. Noteworthy, the geographical separation of diploids and haploids is strikingly similar to patterns found within other haploid Sphagnum species spanning the Northern Hemisphere. Our results confirm a genetic division between the Beringian and the Atlantic that seems to be a general pattern in Sphagnum taxa. The pattern of strong genetic population structuring throughout the distribution range of morphologically similar plants need to be considered in future functional genomic studies of S. magellanicum. PMID:26859563

  4. Very Low Population Structure in a Highly Mobile and Wide-Ranging Endangered Bird Species

    PubMed Central

    Kvistad, Lynna; Ingwersen, Dean; Pavlova, Alexandra; Bull, James K.; Sunnucks, Paul

    2015-01-01

    The loss of biodiversity following fragmentation and degradation of habitat is a major issue in conservation biology. As competition for resources increases following habitat loss and fragmentation, severe population declines may occur even in common, highly mobile species; such demographic decline may cause changes within the population structure of the species. The regent honeyeater, Anthochaera phrygia, is a highly nomadic woodland bird once common in its native southeast Australia. It has experienced a sharp decline in abundance since the late 1970s, following clearing of large areas of its preferred habitat, box-ironbark woodland, within the last 200 years. A captive breeding program has been established as part of efforts to restore this species. This study used genetic data to examine the range-wide population structure of regent honeyeaters, including spatial structure, its change through time, sex differences in philopatry and mobility, and genetic differences between the captive and wild populations. There was low genetic differentiation between birds captured in different geographic areas. Despite the recent demographic decline, low spatial structure appears to have some temporal consistency. Both sexes appear to be highly mobile, and there does not seem to be significant genetic differentiation between the captive and wild populations. We conclude that management efforts for survival of this species, including habitat protection, restoration, and release of captive-bred birds into the wild, can treat the species as effectively a single genetic population. PMID:26649426

  5. Very Low Population Structure in a Highly Mobile and Wide-Ranging Endangered Bird Species.

    PubMed

    Kvistad, Lynna; Ingwersen, Dean; Pavlova, Alexandra; Bull, James K; Sunnucks, Paul

    2015-01-01

    The loss of biodiversity following fragmentation and degradation of habitat is a major issue in conservation biology. As competition for resources increases following habitat loss and fragmentation, severe population declines may occur even in common, highly mobile species; such demographic decline may cause changes within the population structure of the species. The regent honeyeater, Anthochaera phrygia, is a highly nomadic woodland bird once common in its native southeast Australia. It has experienced a sharp decline in abundance since the late 1970s, following clearing of large areas of its preferred habitat, box-ironbark woodland, within the last 200 years. A captive breeding program has been established as part of efforts to restore this species. This study used genetic data to examine the range-wide population structure of regent honeyeaters, including spatial structure, its change through time, sex differences in philopatry and mobility, and genetic differences between the captive and wild populations. There was low genetic differentiation between birds captured in different geographic areas. Despite the recent demographic decline, low spatial structure appears to have some temporal consistency. Both sexes appear to be highly mobile, and there does not seem to be significant genetic differentiation between the captive and wild populations. We conclude that management efforts for survival of this species, including habitat protection, restoration, and release of captive-bred birds into the wild, can treat the species as effectively a single genetic population.

  6. Nutrient availability modifies species abundance and community structure of Fucus-associated littoral benthic fauna.

    PubMed

    Korpinen, Samuli; Jormalainen, Veijo; Pettay, Esko

    2010-01-01

    The brown alga Fucus vesiculosus is a foundation species in the Baltic Sea littoral, hosting a rich faunal community. We compared the species composition and diversity of invertebrate macrofauna living on F. vesiculosus between sites differing in their eutrophication status and exposure to waves at three different times during a season. We determined the size, nitrogen and phlorotannin content of the alga. The invertebrate community differed substantially between sites near fish farms and those in more pristine environment. Snails and bivalves were more abundant on the Fucus stands near fish farms than on control stands, where crustaceans were more abundant. The abundance of molluscs decreased with the increasing shore exposure, while gammaridean amphipods dominated on the exposed shores. Abundance of several taxa increased during the proceeding growing season. The density of the most important herbivore of F. vesiculosus, Idotea balthica, varied 100-fold during the season being the lowest in June and the highest in August when the generation born in the summer started to feed on Fucus. Thus, the diversity and composition of Fucus-associated invertebrate fauna varies both with environmental conditions of the stand and seasonally. Although the negative effects of eutrophication on distribution and abundance of Fucus stands are well documented, a moderate increase of nutrients was found to increase the species richness of Fucus-associated fauna in early summer.

  7. Microsatellite analysis of genetic diversity and population structure of Arabian horse populations.

    PubMed

    Khanshour, Anas; Conant, Eleanore; Juras, Rytis; Cothran, Ernest Gus

    2013-01-01

    The Arabian horse ignites imagination throughout the world. Populations of this breed exist in many countries, and recent genetic work has examined the diversity and ancestry of a few of these populations in isolation. Here, we explore 7 different populations of Arabians represented by 682 horses. Three of these are Middle Eastern populations from near the historical origin of the breed, including Syrian, Persian, and Saudi Arabian. The remaining Western populations are found in Europe (the Shagya Arabian and Polish Arabian) and in America (American Arabian). Analysis of genetic structure was carried out using 15 microsatellite loci. Genetic distances, analysis of molecular variance, factorial correspondence analysis, and a Bayesian method were applied. The results consistently show higher level of diversity within the Middle Eastern populations than the Western populations. The Western Arabian populations were the main source among population variation. Genetic differentiation was not strong among all Middle Eastern populations, but all American Arabians showed differentiation from Middle Eastern populations and were somewhat uniform among themselves. Here, we explore the diversities of many different populations of Arabian horses and find that populations not from the Middle East have noticeably lower levels of diversity, which may adversely affect the health of these populations.

  8. Coronal thermal structure and abundances of supermetal-rich solar-type stars

    NASA Technical Reports Server (NTRS)

    Brickhouse, Nancy S. (Principal Investigator); Mushotzky, Richard F. (Technical Monitor)

    2005-01-01

    This observation is for grating spectroscopy of Tau Boo, a late-type star with very high metallicity (about twice solar). Despite the extreme condition of high metallicity in the photosphere, the abundance ratios of the corona appear consistent with the general picture of a coronal abundance/activity relation. The target was obtained by XMM-Newton on 24 June 2003 for 71900 sec. The European PI Antonio Maggio is responsible for data reduction. Members of our team presented at the Cool Stars Workshop 13 held in Hamburg, Germany in July 2004 and conferred at that time on the publication of results. This project is complete except for the final publication.

  9. Genomic diversity, population structure, and migration following rapid range expansion in the Balsam poplar, Populus balsamifera.

    PubMed

    Keller, Stephen R; Olson, Matthew S; Silim, Salim; Schroeder, William; Tiffin, Peter

    2010-03-01

    Rapid range expansions can cause pervasive changes in the genetic diversity and structure of populations. The postglacial history of the Balsam Poplar, Populus balsamifera, involved the colonization of most of northern North America, an area largely covered by continental ice sheets during the last glacial maximum. To characterize how this expansion shaped genomic diversity within and among populations, we developed 412 SNP markers that we assayed for a range-wide sample of 474 individuals sampled from 34 populations. We complemented the SNP data set with DNA sequence data from 11 nuclear loci from 94 individuals, and used coalescent analyses to estimate historical population size, demographic growth, and patterns of migration. Bayesian clustering identified three geographically separated demes found in the Northern, Central, and Eastern portions of the species' range. These demes varied significantly in nucleotide diversity, the abundance of private polymorphisms, and population substructure. Most measures supported the Central deme as descended from the primary refuge of diversity. Both SNPs and sequence data suggested recent population growth, and coalescent analyses of historical migration suggested a massive expansion from the Centre to the North and East. Collectively, these data demonstrate the strong influence that range expansions exert on genomic diversity, both within local populations and across the range. Our results suggest that an in-depth knowledge of nucleotide diversity following expansion requires sampling within multiple populations, and highlight the utility of combining insights from different data types in population genomic studies.

  10. Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate

    PubMed Central

    Gorochowski, Thomas E.; Ignatova, Zoya; Bovenberg, Roel A.L.; Roubos, Johannes A.

    2015-01-01

    Translation of protein from mRNA is a complex multi-step process that occurs at a non-uniform rate. Variability in ribosome speed along an mRNA enables refinement of the proteome and plays a critical role in protein biogenesis. Detailed single protein studies have found both tRNA abundance and mRNA secondary structure as key modulators of translation elongation rate, but recent genome-wide ribosome profiling experiments have not observed significant influence of either on translation efficiency. Here we provide evidence that this results from an inherent trade-off between these factors. We find codons pairing to high-abundance tRNAs are preferentially used in regions of high secondary structure content, while codons read by significantly less abundant tRNAs are located in lowly structured regions. By considering long stretches of high and low mRNA secondary structure in Saccharomyces cerevisiae and Escherichia coli and comparing them to randomized-gene models and experimental expression data, we were able to distinguish clear selective pressures and increased protein expression for specific codon choices. The trade-off between secondary structure and tRNA-concentration based codon choice allows for compensation of their independent effects on translation, helping to smooth overall translational speed and reducing the chance of potentially detrimental points of excessively slow or fast ribosome movement. PMID:25765653

  11. Population dynamics of bowfin in a south Georgia reservoir: latitudinal comparisons of population structure, growth, and mortality

    USGS Publications Warehouse

    Porter, Nicholas J.; Bonvechio, Timothy F.; McCormick, Joshua L.; Quist, Michael

    2014-01-01

    The objectives of this study were to evaluate the population dynamics of bowfin (Amia calva) in Lake Lindsay Grace, Georgia, and to compare those dynamics to other bowfin populations. Relative abundance of bowfin sampled in 2010 in Lake Lindsay Grace was low and variable (mean±SD; 2.7±4.7 fish per hour of electrofishing). Total length (TL) of bowfin collected in Lake Lindsay Grace varied from 233–683 mm. Age of bowfin in Lake Lindsay Grace varied from 0–5 yr. Total annual mortality (A) was estimated at 68%. Both sexes appeared to be fully mature by age 2 with gonadosomatic index values above 8 for females and close to 1 for males. The majority of females were older, longer, and heavier than males. Bowfin in Lake Lindsay Grace had fast growth up to age 4 and higher total annual mortality than the other populations examined in this study. A chi-square test indicated that size structure of bowfin from Lake Lindsay Grace was different than those of a Louisiana population and two bowfin populations from the upper Mississippi River. To further assess bowfin size structure, we proposed standard length (i.e., TL) categories: stock (200 mm, 8 inches), quality (350 mm, 14 inches), preferred (460 mm, 18 inches), memorable (560 mm, 22, inches), and trophy (710 mm, 28 inches). Because our knowledge of bowfin ecology is limited, additional understanding of bowfin population dynamics provides important insight that can be used in management of bowfin across their distribution.

  12. [On the competition among discrete-structured populations: a matrix model for population dynamics of woodreed and birch growing together].

    PubMed

    Ulanova, N G; Belova, I N; Logofet, D O

    2008-01-01

    Presented is a synthesis of field, theoretical and modelling studies on joint dynamics of two species--common birch (Betula pendula Roth) and wood small reed (Calamagrostis epigeios (L.) Roth)--overgrowing a spruce forest clear-cut. A nonlinear matrix model for population dynamics of two species, which both possess non-trivial population structures and compete for a resource in common was developed as an expansion of the linear models for single-species, age-stage-structured population dynamics. Constant values of the age-stage-specific survival and reproduction rates have been modified with some decreasing functions of the (competitive group) abundances in the competitor species or/and the species itself. Special aggregation of the age-stage structure for each of the competitor species has reduced the dimension of the nonlinear matrix operator down to the level that admits accurate calibration of the model parameters on the observation data, as well as the search for an equilibrium and its stability analysis. When calibrated, the nonlinear model exhibits convergence to the steady equilibrium--a state of the phytocoenosis that is interpreted as young, closed-canopy, birch forest with suppressed woodreed population. The model illustrates the observed course of forest renewal: the appearance of birch germs and the growth of birch population overpass the woodreed competitive resistance and result in formation of young birch forest, where the birch exerts a strong suppressive impact on both the woodreed growth and the own young growth. Remarked is a potential of the model as an object of more general mathematical study and a tool to predict the course of forest renewal.

  13. Practical Bias Correction in Aerial Surveys of Large Mammals: Validation of Hybrid Double-Observer with Sightability Method against Known Abundance of Feral Horse (Equus caballus) Populations

    PubMed Central

    2016-01-01

    Reliably estimating wildlife abundance is fundamental to effective management. Aerial surveys are one of the only spatially robust tools for estimating large mammal populations, but statistical sampling methods are required to address detection biases that affect accuracy and precision of the estimates. Although various methods for correcting aerial survey bias are employed on large mammal species around the world, these have rarely been rigorously validated. Several populations of feral horses (Equus caballus) in the western United States have been intensively studied, resulting in identification of all unique individuals. This provided a rare opportunity to test aerial survey bias correction on populations of known abundance. We hypothesized that a hybrid method combining simultaneous double-observer and sightability bias correction techniques would accurately estimate abundance. We validated this integrated technique on populations of known size and also on a pair of surveys before and after a known number was removed. Our analysis identified several covariates across the surveys that explained and corrected biases in the estimates. All six tests on known populations produced estimates with deviations from the known value ranging from -8.5% to +13.7% and <0.7 standard errors. Precision varied widely, from 6.1% CV to 25.0% CV. In contrast, the pair of surveys conducted around a known management removal produced an estimated change in population between the surveys that was significantly larger than the known reduction. Although the deviation between was only 9.1%, the precision estimate (CV = 1.6%) may have been artificially low. It was apparent that use of a helicopter in those surveys perturbed the horses, introducing detection error and heterogeneity in a manner that could not be corrected by our statistical models. Our results validate the hybrid method, highlight its potentially broad applicability, identify some limitations, and provide insight and guidance

  14. Trends in sea otter population abundance in western Prince William Sound, Alaska: Progress toward recovery following the 1989 Exxon Valdez oil spill

    USGS Publications Warehouse

    Bodkin, J.L.; Ballachey, B.E.; Esslinger, G.G.

    2011-01-01

    Sea otters in western Prince William Sound (WPWS) and elsewhere in the Gulf of Alaska suffered widespread mortality as a result of oiling following the 1989 T/V Exxon Valdez oil spill. Following the spill, extensive efforts have been directed toward identifying and understanding long-term consequences of the spill and the process of recovery. We conducted annual aerial surveys of sea otter abundance from 1993 to 2009 (except for 2001 and 2006) in WPWS. We observed an increasing trend in population abundance at the scale of WPWS through 2000 at an average annual rate of 4 percent: however, at northern Knight Island where oiling was heaviest and sea otter mortality highest, no increase in abundance was evident by 2000. We continued to see significant increase in abundance at the scale of WPWS between 2001 and 2009, with an average annual rate of increase from 1993 to 2009 of 2.6 percent. We estimated the 2009 population size of WPWS to be 3,958 animals (standard error=653), nearly 2,000 animals more than the first post-spill estimate in 1993. Surveys since 2003 also have identified a significant increasing trend at the heavily oiled site in northern Knight Island, averaging about 25 percent annually and resulting in a 2009 estimated population size of 116 animals (standard error=19). Although the 2009 estimate for northern Knight Island remains about 30 percent less than the pre-spill estimate of 165 animals, we interpret this trend as strong evidence of a trajectory toward recovery of spill-affected sea otter populations in WPWS.

  15. Determining population structure and hybridization for two iris species

    PubMed Central

    Hamlin, Jennafer A P; Arnold, Michael L

    2014-01-01

    Identifying processes that promote or limit gene flow can help define the ecological and evolutionary history of a species. Furthermore, defining those factors that make up “species boundaries” can provide a definition of the independent evolutionary trajectories of related taxa. For many species, the historic processes that account for their distribution of genetic variation remain unresolved. In this study, we examine the geographic distribution of genetic diversity for two species of Louisiana Irises, Iris brevicaulis and Iris fulva. Specifically, we asked how populations are structured and if population structure coincides with potential barriers to gene flow. We also asked whether there is evidence of hybridization between these two species outside Louisiana hybrid zones. We used a genotyping-by-sequencing approach and sampled a large number of single nucleotide polymorphisms across these species' genomes. Two different population assignment methods were used to resolve population structure in I. brevicaulis; however, there was considerably less population structure in I. fulva. We used a species tree approach to infer phylogenies both within and between populations and species. For I. brevicaulis, the geography of the collection locality was reflected in the phylogeny. The I. fulva phylogeny reflected much less structure than detected for I. brevicaulis. Lastly, combining both species into a phylogenetic analysis resolved two of six populations of I. brevicaulis that shared alleles with I. fulva. Taken together, our results suggest major differences in the level and pattern of connectivity among populations of these two Louisiana Iris species. PMID:24683457

  16. Skate assemblage on the eastern Patagonian Shelf and Slope: structure, diversity and abundance.

    PubMed

    Arkhipkin, A; Brickle, P; Laptikhovsky, V; Pompert, J; Winter, A

    2012-04-01

    The eastern Patagonian Shelf and continental slope of the south-west Atlantic Ocean support a high biodiversity and abundance of skates. In this study, meso-scale differences in the assemblages, spatial and seasonal distributions of skates are revealed among six habitat zones of the eastern Patagonian Shelf characterized by distinctive oceanographic conditions. Most skates belonged to temperate fauna, and their abundance was much greater in habitats occupied by temperate waters (north-western outer shelf) or mixed waters (northern slope) than in habitats occupied by sub-Antarctic waters (SASW) (south-eastern outer shelf and southern slope). Sub-Antarctic skates were not abundant on the shelf even in habitats occupied by SASW, occurring mainly in deep areas of the lower continental slope. The majority of temperate skates migrated seasonally, shifting northward in winter and spreading southward with warming waters in summer. Most temperate species had two peaks in female maturity (mainly spring and autumn) and spawned in the same habitats where they fed. It is hypothesized that the high biodiversity and abundance of skates on the Patagonian Shelf and Slope are due to the practical absence of their natural competitors, flatfishes, which occupy similar eco-niches elsewhere.

  17. Evolution of extortion in structured populations

    NASA Astrophysics Data System (ADS)

    Szolnoki, Attila; Perc, Matjaž

    2014-02-01

    Extortion strategies can dominate any opponent in an iterated prisoner's dilemma game. But if players are able to adopt the strategies performing better, extortion becomes widespread and evolutionary unstable. It may sometimes act as a catalyst for the evolution of cooperation, and it can also emerge in interactions between two populations, yet it is not the evolutionarily stable outcome. Here we revisit these results in the realm of spatial games. We find that pairwise imitation and birth-death dynamics return known evolutionary outcomes. Myopic best response strategy updating, on the other hand, reveals counterintuitive solutions. Defectors and extortioners coarsen spontaneously, which allows cooperators to prevail even at prohibitively high temptations to defect. Here extortion strategies play the role of a Trojan horse. They may emerge among defectors by chance, and once they do, cooperators become viable as well. These results are independent of the interaction topology, and they highlight the importance of coarsening, checkerboard ordering, and best response updating in evolutionary games.

  18. Heterogeneous road networks have no apparent effect on the genetic structure of small mammal populations.

    PubMed

    Grilo, Clara; Del Cerro, Irene; Centeno-Cuadros, Alejandro; Ramiro, Victor; Román, Jacinto; Molina-Vacas, Guillem; Fernández-Aguilar, Xavier; Rodríguez, Juan; Porto-Peter, Flávia; Fonseca, Carlos; Revilla, Eloy; Godoy, José A

    2016-09-15

    Roads are widely recognized to represent a barrier to individual movements and, conversely, verges can act as potential corridors for the dispersal of many small mammals. Both barrier and corridor effects should generate a clear spatial pattern in genetic structure. Nevertheless, the effect of roads on the genetic structure of small mammal populations still remains unclear. In this study, we examine the barrier effect that different road types (4-lane highway, 2-lane roads and single-lane unpaved roads) may have on the population genetic structure of three species differing in relevant life history traits: southern water vole Arvicola sapidus, the Mediterranean pine vole Microtus duodecimcostatus and the Algerian mouse Mus spretus. We also examine the corridor effect of highway verges on the Mediterranean pine vole and the Algerian mouse. We analysed the population structure through pairwise estimates of FST among subpopulations bisected by roads, identified genetic clusters through Bayesian assignment approaches, and used simple and partial Mantel tests to evaluate the relative barrier or corridor effect of roads. No strong evidences were found for an effect of roads on population structure of these three species. The barrier effect of roads seems to be site-specific and no corridor effect of verges was found for the pine vole and Algerian mouse populations. The lack of consistent results among species and for each road type lead us to believe that the ability of individual dispersers to use those crossing structures or the habitat quality in the highway verges may have a relatively higher influence on gene flow among populations than the presence of crossing structures per se. Further research should include microhabitat analysis and the estimates of species abundance to understand the mechanisms that underlie the genetic structure observed at some sites.

  19. Global population genetic structure and biogeography of the oceanic copepods Eucalanus hyalinus and E. spinifer.

    PubMed

    Goetze, Erica

    2005-11-01

    Although theory dictates that limited gene flow between populations is a necessary precursor to speciation under allopatric and parapatric models, it is currently unclear how genetic differentiation between conspecific populations can arise in open-ocean plankton species. I examined two recently distinguished sympatric, circumglobal sister species, Eucalanus hyalinus and Eucalanus spinifer, for population genetic structure throughout their global biogeographic ranges. Here I show that oceanic zooplankton species can be highly genetically structured on macrogeographic spatial scales, despite experiencing extensive gene flow within features of the large-scale ocean circulation. Mitochondrial DNA analyses of 450 and 383 individuals of E. hyalinus and E. spinifer, respectively, revealed that habitat discontinuities at the boundaries of subtropical gyres in the North and South Pacific, as well as continental land masses, acted as effective barriers to gene flow for both species. However, the impact of specific barriers on population genetic structure varied between the sister species, despite their close phylogenetic relationship and similar circumglobal biogeogeographic distributions. The sister species differed in their oceanographic distributions, with E. spinifer dominating oligotrophic waters of the subtropical gyres and E. hyalinus more abundant along central water mass boundaries and in frontal zones and upwelling systems. This species-specific difference in the oceanographic habitat is an important factor determining the historical and contemporary patterns of dispersal of the two species. I suggest that species-specific ecological differences are likely to be a primary determinant of population genetic structure of open-ocean plankton.

  20. Social and population structure in the ant Cataglyphis emmae.

    PubMed

    Jowers, Michael J; Leniaud, Laurianne; Cerdá, Xim; Alasaad, Samer; Caut, Stephane; Amor, Fernando; Aron, Serge; Boulay, Raphaël R

    2013-01-01

    Dispersal has consequences not only for individual fitness, but also for population dynamics, population genetics and species distribution. Social Hymenoptera show two contrasting colony reproductive strategies, dependent and independent colony foundation modes, and these are often associated to the population structures derived from inter and intra-population gene flow processes conditioned by alternative dispersal strategies. Here we employ microsatellite and mitochondrial markers to investigate the population and social genetic structure and dispersal patterns in the ant Cataglyphis emmae at both, local and regional scales. We find that C. emmae is monogynous and polyandrous. Lack of detection of any population viscosity and population structure with nuclear markers at the local scale suggests efficient dispersal, in agreement with a lack of inbreeding. Contrasting demographic differences before and during the mating seasons suggest that C. emmae workers raise sexuals in peripheric nest chambers to reduce intracolonial conflicts. The high genetic differentiation recovered from the mtDNA haplotypes, together with the significant correlation of such to geographic distance, and presence of new nuclear alleles between areas (valleys) suggest long-term historical isolation between these regions, indicative of limited dispersal at the regional scale. Our findings on the ecological, social and population structure of this species increases our understanding of the patterns and processes involved under independent colony foundation.

  1. Social and Population Structure in the Ant Cataglyphis emmae

    PubMed Central

    Jowers, Michael J.; Leniaud, Laurianne; Cerdá, Xim; Alasaad, Samer; Caut, Stephane; Amor, Fernando; Aron, Serge; Boulay, Raphaël R.

    2013-01-01

    Dispersal has consequences not only for individual fitness, but also for population dynamics, population genetics and species distribution. Social Hymenoptera show two contrasting colony reproductive strategies, dependent and independent colony foundation modes, and these are often associated to the population structures derived from inter and intra-population gene flow processes conditioned by alternative dispersal strategies. Here we employ microsatellite and mitochondrial markers to investigate the population and social genetic structure and dispersal patterns in the ant Cataglyphis emmae at both, local and regional scales. We find that C. emmae is monogynous and polyandrous. Lack of detection of any population viscosity and population structure with nuclear markers at the local scale suggests efficient dispersal, in agreement with a lack of inbreeding. Contrasting demographic differences before and during the mating seasons suggest that C. emmae workers raise sexuals in peripheric nest chambers to reduce intracolonial conflicts. The high genetic differentiation recovered from the mtDNA haplotypes, together with the significant correlation of such to geographic distance, and presence of new nuclear alleles between areas (valleys) suggest long-term historical isolation between these regions, indicative of limited dispersal at the regional scale. Our findings on the ecological, social and population structure of this species increases our understanding of the patterns and processes involved under independent colony foundation. PMID:24039827

  2. Ecological factors influence population genetic structure of European grey wolves.

    PubMed

    Pilot, Malgorzata; Jedrzejewski, Wlodzimierz; Branicki, Wojciech; Sidorovich, Vadim E; Jedrzejewska, Bogumila; Stachura, Krystyna; Funk, Stephan M

    2006-12-01

    Although the mechanisms controlling gene flow among populations are particularly important for evolutionary processes, they are still poorly understood, especially in the case of large carnivoran mammals with extensive continuous distributions. We studied the question of factors affecting population genetic structure in the grey wolf, Canis lupus, one of the most mobile terrestrial carnivores. We analysed variability in mitochondrial DNA and 14 microsatellite loci for a sample of 643 individuals from 59 localities representing most of the continuous wolf range in Eastern Europe. We tested an array of geographical, historical and ecological factors to check whether they may explain genetic differentiation among local wolf populations. We showed that wolf populations in Eastern Europe displayed nonrandom spatial genetic structure in the absence of obvious physical barriers to movement. Neither topographic barriers nor past fragmentation could explain spatial genetic structure. However, we found that the genetic differentiation among local populations was correlated with climate, habitat types, and wolf diet composition. This result shows that ecological processes may strongly influence the amount of gene flow among populations. We suggest natal-habitat-biased dispersal as an underlying mechanism linking population ecology with population genetic structure.

  3. HOW POPULATION STRUCTURE SHAPES NEIGHBORHOOD SEGREGATION*

    PubMed Central

    Bruch, Elizabeth E.

    2014-01-01

    This study investigates how choices about social affiliation based on one attribute can exacerbate or attenuate segregation on another correlated attribute. The specific application is the role of racial and economic factors in generating patterns of racial residential segregation. I identify three population parameters—between-group inequality, within-group inequality, and relative group size—that determine how income inequality between race groups affects racial segregation. I use data from the Panel Study of Income Dynamics to estimate models of individual-level residential mobility, and incorporate these estimates into agent-based models. I then simulate segregation dynamics under alternative assumptions about: (1) the relative size of minority groups; and (2) the degree of correlation between race and income among individuals. I find that income inequality can have offsetting effects at the high and low ends of the income distribution. I demonstrate the empirical relevance of the simulation results using fixed-effects, metro-level regressions applied to 1980-2000 U.S. Census data. PMID:25009360

  4. [Effects of macro-jellyfish abundance dynamics on fishery resource structure in the Yangtze River estuary and its adjacent waters].

    PubMed

    Shan, Xiu-Juan; Zhuang, Zhi-Meng; Jin, Xian-Shi; Dai, Fang-Qun

    2011-12-01

    Based on the bottom trawl survey data in May 2007 and May and June 2008, this paper analyzed the effects of the abundance dynamics of macro-jellyfish on the species composition, distribution, and abundance of fishery resource in the Yangtze River estuary and its adjacent waters. From May 2007 to June 2008, the average catch per haul and the top catch per haul of macro-jellyfish increased, up to 222.2 kg x h(-1) and 1800 kg x h(-1) in June 2008, respectively. The macro-jellyfish were mainly distributed in the areas around 50 m isobath, and not beyond 100 m isobath where was the joint front of the coastal waters of East China Sea, Yangtze River runoff, and Taiwan Warm Current. The main distribution area of macro-jellyfish in June migrated northward, as compared with that in May, and the highest catches of macro-jellyfish in May 2007 and May 2008 were found in the same sampling station (122.5 degrees E, 28.5 degrees N). In the sampling stations with higher abundance of macro-jellyfish, the fishery abundance was low, and the fishery species also changed greatly, mainly composed by small-sized species (Trachurus japonicus, Harpadon nehereus, and Acropoma japonicum) and pelagic species (Psenopsis anomala, Octopus variabilis) and Trichiurus japonicus, and P. anomala accounted for 23.7% of the total catch in June 2008. Larimichthys polyactis also occupied higher proportion of the total catch in sampling stations with higher macro-jellyfish abundance, but the demersal species Lophius litulon was not found, and a few crustaceans were collected. This study showed that macro-jellyfish had definite negative effects on the fishery community structure and abundance in the Yangtze River estuary fishery ecosystem, and further, changed the energy flow patterns of the ecosystem through cascading trophic interactions. Therefore, macro-jellyfish was strongly suggested to be an independent ecological group when the corresponding fishery management measures were considered.

  5. Genetic Variation and Population Structure in Native Americans

    PubMed Central

    Ramachandran, Sohini; Ray, Nicolas; Bedoya, Gabriel; Rojas, Winston; Parra, Maria V; Molina, Julio A; Gallo, Carla; Mazzotti, Guido; Poletti, Giovanni; Hill, Kim; Hurtado, Ana M; Labuda, Damian; Klitz, William; Barrantes, Ramiro; Bortolini, Maria Cátira; Salzano, Francisco M; Petzl-Erler, Maria Luiza; Tsuneto, Luiza T; Llop, Elena; Rothhammer, Francisco; Excoffier, Laurent; Feldman, Marcus W; Rosenberg, Noah A; Ruiz-Linares, Andrés

    2007-01-01

    We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians—signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1) a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2) a relative lack of differentiation between Mesoamerican and Andean populations, (3) a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4) a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas. PMID:18039031

  6. Galactic Structure from Open Clusters: Photometric Characterization of Reddening, Distance and Abundance

    NASA Astrophysics Data System (ADS)

    Anthony-Twarog, Barbara; Twarog, Bruce A.; Schuster, William

    1999-02-01

    Our recent work with open clusters has indicated a surprising demarcation of the Milky Way disk's metallicity as a function of distance from the Galactic center - an apparently abrupt drop in [Fe/H] from solar to -0.3 at R_GC=10 kpc (Twarog, Ashman & Anthony- Twarog 1997). We have asserted that due to uncertain reddenings, distances and abundance data, the step-down in [Fe/H] at 10 kpc has long been masked in previous studies or interpreted as a declining radial gradient in the disk's metallicity. Current work, including observations proposed here, will address these issues for disk clusters by using uvbyCaH(beta) photometry to determine foreground reddenings, abundances and cluster distances.

  7. Plasmodium vivax Diversity and Population Structure across Four Continents

    PubMed Central

    Koepfli, Cristian; Rodrigues, Priscila T.; Antao, Tiago; Orjuela-Sánchez, Pamela; Van den Eede, Peter; Gamboa, Dionicia; van Hong, Nguyen; Bendezu, Jorge; Erhart, Annette; Barnadas, Céline; Ratsimbasoa, Arsène; Menard, Didier; Severini, Carlo; Menegon, Michela; Nour, Bakri Y. M.; Karunaweera, Nadira; Mueller, Ivo; Ferreira, Marcelo U.; Felger, Ingrid

    2015-01-01

    Plasmodium vivax is the geographically most widespread human malaria parasite. To analyze patterns of microsatellite diversity and population structure across countries of different transmission intensity, genotyping data from 11 microsatellite markers was either generated or compiled from 841 isolates from four continents collected in 1999–2008. Diversity was highest in South-East Asia (mean allelic richness 10.0–12.8), intermediate in the South Pacific (8.1–9.9) Madagascar and Sudan (7.9–8.4), and lowest in South America and Central Asia (5.5–7.2). A reduced panel of only 3 markers was sufficient to identify approx. 90% of all haplotypes in South Pacific, African and SE-Asian populations, but only 60–80% in Latin American populations, suggesting that typing of 2–6 markers, depending on the level of endemicity, is sufficient for epidemiological studies. Clustering analysis showed distinct clusters in Peru and Brazil, but little sub-structuring was observed within Africa, SE-Asia or the South Pacific. Isolates from Uzbekistan were exceptional, as a near-clonal parasite population was observed that was clearly separated from all other populations (FST>0.2). Outside Central Asia FST values were highest (0.11–0.16) between South American and all other populations, and lowest (0.04–0.07) between populations from South-East Asia and the South Pacific. These comparisons between P. vivax populations from four continents indicated that not only transmission intensity, but also geographical isolation affect diversity and population structure. However, the high effective population size results in slow changes of these parameters. This persistency must be taken into account when assessing the impact of control programs on the genetic structure of parasite populations. PMID:26125189

  8. The physical structure of Magellanic Cloud H II regions. II. Elemental abundances

    NASA Astrophysics Data System (ADS)

    Vermeij, R.; van der Hulst, J. M.

    2002-09-01

    Based on a new data set of optical and infrared spectra described in Vermeij et al. (\\cite{Ronald}), we analyse the gas-phase elemental abundances of a sample of H Ii regions in the Large and Small Magellanic Cloud. The combined optical and infrared data set gives us access to all the ionization stages of astrophysically important elements such as sulfur and oxygen. We self-consistently determine the electron temperatures and densities for the \\elem{O}{+}, \\elem{S}{++} and \\elem{O}{++} ionization zones, and use these parameters in the derivation of the ionic fractions. We discuss the uncertainties on these ionic fractions. The different relations between the electron temperatures as proposed by Garnett (\\cite{Garnett}) and Thuan et al. (\\cite{Thuan}) are confronted with our results. We find our electron temperatures to be consistent with these relations, although the relation between Te,[S Iii] and Te, [O Iii] might be slightly steeper than predicted. We investigate the reliability of the Ionization Correction Factors (ICFs) used in the derivation of the full elemental abundances of sulfur and neon. We conclude that the prescription for the ICF used to derive the sulfur abundance as given by Stasińska (\\cite{Stas1}) for alpha = 3 is accurate for \\elem{O}{+}/O > 0.20. No conclusions could be drawn for neon. Avoiding the use of ICFs as much as possible, we then proceed to derive the full elemental abundances. We calculate a grid of general photoionization models to compare our results with the ``bright-line'' abundance diagnostics for oxygen (R23) and sulfur (S23(4)). The reliability of the newly proposed S234 parameter (Oey & Shields \\cite{oey}) which includes emission lines from \\elem{S}{+}, \\elem{S}{++} and \\elem{S}{+3} is checked. We find a very good agreement between the S234 models and our analysis results. Finally, we compare the heavy element-to-oxygen ratios of our sample objects to those of giant H Ii regions in a large sample of low

  9. Distribution, Abundance and Population Structuring of Beaked Whales in the Great Bahama Canyon, Northern Bahamas

    DTIC Science & Technology

    2008-01-01

    University of Aberdeen, Scotland, U.K. 129 pp. Evans, D.I. and G.R. England. (2001) Joint interim report Bahamas marine mammal stranding event of 15... Marine Mammal Research Organisation P.O. Box AB-20714 Marsh Harbour Abaco, Bahamas phone: (242) 366-4155 fax: (242) 366-4155 email...Diane.Claridge@bahamaswhales.org Dr. John William Durban National Marine Mammal Laboratory 7600 Sand Point Way NE Seattle, WA 98115 phone: (206) 526

  10. Distribution, Abundance and Population Structuring of Beaked Wales in the Great Bahama Canyon, Northern Bahamas

    DTIC Science & Technology

    2012-09-02

    3) To collect skin and blubber biopsy samples to investigate beaked whale diet through fatty acid, stable isotope and contaminant analyses; and...concentrations of POPs suggests only slight inter-species differences. The levels of contamination in the Bahamas whales were not inordinately high and for...killer whales {Orcinus orcä) in the Gulf of Alaska. Table 4. Comparison of contaminant concentration levels (ng/g lipid) between Blainville’s and

  11. Distribution, Abundance and Population Structuring of Beaked Whales in the Great Bahama Canyon, Northern Bahamas

    DTIC Science & Technology

    2011-09-30

    20714 Marsh Harbour Abaco, Bahamas phone: (242) 366-4155 fax: (242) 366-4155 email: dclaridge@bahamaswhales.org John William Durban, Ph.D...NOAA Southwest Fisheries Science Center 3333 N. Torrey Pines Court La Jolla, CA 92037 phone: (858) 334-2866 email: John.Durban@noaa.gov...Phillip Morin, Ph.D. NOAA Southwest Fisheries Science Center 3333 N. Torrey Pines Court La Jolla, CA 92037 phone: (858) 546-7165 email

  12. Statistical validation of structured population models for Daphnia magna.

    PubMed

    Adoteye, Kaska; Banks, H T; Cross, Karissa; Eytcheson, Stephanie; Flores, Kevin B; LeBlanc, Gerald A; Nguyen, Timothy; Ross, Chelsea; Smith, Emmaline; Stemkovski, Michael; Stokely, Sarah

    2015-08-01

    In this study we use statistical validation techniques to verify density-dependent mechanisms hypothesized for populations of Daphnia magna. We develop structured population models that exemplify specific mechanisms and use multi-scale experimental data in order to test their importance. We show that fecundity and survival rates are affected by both time-varying density-independent factors, such as age, and density-dependent factors, such as competition. We perform uncertainty analysis and show that our parameters are estimated with a high degree of confidence. Furthermore, we perform a sensitivity analysis to understand how changes in fecundity and survival rates affect population size and age-structure.

  13. Patterns of admixture and population structure in native populations of Northwest North America.

    PubMed

    Verdu, Paul; Pemberton, Trevor J; Laurent, Romain; Kemp, Brian M; Gonzalez-Oliver, Angelica; Gorodezky, Clara; Hughes, Cris E; Shattuck, Milena R; Petzelt, Barbara; Mitchell, Joycelynn; Harry, Harold; William, Theresa; Worl, Rosita; Cybulski, Jerome S; Rosenberg, Noah A; Malhi, Ripan S

    2014-08-01

    The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North, Central, and South America. Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendants, reporting on the genomic impact of the history of admixture with colonizing populations of European and African ancestry. However, relatively little genomic research has been conducted on admixture in indigenous North American populations. In this study, we analyze genomic data at 475,109 single-nucleotide polymorphisms sampled in indigenous peoples of the Pacific Northwest in British Columbia and Southeast Alaska, populations with a well-documented history of contact with European and Asian traders, fishermen, and contract laborers. We find that the indigenous populations of the Pacific Northwest have higher gene diversity than Latin American indigenous populations. Among the Pacific Northwest populations, interior groups provide more evidence for East Asian admixture, whereas coastal groups have higher levels of European admixture. In contrast with many Latin American indigenous populations, the variance of admixture is high in each of the Pacific Northwest indigenous populations, as expected for recent and ongoing admixture processes. The results reveal some similarities but notable differences between admixture patterns in the Pacific Northwest and those in Latin America, contributing to a more detailed understanding of the genomic consequences of European colonization events throughout the Americas.

  14. Patterns of Admixture and Population Structure in Native Populations of Northwest North America

    PubMed Central

    Verdu, Paul; Pemberton, Trevor J.; Laurent, Romain; Kemp, Brian M.; Gonzalez-Oliver, Angelica; Gorodezky, Clara; Hughes, Cris E.; Shattuck, Milena R.; Petzelt, Barbara; Mitchell, Joycelynn; Harry, Harold; William, Theresa; Worl, Rosita; Cybulski, Jerome S.; Rosenberg, Noah A.; Malhi, Ripan S.

    2014-01-01

    The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North, Central, and South America. Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendants, reporting on the genomic impact of the history of admixture with colonizing populations of European and African ancestry. However, relatively little genomic research has been conducted on admixture in indigenous North American populations. In this study, we analyze genomic data at 475,109 single-nucleotide polymorphisms sampled in indigenous peoples of the Pacific Northwest in British Columbia and Southeast Alaska, populations with a well-documented history of contact with European and Asian traders, fishermen, and contract laborers. We find that the indigenous populations of the Pacific Northwest have higher gene diversity than Latin American indigenous populations. Among the Pacific Northwest populations, interior groups provide more evidence for East Asian admixture, whereas coastal groups have higher levels of European admixture. In contrast with many Latin American indigenous populations, the variance of admixture is high in each of the Pacific Northwest indigenous populations, as expected for recent and ongoing admixture processes. The results reveal some similarities but notable differences between admixture patterns in the Pacific Northwest and those in Latin America, contributing to a more detailed understanding of the genomic consequences of European colonization events throughout the Americas. PMID:25122539

  15. Amplification on Undirected Population Structures: Comets Beat Stars.

    PubMed

    Pavlogiannis, Andreas; Tkadlec, Josef; Chatterjee, Krishnendu; Nowak, Martin A

    2017-12-01

    The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population. The fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure. Amplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade. In this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Comet-swarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively.

  16. Genetic structure of North American wolverine (Gulo gulo) populations.

    PubMed

    Kyle, C J; Strobeck, C

    2001-02-01

    Wolverines (Gulo gulo) are found in low densities throughout their circumpolar distribution. They are also potentially susceptible to human-caused population fragmentation (development, recreation and fur harvesting). The combination of these factors has contributed to this species being listed as having either vulnerable or endangered status across much of its current range. The effects of inherently low densities and anthropogenic pressures on the genetic structure and variation of wolverine populations are, as yet, unknown. In this study, 461 individuals were typed at 12 microsatellite loci to investigate the population genetic structure of wolverines from north-western Alaska to eastern Manitoba. Levels of gene flow and population differentiation among the sampled regions were estimated via a genotype assignment test, pairwise F(ST), and two genetic distance measures. Our results suggest that wolverine populations from southernmost regions, in which anthropogenic factors are strongest, revealed more genetic structuring than did northern populations. Furthermore, these results suggest that reductions in this species' range may have led to population fragmentation in the extreme reaches of its southern distribution. The continued reduction of suitable habitat for this species may lead to more populations becoming isolated remnants of a larger distribution of northern wolverines, as documented in other North American carnivore species.

  17. Genetic diversity and population structure in contemporary house sparrow populations along an urbanization gradient

    PubMed Central

    Vangestel, C; Mergeay, J; Dawson, D A; Callens, T; Vandomme, V; Lens, L

    2012-01-01

    House sparrow (Passer domesticus) populations have suffered major declines in urban as well as rural areas, while remaining relatively stable in suburban ones. Yet, to date no exhaustive attempt has been made to examine how, and to what extent, spatial variation in population demography is reflected in genetic population structuring along contemporary urbanization gradients. Here we use putatively neutral microsatellite loci to study if and how genetic variation can be partitioned in a hierarchical way among different urbanization classes. Principal coordinate analyses did not support the hypothesis that urban/suburban and rural populations comprise two distinct genetic clusters. Comparison of FST values at different hierarchical scales revealed drift as an important force of population differentiation. Redundancy analyses revealed that genetic structure was strongly affected by both spatial variation and level of urbanization. The results shown here can be used as baseline information for future genetic monitoring programmes and provide additional insights into contemporary house sparrow dynamics along urbanization gradients. PMID:22588131

  18. Sea otter population structure and ecology in Alaska

    USGS Publications Warehouse

    Bodkin, James L.; Monson, Daniel H.

    2002-01-01

    Sea otters are the only fully marine otter. They share a common ancestry with the Old World land otters, but their route of dispersal to the New World is uncertain. The historic range of the species is along the northern Pacific Ocean rim, between central Baja California and the islands of northern Japan. Because they forage almost exclusively on bottom-dwelling marine invertebrates such as clams, snails, crabs, and sea urchins, they predominantly occur near shore. Their offshore distribution is limited by their diving ability; although they are capable of diving to more than 100 meters deep, most of their feeding takes place between the shoreline and depths of 40 meters. They are social animals, generally resting in protected bays or kelp forests in groups, commonly referred to as rafts. Because they are gregarious, possess a fine fur, and occur primarily near shore, they have been exploited by humans for as long as they have co-occupied coastal marine communities.During the late Pleistocene, glacial advances and retreats in the northern latitudes likely influenced genetic exchange within the sea otter’s northern range. When the glaciers were at their maximum, ice sheets extended over large coastal areas, isolating sea otter populations and causing local extinctions. During periods of glacial retreat, sea otters likely recolonized the newly available habitats, allowing exchange of individuals and gene flow between populations.Beginning in about 1750, sea otter populations underwent dramatic declines as a direct result of commercial harvest for their furs. Explorations by Vitus Bering led to the discovery of abundant sea otter populations in the Aleutian Islands. The early harvest, conducted by Russians with enslaved Aleut hunters, began in the eastern Aleutians. Eventually the harvest became multinational and contributed significantly to the exploration and settlement of the North Pacific coastline by Europeans. There were two distinct periods of harvest

  19. Population genetic structure of Aedes albopictus in Penang, Malaysia.

    PubMed

    Zawani, M K N; Abu, H A; Sazaly, A B; Zary, S Y; Darlina, M N

    2014-10-07

    The mosquito Aedes albopictus is indigenous to Southeast Asian and is a vector for arbovirus diseases. Studies examining the population genetics structure of A. albopictus have been conducted worldwide; however, there are no documented reports on the population genetic structure of A. albopictus in Malaysia, particularly in Penang. We examined the population genetics of A. albopictus based on a 445-base pair segment of the mitochondrial DNA cytochrome oxidase 1 gene among 77 individuals from 9 localities representing 4 regions (Seberang Perai Utara, Seberang Perai Tengah, Northeast, and Southwest) of Penang. A total of 37 haplotypes were detected, including 28 unique haplotypes. The other 9 haplotypes were shared among various populations. These shared haplotypes reflect the weak population genetic structure of A. albopictus. The phylogenetic tree showed a low bootstrap value with no genetic structure, which was supported by minimum spanning network analysis. Analysis of mismatch distribution showed poor fit of equilibrium distribution. The genetic distance showed low genetic variation, while pairwise FST values showed no significant difference between all regions in Penang except for some localities. High haplotype diversity and low nucleotide diversity was observed for cytochrome oxidase 1 mtDNA. We conclude that there is no population genetic structure of A. albopictus mosquitoes in the Penang area.

  20. Population genetic structure of Theileria parva field isolates from indigenous cattle populations of Uganda.

    PubMed

    Muwanika, Vincent; Kabi, Fredrick; Masembe, Charles

    2016-03-01

    Theileria parva causes East Coast Fever (ECF) a protozoan infection which manifests as a non-symptomatic syndrome among endemically stable indigenous cattle populations. Knowledge of the current genetic diversity and population structure of T. parva is critical for predicting pathogen evolutionary trends to inform development of effective control strategies. In this study the population genetic structure of 78 field isolates of T. parva from indigenous cattle (Ankole, n=41 and East African shorthorn Zebu (EASZ), n=37) sampled from the different agro ecological zones (AEZs) of Uganda was investigated. A total of eight mini- and micro-satellite markers encompassing the four chromosomes of T. parva were used to genotype the study field isolates. The genetic diversity of the surveyed T. parva populations was observed to range from 0.643±0.55 to 0.663±0.41 among the Central and Western AEZs respectively. The overall Wright's F index showed significant genetic variation between the surveyed T. parva populations based on the different AEZs and indigenous cattle breeds (FST=0.133, p<0.01) and (FST=0.101, p<0.01) respectively. Significant pairwise population genetic differentiations (p<0.05) were observed with FST values ranging from 0.048 to 0.173 between the eastern and northern, eastern and western populations respectively. The principal component analysis (PCA) showed a high level of genetic and geographic sub-structuring among populations. Linkage disequilibrium was observed when populations from all the study AEZs were treated as a single population and when analysed separately. On the overall, the significant genetic diversity and geographic sub-structuring exhibited among the study T. parva isolates has critical implications for ECF control.

  1. Low leopard populations in protected areas of Maputaland: a consequence of poaching, habitat condition, abundance of prey, and a top predator.

    PubMed

    Ramesh, Tharmalingam; Kalle, Riddhika; Rosenlund, Havard; Downs, Colleen T

    2017-03-01

    Identifying the primary causes affecting population densities and distribution of flagship species are necessary in developing sustainable management strategies for large carnivore conservation. We modeled drivers of spatial density of the common leopard (Panthera pardus) using a spatially explicit capture-recapture-Bayesian approach to understand their population dynamics in the Maputaland Conservation Unit, South Africa. We camera-trapped leopards in four protected areas (PAs) of varying sizes and disturbance levels covering 198 camera stations. Ours is the first study to explore the effects of poaching level, abundance of prey species (small, medium, and large), competitors (lion Panthera leo and spotted hyenas Crocuta crocuta), and habitat on the spatial distribution of common leopard density. Twenty-six male and 41 female leopards were individually identified and estimated leopard density ranged from 1.6 ± 0.62/100 km(2) (smallest PA-Ndumo) to 8.4 ± 1.03/100 km(2) (largest PA-western shores). Although dry forest thickets and plantation habitats largely represented the western shores, the plantation areas had extremely low leopard density compared to native forest. We found that leopard density increased in areas when low poaching levels/no poaching was recorded in dry forest thickets and with high abundance of medium-sized prey, but decreased with increasing abundance of lion. Because local leopard populations are vulnerable to extinction, particularly in smaller PAs, the long-term sustainability of leopard populations depend on developing appropriate management strategies that consider a combination of multiple factors to maintain their optimal habitats.

  2. Stage-Structured Population Dynamics of AEDES AEGYPTI

    NASA Astrophysics Data System (ADS)

    Yusoff, Nuraini; Budin, Harun; Ismail, Salemah

    Aedes aegypti is the main vector in the transmission of dengue fever, a vector-borne disease affecting world population living in tropical and sub-tropical countries. Better understanding of the dynamics of its population growth will help in the efforts of controlling the spread of this disease. In looking at the population dynamics of Aedes aegypti, this paper explored the stage-structured modeling of the population growth of the mosquito using the matrix population model. The life cycle of the mosquito was divided into five stages: eggs, larvae, pupae, adult1 and adult2. Developmental rates were obtained for the average Malaysian temperature and these were used in constructing the transition matrix for the matrix model. The model, which was based only on temperature, projected that the population of Aedes aegypti will blow up with time, which is not realistic. For further work, other factors need to be taken into account to obtain a more realistic result.

  3. Effects of Chemical Abundances on the Structure and Dynamics of the Solar Atmosphere

    NASA Astrophysics Data System (ADS)

    Demarque, Pierre; Basu, S.; Robinson, F.; Hunter, C.; Kallinger, T.

    2008-05-01

    This paper presents a comparison between two three-dimensional radiative hydrodynamical (3D RHD) simulations of the solar outer layers using the Grevesse & Sauval (1998; GS98) and the Asplund, Grevesse & Sauval (2005; AGS05) mixtures, respectively. The AGS05 mixture is a revision of the solar abundance mixture using a model atmosphere based on the stratification and dynamics of a solar 3D RHD simulation performed with the GS98 mixture, using the code of Stein & Nordlund (1989, 1998). Our simulations use the same code, and physically realistic treatment of radiative opacities and equation of state as Robinson et al. (2003). A comparison between our GS98 and AGS05 3D simulations shows differences both in the mean vertical temperature gradient and in the turbulent velocity field in the line forming region of the solar atmosphere. The whole superadiabatic layer (SAL) in the AGS05 simulation, including its peak, is shifted outward with respect to the GS98 SAL. Turbulent velocities, critical for absorption line profile calculations, are larger in the AGS05 simulation by about 10%. Since opacities for the AGS05 mixture are lower than those for the GS98 mixture, the T-τ relations derived from the two simulations are different. At 5000K, τ obtained from the GS98 simulation is about 30% larger than that obtained from the AGS05 simulation. These results show the importance of preserving self consistency in the chemical abundances between the model atmosphere and the 3D HRD simulation. When deriving the solar abundances, one must iterate the chemical composition in the model atmosphere, and hence in the 3D simulation on which the atmosphere is based. This research was supported in part by NASA/ATP grant NAG5-13299 (PD and FR) and NSF grant ATM 0348837 to SB.

  4. The chemical abundances of the stellar populations in the Leo I and II dSph galaxies

    NASA Astrophysics Data System (ADS)

    Bosler, Tammy L.; Smecker-Hane, Tammy A.; Stetson, Peter B.

    2007-06-01

    We have obtained calcium abundances and radial velocities for 102 red giant branch (RGB) stars in the Leo I dwarf spheroidal galaxy (dSph) and 74 RGB stars in the Leo II dSph using the low-resolution spectrograph (LRIS) on the Keck I 10-m telescope. We report on the calcium abundances [Ca/H] derived from the strengths of the CaII triplet absorption lines at 8498, 8542 and 8662 Å in the stellar spectra using a new empirical CaII triplet calibration to [Ca/H]. The two galaxies have different average [Ca/H] values of -1.34 +/- 0.02 for Leo I and -1.65 +/- 0.02 for Leo II with intrinsic abundance dispersions of 1.2 and 1.0 dex, respectively. The typical random and total errors in derived abundances are 0.10 and 0.17 dex per star. For comparison to the existing literature, we also converted our CaII measurements to [Fe/H] on the scale of Carretta and Gratton (1997) though we discuss why this may not be the best determinant of metallicity; Leo I has a mean [Fe/H] = -1.34 and Leo II has a mean [Fe/H] = -1.59. The metallicity distribution function of Leo I is approximately Gaussian in shape with an excess at the metal-rich end, while that of Leo II shows an abrupt cut-off at the metal-rich end. The lower mean metallicity of Leo II is consistent with the fact that it has a lower luminosity, hence lower the total mass than Leo I; thus, the evolution of Leo II may have been affected more by mass lost in galactic winds. Our direct and independent measurement of the metallicity distributions in these dSph will allow a more accurate star-formation histories to be derived from future analysis of their colour-magnitude diagrams(CMDs). Data presented herein were obtained at the W.M. Keck Observatory, which is operated as a scientific partnership among the California Institute of Technology, the University of California and the National Aeronautics and Space Administration. The Observatory was made possible by the generous financial support of the W. M. Keck Foundation. E

  5. Pulses of movement across the sea ice: population connectivity and temporal genetic structure in the arctic fox.

    PubMed

    Norén, Karin; Carmichael, Lindsey; Fuglei, Eva; Eide, Nina E; Hersteinsson, Pall; Angerbjörn, Anders

    2011-08-01

    Lemmings are involved in several important functions in the Arctic ecosystem. The Arctic fox (Vulpes lagopus) can be divided into two discrete ecotypes: "lemming foxes" and "coastal foxes". Crashes in lemming abundance can result in pulses of "lemming fox" movement across the Arctic sea ice and immigration into coastal habitats in search for food. These pulses can influence the genetic structure of the receiving population. We have tested the impact of immigration on the genetic structure of the "coastal fox" population in Svalbard by recording microsatellite variation in seven loci for 162 Arctic foxes sampled during the summer and winter over a 5-year period. Genetic heterogeneity and temporal genetic shifts, as inferred by STRUCTURE simulations and deviations from Hardy-Weinberg proportions, respectively, were recorded. Maximum likelihood estimates of movement as well as STRUCTURE simulations suggested that both immigration and genetic mixture are higher in Svalbard than in the neighbouring "lemming fox" populations. The STRUCTURE simulations and AMOVA revealed there are differences in genetic composition of the population between summer and winter seasons, indicating that immigrants are not present in the reproductive portion of the Svalbard population. Based on these results, we conclude that Arctic fox population structure varies with time and is influenced by immigration from neighbouring populations. The lemming cycle is likely an important factor shaping Arctic fox movement across sea ice and the subsequent population genetic structure, but is also likely to influence local adaptation to the coastal habitat and the prevalence of diseases.

  6. Moist convection and the vertical structure and water abundance of Jupiter's atmosphere

    NASA Technical Reports Server (NTRS)

    Del Genio, Anthony D.; Mcgrattan, Kevin B.

    1990-01-01

    The cumulative effects of an ensemble of moist convective plumes on a conditionally unstable atmosphere are predicted by a model of moist convection on Jupiter in which the heating/cooling and drying/moistening of the environment occur through (1) compensating subsidence, (2) detrainment of updraft air at cloud tops, and (3) the evaporation and melting of falling condensate. Parahydrogen is transported as a passive tracer. Pure moist convective, mixed moist-dry convective, and primarily dry convective regimes are possible, depending on the assumed deep-water abundance, efficiency of condensate evaporation, and initial temperature profile.

  7. Abundance, diversity, and seasonal population dynamics of aquatic Coleoptera and Heteroptera in rice fields: effects of direct seeding management.

    PubMed

    Watanabe, Kohei; Koji, Shinsaku; Hidaka, Kazumasa; Nakamura, Koji

    2013-10-01

    Recent introduction of modern drainage systems has produced intensely dry conditions in rice farmlands and has degraded habitats for aquatic animals. In this study, we compared water beetle (Coleoptera) and water bug (Heteroptera) communities within rice fields cultivated under different management regimes: V-furrow no-till direct-seeding (DS) and conventional regimes. In DS fields, rice is sown in well-drained fields, and flooding is performed a month later than in conventional rice fields. DS fields are then continuously flooded until harvesting; unlike in conventional fields, where midseason drainage is performed in summer. We observed that DS fields supported higher densities of water beetles and water bugs than conventional fields, probably because of the high compatibility between the flooding period and the reproductive season of the insects. The species richness of water beetles was higher in DS fields than in conventional fields. Overall, DS fields showed higher water beetle and water bug abundance, but the effect was variable for individual species: seven species were more abundant in DS than in conventional fields, whereas two species showed opposite tendencies. Considering the differential responses among species to the management regimes, a mosaic of DS and conventional fields is preferable to either field alone for the conservation of aquatic insects in rice agroecosystems.

  8. Sulfamethoxazole and COD increase abundance of sulfonamide resistance genes and change bacterial community structures within sequencing batch reactors.

    PubMed

    Guo, Xueping; Pang, Weihai; Dou, Chunling; Yin, Daqiang

    2017-05-01

    The abundant microbial community in biological treatment processes in wastewater treatment plants (WWTPs) may potentially enhance the horizontal gene transfer of antibiotic resistance genes with the presence of antibiotics. A lab-scale sequencing batch reactor was designed to investigate response of sulfonamide resistance genes (sulI, sulII) and bacterial communities to various concentrations of sulfamethoxazole (SMX) and chemical oxygen demand (COD) of wastewater. The SMX concentrations (0.001 mg/L, 0.1 mg/L and 10 mg/L) decreased with treatment time and higher SMX level was more difficult to remove. The presence of SMX also significantly reduced the removal efficiency of ammonia nitrogen, affecting the normal function of WWTPs. All three concentrations of SMX raised both sulI and sulII genes with higher concentrations exhibiting greater increases. The abundance of sul genes was positive correlated with treatment time and followed the second-order reaction kinetic model. Interestingly, these two genes have rather similar activity. SulI and sulII gene abundance also performed similar response to COD. Simpson index and Shannon-Weiner index did not show changes in the microbial community diversity. However, the 16S rRNA gene cloning and sequencing results showed the bacterial community structures varied during different stages. The results demonstrated that influent antibiotics into WWTPs may facilitate selection of ARGs and affect the wastewater conventional treatment as well as the bacteria community structures.

  9. Population genetic structure of mussels from the Baltic Sea

    NASA Astrophysics Data System (ADS)

    Bulnheim, H.-P.; Gosling, E.

    1988-03-01

    In a macrogeographic survey, the population genetic structure of mussels from various regions of the Baltic Sea, a large semi-enclosed brackish-water basin, was examined with reference to Mytilus edulis and M. galloprovincialis samples from the North Sea, Irish coast and southern Portugal. Electrophoretically detectable variation was analysed at 6 polymorphic enzyme loci ( Ap, Est-D, Lap-2, Odh, Pgi and Pgm). Evidence was provided of a remarkably large amount of biochemical genetic differentiation among ecologically and morphologically divergent mussel populations in the Baltic. Patterns of allele frequencies in low-salinity populations from the area of the Baltic Proper were demonstrated to be widely homogeneous but contrast strongly with those of the western Baltic, the latter resembling populations from marine habitats of the North Sea. Associated with a pronounced salinity gradient, the spatial heterogeneity in gene-pool structure is indicated by steep clines of allele frequency changes in the area of the eastern Danish isles. The adaptive significance of the observed allozymic variation is suggested. From genetic distance estimates, the subdivision of population structure is discussed in relation to the significant amount of differentiation detected within Mytilus populations to date and to the evolutionary time required for the divergence of Baltic mussel populations. The allozymic data provide evidence for the genetic distinctiveness of mussels from the low-salinity areas of the Baltic. Their position at the specific or subspecific level of classification requires further consideration.

  10. Abundance and structure of microbial loop components (bacteria and protists) in lakes of different trophic status.

    PubMed

    Ryszard, Chrost J; Tomasz, Adamczewski; Kalinowska, Krystyna; Skowronska, Agnieszka

    2009-09-01

    The abundance, biomass, size distribution, and taxonomic composition of bacterial and protistan (heterotrophic and autotrophic nanoflagellates and ciliates) communities were investigated in six lakes of Masurian Lake District (north-eastern Poland) differing in trophic state. Samples were taken from the trophogenic water layer during summer stratification periods in the years of 2004 and 2006. Image analysis techniques with fluorescent in situ hybridization (FISH) as well as [3H]-methyl-thymidine incorporation methods were applied to analyze differences in the composition and activity of bacterial communities. The greatest differences in trophic parameters were found between the humic lake and remaining non-humic ones. The same bacterial and heterotrophic nanoflagellate (HNF) cell size classes dominated in all the studied lakes. However, distinct increases in the contributions of large bacterial (>1.0 microm) and HNF (>10 microm) cells were observed in eutrophic lakes. The bacterial community was dominated by the beta-Proteobacteria group, which accounted for 27% of total DAPI counts. Ciliate communities were largely composed of Oligotrichida. Positive correlations between bacteria and protists, as well as between nanoflagellates (both heterotrophic and autotrophic) and ciliates, suggest that concentrations of food sources may be important in determining the abundance of protists in the studied lakes.

  11. Genetic diversity and population structure of Scottish Highland red deer (Cervus elaphus) populations: a mitochondrial survey.

    PubMed

    Pérez-Espona, S; Pérez-Barbería, F J; Goodall-Copestake, W P; Jiggins, C D; Gordon, I J; Pemberton, J M

    2009-02-01

    The largest population of red deer (Cervus elaphus) in Europe is found in Scotland. However, human impacts through hunting and introduction of foreign deer stock have disturbed the population's genetics to an unknown extent. In this study, we analysed mitochondrial control region sequences of 625 individuals to assess signatures of human and natural historical influence on the genetic diversity and population structure of red deer in the Scottish Highlands. Genetic diversity was high with 74 haplotypes found in our study area (115 x 87 km). Phylogenetic analyses revealed that none of the individuals had introgressed mtDNA from foreign species or subspecies of deer and only suggested a very few localized red deer translocations among British localities. A haplotype network and population analyses indicated significant genetic structure (Phi(ST)=0.3452, F(ST)=0.2478), largely concordant with the geographical location of the populations. Mismatch distribution analysis and neutrality tests indicated a significant population expansion for one of the main haplogroups found in the study area, approximately dated c. 8200 or 16 400 years ago when applying a fast or slow mutation rate, respectively. Contrary to general belief, our results strongly suggest that native Scottish red deer mtDNA haplotypes have persisted in the Scottish Highlands and that the population retains a largely natural haplotype diversity and structure in our study area.

  12. [Analysis on age structure and dynamics of Kindonia uniflora populations].

    PubMed

    Zhang, Wenhui; Li, Jingxia; Li, Hong; Liu, Xiangjun

    2004-04-01

    Kindonia uniflora is a perennial clone herbaceous plant, and also, a native endangered plant in China. This paper studied its age structure, life table and survivorship curve in different habitats in Taibai mountain area. The results indicated that the age structure and dynamics of K. uniflora populations in the Betula utilis forest at altitude 2500-2700 m, in the Abies fargesii forest at altitude 2700-2900 m, and in the Larix chinensis forest at altitude 2900-3100 m had the similar pattern and developing tendency. The number of younger ramets at 1-2 years old or older than 5 years was less, and the number of ramets at 3-5 years old was the highest in the age structures. The negative values of dx (dead number), qx (mortality rate) and Kx (Killing rate) in the life table showed the increasing rate of the population sizes during the age stage. The survivorship curve of K. uniflora populations in different habitats belonged to Deevey C after 3-5 years old. The mortality rate of populations during 5-10 years stage was higher, and was stable after 10 years old. As for the characters of asexual propagation and clone growth, the rhizomes of the populations were in humus of soil, and developed and expanded as guerilla line style. During growth season, only one leaf grew above ground at every inter-node, and the population growth and development were rarely influenced by external factors. The forest communities, such as Betula utilis, Abies fargesii and Larix chinensis forest, in which K. uniflora populations lived, were at middle or higher mountain, where there were rarely disturbance from human being. Therefore, the habitats for K. uniflora populations to live were relatively stable. As the altitude increased, the disturbances from human being became less, the density of K. uniflora populations increased, the life cycle expanded, the peak of population death delayed, and the population living strategy changed to adapt to the habitats. K. uniflora populations preferred to

  13. Population genetic structure of a colonising, triploid weed, Hieracium lepidulum.

    PubMed

    Chapman, H; Robson, B; Pearson, M L

    2004-03-01

    Understanding the breeding system and population genetic structure of invasive weed species is important for biocontrol, and contributes to our understanding of the evolutionary processes associated with invasions. Hieracium lepidulum is an invasive weed in New Zealand, colonising a diverse range of habitats including native Nothofagus forest, pine plantations, scrubland and tussock grassland. It is competing with native subalpine and alpine grassland and herbfield vegetation. H. lepidulum is a triploid, diplosporous apomict, so theoretically all seed is clonal, and there is limited potential for the creation of variation through recombination. We used intersimple sequence repeats (ISSRs) to determine the population genetic structure of New Zealand populations of H. lepidulum. ISSR analysis of five populations from two regions in the South Island demonstrated high intrapopulation genotypic diversity, and high interpopulation genetic structuring; PhiST = 0.54 over all five populations. No private alleles were found in any of the five populations, and allelic differentiation was correlated to geographic distance. Cladistic compatibility analysis indicated that both recombination and mutation were important in the creation of genotypic diversity. Our data will contribute to any biocontrol program developed for H. lepidulum. It will also be a baseline data set for future comparisons of genetic structure during the course of H. lepidulum invasions.

  14. Effects of Adaptation of In vitro Rumen Culture to Garlic Oil, Nitrate, and Saponin and Their Combinations on Methanogenesis, Fermentation, and Abundances and Diversity of Microbial Populations

    PubMed Central

    Patra, Amlan K.; Yu, Zhongtang

    2015-01-01

    This study investigated the effects of garlic oil (0.25 g/L), nitrate (5 mM), and quillaja saponin (0.6 g/L), alone and in binary or ternary combinations, on methanogenesis, rumen fermentation, and abundances of select microbial populations using in vitro rumen cultures. Potential adaptation to these compounds was also examined by repeated transfers of the cultures on alternate days until day 18. All treatments except saponin alone significantly decreased methanogenesis. Ternary combinations of garlic oil, nitrate, and saponin additively/synergistically suppressed methane production by 65% at day 2 and by 40% at day 18. Feed digestion was not adversely affected by any of the treatments at day 2, but was decreased by the combinations (binary and ternary) of garlic oil with the other inhibitors at days 10 and 18. Saponin, alone or in combinations, and garlic oil alone lowered ammonia concentration at day 2, while nitrate increased ammonia concentration at days 10 and 18. Total volatile fatty acid concentration was decreased by garlic oil alone or garlic oil-saponin combination. Molar proportions of acetate and propionate were affected to different extents by the different treatments. The abundances of methanogens were similar among treatments at day 2; however, garlic oil and its combination with saponin and/or nitrate at day 10 and all treatments except saponin at day 18 significantly decreased the abundances of methanogens. All the inhibitors, either alone or in combinations, did not adversely affect the abundances of total bacteria or Ruminococcus flavefaciens. However, at day 18 the abundances of Fibrobacter succinogenes and Ruminococcus albus were lowered in the presence of garlic oil and saponin, respectively. The results suggest that garlic oil-nitrate-saponin combination (at the doses used in this study) can effectively decreases methanogenesis in the rumen, but its efficacy may decrease while inhibition to feed digestion can increase over time. PMID:26733975

  15. Fine-scale population structure, inbreeding risk and avoidance in a wild insect population.

    PubMed

    Bretman, Amanda; Rodríguez-Muñoz, Rolando; Walling, Craig; Slate, Jon; Tregenza, Tom

    2011-07-01

    The ecological and evolutionary importance of fine-scale genetic structure within populations is increasingly appreciated. However, available data are largely restricted to wild vertebrates and eusocial insects. In addition, there is the expectation that most insects tend to have such large- and high-density populations and are so mobile that they are unlikely to face inbreeding risks through fine-scale population structuring. This has made the growing body of evidence for inbreeding avoidance in insects and its implication in mating systems evolution somewhat enigmatic. We present a 4-year study of a natural population of field crickets. Using detailed video monitoring combined with genotyping, we track the movement of all adults within the population and investigate genetic structure at a fine scale. We find some evidence for relatives being found in closer proximity, both across generations and within a single breeding season. Whilst incestuous matings are not avoided, population inbreeding is low, suggesting that mating is close to random and the limited fine-scale structure does not create significant inbreeding risk. Hence, there is little evidence for selective pressures associated with the evolution of inbreeding avoidance mechanisms in a closely related species.

  16. River mainstem thermal regimes influence population structuring within an Appalachian brook trout population

    USGS Publications Warehouse

    Aunins, Aaron W.; Petty, J. Todd; King, Timothy L.; Schilz, Mariya; Mazik, Patricia M.

    2015-01-01

    Brook trout (Salvelinus fontinalis) often exist as highly differentiated populations, even at small spatial scales, due either to natural or anthropogenic sources of isolation and low rates of dispersal. In this study, we used molecular approaches to describe the unique population structure of brook trout inhabiting the Shavers Fork watershed, located in eastern West Virginia, and contrast it to nearby populations in tributaries of the upper Greenbrier River and North Fork South Branch Potomac Rivers. Bayesian and maximum likelihood clustering methods identified minimal population structuring among 14 collections of brook trout from throughout the mainstem and tributaries of Shavers Fork, highlighting the role of the cold-water mainstem for connectivity and high rates of effective migration among tributaries. In contrast, the Potomac and Greenbrier River collections displayed distinct levels of population differentiation among tributaries, presumably resulting from tributary isolation by warm-water mainstems. Our results highlight the importance of protecting and restoring cold-water mainstem habitats as part of region-wide brook trout conservation efforts. In addition, our results from Shavers Fork provide a contrast to previous genetic studies that characterize Appalachian brook trout as fragmented isolates rather than well-mixed populations. Additional study is needed to determine whether the existence of brook trout as genetically similar populations among tributaries is truly unique and whether connectivity among brook trout populations can potentially be restored within other central Appalachian watersheds.

  17. Influence of warming tendency on Culex pipiens population abundance and on the probability of West Nile fever outbreaks (Israeli Case Study: 2001-2005).

    PubMed

    Paz, Shlomit; Albersheim, Iris

    2008-03-01

    Climate change and West Nile fever (WNV) are both subjects of global importance. Many mosquitoes and the diseases they carry, including West Nile virus (WNV), are sensitive to temperature increase. The current study analyzes the lag correlations between weather conditions (especially air temperature) and 1) Culex pipiens mosquito population abundance, and 2) WNF frequency in humans, between 2001 and 2005 in Israel. These 5 years follow a long period with a documented tendency for temperature increase in the hot season in the country. Monthly anomalies of minimum and maximum temperatures, relative seasonal rainfall contribution, mosquito samplings (hazard level), and WNF cases (hospital admission dates and patients' addresses) were analyzed. Logistic regression was calculated between the climatic data and the mosquito samples, as Spearman correlations and Pearson cross-correlations were calculated between daily temperature values (or daily precipitation amounts) and the hospital admission dates. It was found that the disease appearance reflects the population distribution, while the risk tends to escalate around the metropolis characterized by an urban heat island. Positive anomalies of the temperature during the study period appear to have facilitated the mosquito abundance and, consequently, the disease emergence in humans. An important finding is the potential influence of extreme heat in the early spring on the vector population increase and on the disease's appearance weeks later. Awareness of such situations at the beginning of the spring may help authorities to reduce the disease risk before it becomes a real danger.

  18. Population genetic structure and historical population dynamics of the South American sea lion, Otaria flavescens, in north-central Patagonia.

    PubMed

    Túnez, Juan I; Cappozzo, Humberto L; Nardelli, Maximiliano; Cassini, Marcelo H

    2010-08-01

    The north-central Patagonian coast is the sea lions most abundant area in Argentina. As occurs along the entire Atlantic coast, the distribution of breeding colonies at this smaller geographical scale is also patchy, showing at least three areas with breeding activity. We study the genetic structure and historical population dynamics of the species in five colonies in this area, analysing a 508 base-pair segment of the D-loop control region. Otaria flavescens showed 10 haplotypes with 12 polymorphic sites. The genealogical relationship between haplotypes revealed a shallow pattern of phylogeographic structure. The analysis of molecular variance showed significant differences between colonies, however, pairwise comparisons only indicate significant differences between a pair of colonies belonging to different breeding areas. The pattern of haplotype differentiation and the mismatch distribution analysis suggest a possible bottleneck that would have occurred 64,000 years ago, followed by a demographic expansion of the three southernmost colonies. Thus, the historical population dynamics of O. flavescens in north-central Patagonia appears to be closely related with the dynamics of the Late Pleistocene glaciations.

  19. Universality of fixation probabilities in randomly structured populations.

    PubMed

    Adlam, Ben; Nowak, Martin A

    2014-10-27

    The stage of evolution is the population of reproducing individuals. The structure of the population is known to affect the dynamics and outcome of evolutionary processes, but analytical results for generic random structures have been lacking. The most general result so far, the isothermal theorem, assumes the propensity for change in each position is exactly the same, but realistic biological structures are always subject to variation and noise. We consider a finite population under constant selection whose structure is given by a variety of weighted, directed, random graphs; vertices represent individuals and edges interactions between individuals. By establishing a robustness result for the isothermal theorem and using large deviation estimates to understand the typical structure of random graphs, we prove that for a generalization of the Erdős-Rényi model, the fixation probability of an invading mutant is approximately the same as that of a mutant of equal fitness in a well-mixed population with high probability. Simulations of perturbed lattices, small-world networks, and scale-free networks behave similarly. We conjecture that the fixation probability in a well-mixed population, (1 - r(-1))/(1 - r(-n)), is universal: for many random graph models, the fixation probability approaches the above function uniformly as the graphs become large.

  20. Assessing population genetic structure via the maximisation of genetic distance

    PubMed Central

    2009-01-01

    Background The inference of the hidden structure of a population is an essential issue in population genetics. Recently, several methods have been proposed to infer population structure in population genetics. Methods In this study, a new method to infer the number of clusters and to assign individuals to the inferred populations is proposed. This approach does not make any assumption on Hardy-Weinberg and linkage equilibrium. The implemented criterion is the maximisation (via a simulated annealing algorithm) of the averaged genetic distance between a predefined number of clusters. The performance of this method is compared with two Bayesian approaches: STRUCTURE and BAPS, using simulated data and also a real human data set. Results The simulations show that with a reduced number of markers, BAPS overestimates the number of clusters and presents a reduced proportion of correct groupings. The accuracy of the new method is approximately the same as for STRUCTURE. Also, in Hardy-Weinberg and linkage disequilibrium cases, BAPS performs incorrectly. In these situations, STRUCTURE and the new method show an equivalent behaviour with respect to the number of inferred clusters, although the proportion of correct groupings is slightly better with the new method. Re-establishing equilibrium with the randomisation procedures improves the precision of the Bayesian approaches. All methods have a good precision for FST ≥ 0.03, but only STRUCTURE estimates the correct number of clusters for FST as low as 0.01. In situations with a high number of clusters or a more complex population structure, MGD performs better than STRUCTURE and BAPS. The results for a human data set analysed with the new method are congruent with the geographical regions previously found. Conclusion This new method used to infer the hidden structure in a population, based on the maximisation of the genetic distance and not taking into consideration any assumption about Hardy-Weinberg and linkage equilibrium

  1. Population connectivity and genetic structure of burbot (Lota lota) populations in the Wind River Basin, Wyoming

    USGS Publications Warehouse

    Underwood, Zachary E.; Mandeville, Elizabeth G.; Walters, Annika W.

    2016-01-01

    Burbot (Lota lota) occur in the Wind River Basin in central Wyoming, USA, at the southwestern extreme of the species’ native range in North America. The most stable and successful of these populations occur in six glacially carved mountain lakes on three different tributary streams and one large main stem impoundment (Boysen Reservoir) downstream from the tributary populations. Burbot are rarely found in connecting streams and rivers, which are relatively small and high gradient, with a variety of potential barriers to upstream movement of fish. We used high-throughput genomic sequence data for 11,197 SNPs to characterize the genetic diversity, population structure, and connectivity among burbot populations on the Wind River system. Fish from Boysen Reservoir and lower basin tributary populations were genetically differentiated from those in the upper basin tributary populations. In addition, fish within the same tributary streams fell within the same genetic clusters, suggesting there is movement of fish between lakes on the same tributaries but that populations within each tributary system are isolated and genetically distinct from other populations. Observed genetic differentiation corresponded to natural and anthropogenic barriers, highlighting the importance of barriers to fish population connectivity and gene flow in human-altered linked lake-stream habitats.

  2. Effect of nitrogen and waterlogging on denitrifier gene abundance, community structure and activity in the rhizosphere of wheat.

    PubMed

    Hamonts, Kelly; Clough, Tim J; Stewart, Alison; Clinton, Peter W; Richardson, Alan E; Wakelin, Steven A; O'Callaghan, Maureen; Condron, Leo M

    2013-03-01

    Microbial denitrification plays a key role in determining the availability of soil nitrogen (N) to plants. However, factors influencing the structure and function of denitrifier communities in the rhizosphere remain unclear. Waterlogging can result in root anoxia and increased denitrification, leading to significant N loss from soil and potential nitrous oxide (N(2)O) emissions. This study investigated denitrifier gene abundance, community structure and activity in the rhizosphere of wheat in response to anoxia and N limitation. Denitrifier community structure in the rhizosphere differed from that in bulk soil, and denitrifier gene copy numbers (nirS, nirK, nosZ) and potential denitrification activity were greater in the rhizosphere. Anoxia and N limitation, and in particular a combination of both, reduced the magnitude of this effect on gene abundance (in particular nirS) and activity, with N limitation having greater impact than waterlogging in rhizosphere soil, in contrast to bulk soil where the impact of waterlogging was greater. Increased N supply to anoxic plants improved plant health and increased rhizosphere soil pH, which resulted in enhanced reduction of N(2)O. Both anoxia and N limitation significantly influenced the structure and function of denitrifier communities in the rhizosphere, with reduced root-derived carbon postulated to play an important role.

  3. Correlations in the population structure of music, genes and language.

    PubMed

    Brown, Steven; Savage, Patrick E; Ko, Albert Min-Shan; Stoneking, Mark; Ko, Ying-Chin; Loo, Jun-Hun; Trejaut, Jean A

    2014-01-07

    We present, to our knowledge, the first quantitative evidence that music and genes may have coevolved by demonstrating significant correlations between traditional group-level folk songs and mitochondrial DNA variation among nine indigenous populations of Taiwan. These correlations were of comparable magnitude to those between language and genes for the same populations, although music and language were not significantly correlated with one another. An examination of population structure for genetics showed stronger parallels to music than to language. Overall, the results suggest that music might have a sufficient time-depth to retrace ancient population movements and, additionally, that it might be capturing different aspects of population history than language. Music may therefore have the potential to serve as a novel marker of human migrations to complement genes, language and other markers.

  4. Correlations in the population structure of music, genes and language

    PubMed Central

    Brown, Steven; Savage, Patrick E.; Ko, Albert Min-Shan; Stoneking, Mark; Ko, Ying-Chin; Loo, Jun-Hun; Trejaut, Jean A.

    2014-01-01

    We present, to our knowledge, the first quantitative evidence that music and genes may have coevolved by demonstrating significant correlations between traditional group-level folk songs and mitochondrial DNA variation among nine indigenous populations of Taiwan. These correlations were of comparable magnitude to those between language and genes for the same populations, although music and language were not significantly correlated with one another. An examination of population structure for genetics showed stronger parallels to music than to language. Overall, the results suggest that music might have a sufficient time-depth to retrace ancient population movements and, additionally, that it might be capturing different aspects of population history than language. Music may therefore have the potential to serve as a novel marker of human migrations to complement genes, language and other markers. PMID:24225453

  5. How Obstacles Perturb Population Fronts and Alter Their Genetic Structure

    PubMed Central

    Möbius, Wolfram; Murray, Andrew W.; Nelson, David R.

    2015-01-01

    As populations spread into new territory, environmental heterogeneities can shape the population front and genetic composition. We focus here on the effects of an important building block of heterogeneous environments, isolated obstacles. With a combination of experiments, theory, and simulation, we show how isolated obstacles both create long-lived distortions of the front shape and amplify the effect of genetic drift. A system of bacteriophage T7 spreading on a spatially heterogeneous Escherichia coli lawn serves as an experimental model system to study population expansions. Using an inkjet printer, we create well-defined replicates of the lawn and quantitatively study the population expansion of phage T7. The transient perturbations of the population front found in the experiments are well described by a model in which the front moves with constant speed. Independent of the precise details of the expansion, we show that obstacles create a kink in the front that persists over large distances and is insensitive to the details of the obstacle’s shape. The small deviations between experimental findings and the predictions of the constant speed model can be understood with a more general reaction-diffusion model, which reduces to the constant speed model when the obstacle size is large compared to the front width. Using this framework, we demonstrate that frontier genotypes just grazing the side of an isolated obstacle increase in abundance, a phenomenon we call ‘geometry-enhanced genetic drift’, complementary to the founder effect associated with spatial bottlenecks. Bacterial range expansions around nutrient-poor barriers and stochastic simulations confirm this prediction. The effect of the obstacle on the genealogy of individuals at the front is characterized by simulations and rationalized using the constant speed model. Lastly, we consider the effect of two obstacles on front shape and genetic composition of the population illuminating the effects

  6. Genetic diversity and population structure of cucumber (Cucumis sativus L.).

    PubMed

    Lv, Jing; Qi, Jianjian; Shi, Qiuxiang; Shen, Di; Zhang, Shengping; Shao, Guangjin; Li, Hang; Sun, Zhanyong; Weng, Yiqun; Shang, Yi; Gu, Xingfang; Li, Xixiang; Zhu, Xiaoguo; Zhang, Jinzhe; van Treuren, Robbert; van Dooijeweert, Willem; Zhang, Zhonghua; Huang, Sanwen

    2012-01-01

    Knowing the extent and structure of genetic variation in germplasm collections is essential for the conservation and utilization of biodiversity in cultivated plants. Cucumber is the fourth most important vegetable crop worldwide and is a model system for other Cucurbitaceae, a family that also includes melon, watermelon, pumpkin and squash. Previous isozyme studies revealed a low genetic diversity in cucumber, but detailed insights into the crop's genetic structure and diversity are largely missing. We have fingerprinted 3,342 accessions from the Chinese, Dutch and U.S. cucumber collections with 23 highly polymorphic Simple Sequence Repeat (SSR) markers evenly distributed in the genome. The data reveal three distinct populations, largely corresponding to three geographic regions. Population 1 corresponds to germplasm from China, except for the unique semi-wild landraces found in Xishuangbanna in Southwest China and East Asia; population 2 to Europe, America, and Central and West Asia; and population 3 to India and Xishuangbanna. Admixtures were also detected, reflecting hybridization and migration events between the populations. The genetic background of the Indian germplasm is heterogeneous, indicating that the Indian cucumbers maintain a large proportion of the genetic diversity and that only a small fraction was introduced to other parts of the world. Subsequently, we defined a core collection consisting of 115 accessions and capturing over 77% of the SSR alleles. Insight into the genetic structure of cucumber will help developing appropriate conservation strategies and provides a basis for population-level genome sequencing in cucumber.

  7. Genotypic structure of a Drosophila population for adult locomotor activity

    SciTech Connect

    Grechanyi, G.V.; Korzun, V.M.

    1995-01-01

    Analysis of the variation of adult locomotor activity in four samples taken at different times from a natural population of Drosophila melanogaster showed that the total variation of this trait is relatively stable in time and has a substantial genetic component. Genotypic structure of the population for locomotor activity is characterized by the presence of large groups of genotypes with high and low values of this trait. A possible explanation for the presence of such groups in a population is cyclic density-dependent selection.

  8. Age-structured optimal control in population economics.

    PubMed

    Feichtinger, Gustav; Prskawetz, Alexia; Veliov, Vladimir M

    2004-06-01

    This paper brings both intertemporal and age-dependent features to a theory of population policy at the macro-level. A Lotka-type renewal model of population dynamics is combined with a Solow/Ramsey economy. We consider a social planner who maximizes an aggregate intertemporal utility function which depends on per capita consumption. As control policies we consider migration and saving rate (both age-dependent). By using a new maximum principle for age-structured control systems we derive meaningful results for the optimal migration and saving rate in an aging population. The model used in the numerical calculations is calibrated for Austria.

  9. Population structure and diversity in sexual and asexual populations of the pathogenic fungus Melampsora lini

    PubMed Central

    BARRETT, LUKE G.; THRALL, PETER H.; BURDON, JEREMY J.; NICOTRA, ADRIENNE B.; LINDE, CELESTE C.

    2009-01-01

    Many pathogens undergo both sexual and asexual reproduction to varying degrees, yet the ecological, genetic and evolutionary consequences of different reproductive strategies remain poorly understood. Here we investigate the population genetic structure of wild populations of the plant pathogen Melampsora lini on its host Linum marginale, using amplified fragment length polymorphism (AFLP) markers, two genes underlying pathogen virulence, and phenotypic variation in virulence. In Australia, M. lini occurs as two genetically and geographically divergent lineages (AA and AB), one of which is completely asexual (AB), and the other able to reproduce both clonally and sexually (AA). To quantify the genetic and evolutionary consequences of these different life histories, we sampled five populations in each of two biogeographical regions. Analysis of AFLP data obtained for 275 isolates revealed largely disjunct geographical distributions for the two different lineages, low genetic diversity within lineages, and strong genetic structure among populations within each region. We also detected significant divergence among populations for both Avr genes and virulence phenotypes, although generally these values were lower than those obtained with AFLP markers. Furthermore, isolates belonging to lineage AA collectively harboured significantly higher genotypic and phenotypic diversity than lineage AB isolates. Together these results illustrate the important roles of reproductive modes and geographical structure in the generation and maintenance of virulence diversity in populations of M. lini. PMID:18573166

  10. Recombination Hotspots and Population Structure in Plasmodium falciparum

    PubMed Central

    Mu, Jianbing; Duan, Junhui; McGee, Kate M; Joy, Deirdre A; McVean, Gilean A. T

    2005-01-01

    Understanding the influences of population structure, selection, and recombination on polymorphism and linkage disequilibrium (LD) is integral to mapping genes contributing to drug resistance or virulence in Plasmodium falciparum. The parasite's short generation time, coupled with a high cross-over rate, can cause rapid LD break-down. However, observations of low genetic variation have led to suggestions of effective clonality: selfing, population admixture, and selection may preserve LD in populations. Indeed, extensive LD surrounding drug-resistant genes has been observed, indicating that recombination and selection play important roles in shaping recent parasite genome evolution. These studies, however, provide only limited information about haplotype variation at local scales. Here we describe the first (to our knowledge) chromosome-wide SNP haplotype and population recombination maps for a global collection of malaria parasites, including the 3D7 isolate, whose genome has been sequenced previously. The parasites are clustered according to continental origin, but alternative groupings were obtained using SNPs at 37 putative transporter genes that are potentially under selection. Geographic isolation and highly variable multiple infection rates are the major factors affecting haplotype structure. Variation in effective recombination rates is high, both among populations and along the chromosome, with recombination hotspots conserved among populations at chromosome ends. This study supports the feasibility of genome-wide association studies in some parasite populations. PMID:16144426

  11. Incorporating parasite data in population structure studies of South African sardine Sardinops sagax.

    PubMed

    Van Der Lingen, Carl David; Weston, Laura Frances; Ssempa, Nurudean Norman; Reed, Cecile Catharine

    2015-01-01

    A multidisciplinary approach has been applied to examine the population structure of sardine Sardinops sagax off South Africa, where this species supports significant fisheries and is also of ecological and eco-tourism importance. Observations of discontinuous sardine distribution patterns, discrete spawning grounds and significant spatial differences in a variety of phenotypic characteristics have suggested the existence of discrete western, southern and eastern sardine sub-populations or stocks. The use of parasites as biological tags to elucidate sardine population structure has recently been investigated, and strong spatial gradients around South Africa in the prevalence, mean infection intensity and mean abundance of a digenean 'tetracotyle' type metacercarial endoparasite considered to be of the genus Cardiocephaloides and found in the humours of fish eyes support and have proved particularly convincing evidence for the sardine multiple stock hypothesis. A discontinuous distribution in the occurrence of another parasite, the coccidean Eimeria sardinae found in fish testes, has provided additional but weaker evidence of discrete stocks. These results have contributed to a changed understanding of the population structure of South African sardine and have significant implications for management of the fisheries for this species.

  12. Habitat-specific size structure variations in periwinkle populations ( Littorina littorea) caused by biotic factors

    NASA Astrophysics Data System (ADS)

    Eschweiler, Nina; Molis, Markus; Buschbaum, Christian

    2009-06-01

    Shell size distribution patterns of marine gastropod populations may vary considerably across different environments. We investigated the size and density structure of genetically continuous periwinkle populations ( Littorina littorea) on an exposed rocky and a sheltered sedimentary environment on two nearby islands in the south-eastern North Sea (German Bight). On the sedimentary shore, periwinkle density (917 ± 722 individuals m-2) was about three times higher than on the rocky shore (296 ± 168 individuals m-2). Mean (9.8 ± 3.9 mm) and maximum (22 mm) shell size of L. littorea on the sedimentary shore were smaller than on the rocky shore (21.5 ± 4.2 and 32 mm, respectively), where only few small snails were found. Additionally, periwinkle shells were thicker and stronger on the rocky than on the sedimentary shore. To ascertain mechanisms responsible for differences in population structures, we examined periwinkles in both environments for growth rate, predation pressure, infection with a shell boring polychaete ( Polydora ciliata) and parasitic infestation by trematodes. A crosswise transplantation experiment revealed better growth conditions on the sedimentary than on the rocky shore. However, crab abundance and prevalence of parasites and P. ciliata in adult snails were higher on the sedimentary shore. Previous investigations showed that crabs prefer large periwinkles infested with P. ciliata. Thus, we suggest that parasites and shell boring P. ciliata in conjunction with an increased crab predation pressure are responsible for low abundances of large periwinkles on the sedimentary shore while high wave exposure may explain low densities of juvenile L. littorea on the rocky shore. We conclude that biotic factors may strongly contribute to observed differences in size structure of the L. littorea populations studied on rocky and sedimentary shores.

  13. Ecological specialization in a spatially structured population of the thermophilic cyanobacterium Mastigocladus laminosus.

    PubMed

    Miller, Scott R; Williams, Carin; Strong, Aaron L; Carvey, Darla

    2009-02-01

    Laboratory evolution experiments suggest the potential for microbial populations to contribute significant ecological variation to ecosystems, yet the functional importance of genetic diversity within natural populations of microorganisms is largely unknown. Here, we investigated the distribution of genetic and phenotypic variation for a population of the cyanobacterium Mastigocladus laminosus distributed along the temperature gradient of White Creek, Yellowstone NP. A total of 153 laboratory strains were directly isolated from five sites with mean annual temperatures ranging between 39 and 54 degrees C. Genetic characterization at four nitrogen metabolism genes identified 15 closely related lineages in the population sample. These lineages were distributed nonrandomly along White Creek, but the observed geographic structure could not be explained by limited dispersal capabilities. Temperature performance experiments with six M. laminosus lineages that maximized their respective relative abundances at different positions along the gradient provided evidence for niche differentiation within the population. Niche differentiation included a tradeoff in performance at high and low temperatures, respectively. The physiological variation of these lineages in laboratory culture was generally well matched to the prevailing temperature conditions experienced by these organisms in situ. These results suggest that sympatric diversification along an ecological selection gradient can be a potent source of evolutionary innovation in microbial populations.

  14. Population models for passerine birds: structure, parameterization, and analysis

    USGS Publications Warehouse

    Noon, B.R.; Sauer, J.R.; McCullough, D.R.; Barrett, R.H.

    1992-01-01

    Population models have great potential as management tools, as they use infonnation about the life history of a species to summarize estimates of fecundity and survival into a description of population change. Models provide a framework for projecting future populations, determining the effects of management decisions on future population dynamics, evaluating extinction probabilities, and addressing a variety of questions of ecological and evolutionary interest. Even when insufficient information exists to allow complete identification of the model, the modelling procedure is useful because it forces the investigator to consider the life history of the species when determining what parameters should be estimated from field studies and provides a context for evaluating the relative importance of demographic parameters. Models have been little used in the study of the population dynamics of passerine birds because of: (1) widespread misunderstandings of the model structures and parameterizations, (2) a lack of knowledge of life histories of many species, (3) difficulties in obtaining statistically reliable estimates of demographic parameters for most passerine species, and (4) confusion about functional relationships among demographic parameters. As a result, studies of passerine demography are often designed inappropriately and fail to provide essential data. We review appropriate models for passerine bird populations and illustrate their possible uses in evaluating the effects of management or other environmental influences on population dynamics. We identify environmental influences on population dynamics. We identify parameters that must be estimated from field data, briefly review existing statistical methods for obtaining valid estimates, and evaluate the present status of knowledge of these parameters.

  15. Determinants of the abundance of invasive annual weeds: community structure and non-equilibrium dynamics.

    PubMed

    Freckleton, R P; Watkinson, A R; Dowling, P M; Ley, A R

    2000-06-07

    The dynamics of an annual pasture community are described from a five-year experimental and monitoring study. The community was dominated by two grasses (Lolium rigidum and Vulpia bromoides) and a legume (Trifolium subterraneum). Fits of population dynamic models to per capita rates of population change indicate that interactions between the grasses were generally strong, while interactions between the grasses and legumes were weaker. Most, but not all, of the net effects of competition on population growth could be attributed to interactions occurring during plant growth. Phase-plane analysis indicated that, for a constant environment, a joint equilibrium of the two grasses is unstable since interspecific competition between Lolium and Vulpia is stronger than intraspecific competition. Consequently, the community will tend to a mixture of only one or other of the grass species and T. subterraneum, depending on the founding composition of the pasture. Analysis of data taken from a year in which a drought occurred (1993-1994) demonstrated profound effects on all three species. Modelling of the long-term impacts of the effects of repeated droughts showed that disturbance of this form overrides the founder effect observed under constant conditions. Consequently, Vulpia is ultimately able to invade any mixture of the other species in environments where stochastic disturbances occur.

  16. Genetic variation and population structure in Scandinavian wolverine (Gulo gulo) populations.

    PubMed

    Walker, C W; Vilà, C; Landa, A; Lindén, M; Ellegren, H

    2001-01-01

    Wolverine (Gulo gulo) numbers in Scandinavia were significantly reduced during the early part of the century as a result of predator removal programmes and hunting. Protective legislation in both Sweden and Norway in the 1960s and 1970s has now resulted in increased wolverine densities in Scandinavia. We report here the development of 15 polymorphic microsatellite markers in wolverine and their use to examine the population sub-structure and genetic variability in free-ranging Scandinavian wolverine populations as well as in a sample of individuals collected before 1970. Significant subdivision between extant populations was discovered, in particular for the small and isolated population of southern Norway, which represents a recent recolonization. Overall genetic variability was found to be lower than previously reported for other mustelids, with only two to five alleles per locus and observed heterozygosities (H(O)) ranging from 0.269 to 0.376 across the examined populations, being lowest in southern Norway. Analysis of the mitochondrial DNA control region revealed no variation throughout the surveyed populations. As the historical sample did not show higher levels of genetic variability, our results are consistent with a reduction in the genetic variation in Scandinavian wolverines that pre-dates the demographic bottleneck observed during the last century. The observed subdivision between populations calls for management caution when issuing harvest quotas, especially for the geographically isolated south Norwegian population.

  17. Ethnicity and Population Structure in Personal Naming Networks

    PubMed Central

    Mateos, Pablo; Longley, Paul A.; O'Sullivan, David

    2011-01-01

    Personal naming practices exist in all human groups and are far from random. Rather, they continue to reflect social norms and ethno-cultural customs that have developed over generations. As a consequence, contemporary name frequency distributions retain distinct geographic, social and ethno-cultural patterning that can be exploited to understand population structure in human biology, public health and social science. Previous attempts to detect and delineate such structure in large populations have entailed extensive empirical analysis of naming conventions in different parts of the world without seeking any general or automated methods of population classification by ethno-cultural origin. Here we show how ‘naming networks’, constructed from forename-surname pairs of a large sample of the contemporary human population in 17 countries, provide a valuable representation of cultural, ethnic and linguistic population structure around the world. This innovative approach enriches and adds value to automated population classification through conventional national data sources such as telephone directories and electoral registers. The method identifies clear social and ethno-cultural clusters in such naming networks that extend far beyond the geographic areas in which particular names originated, and that are preserved even after international migration. Moreover, one of the most striking findings of this approach is that these clusters simply ‘emerge’ from the aggregation of millions of individual decisions on parental naming practices for their children, without any prior knowledge introduced by the researcher. Our probabilistic approach to community assignment, both at city level as well as at a global scale, helps to reveal the degree of isolation, integration or overlap between human populations in our rapidly globalising world. As such, this work has important implications for research in population genetics, public health, and social science adding new

  18. Structure of the New England herring gull population

    USGS Publications Warehouse

    Kadlec, J.A.; Drury, W.H.

    1968-01-01

    Measurements of the rates of population increase, reproduction, and mortality together with an observed age ratio, were used to analyze the population of the Herring Gull in New England. Data from sporadic censuses prior to this study, aerial censuses by the authors, and National Audubon Society Christmas Bird Count indicated that the New England breeding population has been doubling every 12 to 15 years since the early 1900's. This increase has involved founding new colonies and expanding the breeding range There is evidence that 15 to 30% of the adults do not breed in any given year. Sixty-one productivity measurements on 43 islands from 1963 through 1966, involving almost 13,000 nests, showed that from 0.8 to 1.4 young/breeding pair/year is the usual range of rate of production. The age distribution in the population was determined by classifying Herring Gulls by plumage category on an aerial census of the coast from Tampico, Mexico, to Cape Sable, Nova Scotia. Of the 622,000 gulls observed, 68% were adults, 17% were second- and third-year birds, and 15% were first-year birds. Mortality rates derived from band recovery data were too high to be consistent with the observed rate of population growth, productivity, and age structure. Loss of bands increasing to the rate of about 20%/year 5 years after banding eliminates most of the discrepancy. The age structure and rate of population increase indicate a mortality rate of 4 to 9% for gulls 2 years old or older, compared with the 25 to 30% indicated by band recoveries. The population structure we have developed fits everything we have observed about Herring Gull population dynamics, except mortality based on band recoveries.

  19. Ethnicity and population structure in personal naming networks.

    PubMed

    Mateos, Pablo; Longley, Paul A; O'Sullivan, David

    2011-01-01

    Personal naming practices exist in all human groups and are far from random. Rather, they continue to reflect social norms and ethno-cultural customs that have developed over generations. As a consequence, contemporary name frequency distributions retain distinct geographic, social and ethno-cultural patterning that can be exploited to understand population structure in human biology, public health and social science. Previous attempts to detect and delineate such structure in large populations have entailed extensive empirical analysis of naming conventions in different parts of the world without seeking any general or automated methods of population classification by ethno-cultural origin. Here we show how 'naming networks', constructed from forename-surname pairs of a large sample of the contemporary human population in 17 countries, provide a valuable representation of cultural, ethnic and linguistic population structure around the world. This innovative approach enriches and adds value to automated population classification through conventional national data sources such as telephone directories and electoral registers. The method identifies clear social and ethno-cultural clusters in such naming networks that extend far beyond the geographic areas in which particular names originated, and that are preserved even after international migration. Moreover, one of the most striking findings of this approach is that these clusters simply 'emerge' from the aggregation of millions of individual decisions on parental naming practices for their children, without any prior knowledge introduced by the researcher. Our probabilistic approach to community assignment, both at city level as well as at a global scale, helps to reveal the degree of isolation, integration or overlap between human populations in our rapidly globalising world. As such, this work has important implications for research in population genetics, public health, and social science adding new

  20. Vertical changes in abundance, biomass and community structure of copepods down to 3000 m in the southern Bering Sea

    NASA Astrophysics Data System (ADS)

    Homma, Tomoe; Yamaguchi, Atsushi

    2010-08-01

    Vertical changes in abundance, biomass and community structure of copepods down to 3000 m depth were studied at a single station of the Aleutian Basin of the Bering Sea (53°28'N, 177°00'W, depth 3779 m) on the 14th June 2006. Both abundance and biomass of copepods were greatest near the surface layer and decreased with increase in depth. Abundance and biomass of copepods integrated over 0-3000 m were 1,390,000 inds. m -2 and 5056 mg C m -2, respectively. Copepod carcasses occurred throughout the layer, and the carcass:living specimen ratio was the greatest in the oxygen minimum layer (750-100 m, the ratio was 2.3). A total of 72 calanoid copepod species belonging to 34 genera and 15 families occurred in the 0-3000 m water column (Cyclopoida, Harpacticoida and Poecilostomatoida were not identified to species level). Cluster analysis separated calanoid copepod communities into 5 groups (A-E). Each group was separated by depth, and the depth range of each group was at 0-75 m (A), 75-500 m (B), 500-750 m (C), 750-1500 m (D) and 1500-3000 m (E). Copepods were divided into four types based on the feeding pattern: suspension feeders, suspension feeders in diapause, detritivores and carnivores. In terms of abundance the most dominant group was suspension feeders (mainly Cyclopoida) in the epipelagic zone, and detritivores (mainly Poecilostomatoida) were dominant in the meso- and bathypelagic zones. In terms of biomass, suspension feeders in diapause (calanoid copepods Neocalanus spp. and Eucalanus bungii) were the major component (ca. 10-45%), especially in the 250-3000 m depth. These results are compared with the previous studies in the same region and that down to greater depths in the worldwide oceans.

  1. Models of earth structure inferred from neodymium and strontium isotopic abundances

    PubMed Central

    Wasserburg, G. J.; DePaolo, D. J.

    1979-01-01

    A simplified model of earth structure based on the Nd and Sr isotopic characteristics of oceanic and continental tholeiitic flood basalts is presented, taking into account the motion of crustal plates and a chemical balance for trace elements. The resulting structure that is inferred consists of a lower mantle that is still essentially undifferentiated, overlain by an upper mantle that is the residue of the original source from which the continents were derived. PMID:16592688

  2. Genetic Determinants for Enzymatic Digestion of Lignocellulosic Biomass Are Independent of Those for Lignin Abundance in a Maize Recombinant Inbred Population

    SciTech Connect

    Penning, Bryan W.; Sykes, Robert W.; Babcock, Nicholas C.; Dugard, Christopher K.; Held, Michael A.; Klimek, John F.; Shreve, Jacob T.; Fowler, Matthew; Ziebell, Angela; Davis, Mark F.; Decker, Stephen R.; Turner, Geoffrey B.; Mosier, Nathan S.; Springer, Nathan M.; Thimmapuram, Jyothi; Weil, Clifford F.; McCann, Maureen C.; Carpita, Nicholas C.

    2014-06-27

    Biotechnological approaches to reduce or modify lignin in biomass crops are predicated on the assumption that it is the principal determinant of the recalcitrance of biomass to enzymatic digestion for biofuels production. We defined quantitative trait loci (QTL) in the Intermated B73 x 3 Mo17 recombinant inbred maize (Zea mays) population using pyrolysis molecular-beam mass spectrometry to establish stem lignin content and an enzymatic hydrolysis assay to measure glucose and xylose yield. Among five multiyear QTL for lignin abundance, two for 4-vinylphenol abundance, and four for glucose and/or xylose yield, not a single QTL for aromatic abundance and sugar yield was shared. A genome-wide association study for lignin abundance and sugar yield of the 282- member maize association panel provided candidate genes in the 11 QTL of the B73 and Mo17 parents but showed that many other alleles impacting these traits exist among this broader pool of maize genetic diversity. B73 and Mo17 genotypes exhibited large differences in gene expression in developing stem tissues independent of allelic variation. Combining these complementary genetic approaches provides a narrowed list of candidate genes. A cluster of SCARECROW-LIKE9 and SCARECROW-LIKE14 transcription factor genes provides exceptionally strong candidate genes emerging from the genome-wide association study. In addition to these and genes associated with cell wall metabolism, candidates include several other transcription factors associated with vascularization and fiber formation and components of cellular signaling pathways. Finally, these results provide new insights and strategies beyond the modification of lignin to enhance yields of biofuels from genetically modified biomass.

  3. Genetic Determinants for Enzymatic Digestion of Lignocellulosic Biomass Are Independent of Those for Lignin Abundance in a Maize Recombinant Inbred Population

    DOE PAGES

    Penning, Bryan W.; Sykes, Robert W.; Babcock, Nicholas C.; ...

    2014-06-27

    Biotechnological approaches to reduce or modify lignin in biomass crops are predicated on the assumption that it is the principal determinant of the recalcitrance of biomass to enzymatic digestion for biofuels production. We defined quantitative trait loci (QTL) in the Intermated B73 x 3 Mo17 recombinant inbred maize (Zea mays) population using pyrolysis molecular-beam mass spectrometry to establish stem lignin content and an enzymatic hydrolysis assay to measure glucose and xylose yield. Among five multiyear QTL for lignin abundance, two for 4-vinylphenol abundance, and four for glucose and/or xylose yield, not a single QTL for aromatic abundance and sugar yieldmore » was shared. A genome-wide association study for lignin abundance and sugar yield of the 282- member maize association panel provided candidate genes in the 11 QTL of the B73 and Mo17 parents but showed that many other alleles impacting these traits exist among this broader pool of maize genetic diversity. B73 and Mo17 genotypes exhibited large differences in gene expression in developing stem tissues independent of allelic variation. Combining these complementary genetic approaches provides a narrowed list of candidate genes. A cluster of SCARECROW-LIKE9 and SCARECROW-LIKE14 transcription factor genes provides exceptionally strong candidate genes emerging from the genome-wide association study. In addition to these and genes associated with cell wall metabolism, candidates include several other transcription factors associated with vascularization and fiber formation and components of cellular signaling pathways. Finally, these results provide new insights and strategies beyond the modification of lignin to enhance yields of biofuels from genetically modified biomass.« less

  4. Demography and genetic structure of a recovering grizzly bear population

    USGS Publications Warehouse

    Kendall, K.C.; Stetz, J.B.; Boulanger, J.; Macleod, A.C.; Paetkau, David; White, Gary C.

    2009-01-01

    Grizzly bears (brown bears; Ursus arctos) are imperiled in the southern extent of their range worldwide. The threatened population in northwestern Montana, USA, has been managed for recovery since 1975; yet, no rigorous data were available to monitor program success. We used data from a large noninvasive genetic sampling effort conducted in 2004 and 33 years of physical captures to assess abundance, distribution, and genetic health of this population. We combined data from our 3 sampling methods (hair trap, bear rub, and physical capture) to construct individual bear encounter histories for use in Huggins-Pledger closed mark-recapture models. Our population estimate, N?? = 765 (95% CI = 715-831) was more than double the existing estimate derived from sightings of females with young. Based on our results, the estimated known, human-caused mortality rate in 2004 was 4.6% (95% CI = 4.2-4.9%), slightly above the 4% considered sustainable; however, the high proportion of female mortalities raises concern. We used location data from telemetry, confirmed sightings, and genetic sampling to estimate occupied habitat. We found that grizzly bears occupied 33,480 km2 in the Northern Continental Divide Ecosystem (NCDE) during 1994-2007, including 10,340 km beyond the Recovery Zone. We used factorial correspondence analysis to identify potential barriers to gene flow within this population. Our results suggested that genetic interchange recently increased in areas with low gene flow in the past; however, we also detected evidence of incipient fragmentation across the major transportation corridor in this ecosystem. Our results suggest that the NCDE population is faring better than previously thought, and they highlight the need for a more rigorous monitoring program.

  5. Abundance of stable periodic behavior in a Red Grouse population model with delay: A consequence of homoclinicity

    NASA Astrophysics Data System (ADS)

    Slipantschuk, Julia; Ullner, Ekkehard; Baptista, Murilo da Silva; Zeineddine, Mohammed; Thiel, Marco

    2010-12-01

    Shrimp-shaped periodic regions embedded in chaotic regions in two-dimensional parameter spaces are of specific interest for physical and biological systems. We provide the first observation of these shrimp-shaped stability regions in a parameter space of a continuous time-delayed population model, obtained by taking the delays as bifurcation parameters. The parameter space organization is governed by the presence of infinitely many periodicity hubs, which trigger the spiraling organization of these shrimp-shaped periodic regions around them. We provide evidence that this spiraling organization in the parameter space is a consequence of the existence of homoclinic orbits in the phase space.

  6. The genetic structure of a relict population of wood frogs

    USGS Publications Warehouse

    Scherer, Rick; Muths, Erin; Noon, Barry; Oyler-McCance, Sara

    2012-01-01

    Habitat fragmentation and the associated reduction in connectivity between habitat patches are commonly cited causes of genetic differentiation and reduced genetic variation in animal populations. We used eight microsatellite markers to investigate genetic structure and levels of genetic diversity in a relict population of wood frogs (Lithobates sylvatica) in Rocky Mountain National Park, Colorado, where recent disturbances have altered hydrologic processes and fragmented amphibian habitat. We also estimated migration rates among subpopulations, tested for a pattern of isolation-by-distance, and looked for evidence of a recent population bottleneck. The results from the clustering algorithm in Program STRUCTURE indicated the population is partitioned into two genetic clusters (subpopulations), and this result was further supported by factorial component analysis. In addition, an estimate of FST (FST = 0.0675, P value \\0.0001) supported the genetic differentiation of the two clusters. Estimates of migration rates among the two subpopulations were low, as were estimates of genetic variability. Conservation of the population of wood frogs may be improved by increasing the spatial distribution of the population and improving gene flow between the subpopulations. Construction or restoration of wetlands in the landscape between the clusters has the potential to address each of these objectives.

  7. The relationship between Baylisascaris procyonis prevalence and raccoon population structure.

    PubMed

    Page, L Kristen; Gehrt, Stanley D; Cascione, Andrea; Kellner, Kenneth F

    2009-12-01

    Parasite transmission is a dynamic process that can be affected by factors including host and parasite population dynamics. Raccoons ( Procyon lotor ) are the definitive host of Baylisascaris procyonis , an intestinal roundworm. Transmission of this parasite has been linked to raccoon behavior and human land-use patterns; however, we do not know the importance of host population structure. Therefore, the objective of this study was to determine the relationship between raccoon population attributes and prevalence of B. procyonis. We necropsied 307 trapped or road-killed raccoons collected during 2000-2006 from the Chicago area. In addition, we examined, via fecal samples (n  =  433), the patterns of B. procyonis prevalence as they relate to population dynamics among 3 subpopulations within the larger study. Baylisascaris procyonis was seen in 39% of 307 necropsied raccoons. There were differences in prevalence as a function of host age and sex. Baylisascaris procyonis was observed in 18% of 433 fecal samples obtained from live-trapped raccoons, and there were differences according to age, but not by sex. We found that the host populations consistently differed in density across study areas, but were similar regarding sex and age structure. Differences in host density were associated with differences in prevalence, suggesting that possible differences between populations, as well as ecological differences in sites and raccoon behavior, may have influenced parasite prevalence.

  8. Shallow Population Genetic Structures of Thread-sail Filefish (Stephanolepis cirrhifer) Populations from Korean Coastal Waters.

    PubMed

    Yoon, M; Park, W; Nam, Y K; Kim, D S

    2012-02-01

    Genetic diversities, population genetic structures and demographic histories of the thread-sail filefish Stephanolepis cirrhifer were investigated by nucleotide sequencing of 336 base pairs of the mitochondrial DNA (mtDNA) control region in 111 individuals collected from six populations in Korean coastal waters. A total of 70 haplotypes were defined by 58 variable nucleotide sites. The neighbor-joining tree of the 70 haplotypes was shallow and did not provide evidence of geographical associations. Expansion of S. cirrhifer populations began approximate 51,000 to 102,000 years before present, correlating with the period of sea level rise since the late Pleistocene glacial maximum. High levels of haplotype diversities (0.974±0.029 to 1.000±0.076) and nucleotide diversities (0.014 to 0.019), and low levels of genetic differentiation among populations inferred from pairwise population F ST values (-0.007 to 0.107), support an expansion of the S. cirrhifer population. Hierarchical analysis of molecular variance (AMOVA) revealed weak but significant genetic structures among three groups (F CT = 0.028, p<0.05), and no genetic variation within groups (0.53%; F SC = 0.005, p = 0.23). These results may help establish appropriate fishery management strategies for stocks of S. cirrhifer and related species.

  9. Origin, genetic diversity, and population structure of Chinese domestic sheep.

    PubMed

    Chen, Shan-Yuan; Duan, Zi-Yuan; Sha, Tao; Xiangyu, Jinggong; Wu, Shi-Fang; Zhang, Ya-Ping

    2006-07-19

    To characterize the origin, genetic diversity, and phylogeographic structure of Chinese domestic sheep, we here analyzed a 531-bp fragment of mtDNA control region of 449 Chinese autochthonous sheep from 19 breeds/populations from 13 geographic regions, together with previously reported 44 sequences from Chinese indigenous sheep. Phylogenetic analysis showed that all three previously defined lineages A, B, and C were found in all sampled Chinese sheep populations, except for the absence of lineage C in four populations. Network profiles revealed that the lineages B and C displayed a star-like phylogeny with the founder haplotype in the centre, and that two star-like subclades with two founder haplotypes were identified in lineage A. The pattern of genetic variation in lineage A, together with the divergence time between the two central founder haplotypes suggested that two independent domestication events have occurred in sheep lineage A. Considerable mitochondrial diversity was observed in Chinese sheep. Weak structuring was observed either among Chinese indigenous sheep populations or between Asian and European sheep and this can be attributable to long-term strong gene flow induced by historical human movements. The high levels of intra-population diversity in Chinese sheep and the weak phylogeographic structuring indicated three geographically independent domestication events have occurred and the domestication place was not only confined to the Near East, but also occurred in other regions.

  10. Population genetic analysis and sub-structuring in Babesia bovis.

    PubMed

    Simuunza, Martin; Bilgic, Huseyin; Karagenc, Tulin; Syakalima, Michelo; Shiels, Brian; Tait, Andy; Weir, William

    2011-06-01

    The tick-borne protozoan parasite, Babesia bovis is one of the causes of bovine babesiosis, an economically important disease of cattle in tropical and sub-tropical countries. Using the recently published genome sequence of the parasite, we developed a panel of eight mini- and micro-satellite markers and used these to investigate the role of genetic exchange in the population structure and diversity of the parasite using isolates from Zambia and Turkey. This population genetic analysis showed that genetic exchange occurs and that there are high levels of genetic diversity, with geographical sub-structuring quantified using Wright's F Index. Linkage disequilibrium was observed when isolates from both countries were treated as one population, but when isolates from Zambia were analysed separately linkage equilibrium was observed. The Turkish isolates were sub-structured, containing two genetically distinct sub-groups, both of which appeared to be in linkage equilibrium. The results of the Zambian study suggest that a sub-set of the parasite population is responsible for the westward spread of babesiosis into the previously disease-free central region of the country. The Zambian isolates had a significantly higher number of genotypes per sample than those from Turkey and age was found to be a significant predictor of the multiplicity of infection. The high levels of diversity seen in the Zambian and Turkish B. bovis populations have implications in the development of subunit vaccines against the disease and the spread of drug resistance.

  11. The subtle role of climate change on population genetic structure in Canada lynx.

    PubMed

    Row, Jeffrey R; Wilson, Paul J; Gomez, Celine; Koen, Erin L; Bowman, Jeff; Thornton, Daniel; Murray, Dennis L

    2014-07-01

    Anthropogenically driven climatic change is expected to reshape global patterns of species distribution and abundance. Given recent links between genetic variation and environmental patterns, climate change may similarly impact genetic population structure, but we lack information on the spatial and mechanistic underpinnings of genetic-climate associations. Here, we show that current genetic variability of Canada lynx (Lynx canadensis) is strongly correlated with a winter climate gradient (i.e. increasing snow depth and winter precipitation from west-to-east) across the Pacific-North American (PNO) to North Atlantic Oscillation (NAO) climatic systems. This relationship was stronger than isolation by distance and not explained by landscape variables or changes in abundance. Thus, these patterns suggest that individuals restricted dispersal across the climate boundary, likely in the absence of changes in habitat quality. We propose habitat imprinting on snow conditions as one possible explanation for this unusual phenomenon. Coupling historical climate data with future projections, we also found increasingly diverging snow conditions between the two climate systems. Based on genetic simulations using projected climate data (2041-2070), we predicted that this divergence could lead to a threefold increase in genetic differentiation, potentially leading to isolated east-west populations of lynx in North America. Our results imply that subtle genetic structure can be governed by current climate and that substantive genetic differentiation and related ecological divergence may arise from changing climate patterns.

  12. Microsatellite and Wolbachia analysis in Rhagoletis cerasi natural populations: population structuring and multiple infections

    PubMed Central

    Augustinos, Antonios A; Asimakopoulou, Anastasia K; Moraiti, Cleopatra A; Mavragani-Tsipidou, Penelope; Papadopoulos, Nikolaos T; Bourtzis, Kostas

    2014-01-01

    Rhagoletis cerasi (Diptera: Tephritidae) is a major pest of sweet and sour cherries in Europe and parts of Asia. Despite its economic significance, there is a lack of studies on the genetic structure of R. cerasi populations. Elucidating the genetic structure of insects of economic importance is crucial for developing phenological-predictive models and environmental friendly control methods. All natural populations of R. cerasi have been found to harbor the endosymbiont Wolbachia pipientis, which widely affects multiple biological traits contributing to the evolution of its hosts, and has been suggested as a tool for the biological control of insect pests and disease vectors. In the current study, the analysis of 18 R. cerasi populations collected in Greece, Germany, and Russia using 13 microsatellite markers revealed structuring of R. cerasi natural populations, even at close geographic range. We also analyzed the Wolbachia infection status of these populations using 16S rRNA-, MLST- and wsp-based approaches. All 244 individuals screened were positive for Wolbachia. Our results suggest the fixation of the wCer1 strain in Greece while wCer2, wCer4, wCer5, and probably other uncharacterized strains were also detected in multiply infected individuals. The role of Wolbachia and its potential extended phenotypes needs a thorough investigation in R. cerasi. Our data suggest an involvement of this symbiont in the observed restriction in the gene flow in addition to a number of different ecological factors. PMID:24963388

  13. Evolutionary snowdrift game incorporating costly punishment in structured populations

    NASA Astrophysics Data System (ADS)

    Chan, Nat W. H.; Xu, C.; Tey, Siew Kian; Yap, Yee Jiun; Hui, P. M.

    2013-01-01

    The role of punishment and the effects of a structured population in promoting cooperation are important issues. Within a recent model of snowdrift game (SG) incorporating a costly punishing strategy (P), we study the effects of a population connected through a square lattice. The punishers, who carry basically a cooperative (C) character, are willing to pay a cost α so as to punish a non-cooperative (D) opponent by β. Depending on α, β, the cost-to-benefit ratio r in SG, and the initial conditions, the system evolves into different phases that could be homogeneous or inhomogeneous. The spatial structure imposes geometrical constraint on how one agent is affected by neighboring agents. Results of extensive numerical simulations, both for the steady state and the dynamics, are presented. Possible phases are identified and discussed, and isolated phases in the r-β space are identified as special local structures of strategies that are stable due to the lattice structure. In contrast to a well-mixed population where punishers are suppressed due to the cost of punishment, the altruistic punishing strategy can flourish and prevail for appropriate values of the parameters, implying an enhancement in cooperation by imposing punishments in a structured population. The system could evolve to a phase corresponding to the coexistence of C, D, and P strategies at some particular payoff parameters, and such a phase is absent in a well-mixed population. The pair approximation, a commonly used analytic approach, is extended from a two-strategy system to a three-strategy system. We show that the pair approximation can, at best, capture the numerical results only qualitatively. Due to the improper way of including spatial correlation imposed by the lattice structure, the approximation does not give the frequencies of C, D, and P accurately and fails to give the homogeneous AllD and AllP phases.

  14. Population structure of barley landrace populations and gene-flow with modern varieties.

    PubMed

    Bellucci, Elisa; Bitocchi, Elena; Rau, Domenico; Nanni, Laura; Ferradini, Nicoletta; Giardini, Alessandro; Rodriguez, Monica; Attene, Giovanna; Papa, Roberto

    2013-01-01

    Landraces are heterogeneous plant varieties that are reproduced by farmers as populations that are subject to both artificial and natural selection. Landraces are distinguished by farmers due to their specific traits, and different farmers often grow different populations of the same landrace. We used simple sequence repeats (SSRs) to analyse 12 barley landrace populations from Sardinia from two collections spanning 10 years. We analysed the population structure, and compared the population diversity of the landraces that were collected at field level (population). We used a representative pool of barley varieties for diversity comparisons and to analyse the effects of gene flow from modern varieties. We found that the Sardinian landraces are a distinct gene pool from those of both two-row and six-row barley varieties. There is also a low, but significant, mean level and population-dependent level of introgression from the modern varieties into the Sardinian landraces. Moreover, we show that the Sardinian landraces have the same level of gene diversity as the representative sample of modern commercial varieties grown in Italy in the last decades, even within population level. Thus, these populations represent crucial sources of germplasm that will be useful for crop improvement and for population genomics studies and association mapping, to identify genes, loci and genome regions responsible for adaptive variations. Our data also suggest that landraces are a source of valuable germplasm for sustainable agriculture in the context of future climate change, and that in-situ conservation strategies based on farmer use can preserve the genetic identity of landraces while allowing adaptation to local environments.

  15. Evaluating Functional Diversity: Missing Trait Data and the Importance of Species Abundance Structure and Data Transformation

    PubMed Central

    Bryndová, Michala; Kasari, Liis; Norberg, Anna; Weiss, Matthias; Bishop, Tom R.; Luke, Sarah H.; Sam, Katerina; Le Bagousse-Pinguet, Yoann; Lepš, Jan; Götzenberger, Lars; de Bello, Francesco

    2016-01-01

    Functional diversity (FD) is an important component of biodiversity that quantifies the difference in functional traits between organisms. However, FD studies are often limited by the availability of trait data and FD indices are sensitive to data gaps. The distribution of species abundance and trait data, and its transformation, may further affect the accuracy of indices when data is incomplete. Using an existing approach, we simulated the effects of missing trait data by gradually removing data from a plant, an ant and a bird community dataset (12, 59, and 8 plots containing 62, 297 and 238 species respectively). We ranked plots by FD values calculated from full datasets and then from our increasingly incomplete datasets and compared the ranking between the original and virtually reduced datasets to assess the accuracy of FD indices when used on datasets with increasingly missing data. Finally, we tested the accuracy of FD indices with and without data transformation, and the effect of missing trait data per plot or per the whole pool of species. FD indices became less accurate as the amount of missing data increased, with the loss of accuracy depending on the index. But, where transformation improved the normality of the trait data, FD values from incomplete datasets were more accurate than before transformation. The distribution of data and its transformation are therefore as important as data completeness and can even mitigate the effect of missing data. Since the effect of missing trait values pool-wise or plot-wise depends on the data distribution, the method should be decided case by case. Data distribution and data transformation should be given more careful consideration when designing, analysing and interpreting FD studies, especially where trait data are missing. To this end, we provide the R package “traitor” to facilitate assessments of missing trait data. PMID:26881747

  16. Recurrence and Frequency of Disturbance have Cumulative Effect on Methanotrophic Activity, Abundance, and Community Structure

    PubMed Central

    Ho, Adrian; van den Brink, Erik; Reim, Andreas; Krause, Sascha M. B.; Bodelier, Paul L. E.

    2016-01-01

    Alternate prolonged drought and heavy rainfall is predicted to intensify with global warming. Desiccation-rewetting events alter the soil quality and nutrient concentrations which drive microbial-mediated processes, including methane oxidation, a key biogeochemical process catalyzed by methanotrophic bacteria. Although aerobic methanotrophs showed remarkable resilience to a suite of physical disturbances induced as a single event, their resilience to recurring disturbances is less known. Here, using a rice field soil in a microcosm study, we determined whether recurrence and frequency of desiccation-rewetting impose an accumulating effect on the methanotrophic activity. The response of key aerobic methanotroph subgroups (type Ia, Ib, and II) were monitored using qPCR assays, and was supported by a t-RFLP analysis. The methanotrophic activity was resilient to recurring desiccation-rewetting, but increasing the frequency of the disturbance by twofold significantly decreased methane uptake rate. Both the qPCR and t-RFLP analyses were congruent, showing the dominance of type Ia/Ib methanotrophs prior to disturbance, and after disturbance, the recovering community was predominantly comprised of type Ia (Methylobacter) methanotrophs. Both type Ib and type II (Methylosinus/Methylocystis) methanotrophs were adversely affected by the disturbance, but type II methanotrophs showed recovery over time, indicating relatively higher resilience to the disturbance. This revealed distinct, yet unrecognized traits among the methanotroph community members. Our results show that recurring desiccation-rewetting before a recovery in community abundance had an accumulated effect, compromising methanotrophic activity. While methanotrophs may recover well following sporadic disturbances, their resilience may reach a ‘tipping point’ where activity no longer recovered if disturbance persists and increase in frequency. PMID:26779148

  17. Evaluating Functional Diversity: Missing Trait Data and the Importance of Species Abundance Structure and Data Transformation.

    PubMed

    Májeková, Maria; Paal, Taavi; Plowman, Nichola S; Bryndová, Michala; Kasari, Liis; Norberg, Anna; Weiss, Matthias; Bishop, Tom R; Luke, Sarah H; Sam, Katerina; Le Bagousse-Pinguet, Yoann; Lepš, Jan; Götzenberger, Lars; de Bello, Francesco

    2016-01-01

    Functional diversity (FD) is an important component of biodiversity that quantifies the difference in functional traits between organisms. However, FD studies are often limited by the availability of trait data and FD indices are sensitive to data gaps. The distribution of species abundance and trait data, and its transformation, may further affect the accuracy of indices when data is incomplete. Using an existing approach, we simulated the effects of missing trait data by gradually removing data from a plant, an ant and a bird community dataset (12, 59, and 8 plots containing 62, 297 and 238 species respectively). We ranked plots by FD values calculated from full datasets and then from our increasingly incomplete datasets and compared the ranking between the original and virtually reduced datasets to assess the accuracy of FD indices when used on datasets with increasingly missing data. Finally, we tested the accuracy of FD indices with and without data transformation, and the effect of missing trait data per plot or per the whole pool of species. FD indices became less accurate as the amount of missing data increased, with the loss of accuracy depending on the index. But, where transformation improved the normality of the trait data, FD values from incomplete datasets were more accurate than before transformation. The distribution of data and its transformation are therefore as important as data completeness and can even mitigate the effect of missing data. Since the effect of missing trait values pool-wise or plot-wise depends on the data distribution, the method should be decided case by case. Data distribution and data transformation should be given more careful consideration when designing, analysing and interpreting FD studies, especially where trait data are missing. To this end, we provide the R package "traitor" to facilitate assessments of missing trait data.

  18. Turkish population structure and genetic ancestry reveal relatedness among Eurasian populations.

    PubMed

    Hodoğlugil, Uğur; Mahley, Robert W

    2012-03-01

    Turkey has experienced major population movements. Population structure and genetic relatedness of samples from three regions of Turkey, using over 500,000 SNP genotypes, were compared together with Human Genome Diversity Panel (HGDP) data. To obtain a more representative sampling from Central Asia, Kyrgyz samples (Bishkek, Kyrgyzstan) were genotyped and analysed. Principal component (PC) analysis reveals a significant overlap between Turks and Middle Easterners and a relationship with Europeans and South and Central Asians; however, the Turkish genetic structure is unique. FRAPPE, STRUCTURE, and phylogenetic analyses support the PC analysis depending upon the number of parental ancestry components chosen. For example, supervised STRUCTURE (K=3) illustrates a genetic ancestry for the Turks of 45% Middle Eastern (95% CI, 42-49), 40% European (95% CI, 36-44) and 15% Central Asian (95% CI, 13-16), whereas at K=4 the genetic ancestry of the Turks was 38% European (95% CI, 35-42), 35% Middle Eastern (95% CI, 33-38), 18% South Asian (95% CI, 16-19) and 9% Central Asian (95% CI, 7-11). PC analysis and FRAPPE/STRUCTURE results from three regions in Turkey (Aydin, Istanbul and Kayseri) were superimposed, without clear subpopulation structure, suggesting sample homogeneity. Thus, this study demonstrates admixture of Turkish people reflecting the population migration patterns.

  19. Genetic population structure in the yellow mongoose, Cynictis penicillata.

    PubMed

    Van Vuuren, B J; Robinson, T J

    1997-12-01

    Phylogeographic structure was determined for the yellow mongoose, Cynictis penicillata, using mtDNA RFLPs and control region sequences. The RFLP analysis revealed 13 haplotypes which showed weak geographical patterning consistent with a recent range expansion from a refugial population(s). An analysis of molecular variance (AMOVA) revealed no correspondence between mtDNA phylogeography and subspecies delimitation, nor between matrilines and areas characterized by a high incidence of the viverrid-type rabies, of which the yellow mongoose is the principal vector. The lack of structure was also shown by control region sequences although four of the maternal lineages shared a near-perfect 81 bp repeat. We speculate that regional hot spots of the viverrid rabies biotype reflect population density differences in the yellow mongoose that are not underscored by genetic partitioning, at least at the level of resolution provided by our analyses.

  20. The Significance of Myriophyllum elatinoides for Swine Wastewater Treatment: Abundance and Community Structure of Ammonia-Oxidizing Microorganisms in Sediments

    PubMed Central

    Li, Xi; Zhang, Miaomiao; Liu, Feng; Li, Yong; He, Yang; Zhang, Shunan; Wu, Jinshui

    2015-01-01

    Myriophyllum elatinoides was reported to effectively treat wastewater by removing nitrogen (N) and phosphorus (P). However, little is known about the abundance and community structure of ammonia-oxidizing microorganisms associated with M. elatinoides purification systems. The objective of this research was to characterize the abundance and community structure of ammonia-oxidizing microorganisms in swine wastewater and determine the main nitrogen removal pathways. In this study, five different waters were treated by M. elatinoides in microcosms for one month. The five waters included tap water (Control), swine wastewater (SW), 50% diluted swine wastewater (50% SW), and two synthetic wastewaters: 200 mg NH4+-N L−1 (200 NH4+-N) and 400 mg NH4+-N L−1 (400 NH4+-N). The most dramatic changes were in NH4+-N and total N (TN) concentrations, with average removal rates of 84% and 90%, respectively, in the treatments containing swine wastewater. On days 7, 14, and 28, the dissolved oxygen (DO) increased by 81.8%, 210.4% and 136.5%, respectively, compared with on day 0, in the swine wastewater. The results also showed that the bacterial amoA (AOB) copy numbers in the sediments of the treatments were significantly higher than those of archaeal amoA (AOA) copy numbers (p = 0.015). In addition, the high DO concentrations in swine wastewater responded well to the high abundance of AOB. The AOA and AOB community distributions were positively related with NO3-N and were negatively related with DO in swine wastewater treatments. In summary, our experimental results suggested that the M. elatinoides purification system could improve the activity of ammonia-oxidizing microorganisms and consequently might contribute to the significant N removal from the swine wastewater. PMID:26444015

  1. Decreasing Abundance, Increasing Diversity and Changing Structure of the Wild Bee Community (Hymenoptera: Anthophila) along an Urbanization Gradient

    PubMed Central

    Fortel, Laura; Henry, Mickaël; Guilbaud, Laurent; Guirao, Anne Laure; Kuhlmann, Michael; Mouret, Hugues; Rollin, Orianne; Vaissière, Bernard E.

    2014-01-01

    Background Wild bees are important pollinators that have declined in diversity and abundance during the last decades. Habitat destruction and fragmentation associated with urbanization are reported as part of the main causes of this decline. Urbanization involves dramatic changes of the landscape, increasing the proportion of impervious surface while decreasing that of green areas. Few studies have investigated the effects of urbanization on bee communities. We assessed changes in the abundance, species richness, and composition of wild bee community along an urbanization gradient. Methodology/Principal Findings Over two years and on a monthly basis, bees were sampled with colored pan traps and insect nets at 24 sites located along an urbanization gradient. Landscape structure within three different radii was measured at each study site. We captured 291 wild bee species. The abundance of wild bees was negatively correlated with the proportion of impervious surface, while species richness reached a maximum at an intermediate (50%) proportion of impervious surface. The structure of the community changed along the urbanization gradient with more parasitic species in sites with an intermediate proportion of impervious surface. There were also greater numbers of cavity-nesting species and long-tongued species in sites with intermediate or higher proportion of impervious surface. However, urbanization had no effect on the occurrence of species depending on their social behavior or body size. Conclusions/Significance We found nearly a third of the wild bee fauna known from France in our study sites. Indeed, urban areas supported a diverse bee community, but sites with an intermediate level of urbanization were the most speciose ones, including greater proportion of parasitic species. The presence of a diverse array of bee species even in the most urbanized area makes these pollinators worthy of being a flagship group to raise the awareness of urban citizens about

  2. Galactic Chemical Evolution and Solar s-process Abundances: Dependence on the 13C-pocket Structure

    NASA Astrophysics Data System (ADS)

    Bisterzo, S.; Travaglio, C.; Gallino, R.; Wiescher, M.; Käppeler, F.

    2014-05-01

    We study the s-process abundances (A >~ 90) at the epoch of the solar system formation. Asymptotic giant branch yields are computed with an updated neutron capture network and updated initial solar abundances. We confirm our previous results obtained with a Galactic chemical evolution (GCE) model: (1) as suggested by the s-process spread observed in disk stars and in presolar meteoritic SiC grains, a weighted average of s-process strengths is needed to reproduce the solar s distribution of isotopes with A > 130; and (2) an additional contribution (of about 25%) is required in order to represent the solar s-process abundances of isotopes from A = 90 to 130. Furthermore, we investigate the effect of different internal structures of the 13C pocket, which may affect the efficiency of the 13C(α, n)16O reaction, the major neutron source of the s process. First, keeping the same 13C profile adopted so far, we modify by a factor of two the mass involved in the pocket; second, we assume a flat 13C profile in the pocket, and we test again the effects of the variation of the mass of the pocket. We find that GCE s predictions at the epoch of the solar system formation marginally depend on the size and shape of the 13C pocket once a different weighted range of 13C-pocket strengths is assumed. We obtain that, independently of the internal structure of the 13C pocket, the missing solar system s-process contribution in the range from A = 90 to 130 remains essentially the same.

  3. The Significance of Myriophyllum elatinoides for Swine Wastewater Treatment: Abundance and Community Structure of Ammonia-Oxidizing Microorganisms in Sediments.

    PubMed

    Li, Xi; Zhang, Miaomiao; Liu, Feng; Li, Yong; He, Yang; Zhang, Shunan; Wu, Jinshui

    2015-01-01

    Myriophyllum elatinoides was reported to effectively treat wastewater by removing nitrogen (N) and phosphorus (P). However, little is known about the abundance and community structure of ammonia-oxidizing microorganisms associated with M. elatinoides purification systems. The objective of this research was to characterize the abundance and community structure of ammonia-oxidizing microorganisms in swine wastewater and determine the main nitrogen removal pathways. In this study, five different waters were treated by M. elatinoides in microcosms for one month. The five waters included tap water (Control), swine wastewater (SW), 50% diluted swine wastewater (50% SW), and two synthetic wastewaters: 200 mg NH4+-N L(-1) (200 NH4+-N) and 400 mg NH4+-N L(-1) (400 NH4+-N). The most dramatic changes were in NH4+-N and total N (TN) concentrations, with average removal rates of 84% and 90%, respectively, in the treatments containing swine wastewater. On days 7, 14, and 28, the dissolved oxygen (DO) increased by 81.8%, 210.4% and 136.5%, respectively, compared with on day 0, in the swine wastewater. The results also showed that the bacterial amoA (AOB) copy numbers in the sediments of the treatments were significantly higher than those of archaeal amoA (AOA) copy numbers (p = 0.015). In addition, the high DO concentrations in swine wastewater responded well to the high abundance of AOB. The AOA and AOB community distributions were positively related with NO3-N and were negatively related with DO in swine wastewater treatments. In summary, our experimental results suggested that the M. elatinoides purification system could improve the activity of ammonia-oxidizing microorganisms and consequently might contribute to the significant N removal from the swine wastewater.

  4. Host Mobility Drives Pathogen Competition in Spatially Structured Populations

    PubMed Central

    Poletto, Chiara; Meloni, Sandro; Colizza, Vittoria; Moreno, Yamir; Vespignani, Alessandro

    2013-01-01

    Interactions among multiple infectious agents are increasingly recognized as a fundamental issue in the understanding of key questions in public health regarding pathogen emergence, maintenance, and evolution. The full description of host-multipathogen systems is, however, challenged by the multiplicity of factors affecting the interaction dynamics and the resulting competition that may occur at different scales, from the within-host scale to the spatial structure and mobility of the host population. Here we study the dynamics of two competing pathogens in a structured host population and assess the impact of the mobility pattern of hosts on the pathogen competition. We model the spatial structure of the host population in terms of a metapopulation network and focus on two strains imported locally in the system and having the same transmission potential but different infectious periods. We find different scenarios leading to competitive success of either one of the strain or to the codominance of both strains in the system. The dominance of the strain characterized by the shorter or longer infectious period depends exclusively on the structure of the population and on the the mobility of hosts across patches. The proposed modeling framework allows the integration of other relevant epidemiological, environmental and demographic factors, opening the path to further mathematical and computational studies of the dynamics of multipathogen systems. PMID:23966843

  5. Population structure and cultural geography of a folktale in Europe.

    PubMed

    Ross, Robert M; Greenhill, Simon J; Atkinson, Quentin D

    2013-04-07

    Despite a burgeoning science of cultural evolution, relatively little work has focused on the population structure of human cultural variation. By contrast, studies in human population genetics use a suite of tools to quantify and analyse spatial and temporal patterns of genetic variation within and between populations. Human genetic diversity can be explained largely as a result of migration and drift giving rise to gradual genetic clines, together with some discontinuities arising from geographical and cultural barriers to gene flow. Here, we adapt theory and methods from population genetics to quantify the influence of geography and ethnolinguistic boundaries on the distribution of 700 variants of a folktale in 31 European ethnolinguistic populations. We find that geographical distance and ethnolinguistic affiliation exert significant independent effects on folktale diversity and that variation between populations supports a clustering concordant with European geography. This pattern of geographical clines and clusters parallels the pattern of human genetic diversity in Europe, although the effects of geographical distance and ethnolinguistic boundaries are stronger for folktales than genes. Our findings highlight the importance of geography and population boundaries in models of human cultural variation and point to key similarities and differences between evolutionary processes operating on human genes and culture.

  6. Evolutionary dynamics for persistent cooperation in structured populations

    NASA Astrophysics Data System (ADS)

    Li, Yan; Liu, Xinsheng; Claussen, Jens Christian; Guo, Wanlin

    2015-06-01

    The emergence and maintenance of cooperative behavior is a fascinating topic in evolutionary biology and social science. The public goods game (PGG) is a paradigm for exploring cooperative behavior. In PGG, the total resulting payoff is divided equally among all participants. This feature still leads to the dominance of defection without substantially magnifying the public good by a multiplying factor. Much effort has been made to explain the evolution of cooperative strategies, including a recent model in which only a portion of the total benefit is shared by all the players through introducing a new strategy named persistent cooperation. A persistent cooperator is a contributor who is willing to pay a second cost to retrieve the remaining portion of the payoff contributed by themselves. In a previous study, this model was analyzed in the framework of well-mixed populations. This paper focuses on discussing the persistent cooperation in lattice-structured populations. The evolutionary dynamics of the structured populations consisting of three types of competing players (pure cooperators, defectors, and persistent cooperators) are revealed by theoretical analysis and numerical simulations. In particular, the approximate expressions of fixation probabilities for strategies are derived on one-dimensional lattices. The phase diagrams of stationary states, and the evolution of frequencies and spatial patterns for strategies are illustrated on both one-dimensional and square lattices by simulations. Our results are consistent with the general observation that, at least in most situations, a structured population facilitates the evolution of cooperation. Specifically, here we find that the existence of persistent cooperators greatly suppresses the spreading of defectors under more relaxed conditions in structured populations compared to that obtained in well-mixed populations.

  7. Population Structure Shapes Copy Number Variation in Malaria Parasites

    PubMed Central

    Cheeseman, Ian H.; Miller, Becky; Tan, John C.; Tan, Asako; Nair, Shalini; Nkhoma, Standwell C.; De Donato, Marcos; Rodulfo, Hectorina; Dondorp, Arjen; Branch, Oralee H.; Mesia, Lastenia Ruiz; Newton, Paul; Mayxay, Mayfong; Amambua-Ngwa, Alfred; Conway, David J.; Nosten, François; Ferdig, Michael T.; Anderson, Tim J. C.

    2016-01-01

    If copy number variants (CNVs) are predominantly deleterious, we would expect them to be more efficiently purged from populations with a large effective population size (Ne) than from populations with a small Ne. Malaria parasites (Plasmodium falciparum) provide an excellent organism to examine this prediction, because this protozoan shows a broad spectrum of population structures within a single species, with large, stable, outbred populations in Africa, small unstable inbred populations in South America and with intermediate population characteristics in South East Asia. We characterized 122 single-clone parasites, without prior laboratory culture, from malaria-infected patients in seven countries in Africa, South East Asia and South America using a high-density single-nucleotide polymorphism/CNV microarray. We scored 134 high-confidence CNVs across the parasite exome, including 33 deletions and 102 amplifications, which ranged in size from <500 bp to 59 kb, as well as 10,107 flanking, biallelic single-nucleotide polymorphisms. Overall, CNVs were rare, small, and skewed toward low frequency variants, consistent with the deleterious model. Relative to African and South East Asian populations, CNVs were significantly more common in South America, showed significantly less skew in allele frequencies, and were significantly larger. On this background of low frequency CNV, we also identified several high-frequency CNVs under putative positive selection using an FST outlier analysis. These included known adaptive CNVs containing rh2b and pfmdr1, and several other CNVs (e.g., DNA helicase and three conserved proteins) that require further investigation. Our data are consistent with a significant impact of genetic structure on CNV burden in an important human pathogen. PMID:26613787

  8. Population Structure Shapes Copy Number Variation in Malaria Parasites.

    PubMed

    Cheeseman, Ian H; Miller, Becky; Tan, John C; Tan, Asako; Nair, Shalini; Nkhoma, Standwell C; De Donato, Marcos; Rodulfo, Hectorina; Dondorp, Arjen; Branch, Oralee H; Mesia, Lastenia Ruiz; Newton, Paul; Mayxay, Mayfong; Amambua-Ngwa, Alfred; Conway, David J; Nosten, François; Ferdig, Michael T; Anderson, Tim J C

    2016-03-01

    If copy number variants (CNVs) are predominantly deleterious, we would expect them to be more efficiently purged from populations with a large effective population size (Ne) than from populations with a small Ne. Malaria parasites (Plasmodium falciparum) provide an excellent organism to examine this prediction, because this protozoan shows a broad spectrum of population structures within a single species, with large, stable, outbred populations in Africa, small unstable inbred populations in South America and with intermediate population characteristics in South East Asia. We characterized 122 single-clone parasites, without prior laboratory culture, from malaria-infected patients in seven countries in Africa, South East Asia and South America using a high-density single-nucleotide polymorphism/CNV microarray. We scored 134 high-confidence CNVs across the parasite exome, including 33 deletions and 102 amplifications, which ranged in size from <500 bp to 59 kb, as well as 10,107 flanking, biallelic single-nucleotide polymorphisms. Overall, CNVs were rare, small, and skewed toward low frequency variants, consistent with the deleterious model. Relative to African and South East Asian populations, CNVs were significantly more common in South America, showed significantly less skew in allele frequencies, and were significantly larger. On this background of low frequency CNV, we also identified several high-frequency CNVs under putative positive selection using an FST outlier analysis. These included known adaptive CNVs containing rh2b and pfmdr1, and several other CNVs (e.g., DNA helicase and three conserved proteins) that require further investigation. Our data are consistent with a significant impact of genetic structure on CNV burden in an important human pathogen.

  9. Effects of structural complexity enhancement on eastern red-backed salamander (Plethodon cinereus) populations in northern hardwood forests

    USGS Publications Warehouse

    McKenny, H.C.; Keeton, W.S.; Donovan, T.M.

    2006-01-01

    Managing for stand structural complexity in northern hardwood forests has been proposed as a method for promoting microhabitat characteristics important to eastern red-backed salamanders (Plethodon cinereus). We evaluated the effects of alternate, structure-based silvicultural systems on red-backed salamander populations at two research sites in northwestern Vermont. Treatments included two uneven-aged approaches (single-tree selection and group-selection) and one unconventional approach, termed "structural complexity enhancement" (SCE), that promotes development of late-successional structure, including elevated levels of coarse woody debris (CWD). Treatments were applied to 2 ha units and were replicated two to four times depending on treatment. We surveyed red-backed salamanders with a natural cover search method of transects nested within vegetation plots 1 year after logging. Abundance estimates corrected for detection probability were calculated from survey data with a binomial mixture model. Abundance estimates differed between study areas and were influenced by forest structural characteristics. Model selection was conducted using Akaike Information Criteria, corrected for over-dispersed data and small sample size (QAICc). We found no difference in abundance as a response to treatment as a whole, suggesting that all of the uneven-aged silvicultural systems evaluated can maintain salamander populations after harvest. However, abundance was tied to specific structural habitat attributes associated with study plots within treatments. The most parsimonious model of habitat covariates included site, relative density of overstory trees, and density of more-decayed and less-decayed downed CWD. Abundance responded positively to the density of downed, well-decayed CWD and negatively to the density of poorly decayed CWD and to overstory relative density. CWD volume was not a strong predictor of salamander abundance. We conclude that structural complexity enhancement

  10. Impact of the 2010 Deepwater Horizon oil spill on population size and genetic structure of horse flies in Louisiana marshes.

    PubMed

    Husseneder, Claudia; Donaldson, Jennifer R; Foil, Lane D

    2016-01-12

    The greenhead horse fly, Tabanus nigrovittatus Macquart, is frequently found in coastal marshes of the Eastern United States. The greenhead horse fly larvae are top predators in the marsh and thus vulnerable to changes in the environment, and the adults potentially are attracted to polarized surfaces like oil. Therefore, horse fly populations could serve as bioindicators of marsh health and toxic effects of oil intrusion. In this study, we describe the impact of the April 2010 Deep Water Horizon oil spill in the Gulf of Mexico on tabanid population abundance and genetics as well as mating structure. Horse fly populations were sampled biweekly from oiled and unaffected locations immediately after the oil spill in June 2010 until October 2011. Horse fly abundance estimates showed severe crashes of tabanid populations in oiled areas. Microsatellite genotyping of six pristine and seven oiled populations at ten polymorphic loci detected genetic bottlenecks in six of the oiled populations in association with fewer breeding parents, reduced effective population size, lower number of family clusters and fewer migrants among populations. This is the first study assessing the impact of oil contamination at the level of a top arthropod predator of the invertebrate community in salt marshes.

  11. Impact of the 2010 Deepwater Horizon oil spill on population size and genetic structure of horse flies in Louisiana marshes

    PubMed Central

    Husseneder, Claudia; Donaldson, Jennifer R.; Foil, Lane D.

    2016-01-01

    The greenhead horse fly, Tabanus nigrovittatus Macquart, is frequently found in coastal marshes of the Eastern United States. The greenhead horse fly larvae are top predators in the marsh and thus vulnerable to changes in the environment, and the adults potentially are attracted to polarized surfaces like oil. Therefore, horse fly populations could serve as bioindicators of marsh health and toxic effects of oil intrusion. In this study, we describe the impact of the April 2010 Deep Water Horizon oil spill in the Gulf of Mexico on tabanid population abundance and genetics as well as mating structure. Horse fly populations were sampled biweekly from oiled and unaffected locations immediately after the oil spill in June 2010 until October 2011. Horse fly abundance estimates showed severe crashes of tabanid populations in oiled areas. Microsatellite genotyping of six pristine and seven oiled populations at ten polymorphic loci detected genetic bottlenecks in six of the oiled populations in association with fewer breeding parents, reduced effective population size, lower number of family clusters and fewer migrants among populations. This is the first study assessing the impact of oil contamination at the level of a top arthropod predator of the invertebrate community in salt marshes. PMID:26755069

  12. Impact of the 2010 Deepwater Horizon oil spill on population size and genetic structure of horse flies in Louisiana marshes

    NASA Astrophysics Data System (ADS)

    Husseneder, Claudia; Donaldson, Jennifer R.; Foil, Lane D.

    2016-01-01

    The greenhead horse fly, Tabanus nigrovittatus Macquart, is frequently found in coastal marshes of the Eastern United States. The greenhead horse fly larvae are top predators in the marsh and thus vulnerable to changes in the environment, and the adults potentially are attracted to polarized surfaces like oil. Therefore, horse fly populations could serve as bioindicators of marsh health and toxic effects of oil intrusion. In this study, we describe the impact of the April 2010 Deep Water Horizon oil spill in the Gulf of Mexico on tabanid population abundance and genetics as well as mating structure. Horse fly populations were sampled biweekly from oiled and unaffected locations immediately after the oil spill in June 2010 until October 2011. Horse fly abundance estimates showed severe crashes of tabanid populations in oiled areas. Microsatellite genotyping of six pristine and seven oiled populations at ten polymorphic loci detected genetic bottlenecks in six of the oiled populations in association with fewer breeding parents, reduced effective population size, lower number of family clusters and fewer migrants among populations. This is the first study assessing the impact of oil contamination at the level of a top arthropod predator of the invertebrate community in salt marshes.

  13. Effects of oxytetracycline on the abundance and community structure of nitrogen-fixing bacteria during cattle manure composting.

    PubMed

    Sun, Jiajun; Qian, Xun; Gu, Jie; Wang, Xiaojuan; Gao, Hua

    2016-09-01

    The effects of oxytetracycline (OTC) on nitrogen-fixing bacterial communities were investigated during cattle manure composting. The abundance and community structure of nitrogen-fixing bacteria were determined by qPCR and denaturing gradient gel electrophoresis (DGGE), respectively. The matrix was spiked with OTC at four levels: no OTC, 10mg/kg dry weight (DW) OTC (L), 60mg/kg DW OTC (M), and 200mg/kg DW OTC (H). The high temperature period of composting was shorter with M and H, and the decline in temperature during the cooling stage was accelerated by OTC. OTC had a concentration-dependent inhibitory effect on the nitrogenase activity during early composting, and the nifH gene abundance declined significantly during the later composting stage. The DGGE profile and statistical analysis showed that OTC changed the nitrogen-fixing bacterial community succession and reduced the community richness and dominance. The nitrogen-fixing bacterial community structure was affected greatly by the high level of OTC.

  14. Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa.

    PubMed

    Khanyile, Khulekani S; Dzomba, Edgar F; Muchadeyi, Farai C

    2015-01-01

    Extensively raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years that ought to be characterized and utilized. Surveys that can reveal a population's genetic structure and provide an insight into its demographic history will give valuable information that can be used to manage and conserve important indigenous animal genetic resources. This study reports population diversity and structure, linkage disequilibrium and effective population sizes of Southern African village chickens and conservation flocks from South Africa. DNA samples from 312 chickens from South African village and conservation flocks (n = 146), Malawi (n = 30) and Zimbabwe (n = 136) were genotyped using the Illumina iSelect chicken SNP60K BeadChip. Population genetic structure analysis distinguished the four conservation flocks from the village chicken populations. Of the four flocks, the Ovambo clustered closer to the village chickens particularly those sampled from South Africa. Clustering of the village chickens followed a geographic gradient whereby South African chickens were closer to those from Zimbabwe than to chickens from Malawi. Different conservation flocks seemed to have maintained different components of the ancestral genomes with a higher proportion of village chicken diversity found in the Ovambo population. Overall population LD averaged over chromosomes ranged from 0.03 ± 0.07 to 0.58 ± 0.41 and averaged 0.15 ± 0.16. Higher LD, ranging from 0.29 to 0.36, was observed between SNP markers that were less than 10 kb apart in the conservation flocks. LD in the conservation flocks steadily decreased to 0.15 (PK) and 0.24 (VD) at SNP marker interval of 500 kb. Genomewide LD decay in the village chickens from Malawi, Zimbabwe and South Africa followed a similar trend as the conservation flocks although the mean LD values for the investigated SNP intervals were lower. The results suggest low effective

  15. Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa

    PubMed Central

    Khanyile, Khulekani S.; Dzomba, Edgar F.; Muchadeyi, Farai C.

    2015-01-01

    Extensively raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years that ought to be characterized and utilized. Surveys that can reveal a population's genetic structure and provide an insight into its demographic history will give valuable information that can be used to manage and conserve important indigenous animal genetic resources. This study reports population diversity and structure, linkage disequilibrium and effective population sizes of Southern African village chickens and conservation flocks from South Africa. DNA samples from 312 chickens from South African village and conservation flocks (n = 146), Malawi (n = 30) and Zimbabwe (n = 136) were genotyped using the Illumina iSelect chicken SNP60K BeadChip. Population genetic structure analysis distinguished the four conservation flocks from the village chicken populations. Of the four flocks, the Ovambo clustered closer to the village chickens particularly those sampled from South Africa. Clustering of the village chickens followed a geographic gradient whereby South African chickens were closer to those from Zimbabwe than to chickens from Malawi. Different conservation flocks seemed to have maintained different components of the ancestral genomes with a higher proportion of village chicken diversity found in the Ovambo population. Overall population LD averaged over chromosomes ranged from 0.03 ± 0.07 to 0.58 ± 0.41 and averaged 0.15 ± 0.16. Higher LD, ranging from 0.29 to 0.36, was observed between SNP markers that were less than 10 kb apart in the conservation flocks. LD in the conservation flocks steadily decreased to 0.15 (PK) and 0.24 (VD) at SNP marker interval of 500 kb. Genomewide LD decay in the village chickens from Malawi, Zimbabwe and South Africa followed a similar trend as the conservation flocks although the mean LD values for the investigated SNP intervals were lower. The results suggest low effective

  16. Emergent patterns of population genetic structure for a coral reef community.

    PubMed

    Selkoe, Kimberly A; Gaggiotti, Oscar E; Bowen, Brian W; Toonen, Robert J

    2014-06-01

    What shapes variation in genetic structure within a community of codistributed species is a central but difficult question for the field of population genetics. With a focus on the isolated coral reef ecosystem of the Hawaiian Archipelago, we assessed how life history traits influence population genetic structure for 35 reef animals. Despite the archipelago's stepping stone configuration, isolation by distance was the least common type of genetic structure, detected in four species. Regional structuring (i.e. division of sites into genetically and spatially distinct regions) was most common, detected in 20 species and nearly in all endemics and habitat specialists. Seven species displayed chaotic (spatially unordered) structuring, and all were nonendemic generalist species. Chaotic structure also associated with relatively high global FST. Pelagic larval duration (PLD) was not a strong predictor of variation in population structure (R2=0.22), but accounting for higher FST values of chaotic and invertebrate species, compared to regionally structured and fish species, doubled the power of PLD to explain variation in global FST (adjusted R2=0.50). Multivariate correlation of eight species traits to six genetic traits highlighted dispersal ability, taxonomy (i.e. fish vs. invertebrate) and habitat specialization as strongest influences on genetics, but otherwise left much variation in genetic traits unexplained. Considering that the study design controlled for many sampling and geographical factors, the extreme interspecific variation in spatial genetic patterns observed for Hawaìi marine species may be generated by demographic variability due to species-specific abundance and migration patterns and/or seascape and historical factors.

  17. Regional patterns and controlling factors on summer population structure of Calanus glacialis in the western Arctic Ocean

    NASA Astrophysics Data System (ADS)

    Matsuno, Kohei; Abe, Yoshiyuki; Yamaguchi, Atsushi; Kikuchi, Takashi

    2016-12-01

    In the Arctic Ocean, Calanus glacialis is the most dominant species in zooplankton biomass. While important, little information is available concerning the factors controlling their population. In this study, we evaluated regional patterns and environmental factors controlling the population structure of C. glacialis in the western Arctic Ocean in summer months (July-October) in 1991, 1992, 2007, 2008, 2010, 2012, 2013 and 2014. To evaluate regional patterns, environmental parameters (temperature, salinity and chlorophyll a) and C. glacialis population parameters (abundance, biomass, mean copepodid stage and lipid accumulation) were divided into three latitudinal regions. In all three regions from July to October, chlorophyll a decreased, while the mean copepodid stage increased. These results suggest phytoplankton blooms occurred early in the sampling period, and C. glacialis grew during the period. From Structural Equation Model (SEM) analysis, the controlling factors on the C. glacialis population were evaluated. The results of the SEM analysis indicated positive correlations between abundance and biomass; Julian day and mean copepodid stage; and temperature and mean copepodid stage. Additionally, a negative correlation between abundance and mean copepodid stage was observed.

  18. Expert Group Meeting on Population Growth and Demographic Structure.

    PubMed

    1993-01-01

    As part of the preparation for the forth-coming UN International Conference on Population and Development, an expert group met in Paris, France, in November 1992 to discuss population growth and demographic structure. As part of the demographic background for the meeting provided by the UN Population Division, participants were informed that although the world population growth rate began to decline in the late 1970s, this decline has not yet resulted in declining absolute numbers, and the annual increment to the world population was not expected to decline to the level that existed in 1985 until the period 2020-25. World population increased from 2.5 billion in 1950 to 5.3 billion in 1990. The medium variant population projection of the UN shows world population at 6.3 billion in 2000 and 8.5 billion in 2025 (the high variant shows 9.4 billion in 2025 and the low variant shows 7.6 billion). Population aging is expected to reach unparalleled levels in 2010-20. The meeting then considered the topics of population growth and socioeconomic development, confronting poverty in developing countries, demographic impacts of development patterns, demographic and health transitions, population growth and employment, social change and the elderly in developing countries, and social development and ageing in developed countries, The expert group meeting then prepared 19 recommendations aimed at governments, social institutions, and the international community. The recommendations call for political commitment to human resources development and population and development programs, especially in least developed countries, alleviation of poverty and social inequality, and equality of access to social and health resources that will lead to reduced mortality and fertility. Governments are urged to place a high priority on education and on increasing women's access to education and to remove barriers to economic independence for women. Health-sector priorities should be reassessed

  19. Abundance, distribution, and population trends of the iconic Hawaiian Honeycreeper, the ʻIʻiwi (Vestiaria coccinea) throughout the Hawaiian Islands

    USGS Publications Warehouse

    Paxton, Eben H.; Gorresen, P. Marcos; Camp, Richard J.

    2013-01-01

    Naturalists in the 1800s described the ʻIʻiwi (Vestiaria coccinea) as one of the most abundant forest birds, detected in forested areas from sea level to tree line across all the major Hawaiian Islands. However, in the late 1800s, ʻIʻiwi began to disappear from low elevation forests, and by the mid-1900s, the species was largely absent from low- and mid-elevation areas. Today, ʻIʻiwi are restricted to high-elevation forests on the islands of Hawaiʻi, east Maui, and Kauaʻi, with a few birds apparently persisting on Oʻahu, Molokaʻi, and west Maui. ʻIʻiwi are highly vulnerable to introduced disease, and the prevalence of avian malaria in low and mid-elevations is believed to be the cause of ʻIʻiwi being restricted to high elevations where temperatures are too cold for the development of the disease and its mosquito vector. With global warming, it is feared that the disease will move quickly into the high-elevation forests where the last ʻIʻiwi reside, threatening their viability. The U.S. Fish and Wildlife Service was petitioned to list the ʻIʻiwi as an Endangered Species in 2010, and this report provides a comprehensive review of the abundance, distribution, and trends using historical survey data as well as the most recently available survey information (up to 2012). We estimate the total population size of ‘I‘iwi at 550,972–659,864 (mean = 605,418) individuals. Of these, 90 percent are on the island of Hawaiʻi, followed by east Maui (about 10 percent), with less than 1 percent on Kauaʻi. ʻIʻiwi population trends vary across the islands. ʻIʻiwi population in Kauaʻi has experienced sharp declines, with a projected trend of 92 percent decline over a 25 year period based on the 2000–2012 surveys. On East Maui, the northeastern region has experienced declines (34 percent over a 25 year period), while the southeastern region has been stable to moderately increasing. On the island of Hawaiʻi, population trends are mixed. On the windward

  20. How detectable is predation in stage-structured populations? Insights from a simulation-testing analysis.

    PubMed

    Oken, Kiva L; Essington, Timothy E

    2015-01-01

    The potential of predation to structure marine food webs is widely acknowledged. However, available tools to detect the regulation of prey population dynamics by predation are limited, partly because available population data often aggregate a population's age structure into a single biomass or abundance metric. Additionally, many food webs are relatively complex, with prey species subject to different assemblages of predators throughout their ontogeny. The goal of this study was to evaluate the extent to which stage-structured predation could be reliably detected from time series of total biomass of predators and prey. We simulated age-structured populations of four mid-trophic-level fish species with distinct life-history traits, exposed them to variable predation at different life stages and fit production models to resulting population biomass to determine how reliably the effects of predators could be detected. Predation targeting early life history and juvenile life stages generally led to larger fluctuations in annual production and was therefore more detectable. However, ecologically realistic levels of observation error and environmental stochasticity masked most predator signals. The addition of predation at a second life stage sharply decreased the ability to detect the effect of each predator. We conclude that the absence of detectable species interactions from biomass time series may be partly due to the interactive effects of environmental variability and complex food web linkages and life histories. We also note that predation signals are most robust for predator-prey systems where predators primarily act on mortality of submature life-history stages. Simulation testing can be applied widely to evaluate the statistical power of analyses to detect predation effects.

  1. Intraspecific phytochemical variation shapes community and population structure for specialist caterpillars.

    PubMed

    Glassmire, Andrea E; Jeffrey, Christopher S; Forister, Matthew L; Parchman, Thomas L; Nice, Chris C; Jahner, Joshua P; Wilson, Joseph S; Walla, Thomas R; Richards, Lora A; Smilanich, Angela M; Leonard, Michael D; Morrison, Colin R; Simbaña, Wilmer; Salagaje, Luis A; Dodson, Craig D; Miller, Jim S; Tepe, Eric J; Villamarin-Cortez, Santiago; Dyer, Lee A

    2016-10-01

    Chemically mediated plant-herbivore interactions contribute to the diversity of terrestrial communities and the diversification of plants and insects. While our understanding of the processes affecting community structure and evolutionary diversification has grown, few studies have investigated how trait variation shapes genetic and species diversity simultaneously in a tropical ecosystem. We investigated secondary metabolite variation among subpopulations of a single plant species, Piper kelleyi (Piperaceae), using high-performance liquid chromatography (HPLC), to understand associations between plant phytochemistry and host-specialized caterpillars in the genus Eois (Geometridae: Larentiinae) and associated parasitoid wasps and flies. In addition, we used a genotyping-by-sequencing approach to examine the genetic structure of one abundant caterpillar species, Eois encina, in relation to host phytochemical variation. We found substantive concentration differences among three major secondary metabolites, and these differences in chemistry predicted caterpillar and parasitoid community structure among host plant populations. Furthermore, E. encina populations located at high elevations were genetically different from other populations. They fed on plants containing high concentrations of prenylated benzoic acid. Thus, phytochemistry potentially shapes caterpillar and wasp community composition and geographic variation in species interactions, both of which can contribute to diversification of plants and insects.

  2. Seasonal Variation in Population Abundance and Chytrid Infection in Stream-Dwelling Frogs of the Brazilian Atlantic Forest

    PubMed Central

    Ruggeri, Joice; Longo, Ana V.; Gaiarsa, Marília P.; Alencar, Laura R. V.; Lambertini, Carolina; Leite, Domingos S.; Carvalho-e-Silva, Sergio P.; Zamudio, Kelly R.; Toledo, Luís Felipe; Martins, Marcio

    2015-01-01

    Enigmatic amphibian declines were first reported in southern and southeastern Brazil in the late 1980s and included several species of stream-dwelling anurans (families Hylodidae and Cycloramphidae). At that time, we were unaware of the amphibian-killing fungus Batrachochytrium dendrobatidis (Bd); therefore, pollution, habitat loss, fragmentation and unusual climatic events were hypothesized as primary causes of these declines. We now know that multiple lineages of Bd have infected amphibians of the Brazilian Atlantic forest for over a century, yet declines have not been associated specifically with Bd outbreaks. Because stream-dwelling anurans occupy an environmental hotspot ideal for disease transmission, we investigated temporal variation in population and infection dynamics of three stream-adapted species (Hylodes asper, H. phyllodes, and Cycloramphus boraceiensis) on the northern coast of São Paulo state, Brazil. We surveyed standardized transects along streams for four years, and show that fluctuations in the number of frogs correlate with specific climatic variables that also increase the likelihood of Bd infections. In addition, we found that Bd infection probability in C. boraceiensis, a nocturnal species, was significantly higher than in Hylodes spp., which are diurnal, suggesting that the nocturnal activity may either facilitate Bd zoospore transmission or increase susceptibility of hosts. Our findings indicate that, despite long-term persistence of Bd in Brazil, some hosts persist with seasonally variable infections, and thus future persistence in the face of climate change will depend on the relative effect of those changes on frog recruitment and pathogen proliferation. PMID:26161777

  3. Molecular Population Genetic Structure in the Piping Plover

    USGS Publications Warehouse

    Miller, Mark P.; Haig, Susan M.; Gratto-Trevor, Cheri L.; Mullins, Thomas D.

    2009-01-01

    The Piping Plover (Charadrius melodus) is a migratory shorebird currently listed as Endangered in Canada and the U.S. Great Lakes, and threatened throughout the remainder of its U.S. breeding and winter range. In this study, we undertook the first comprehensive molecular genetic-based investigation of Piping Plovers. Our primary goals were to (1) address higher level subspecific taxonomic issues, (2) characterize population genetic structure, and (3) make inferences regarding past bottlenecks or population expansions that have occurred within this species. Our analyses included samples of individuals from 23 U.S. States and Canadian Provinces, and were based on mitochondrial DNA sequences (580 bp, n = 245 individuals) and eight nuclear microsatellite loci (n = 229 individuals). Our findings illustrate strong support for separate Atlantic and Interior Piping Plover subspecies (C. m. melodus and C. m. circumcinctus, respectively). Birds from the Great Lakes region were allied with the Interior subspecies group and should be taxonomically referred to as C. m. circumcinctus. Population genetic analyses suggested that genetic structure was stronger among Atlantic birds relative to the Interior group. This pattern indicates that natal and breeding site fidelity may be reduced among Interior birds. Furthermore, analyses suggested that Interior birds have previously experienced genetic bottlenecks, whereas no evidence for such patterns existed among the Atlantic subspecies. Likewise, genetic analyses indicated that the Great Lakes region has experienced a population expansion. This finding may be interpreted as population growth following a previous bottleneck event. No genetic evidence for population expansions was found for Atlantic, Prairie Canada, or U.S. Northern Great Plains individuals. We interpret our population history insights in light of 25 years of Piping Plover census data. Overall, differences observed between Interior and Atlantic birds may reflect

  4. Genetic diversity and population structure of Yucca filamentosa (Agavaceae).

    PubMed

    Massey, L; Hamrick, J

    1998-03-01

    Using 19 allozyme loci we studied genetic diversity in 18 populations of Yucca filamentosa (Agavaceae) from the southeastern United States. Of the 19 loci surveyed, 17 (89.5%) were polymorphic in at least one of the populations sampled. There was considerable variation among populations in the percentage of polymorphic loci (range = 31.6-84.2%, mean = 67.6%). Similar heterogeneity among populations was observed for mean number of alleles per polymorphic locus (range = 2.0-3.0; mean = 2.48) and mean expected heterozygosity (range = 0.113-0.288; mean = 0.213). On average, 83% of the total genetic diversity was found within populations. Duplications of three allozyme loci were detected in several populations. The life-history characteristics of Y. filamentosa (a long-lived, semiwoody, predominantly outcrossing monocot with a large geographical range) may contribute to the maintenance of such high levels of genetic diversity. These results contradict expectations of the genetic structure of Y. filamentosa based on observations of the dispersal and pollination behavior of its sole pollinator, Tegeticula yuccasella, the yucca moth.

  5. Population structure of the giant garter snake, Thamnophis gigas

    USGS Publications Warehouse

    Paquin, M.M.; Wylie, G.D.; Routman, E.J.

    2006-01-01

    The giant garter snake, Thamnophis gigas, is a threatened species endemic to California's Central Valley. We tested the hypothesis that current watershed boundaries have caused genetic differentiation among populations of T. gigas. We sampled 14 populations throughout the current geographic range of T. gigas and amplified 859 bp from the mitochondrial gene ND4 and one nuclear microsatellite locus. DNA sequence variation from the mitochondrial gene indicates there is some genetic structuring of the populations, with high F ST values and unique haplotypes occurring at high frequency in several populations. We found that clustering populations by watershed boundary results in significant between-region genetic variance for mtDNA. However, analysis of allele frequencies at the microsatellite locus NSU3 reveals very low F ST values and little between-region variation in allele frequencies. The discordance found between mitochondrial and microsatellite data may be explained by aspects of molecular evolution and/or T. gigas life history characteristics. Differences in effective population size between mitochondrial and nuclear DNA, or male-biased gene flow, result in a lower migration rate of mitochondrial haplotypes relative to nuclear alleles. However, we cannot exclude homoplasy as one explanation for homogeneity found for the single microsatellite locus. The mitochondrial nucleotide sequence data supports conservation practices that identify separate management units for T. gigas. ?? Springer 2006.

  6. A Spatial Framework for Understanding Population Structure and Admixture

    PubMed Central

    Bradburd, Gideon S.; Ralph, Peter L.; Coop, Graham M.

    2016-01-01

    Geographic patterns of genetic variation within modern populations, produced by complex histories of migration, can be difficult to infer and visually summarize. A general consequence of geographically limited dispersal is that samples from nearby locations tend to be more closely related than samples from distant locations, and so genetic covariance often recapitulates geographic proximity. We use genome-wide polymorphism data to build “geogenetic maps,” which, when applied to stationary populations, produces a map of the geographic positions of the populations, but with distances distorted to reflect historical rates of gene flow. In the underlying model, allele frequency covariance is a decreasing function of geogenetic distance, and nonlocal gene flow such as admixture can be identified as anomalously strong covariance over long distances. This admixture is explicitly co-estimated and depicted as arrows, from the source of admixture to the recipient, on the geogenetic map. We demonstrate the utility of this method on a circum-Tibetan sampling of the greenish warbler (Phylloscopus trochiloides), in which we find evidence for gene flow between the adjacent, terminal populations of the ring species. We also analyze a global sampling of human populations, for which we largely recover the geography of the sampling, with support for significant histories of admixture in many samples. This new tool for understanding and visualizing patterns of population structure is implemented in a Bayesian framework in the program SpaceMix. PMID:26771578

  7. Population structure of loggerhead shrikes in the California Channel Islands.

    PubMed

    Eggert, Lori S; Mundy, Nicholas I; Woodruff, David S

    2004-08-01

    The loggerhead shrike (Lanius ludovicianus), a songbird that hunts like a small raptor, maintains breeding populations on seven of the eight California Channel Islands. One of the two subspecies, L. l. anthonyi, was described as having breeding populations on six of the islands while a second subspecies, L. l. mearnsi, was described as being endemic to San Clemente Island. Previous genetic studies have demonstrated that the San Clemente Island loggerhead shrike is well differentiated genetically from both L. l. anthonyi and mainland populations, despite the fact that birds from outside the population are regular visitors to the island. Those studies, however, did not include a comparison between San Clemente Island shrikes and the breeding population on Santa Catalina Island, the closest island to San Clemente. Here we use mitochondrial control region sequences and nuclear microsatellites to investigate the population structure of loggerhead shrikes in the Channel Islands. We confirm the genetic distinctiveness of the San Clemente Island loggerhead shrike and, using Bayesian clustering analysis, demonstrate the presence and infer the source of the nonbreeding visitors. Our results indicate that Channel Island loggerhead shrikes comprise three distinct genetic clusters that inhabit: (i) San Clemente Island, (ii) Santa Catalina Island and (iii) the Northern Channel Islands and nearby mainland; they do not support a recent suggestion that all Channel Island loggerhead shrikes should be managed as a single entity.

  8. Population Structure, Diversity and Reproductive Mode of the Grape Phylloxera (Daktulosphaira vitifoliae) across Its Native Range

    PubMed Central

    Walker, M. Andrew

    2017-01-01

    Grape Phylloxera, Daktulosphaira vitifoliae, is a gall-forming insect that feeds on the leaves and roots of many Vitis species. The roots of the cultivated V. vinifera cultivars and hybrids are highly susceptible to grape phylloxera feeding damage. The native range of this insect covers most of North America, and it is particularly abundant in the eastern and central United States. Phylloxera was introduced from North America to almost all grape-growing regions across five of the temperate zone continents. It devastated vineyards in each of these regions causing large-scale disruptions to grape growers, wine makers and national economies. In order to understand the population diversity of grape phylloxera in its native range, more than 500 samples from 19 States and 34 samples from the introduced range (northern California, Europe and South America) were genotyped with 32 simple sequence repeat markers. STRUCTURE, a model based clustering method identified five populations within these samples. The five populations were confirmed by a neighbor-joining tree and principal coordinate analysis (PCoA). These populations were distinguished by their Vitis species hosts and their geographic locations. Samples collected from California, Europe and South America traced back to phylloxera sampled in the northeastern United States on V. riparia, with some influence from phylloxera collected along the Atlantic Coast and Central Plains on V. vulpina. Reproductive statistics conclusively confirmed that sexual reproduction is common in the native range and is combined with cyclical parthenogenesis. Native grape phylloxera populations were identified to be under Hardy-Weinberg equilibrium. The identification of admixed samples between many of these populations indicates that shared environments facilitate sexual reproduction between different host associated populations to create new genotypes of phylloxera. This study also found that assortative mating might occur across the

  9. Evolution in a spatially structured population subject to rare epidemics.

    PubMed

    Socolar, J E; Richards, S; Wilson, W G

    2001-04-01

    We study a model that gives rise to spatially inhomogeneous population densities in a system of host individuals subject to rare, randomly distributed disease events. For stationary hosts that disperse offspring over short distances, evolutionary dynamics can lead to persistent populations with a variety of spatial structures. A mean-field analysis is shown to account for the behavior observed in simulations of a one-dimensional system, where the evolutionarily stable state corresponds to the solution of a straightforward optimization problem. In two dimensions, evolution drives the system to a stable critical state that is less well understood.

  10. Dimensions of global population projections: what do we know about future population trends and structures?

    PubMed

    Lutz, Wolfgang; K C, Samir

    2010-09-27

    The total size of the world population is likely to increase from its current 7 billion to 8-10 billion by 2050. This uncertainty is because of unknown future fertility and mortality trends in different parts of the world. But the young age structure of the population and the fact that in much of Africa and Western Asia, fertility is still very high makes an increase by at least one more billion almost certain. Virtually, all the increase will happen in the developing world. For the second half of the century, population stabilization and the onset of a decline are likely. In addition to the future size of the population, its distribution by age, sex, level of educational attainment and place of residence are of specific importance for studying future food security. The paper provides a detailed discussion of different relevant dimensions in population projections and an evaluation of the methods and assumptions used in current global population projections and in particular those produced by the United Nations and by IIASA.

  11. Modulation of Na(+)-K(+)-ATPase cell surface abundance through structural determinants on the α1-subunit.

    PubMed

    Pierre, Sandrine V; Belliard, Aude; Sottejeau, Yoann

    2011-01-01

    Through their ion-pumping and non-ion-pumping functions, Na(+)-K(+)-ATPase protein complexes at the plasma membrane are critical to intracellular homeostasis and to the physiological and pharmacological actions of cardiotonic steroids. Alteration of the abundance of Na(+)-K(+)-ATPase units at the cell surface is one of the mechanisms for Na(+)-K(+)-ATPase regulation in health and diseases that has been closely examined over the past few decades. We here summarize these findings, with emphasis on studies that explicitly tested the involvement of defined regions or residues on the Na(+)-K(+)-ATPase α1 polypeptide. We also report new findings on the effect of manipulating Na(+)-K(+)-ATPase membrane abundance by targeting one of these defined regions: a dileucine motif of the form [D/E]XXXL[L/I]. In this study, opossum kidney cells stably expressing rat α1 Na(+)-K(+)-ATPase or a mutant where the motif was disrupted (α1-L499V) were exposed to 30 min of substrate/coverslip-induced-ischemia followed by reperfusion (I-R). Biotinylation studies suggested that I-R itself acted as an inducer of Na(+)-K(+)-ATPase internalization and that surface expression of the mutant was higher than the native Na(+)-K(+)-ATPase before and after ischemia. Annexin V/propidium iodide staining and lactate dehydrogenase release suggested that I-R injury was reduced in α1-L499V-expressing cells compared with α1-expressing cells. Hence, modulation of Na(+)-K(+)-ATPase cell surface abundance through structural determinants on the α-subunit is an important mechanism of regulation of cellular Na(+)-K(+)-ATPase in various physiological and pathophysiological conditions, with a significant impact on cell survival in face of an ischemic stress.

  12. Effects of different fertilizers on the abundance and community structure of ammonia oxidizers in a yellow clay soil.

    PubMed

    Yao, Huaiying; Huang, Sha; Qiu, Qiongfen; Li, Yaying; Wu, Lianghuan; Mi, Wenhai; Dai, Feng

    2016-08-01

    Yellow clay paddy soil (Oxisols) is a typical soil with low productivity in southern China. Nitrification inhibitors and slow release fertilizers have been used to improve nitrogen fertilizer utilization and reduce environmental impaction of the paddy soil. However, their effects on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in paddy soil have rarely been investigated. In the present work, we compared the influences of several slow release fertilizers and nitrification inhibitors on the community structure and activities of the ammonia oxidizers in yellow clay soil. The abundances and community compositions of AOA and AOB were determined with qPCR, terminal restriction fragment length polymorphism (T-RFLP), and clone library approaches. Our results indicated that the potential nitrification rate (PNR) of the soil was significantly related to the abundances of both AOA and AOB. Nitrogen fertilizer application stimulated the growth of AOA and AOB, and the combinations of nitrapyrin with urea (NPU) and urea-formaldehyde (UF) inhibited the growth of AOA and AOB, respectively. Compared with other treatments, the applications of NPU and UF also led to significant shifts in the community compositions of AOA and AOB, respectively. NPU showed an inhibitory effect on AOA T-RF 166 bp that belonged to Nitrosotalea. UF had a negative effect on AOB T-RF 62 bp that was assigned to Nitrosospira. These results suggested that NPU inhibited PNR and increased nitrogen use efficiency (NUE) by inhibiting the growth of AOA and altering AOA community. UF showed no effect on NUE but decreased AOB abundance and shifted AOB community.

  13. Profiling of the molecular weight and structural isomer abundance of macroalgae-derived phlorotannins.

    PubMed

    Heffernan, Natalie; Brunton, Nigel P; FitzGerald, Richard J; Smyth, Thomas J

    2015-01-16

    Phlorotannins are a group of complex polymers of phloroglucinol (1,3,5-trihydroxybenzene) unique to macroalgae. These phenolic compounds are integral structural components of the cell wall in brown algae, but also play many secondary ecological roles such as protection from UV radiation and defense against grazing. This study employed Ultra Performance Liquid Chromatography (UPLC) with tandem mass spectrometry to investigate isomeric complexity and observed differences in phlorotannins derived from macroalgae harvested off the Irish coast (Fucus serratus, Fucus vesiculosus, Himanthalia elongata and Cystoseira nodicaulis). Antioxidant activity and total phenolic content assays were used as an index for producing phlorotannin fractions, enriched using molecular weight cut-off dialysis with subsequent flash chromatography to profile phlorotannin isomers in these macroalgae. These fractions were profiled using UPLC-MS with multiple reaction monitoring (MRM) and the level of isomerization for specific molecular weight phlorotannins between 3 and 16 monomers were determined. The majority of the low molecular weight (LMW) phlorotannins were found to have a molecular weight range equivalent to 4-12 monomers of phloroglucinol. The level of isomerization within the individual macroalgal species differed, resulting in substantially different numbers of phlorotannin isomers for particular molecular weights. F. vesiculosus had the highest number of isomers of 61 at one specific molecular mass, corresponding to 12 phloroglucinol units (PGUs). These results highlight the complex nature of these extracts and emphasize the challenges involved in structural elucidation of these compounds.

  14. Evaluation of Fish Movements, Migration Patterns and Populations Abundance with Streamwidth PIT Tag Interrogation Systems, Final Report 2002.

    SciTech Connect

    Zydlewski, Gayle B.; Casey, Sean

    2003-02-01

    (approximately 5,400). All species used the faster moving/deeper section of the creek at both SPIs. A backpack PIT tag detector was also developed and used as another remote ''recapture'' for additional accuracy in estimating population survival and recapture probability. This unit was used at an approximate efficiency of 24% to survey the creek after the Spring migration. Twenty-five individual fish were re-located. All PIT tag data were used to calculate survival and recapture probabilities using the Cormack-Jolly-Seber population model. Survival for steelhead was high and recapture probability depended greatly on season. Probability of recapture was highest in Spring (29.5%) and relatively low in all other seasons (< 7% in Fall, Winter, and Summer). Wild steelhead PIT tagged in the field and returned to the laboratory had a tag retention rate of 97.6%. A laboratory study was designed to determine the effects of 3-sized PIT tags (12 mm, 20 mm, and 23 mm) on survival and growth of individuals. Survival from surgical implantation of 23 mm PIT tags was > 98% for fish (coho salmon and steelhead). Retention of 23 mm PIT tags was 100% for coho salmon and 89% for steelhead. For both coho and steelhead, growth rates during the first month were affected by tagging, but by the end of 2 months growth effects equalized for all tag sizes. Life history characteristics quantified with SPI techniques are comparable to standard techniques. For example, peaks of Spring migration for steelhead and cutthroat were amazingly similar to those reported from the screw trap. These techniques will enable application of less laborious methods which are more accurate at estimating life history parameters.

  15. Evaluation of Fish Movements, Migration Patterns, and Population Abundance with Streamwidth PIT Tag Interrogation Systems, Final Report 2002.

    SciTech Connect

    Zydlewski, Gayle; Winter, Christiane; McClanahan, Dee

    2003-02-01

    (approximately 5,400). All species used the faster moving/deeper section of the creek at both SPIs. A backpack PIT tag detector was also developed and used as another remote 'recapture' for additional accuracy in estimating population survival and recapture probability. This unit was used at an approximate efficiency of 24% to survey the creek after the Spring migration. Twenty-five individual fish were re-located. All PIT tag data were used to calculate survival and recapture probabilities using the Cormack-Jolly-Seber population model. Survival for steelhead was high and recapture probability depended greatly on season. Probability of recapture was highest in Spring (29.5%) and relatively low in all other seasons (< 7% in Fall, Winter, and Summer). Wild steelhead PIT tagged in the field and returned to the laboratory had a tag retention rate of 97.6%. A laboratory study was designed to determine the effects of 3-sized PIT tags (12 mm, 20 mm, and 23 mm) on survival and growth of individuals. Survival from surgical implantation of 23 mm PIT tags was > 98% for fish (coho salmon and steelhead). Retention of 23 mm PIT tags was 100% for coho salmon and 89% for steelhead. For both coho and steelhead, growth rates during the first month were affected by tagging, but by the end of 2 months growth effects equalized for all tag sizes. Life history characteristics quantified with SPI techniques are comparable to standard techniques. For example, peaks of Spring migration for steelhead and cutthroat were amazingly similar to those reported from the screw trap. These techniques will enable application of less laborious methods which are more accurate at estimating life history parameters.

  16. fastSTRUCTURE: variational inference of population structure in large SNP data sets.

    PubMed

    Raj, Anil; Stephens, Matthew; Pritchard, Jonathan K

    2014-06-01

    Tools for estimating population structure from genetic data are now used in a wide variety of applications in population genetics. However, inferring population structure in large modern data sets imposes severe computational challenges. Here, we develop efficient algorithms for approximate inference of the model underlying the STRUCTURE program using a variational Bayesian framework. Variational methods pose the problem of computing relevant posterior distributions as an optimization problem, allowing us to build on recent advances in optimization theory to develop fast inference tools. In addition, we propose useful heuristic scores to identify the number of populations represented in a data set and a new hierarchical prior to detect weak population structure in the data. We test the variational algorithms on simulated data and illustrate using genotype data from the CEPH-Human Genome Diversity Panel. The variational algorithms are almost two orders of magnitude faster than STRUCTURE and achieve accuracies comparable to those of ADMIXTURE. Furthermore, our results show that the heuristic scores for choosing model complexity provide a reasonable range of values for the number of populations represented in the data, with minimal bias toward detecting structure when it is very weak. Our algorithm, fastSTRUCTURE, is freely available online at http://pritchardlab.stanford.edu/structure.html.

  17. Demographic analysis from summaries of an age-structured population.

    PubMed

    Link, William A; Royle, J Andrew; Hatfield, Jeff S

    2003-12-01

    Demographic analyses of age-structured populations typically rely on life history data for individuals, or when individual animals are not identified, on information about the numbers of individuals in each age class through time. While it is usually difficult to determine the age class of a randomly encountered individual, it is often the case that the individual can be readily and reliably assigned to one of a set of age classes. For example, it is often possible to distinguish first-year from older birds. In such cases, the population age structure can be regarded as a latent variable governed by a process prior, and the data as summaries of this latent structure. In this article, we consider the problem of uncovering the latent structure and estimating process parameters from summaries of age class information. We present a demographic analysis for the critically endangered migratory population of whooping cranes (Grus americana), based only on counts of first-year birds and of older birds. We estimate age and year-specific survival rates. We address the controversial issue of whether management action on the breeding grounds has influenced recruitment, relating recruitment rates to the number of seventh-year and older birds, and examining the pattern of variation through time in this rate.

  18. Demographic analysis from summaries of an age-structured population

    USGS Publications Warehouse

    Link, William A.; Royle, J. Andrew; Hatfield, Jeff S.

    2003-01-01

    Demographic analyses of age-structured populations typically rely on life history data for individuals, or when individual animals are not identified, on information about the numbers of individuals in each age class through time. While it is usually difficult to determine the age class of a randomly encountered individual, it is often the case that the individual can be readily and reliably assigned to one of a set of age classes. For example, it is often possible to distinguish first-year from older birds. In such cases, the population age structure can be regarded as a latent variable governed by a process prior, and the data as summaries of this latent structure. In this article, we consider the problem of uncovering the latent structure and estimating process parameters from summaries of age class information. We present a demographic analysis for the critically endangered migratory population of whooping cranes (Grus americana), based only on counts of first-year birds and of older birds. We estimate age and year-specific survival rates. We address the controversial issue of whether management action on the breeding grounds has influenced recruitment, relating recruitment rates to the number of seventh-year and older birds, and examining the pattern of variation through time in this rate.

  19. Modelling malaria population structure and its implications for control.

    PubMed

    Buckee, Caroline O; Gupta, Sunetra

    2010-01-01

    Mathematical models of malaria transmission have been used to inform the design of malaria control programs since the mid 20th century, and many of these models have provided useful insights into the complexity of the disease. Among developing countries, however and particularly in sub-Saharan Africa, malaria remains a major cause of morbidity and mortality. One of the main difficulties in controlling the most virulent human malaria parasite, Plasmodium falciparum, is its genetic diversity, which confounds attempts to design an effective vaccine. The population structure of P. falciparum remains poorly understood but plays a key role in determining epidemiological patterns of disease and the development of immunity. We discuss the seminal model of malaria transmission developed by Ross and MacDonald, and the modifications that have been made since to include more realism. We show that age profiles of disease and serological data support a theoretical model in which the parasite population is diverse and structured into several antigenic types and highlight the implications of this structure for controlling malaria. Lastly, we discuss the current sequence data on parasite antigen genes that are important for the aquisition of immunity, and the results of a new analysis of P. falciparum population structure at the genomic level.

  20. Narrow-line Seyfert Galaxies. Connection between abundance and the large-scale structure

    NASA Astrophysics Data System (ADS)

    Ermash, A. A.; Komberg, B. V.

    2014-12-01

    Utilizing methods, developed by the author the correlations between spatial concentrations of active nuclei (NLS and BLS) and concentration of galaxies of full uniform sample were obtained. Galaxies of this uniform sample trace the large-scale structure. We used SDSS DR 7 data. The correlations obtained are linear and the NLS/BLS ratio is constant. That leads to conclusion that amounts NLS and BLS are some fixed portion of all galaxies independent on the density of large-scale environment. In order to check validity of our results we also confirmed the well known result that fraction of red galaxies increases with density of environment. Also it was confirmed that this trend is more prominent for less massive galaxies.

  1. Variations in the abundance of fisheries resources and ecosystem structure in the Japan/East Sea

    NASA Astrophysics Data System (ADS)

    Zhang, Chang Ik; Lee, Jae Bong; Seo, Young Il; Yoon, Sang Cheol; Kim, Suam

    2004-05-01

    Evidence supports the hypothesis that two climatic regime shifts in the North Pacific and the Japan/East Sea, have affected the dynamics of the marine ecosystem and fisheries resources from 1960 to 2000. Changes in both mixed layer depth (MLD) and primary production were detected in the Japan/East Sea after 1976. The 1976 regime shift appears to have caused the biomass replacement with changes in catch production of major exploited fisheries resources, including Pacific saury, Pacific sardine and filefish. Both fisheries yield and fish distribution are reflected in these decadal fluctuations. In the 1960s and 1990s, common squid dominated the catches whereas in the 1970s and 1980s, it was replaced by walleye pollock. In the post-1988 regime shift, the distribution of horse mackerel shifted westward and southward and its distributional overlap with common mackerel decreased. The habitat of Pacific sardine also shifted away from mackerel habitats during this period. To evaluate changes in the organization and structure of the ecosystem in the Japan/East Sea, a mass-balanced model, Ecopath, was employed. Based on two mass-balanced models, representing before (1970-75) and after (1978-84) the 1976 regime shift, the weighted mean trophic level of catch increased from 3.09 before to 3.28 after. Total biomass of species groups in the Japan/East Sea ecosystem increased by 15% and total catch production increased by 48% due to the 1976 regime shift. The largest changes occurred at mid-trophic levels, occupied by fishes and cephalopods. The dominant predatory species shifted from cephalopods to walleye pollock due to the 1976 regime shift. It is concluded that the climatic regime shifts caused changes in the structure of the ecosystem and the roles of major species, as well as, large variations in biomass and production of fisheries resources.

  2. A Comparison of Anammox Bacterial Abundance and Community Structures in Three Different Emerged Plants-Related Sediments.

    PubMed

    Chu, Jinyu; Zhang, Jinping; Zhou, Xiaohong; Liu, Biao; Li, Yimin

    2015-09-01

    Quantitative polymerase chain reaction (qPCR) assays and 16S rRNA gene clone libraries were used to document the abundance, diversity and community structure of anaerobic ammonia-oxidising (anammox) bacteria in the rhizosphere and non-rhizosphere sediments of three emergent macrophyte species (Iris pseudacorus, Thalia dealbata and Typha orientalis). The qPCR results confirmed the existence of anammox bacteria (AMX) with observed log number of gene copies per dry gram sediment ranging from 5.00 to 6.78. AMX was more abundant in T. orientalis-associated sediments than in the other two plant species. The I. pseudacorus- and T. orientalis-associated sediments had higher Shannon diversity values, indicating higher AMX diversity in these sediments. Based on the 16S rRNA gene, Candidatus 'Brocadia', Candidatus 'Kuenenia', Candidatus 'Jettenia' and new clusters were observed with the predominant Candidatus 'Kuenenia' cluster. The I. pseudacorus-associated sediments contained all the sequences of the C. 'Jettenia' cluster. Sequences obtained from T. orientalis-associated sediments contributed more than 90 % sequences in the new cluster, whereas none was found from I. pseudacorus. The new cluster was distantly related to known sequences; thus, this cluster was grouped outside the known clusters, indicating that the new cluster may be a new Planctomycetales genus. Further studies should be undertaken to confirm this finding.

  3. THE C+N+O ABUNDANCE OF {omega} CENTAURI GIANT STARS: IMPLICATIONS FOR THE CHEMICAL-ENRICHMENT SCENARIO AND THE RELATIVE AGES OF DIFFERENT STELLAR POPULATIONS

    SciTech Connect

    Marino, A. F.; Milone, A. P.; Aparicio, A.; Piotto, G.; Cassisi, S.; D'Antona, F.; Anderson, J.; Bedin, L. R.; Renzini, A.; Villanova, S. E-mail: milone@iac.es E-mail: giampaolo.piotto@unipd.it E-mail: dantona@oa-roma.inaf.it E-mail: luigi.bedin@oapd.inaf.it E-mail: svillanova@astro-udec.cl

    2012-02-10

    We present a chemical-composition analysis of 77 red-giant stars in Omega Centauri. We have measured abundances for carbon and nitrogen, and combined our results with abundances of O, Na, La, and Fe that we determined in our previous work. Our aim is to better understand the peculiar chemical-enrichment history of this cluster by studying how the total C+N+O content varies among the different metallicity stellar groups, and among stars at different places along the Na-O anticorrelation. We find that the (anti)correlations among the light elements that would be expected on theoretical grounds for matter that has been nuclearly processed via high-temperature proton captures. The overall [(C+N+O)/Fe] increases by {approx}0.5 dex from [Fe/H] {approx}-2.0 to [Fe/H] {approx}-0.9. Our results provide insight into the chemical-enrichment history of the cluster, and the measured CNO variations provide important corrections for estimating the relative ages of the different stellar populations.

  4. Visualizing spatial population structure with estimated effective migration surfaces.

    PubMed

    Petkova, Desislava; Novembre, John; Stephens, Matthew

    2016-01-01

    Genetic data often exhibit patterns broadly consistent with 'isolation by distance'-a phenomenon where genetic similarity decays with geographic distance. In a heterogeneous habitat, this may occur more quickly in some regions than in others: for example, barriers to gene flow can accelerate differentiation between neighboring groups. We use the concept of 'effective migration' to model the relationship between genetics and geography. In this paradigm, effective migration is low in regions where genetic similarity decays quickly. We present a method to visualize variation in effective migration across a habitat from geographically indexed genetic data. Our approach uses a population genetic model to relate effective migration rates to expected genetic dissimilarities. We illustrate its potential and limitations using simulations and data from elephant, human and Arabidopsis thaliana populations. The resulting visualizations highlight important spatial features of population structure that are difficult to discern using existing methods for summarizing genetic variation.

  5. Visualizing spatial population structure with estimated effective migration surfaces

    PubMed Central

    Petkova, Desislava; Novembre, John; Stephens, Matthew

    2015-01-01

    Genetic data often exhibit patterns broadly consistent with “isolation by distance” – a phenomenon where genetic similarity decays with geographic distance. In a heterogeneous habitat this may occur more quickly in some regions than others: for example, barriers to gene flow can accelerate differentiation between neighboring groups. We use the concept of “effective migration” to model the relationship between genetics and geography: in this paradigm, effective migration is low in regions where genetic similarity decays quickly. We present a method to visualize variation in effective migration across the habitat from geographically indexed genetic data. Our approach uses a population genetic model to relate effective migration rates to expected genetic dissimilarities. We illustrate its potential and limitations using simulations and data from elephant, human and A. thaliana populations. The resulting visualizations highlight important spatial features of population structure that are difficult to discern using existing methods for summarizing genetic variation. PMID:26642242

  6. Effects of polycyclic aromatic hydrocarbons on microbial community structure and PAH ring hydroxylating dioxygenase gene abundance in soil.

    PubMed

    Sawulski, Przemyslaw; Clipson, Nicholas; Doyle, Evelyn

    2014-11-01

    Development of successful bioremediation strategies for environments contaminated with recalcitrant pollutants requires in-depth knowledge of the microorganisms and microbial processes involved in degradation. The response of soil microbial communities to three polycyclic aromatic hydrocarbons, phenanthrene (3-ring), fluoranthene (4-ring) and benzo(a)pyrene (5-ring), was examined. Profiles of bacterial, archaeal and fungal communities were generated using molecular fingerprinting techniques (TRFLP, ARISA) and multivariate statistical tools were employed to interpret the effect of PAHs on community dynamics and composition. The extent and rate of PAH removal was directly related to the chemical structure, with the 5-ring PAH benzo(a)pyrene degraded more slowly than phenathrene or fluoranthene. Bacterial, archaeal and fungal communities were all significantly affected by PAH amendment, time and their interaction. Based on analysis of clone libraries, Actinobacteria appeared to dominate in fluoranthene amended soil, although they also represented a significant portion of the diversity in phenanthrene amended and unamended soils. In addition there appeared to be more γ-Proteobacteria and less Bacteroidetes in soil amended with either PAH compared to the control. The soil bacterial community clearly possessed the potential to degrade PAHs as evidenced by the abundance of PAH ring hydroxylating (PAH-RHDα) genes from both gram negative (GN) and gram positive (GP) bacteria in PAH-amended and control soils. Although the dioxygenase gene from GP bacteria was less abundant in soil than the gene associated with GN bacteria, significant (p < 0.001) increases in the abundance of the GP PAH-RHDα gene were observed during phenanthrene and fluoranthene degradation, whereas there was no significant difference in the abundance of the GN PAH-RHDα gene during the course of the experiment. Few studies to-date have examined the effect of pollutants on more than one microbial

  7. Temporal changes in kin structure through a population cycle in a territorial bird, the red grouse Lagopus lagopus scoticus.

    PubMed

    Piertney, Stuart B; Lambin, Xavier; Maccoll, Andrew D C; Lock, Kerry; Bacon, Philip J; Dallas, John F; Leckie, Fiona; Mougeot, Francois; Racey, Paul A; Redpath, Steve; Moss, Robert

    2008-05-01

    Populations of red grouse (Lagopus lagopus scoticus) undergo regular multiannual cycles in abundance. The 'kinship hypothesis' posits that such cycles are caused by changes in kin structure among territorial males producing delayed density-dependent changes in aggressiveness, which in turn influence recruitment and regulate density. The kinship hypothesis makes several specific predictions about the levels of kinship, aggressiveness and recruitment through a population cycle: (i) kin structure will build up during the increase phase of a cycle, but break down prior to peak density; (ii) kin structure influences aggressiveness, such that there will be a negative relationship between kinship and aggressiveness over the years; (iii) as aggressiveness regulates recruitment and density, there will be a negative relationship between aggressiveness in one year and both recruitment and density in the next; (iv) as kin structure influences recruitment via an affect on aggressiveness, there will be a positive relationship between kinship in one year and recruitment the next. Here we test these predictions through the course of an 8-year cycle in a natural population of red grouse in northeast Scotland, using microsatellite DNA markers to resolve changing patterns of kin structure, and supra-orbital comb height of grouse as an index of aggressiveness. Both kin structure and aggressiveness were dynamic through the course of the cycle, and changing patterns were entirely consistent with the expectations of the kinship hypothesis. Results are discussed in relation to potential drivers of population regulation and implications of dynamic kin structure for population genetics.

  8. Aedes albopictus (Diptera: Culicidae) population density and structure in southwest Louisiana.

    PubMed

    Willis, F S; Nasci, R S

    1994-07-01

    Pupal density, wing length at emergence, host-seeking female abundance, and host-seeking female wing length and parity were determined monthly for a population of Aedes albopictus (Skuse) in a southwestern Louisiana tire dump from January 1988 through January 1989. Pupae and host-seeking females were first collected in April. Pupal densities were consistently high from June through September. Host-seeking female abundance was highest during July and August. Average female wing length was longest during spring, declined in midsummer, and increased slightly during fall. Average wing length was negatively correlated with average pupal density during the month of collection and with average air temperature recorded the previous month. Host-seeking females had consistently longer wings than emerging females, and parous host-seeking females had longer wings than nulliparous host-seeking females. Average wing length of the parous host-seeking females was consistently long throughout the season. Parity of host-seeking females parity was highest during July when approximately 21 parous host-seeking females were collected per hour. These results indicate that seasonal patterns in immature population density influence average body size and parity structure in Ae. albopictus.

  9. Campylobacter jejuni colonization and population structure in urban populations of ducks and starlings in New Zealand

    PubMed Central

    Mohan, Vathsala; Stevenson, Mark; Marshall, Jonathan; Fearnhead, Paul; Holland, Barbara R; Hotter, Grant; French, Nigel P

    2013-01-01

    Abstract A repeated cross-sectional study was conducted to determine the prevalence of Campylobacter spp. and the population structure of C. jejuni in European starlings and ducks cohabiting multiple public access sites in an urban area of New Zealand. The country's geographical isolation and relatively recent history of introduction of wild bird species, including the European starling and mallard duck, create an ideal setting to explore the impact of geographical separation on the population biology of C. jejuni, as well as potential public health implications. A total of 716 starling and 720 duck fecal samples were collected and screened for C. jejuni over a 12 month period. This study combined molecular genotyping, population genetics and epidemiological modeling and revealed: (i) higher Campylobacter spp. isolation in starlings (46%) compared with ducks (30%), but similar isolation of C. jejuni in ducks (23%) and starlings (21%), (ii) significant associations between the isolation of Campylobacter spp. and host species, sampling location and time of year using logistic regression, (iii) evidence of population differentiation, as indicated by FST, and host-genotype association with clonal complexes CC ST-177 and CC ST-682 associated with starlings, and clonal complexes CC ST-1034, CC ST-692, and CC ST-1332 associated with ducks, and (iv) greater genetic diversity and genotype richness in ducks compared with starlings. These findings provide evidence that host-associated genotypes, such as the starling-associated ST-177 and ST-682, represent lineages that were introduced with the host species in the 19th century. The isolation of sequence types associated with human disease in New Zealand indicate that wild ducks and starlings need to be considered as a potential public health risk, particularly in urban areas. We applied molecular epidemiology and population genetics to obtain insights in to the population structure, host-species relationships, gene flow and

  10. Rivers influence the population genetic structure of bonobos (Pan paniscus).

    PubMed

    Eriksson, J; Hohmann, G; Boesch, C; Vigilant, L

    2004-11-01

    Bonobos are large, highly mobile primates living in the relatively undisturbed, contiguous forest south of the Congo River. Accordingly, gene flow among populations is assumed to be extensive, but may be impeded by large, impassable rivers. We examined mitochondrial DNA control region sequence variation in individuals from five distinct localities separated by rivers in order to estimate relative levels of genetic diversity and assess the extent and pattern of population genetic structure in the bonobo. Diversity estimates for the bonobo exceed those for humans, but are less than those found for the chimpanzee. All regions sampled are significantly differentiated from one another, according to genetic distances estimated as pairwise FSTs, with the greatest differentiation existing between region East and each of the two Northern populations (N and NE) and the least differentiation between regions Central and South. The distribution of nucleotide diversity shows a clear signal of population structure, with some 30% of the variance occurring among geographical regions. However, a geographical patterning of the population structure is not obvious. Namely, mitochondrial haplotypes were shared among all regions excepting the most eastern locality and the phylogenetic analysis revealed a tree in which haplotypes were intermixed with little regard to geographical origin, with the notable exception of the close relationships among the haplotypes found in the east. Nonetheless, genetic distances correlated with geographical distances when the intervening distances were measured around rivers presenting effective current-day barriers, but not when straight-line distances were used, suggesting that rivers are indeed a hindrance to gene flow in this species.

  11. Seasonal abundance, species composition, and population dynamics of stink bugs in production fields of early and late soybean in South Arkansas.

    PubMed

    Smith, J F; Luttrell, R G; Greene, J K

    2009-02-01

    From 2003 through 2007, densities of stink bugs were monitored weekly in 297 commercial production fields of early and late soybean, Glycine max L. Merrill, in southeast and southwest Arkansas. The goal of this research was to better understand seasonal abundance, species composition, and population dynamics of pentatomids as a benchmark reference for future management systems. Thirty-five percent of all the 25-sweep samples taken in soybean contained at least one stink bug specimen. The average density (mean +/- SEM) of stink bugs across all soybean samples was 1.84 +/- 0.06 per 25 sweeps. Overall, Nezara viridula L. was the most abundant species, although Euschistus serous (Say) was frequently found in soybean samples (18% of all samples). Peak densities of stink bugs in soybean were observed during the full-pod (R7) developmental stage. Approximately 25% of all soybean fields sampled had threshold densities (nine or more per 25 sweeps) at some time during the year, although 82 and 78% of fields in 2006 and 2007, respectively, reached threshold. At low densities (one to three stink bugs per 25 sweeps), E. serous comprised 50% of total stink bugs, but at high densities (> 71 stink bugs per 25 sweeps), N. viridula comprised 81% of total stink bugs. Piezodorus guildinii (Westwood) was observed as a pest of Arkansas soybean in 2005, and reproduction in soybean was documented in 2006 and 2007. Stink bugs seem to be a serious and increasingly important pest of soybean in southern Arkansas. Crop phenological development is a key factor in predicting colonization and population growth of stink bugs on Arkansas soybean, regardless of geographic region or type of soybean production system.

  12. Different perceptions of social dilemmas: Evolutionary multigames in structured populations

    NASA Astrophysics Data System (ADS)

    Wang, Zhen; Szolnoki, Attila; Perc, Matjaž

    2014-09-01

    Motivated by the fact that the same social dilemma can be perceived differently by different players, we here study evolutionary multigames in structured populations. While the core game is the weak prisoner's dilemma, a fraction of the population adopts either a positive or a negative value of the sucker's payoff, thus playing either the traditional prisoner's dilemma or the snowdrift game. We show that the higher the fraction of the population adopting a different payoff matrix the more the evolution of cooperation is promoted. The microscopic mechanism responsible for this outcome is unique to structured populations, and it is due to the payoff heterogeneity, which spontaneously introduces strong cooperative leaders that give rise to an asymmetric strategy imitation flow in favor of cooperation. We demonstrate that the reported evolutionary outcomes are robust against variations of the interaction network, and they also remain valid if players are allowed to vary which game they play over time. These results corroborate existing evidence in favor of heterogeneity-enhanced network reciprocity, and they reveal how different perceptions of social dilemmas may contribute to their resolution.

  13. Argentine Population Genetic Structure: Large Variance in Amerindian Contribution

    PubMed Central

    Seldin, Michael F.; Tian, Chao; Shigeta, Russell; Scherbarth, Hugo R.; Silva, Gabriel; Belmont, John W.; Kittles, Rick; Gamron, Susana; Allevi, Alberto; Palatnik, Simon A.; Alvarellos, Alejandro; Paira, Sergio; Caprarulo, Cesar; Guillerón, Carolina; Catoggio, Luis J.; Prigione, Cristina; Berbotto, Guillermo A.; García, Mercedes A.; Perandones, Carlos E.; Pons-Estel, Bernardo A.; Alarcon-Riquelme, Marta E.

    2011-01-01

    Argentine population genetic structure was examined using a set of 78 ancestry informative markers (AIMs) to assess the contributions of European, Amerindian, and African ancestry in 94 individuals members of this population. Using the Bayesian clustering algorithm STRUCTURE, the mean European contribution was 78%, the Amerindian contribution was 19.4%, and the African contribution was 2.5%. Similar results were found using weighted least mean square method: European, 80.2%; Amerindian, 18.1%; and African, 1.7%. Consistent with previous studies the current results showed very few individuals (four of 94) with greater than 10% African admixture. Notably, when individual admixture was examined, the Amerindian and European admixture showed a very large variance and individual Amerindian contribution ranged from 1.5 to 84.5% in the 94 individual Argentine subjects. These results indicate that admixture must be considered when clinical epidemiology or case control genetic analyses are studied in this population. Moreover, the current study provides a set of informative SNPs that can be used to ascertain or control for this potentially hidden stratification. In addition, the large variance in admixture proportions in individual Argentine subjects shown by this study suggests that this population is appropriate for future admixture mapping studies. PMID:17177183

  14. Spatial structure of lemming populations (Dicrostonyx groenlandicus) fluctuating in density.

    PubMed

    Ehrich, D; Jorde, P E; Krebs, C J; Kenney, A J; Stacy, J E; Stenseth, N C

    2001-02-01

    The pattern and scale of the genetic structure of populations provides valuable information for the understanding of the spatial ecology of populations, including the spatial aspects of density fluctuations. In the present paper, the genetic structure of periodically fluctuating lemmings (Dicrostonyx groenlandicus) in the Canadian Arctic was analysed using mitochondrial DNA (mtDNA) control region sequences and four nuclear microsatellite loci. Low genetic variability was found in mtDNA, while microsatellite loci were highly variable in all localities, including localities on isolated small islands. For both genetic markers the genetic differentiation was clear among geographical regions but weaker among localities within regions. Such a pattern implies gene flow within regions. Based on theoretical calculations and population census data from a snap-trapping survey, we argue that the observed genetic variability on small islands and the low level of differentiation among these islands cannot be explained without invoking long distance dispersal of lemmings over the sea ice. Such dispersal is unlikely to occur only during population density peaks.

  15. Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent.

    PubMed

    McLellan, S L; Huse, S M; Mueller-Spitz, S R; Andreishcheva, E N; Sogin, M L

    2010-02-01

    The release of untreated sewage introduces non-indigenous microbial populations of uncertain composition into surface waters. We used massively parallel 454 pyrosequencing of hypervariable regions in rRNA genes to profile microbial communities from eight untreated sewage influent samples of two wastewater treatment plants (WWTPs) in metropolitan Milwaukee. The sewage profiles included a discernible human faecal signature made up of several taxonomic groups including multiple Bifidobacteriaceae, Coriobacteriaceae, Bacteroidaceae, Lachnospiraceae and Ruminococcaceae genera. The faecal signature made up a small fraction of the taxa present in sewage but the relative abundance of these sequence tags mirrored the population structures of human faecal samples. These genera were much more prevalent in the sewage influent than standard indicators species. High-abundance sequences from taxonomic groups within the Beta- and Gammaproteobacteria dominated the sewage samples but occurred at very low levels in faecal and surface water samples, suggesting that these organisms proliferate within the sewer system. Samples from Jones Island (JI--servicing residential plus a combined sewer system) and South Shore (SS--servicing a residential area) WWTPs had very consistent community profiles, with greater similarity between WWTPs on a given collection day than the same plant collected on different days. Rainfall increased influent flows at SS and JI WWTPs, and this corresponded to greater diversity in the community at both plants. Overall, the sewer system appears to be a defined environment with both infiltration of rainwater and stormwater inputs modulating community composition. Microbial sewage communities represent a combination of inputs from human faecal microbes and enrichment of specific microbes from the environment to form a unique population structure.

  16. Abundant off-fault seismicity and orthogonal structures in the San Jacinto fault zone

    PubMed Central

    Ross, Zachary E.; Hauksson, Egill; Ben-Zion, Yehuda

    2017-01-01

    The trifurcation area of the San Jacinto fault zone has produced more than 10% of all earthquakes in southern California since 2000, including the June 2016 Mw (moment magnitude) 5.2 Borrego Springs earthquake. In this area, the fault splits into three subparallel strands and is associated with broad VP/VS anomalies. We synthesize spatiotemporal properties of historical background seismicity and aftershocks of the June 2016 event. A template matching technique is used to detect and locate more than 23,000 aftershocks, which illuminate highly complex active fault structures in conjunction with a high-resolution regional catalog. The hypocenters form dipping seismicity lineations both along strike and nearly orthogonal to the main fault, and are composed of interlaced strike-slip and normal faults. The primary faults change dip with depth and become listric by transitioning to a dip of ~70° near a depth of 10 km. The Mw 5.2 Borrego Springs earthquake and past events with M > 4.0 occurred on the main faults, whereas most of the low-magnitude events are located in a damage zone (several kilometers wide) at seismogenic depths. The lack of significant low-magnitude seismicity on the main fault traces suggests that they do not creep. The very high rate of aftershocks likely reflects the large geometrical fault complexity and perhaps a relatively high stress due to a significant length of time elapsed since the last major event. The results provide important insights into the physics of faulting near the brittle-ductile transition. PMID:28345036

  17. Abundant off-fault seismicity and orthogonal structures in the San Jacinto fault zone.

    PubMed

    Ross, Zachary E; Hauksson, Egill; Ben-Zion, Yehuda

    2017-03-01

    The trifurcation area of the San Jacinto fault zone has produced more than 10% of all earthquakes in southern California since 2000, including the June 2016 Mw (moment magnitude) 5.2 Borrego Springs earthquake. In this area, the fault splits into three subparallel strands and is associated with broad VP /VS anomalies. We synthesize spatiotemporal properties of historical background seismicity and aftershocks of the June 2016 event. A template matching technique is used to detect and locate more than 23,000 aftershocks, which illuminate highly complex active fault structures in conjunction with a high-resolution regional catalog. The hypocenters form dipping seismicity lineations both along strike and nearly orthogonal to the main fault, and are composed of interlaced strike-slip and normal faults. The primary faults change dip with depth and become listric by transitioning to a dip of ~70° near a depth of 10 km. The Mw 5.2 Borrego Springs earthquake and past events with M > 4.0 occurred on the main faults, whereas most of the low-magnitude events are located in a damage zone (several kilometers wide) at seismogenic depths. The lack of significant low-magnitude seismicity on the main fault traces suggests that they do not creep. The very high rate of aftershocks likely reflects the large geometrical fault complexity and perhaps a relatively high stress due to a significant length of time elapsed since the last major event. The results provide important insights into the physics of faulting near the brittle-ductile transition.

  18. Development of paradigms for the dynamics of structured populations

    SciTech Connect

    Not Available

    1994-10-01

    This is a technical progress report on the dynamics of predator-prey systems in a patchy environment. A new phenomenon that might contribute to outbreaks in systems of discrete patches has been determined using a discrete time model with both spatial and age structure. A model for a single species in a patchy environment with migration, local population growth and disasters with in patches has been formulated and a brief description is included.

  19. Genetic structuring among silverside fish (Atherinella brasiliensis) populations from different Brazilian regions

    NASA Astrophysics Data System (ADS)

    da Silva Cortinhas, Maria Cristina; Kersanach, Ralf; Proietti, Maíra; Dumont, Luiz Felipe Cestari; D'Incao, Fernando; Lacerda, Ana Luzia F.; Prata, Pedro Sanmartin; Matoso, Daniele Aparecida; Noleto, Rafael Bueno; Ramsdorf, Wanessa; Boni, Talge Aiex; Prioli, Alberto José; Cestari, Marta Margarete

    2016-09-01

    Estuaries are dynamic environments, key for the survival of innumerous ecologically or economically important fish species. Among these species are Neotropical silversides (Atherinella brasiliensis), which are resident and abundant in Brazilian estuaries and used as a complementary source of income and food for local communities. To better understand silverside populations in Brazil, we evaluated the genetic diversity, structure and demography of fish sampled at six estuaries from the northeastern to the southern coast, using Random Amplified Polymorphic DNA and mitochondrial DNA (D-loop) markers. High haplotype diversities (h ranging from 0.75 to 0.99) were found in all populations except Carapebus, located in Southeast Brazil (h = 0.54). A total of 69 mtDNA haplotypes were found, with Itaparica (Northeast Brazil) and Carapebus presenting only exclusive haplotypes, while some were shared among populations in the South. Strong regional structure was observed, with very high differentiation between Itaparica and Carapebus, as well as among these two populations and the ones from the Southern region (Paranaguá, Conceição, Camacho and Patos). Among southern areas, low/moderate structure was detected. Most populations showed unimodal mismatch distributions indicating recent demographic expansion, while Carapebus presented a multimodal distribution characteristic of a stable or bottlenecked population. Times since possible population expansion were highest in Itaparica (32,500 ya) and Carapebus (29,540 ya), while in the Southern region longest time was observed at Conceição (25,540 ya) and shortest at Patos (9720 ya). In a general manner, haplotype diversities were directly related to times since population expansions; again, Carapebus was the exception, displaying long time since expansion but low diversity, possibly due to a recent bottleneck caused by the isolation and human impacts this lagoon is subject to. Isolation by Distance was significant for Itaparica

  20. Population structure and minimum core genome typing of Legionella pneumophila

    PubMed Central

    Qin, Tian; Zhang, Wen; Liu, Wenbin; Zhou, Haijian; Ren, Hongyu; Shao, Zhujun; Lan, Ruiting; Xu, Jianguo

    2016-01-01

    Legionella pneumophila is an important human pathogen causing Legionnaires’ disease. In this study, whole genome sequencing (WGS) was used to study the characteristics and population structure of L. pneumophila strains. We sequenced and compared 53 isolates of L. pneumophila covering different serogroups and sequence-based typing (SBT) types (STs). We found that 1,896 single-copy orthologous genes were shared by all isolates and were defined as the minimum core genome (MCG) of L. pneumophila. A total of 323,224 single-nucleotide polymorphisms (SNPs) were identified among the 53 strains. After excluding 314,059 SNPs which were likely to be results of recombination, the remaining 9,165 SNPs were referred to as MCG SNPs. Population Structure analysis based on MCG divided the 53 L. pneumophila into nine MCG groups. The within-group distances were much smaller than the between-group distances, indicating considerable divergence between MCG groups. MCG groups were also supplied by phylogenetic analysis and may be considered as robust taxonomic units within L. pneumophila. Among the nine MCG groups, eight showed high intracellular growth ability while one showed low intracellular growth ability. Furthermore, MCG typing also showed high resolution in subtyping ST1 strains. The results obtained in this study provided significant insights into the evolution, population structure and pathogenicity of L. pneumophila. PMID:26888563

  1. Effects of Habitat Structure and Fragmentation on Diversity and Abundance of Primates in Tropical Deciduous Forests in Bolivia.

    PubMed

    Pyritz, Lennart W; Büntge, Anna B S; Herzog, Sebastian K; Kessler, Michael

    2010-10-01

    Habitat structure and anthropogenic disturbance are known to affect primate diversity and abundance. However, researchers have focused on lowland rain forests, whereas endangered deciduous forests have been neglected. We aimed to investigate the relationships between primate diversity and abundance and habitat parameters in 10 deciduous forest fragments southeast of Santa Cruz, Bolivia. We obtained primate data via line-transect surveys and visual and acoustic observations. In addition, we assessed the vegetation structure (canopy height, understory density), size, isolation time, and surrounding forest area of the fragments. We interpreted our results in the context of the historical distribution data for primates in the area before fragmentation and interviews with local people. We detected 5 of the 8 historically observed primate species: Alouatta caraya, Aotus azarae boliviensis, Callithrix melanura, Callicebus donacophilus, and Cebus libidinosus juruanus. Total species number and detection rates decreased with understory density. Detection rates also negatively correlated with forest areas in the surroundings of a fragment, which may be due to variables not assessed, i.e., fragment shape, distance to nearest town. Observations for Alouatta and Aotus were too few to conduct further statistics. Cebus and Callicebus were present in 90% and 70% of the sites, respectively, and their density did not correlate with any of the habitat variables assessed, signaling high ecological plasticity and adaptability to anthropogenic impact in these species. Detections of Callithrix were higher in areas with low forest strata. Our study provides baseline data for future fragmentation studies in Neotropical dry deciduous forests and sets a base for specific conservation measures.

  2. Effects of Habitat Structure and Fragmentation on Diversity and Abundance of Primates in Tropical Deciduous Forests in Bolivia

    PubMed Central

    Büntge, Anna B. S.; Herzog, Sebastian K.; Kessler, Michael

    2010-01-01

    Habitat structure and anthropogenic disturbance are known to affect primate diversity and abundance. However, researchers have focused on lowland rain forests, whereas endangered deciduous forests have been neglected. We aimed to investigate the relationships between primate diversity and abundance and habitat parameters in 10 deciduous forest fragments southeast of Santa Cruz, Bolivia. We obtained primate data via line-transect surveys and visual and acoustic observations. In addition, we assessed the vegetation structure (canopy height, understory density), size, isolation time, and surrounding forest area of the fragments. We interpreted our results in the context of the historical distribution data for primates in the area before fragmentation and interviews with local people. We detected 5 of the 8 historically observed primate species: Alouatta caraya, Aotus azarae boliviensis, Callithrix melanura, Callicebus donacophilus, and Cebus libidinosus juruanus. Total species number and detection rates decreased with understory density. Detection rates also negatively correlated with forest areas in the surroundings of a fragment, which may be due to variables not assessed, i.e., fragment shape, distance to nearest town. Observations for Alouatta and Aotus were too few to conduct further statistics. Cebus and Callicebus were present in 90% and 70% of the sites, respectively, and their density did not correlate with any of the habitat variables assessed, signaling high ecological plasticity and adaptability to anthropogenic impact in these species. Detections of Callithrix were higher in areas with low forest strata. Our study provides baseline data for future fragmentation studies in Neotropical dry deciduous forests and sets a base for specific conservation measures. PMID:20949116

  3. Comparison of the abundance and community structure of ammonia oxidizing prokaryotes in rice rhizosphere under three different irrigation cultivation modes.

    PubMed

    Zhang, Jinping; Zhou, Xiaohong; Chen, Lei; Chen, Zhigang; Chu, Jinyu; Li, Yimin

    2016-05-01

    The abundance, diversity and community structure of ammonia oxidizing archaea (AOA) and bacteria (AOB) in rice rhizosphere soils under three different irrigation cultivated modes, named continuous irrigation mode (C), intermittent irrigation mode (I) and semi-arid mode (M), respectively, were investigated using amoA gene as a molecular biomarker. Clone libraries and quantitative polymerase chain reaction results indicated the highest number of archaeal amoA gene copy was detected in M cultivation mode, then in I and C, whereas, their order of amoA gene copy numbers were I > M > C for AOB, and those were obvious higher than in the bulk soil. The ratios of AOA/AOB were greater than 1 for all samples, suggested the predominance of AOA throughout the period of rice growth in the three different irrigation cultivation modes. Diversity index (SChao1 and Shannon H) have an obvious variation in three different irrigation cultivation modes. For AOA, SChao1 was highest in M and lowest in I mode, whereas, Shannon H was highest in M cultivation mode and lowest in C mode. For AOB, mode M exhibited the highest diversity index (SChao1 and Shannon H), while C showed the lowest highest diversity, suggested long-term water input (continuous mode) may decrease diversity of ammonia oxidizers, whereas mode M may be more appropriate for them. In addition, AOA sequences fall within Nitrososphaera, Nitrosopumilus and Nitrosotalea cluster with proportion of 89.38, 8.85 and 1.77 %, respectively. AOB gene sequences belonged to the Nitrosomonas and Nitrosospira genera with proportion of 90.97 and 9.03 %, respectively. In addition, the abundances, diversity and community structure had an obvious temporal variation in three developmental stages of rice, further suggested rice growth obviously affected the ammonia oxidizing prokaryotes in their rhizosphere soil.

  4. Abundance of non-native crabs in intertidal habitats of New England with natural and artificial structure

    PubMed Central

    Lovely, Christina M.; Judge, Michael L.

    2015-01-01

    Marine habitats containing complex physical structure (e.g., crevices) can provide shelter from predation for benthic invertebrates. To examine effects of natural and artificial structure on the abundance of intertidal juvenile crabs, 2 experiments were conducted in Kingston Bay, Massachusetts, USA, from July to September, 2012. In the first experiment, structure was manipulated in a two-factor design that was placed in the high intertidal for 3 one-week periods to test for both substrate type (sand vs. rock) and the presence or absence of artificial structure (mesh grow-out bags used in aquaculture, ∼0.5 m2 with 62 mm2 mesh openings). The Asian shore crab, Hemigrapsus sanguineus, and small individuals of the green crab, Carcinus maenas, were observed only in the treatments of rocks and mesh bag plus rocks. Most green crabs were small (<6 mm in carapace width) whereas H. sanguineus occurred in a wide range of sizes. In the second experiment, 3 levels of oyster-shell treatments were established using grow-out bags placed on a muddy sand substrate in the low intertidal zone: mesh grow-out bags without shells, grow-out bags with oyster shells, and grow-out bags containing live oysters. Replicate bags were deployed weekly for 7 weeks in a randomized complete block design. All crabs collected in the bags were juvenile C. maenas (1–15 mm carapace width), and numbers of crabs differed 6-fold among treatments, with most crabs present in bags with live oysters (29.5 ± 10.6 m−2 [mean ± S.D.]) and fewest in bags without shells (4.9 ± 3.7 m−2). Both C. maenas and H. sanguineus occurred in habitats with natural structure (cobble rocks). The attraction of juvenile C. maenas to artificial structure consisting of plastic mesh bags containing both oyster shells and living oysters could potentially impact oyster aquaculture operations. PMID:26401456

  5. Abundance of non-native crabs in intertidal habitats of New England with natural and artificial structure.

    PubMed

    Lovely, Christina M; O'Connor, Nancy J; Judge, Michael L

    2015-01-01

    Marine habitats containing complex physical structure (e.g., crevices) can provide shelter from predation for benthic invertebrates. To examine effects of natural and artificial structure on the abundance of intertidal juvenile crabs, 2 experiments were conducted in Kingston Bay, Massachusetts, USA, from July to September, 2012. In the first experiment, structure was manipulated in a two-factor design that was placed in the high intertidal for 3 one-week periods to test for both substrate type (sand vs. rock) and the presence or absence of artificial structure (mesh grow-out bags used in aquaculture, ∼0.5 m(2) with 62 mm(2) mesh openings). The Asian shore crab, Hemigrapsus sanguineus, and small individuals of the green crab, Carcinus maenas, were observed only in the treatments of rocks and mesh bag plus rocks. Most green crabs were small (<6 mm in carapace width) whereas H. sanguineus occurred in a wide range of sizes. In the second experiment, 3 levels of oyster-shell treatments were established using grow-out bags placed on a muddy sand substrate in the low intertidal zone: mesh grow-out bags without shells, grow-out bags with oyster shells, and grow-out bags containing live oysters. Replicate bags were deployed weekly for 7 weeks in a randomized complete block design. All crabs collected in the bags were juvenile C. maenas (1-15 mm carapace width), and numbers of crabs differed 6-fold among treatments, with most crabs present in bags with live oysters (29.5 ± 10.6 m(-2) [mean ± S.D.]) and fewest in bags without shells (4.9 ± 3.7 m(-2)). Both C. maenas and H. sanguineus occurred in habitats with natural structure (cobble rocks). The attraction of juvenile C. maenas to artificial structure consisting of plastic mesh bags containing both oyster shells and living oysters could potentially impact oyster aquaculture operations.

  6. Temporal Variation in Genetic Diversity and Structure of a Lotic Population of Burkholderia (Pseudomonas) cepacia

    PubMed Central

    Wise, M. G.; McArthur, J. V.; Wheat, C.; Shimkets, L. J.

    1996-01-01

    The genetic structure and temporal patterns of genetic diversity in a population of Burkholderia (Pseudomonas) cepacia, isolated from a southeastern blackwater stream, were investigated by multilocus enzyme electrophoresis. Allelic variation in seven structural gene loci was monitored at a single stream location at 0, 6, 12, and 24 h and at 2, 4, 8, 16, and 32 days. Over the length of the study, 217 isolates were collected, from which 65 unique electrophoretic types (ETs) were identified. Most of these ETs were present at only one or two time periods and were considered transients; however, one resident ET was particularly abundant (64 of the 217 isolates [29.4%]) and was found at all time points except day 32. The mean genetic diversity of the entire population was 0.520, and the index of association (a measure of multilocus linkage disequilibrium) was 1.33. These results, taken in conjunction with a previous study focusing on spatial patterns of genetic diversity in lotic B. cepacia, show that these bacterial populations exhibit greater variability among sites than within a site over time, suggesting relative stability over short time periods. PMID:16535308

  7. Competitive advantage and higher fitness in native populations of genetically structured planktonic diatoms.

    PubMed

    Sildever, Sirje; Sefbom, Josefin; Lips, Inga; Godhe, Anna

    2016-12-01

    It has been shown that the planktonic diatom Skeletonema from neighbouring areas are genetically differentiated despite absence of physical dispersal barriers. We revisited two sites, Mariager Fjord and Kattegat, NE Atlantic, and isolated new strains. Microsatellite genotyping and F-statistics revealed that the populations were genetically differentiated. An experiment was designed to investigate if populations are locally adapted and have a native competitive advantage. Ten strains from each location were grown individually in native and foreign water to investigate differences in produced biomass. Additionally, we mixed six pairs, one strain from each site, and let them grow together in native and foreign water. Strains from Mariager Fjord and Kattegat produced higher biomass in native water. In the competition experiment, strains from both sites displayed higher relative abundance and demonstrated competitive advantage in their native water. The cause of the differentiated growth is unknown, but could possibly be attributed to differences in silica concentration or viruses in the two water types. Our data show that dispersal potential does not influence the genetic structure of the populations. We conclude that genetic adaptation has not been overruled by gene flow, but instead the responses to different selection conditions are enforcing the observed genetic structure.

  8. Lonely populations in the deep: genetic structure of red gorgonians at the heads of submarine canyons in the north-western Mediterranean Sea

    NASA Astrophysics Data System (ADS)

    Pérez-Portela, Rocío; Cerro-Gálvez, Elena; Taboada, Sergi; Tidu, Carlo; Campillo-Campbell, Carolina; Mora, Joan; Riesgo, Ana

    2016-09-01

    The red gorgonian Paramuricea clavata plays a central role in coralligenous ecosystems of the Mediterranean Sea, being relatively abundant in shallow habitats (5-35 m depth). Recently, deeper populations have been discovered at the heads of submarine canyons in the north-western Mediterranean Sea, between 50 and 70 m deep. Colonies from some of these deeper populations were exceptionally large (>1 m high), contrasting with the general prevalence of smaller size classes in shallower populations. Importantly, the high pressure of trawling activities on the nearby continental shelf could threaten these populations of large and old colonies. Although the genetic diversity and structure of populations in shallow habitats is relatively well known, very little is known about deeper populations. We aimed to assess the genetic structure, connectivity and potential demographic decline of six deep populations of P. clavata located at the heads of La Fonera, Blanes and Arenys de Mar submarine canyons, as well as potential gene flow between those and the two nearest shallow populations. A total of 188 individuals were genotyped using nine microsatellite loci. Results showed strong genetic differentiation among populations in different submarine canyons, among populations within one of the canyons and between shallow and deep populations. Gene flow among populations was very limited, estimates of effective population size in some populations were small, and evidence of recent population reductions (bottlenecks) was detected in several populations. The large genetic differentiation in populations of P. clavata among canyons is related to limited effective dispersal.

  9. Four types of interference competition and their impacts on the ecology and evolution of size-structured populations and communities.

    PubMed

    Zhang, Lai; Andersen, Ken H; Dieckmann, Ulf; Brännström, Åke

    2015-09-07

    We investigate how four types of interference competition - which alternatively affect foraging, metabolism, survival, and reproduction - impact the ecology and evolution of size-structured populations. Even though all four types of interference competition reduce population biomass, interference competition at intermediate intensity sometimes significantly increases the abundance of adult individuals and the population׳s reproduction rate. We find that foraging and metabolic interference evolutionarily favor smaller maturation size when interference is weak and larger maturation size when interference is strong. The evolutionary response to survival interference and reproductive interference is always larger maturation size. We also investigate how the four types of interference competition impact the evolutionary dynamics and resultant diversity and trophic structure of size-structured communities. Like other types of trait-mediated competition, all four types of interference competition can induce disruptive selection and thus promote initial diversification. Even though foraging interference and reproductive interference are more potent in promoting initial diversification, they catalyze the formation of diverse communities with complex trophic structure only at high levels of interference intensity. By contrast, survival interference does so already at intermediate levels, while reproductive interference can only support relatively smaller communities with simpler trophic structure. Taken together, our results show how the type and intensity of interference competition jointly affect coexistence patterns in structured population models.

  10. Age-structured mark-recapture analysis: A virtual-population-analysis-based model for analyzing age-structured capture-recapture data

    USGS Publications Warehouse

    Coggins, L.G.; Pine, William E.; Walters, C.J.; Martell, S.J.D.

    2006-01-01

    We present a new model to estimate capture probabilities, survival, abundance, and recruitment using traditional Jolly-Seber capture-recapture methods within a standard fisheries virtual population analysis framework. This approach compares the numbers of marked and unmarked fish at age captured in each year of sampling with predictions based on estimated vulnerabilities and abundance in a likelihood function. Recruitment to the earliest age at which fish can be tagged is estimated by using a virtual population analysis method to back-calculate the expected numbers of unmarked fish at risk of capture. By using information from both marked and unmarked animals in a standard fisheries age structure framework, this approach is well suited to the sparse data situations common in long-term capture-recapture programs with variable sampling effort. ?? Copyright by the American Fisheries Society 2006.

  11. Visualizing Transient Low-Populated Structures of RNA

    PubMed Central

    Dethoff, Elizabeth A.; Petzold, Katja; Chugh, Jeetender; Casiano-Negroni, Anette; Al-Hashimi, Hashim M.

    2012-01-01

    The visualization of RNA conformational changes has provided fundamental insights into how regulatory RNAs carry out their biological functions. The RNA structural transitions that have been characterized to date involve long-lived species that can be captured by structure characterization techniques. Here, we report the Nuclear Magnetic Resonance visualization of RNA transitions towards invisible ‘excited states’ (ES), which exist in too little abundance (2–13%) and for too short periods of time (45–250 μs) to allow structural characterization by conventional techniques. Transitions towards ESs result in localized rearrangements in base-pairing that alter building block elements of RNA architecture, including helix-junction-helix motifs and apical loops. The ES can inhibit function by sequestering residues involved in recognition and signaling or promote ATP-independent strand exchange. Thus, RNAs do not adopt a single conformation, but rather exist in rapid equilibrium with alternative ESs, which can be stabilized by cellular cues to affect functional outcomes. PMID:23041928

  12. Population genetic structure in apricot (Prunus armeniaca L.) cultivars revealed by fluorescent-AFLP markers in southern Xinjiang, China.

    PubMed

    Yuan, Zhaohe; Chen, Xuesen; He, Tianming; Feng, Jianrong; Feng, Tao; Zhang, Chunyu

    2007-11-01

    Population-wide genetic structure was studied using fluorescent-AFLP markers on 85 apricot (Prunus armeniaca L.) cultivars collected from Kuche, Kashi, Hetian in the Tarim Basin, southern Xinjiang Uygur Autonomous Region of China. The purpose of this study was to determine the genetic structure and genotypic diversity among the different eco-geographical populations. Based on the results from this study, 8 pairs of fluorescent-AFLP primers showed clear electrophoregram and high polymorphism amongst the 64 pairs of EcoR|/Mse|(Mse|--a FAM fluorescent marked primer) primers screened. There was a significant polymorphic difference for the same primer pair in different populations and for the same population with different primer pairs. The percentage of polymorphic loci (P) at species level was higher than Kuche, Hetian, Kashi population levels, respectively. The Nei's gene diversity index (H) and Shannon's information index (I) at species level were higher than those of Kuche, Hetian, and Kashi at population level, respectively. H and I of Kuche population were the highest amongst the three populations. Apricot population genetic diversity was found mainly within the population. Genetic differentiation coefficient between populations (G(ST)) was 0.0882. Gene flow Nm between the populations was 5.1689. Population genetic identity was between 0.9772-0.9811 and genetic distance was between 0.0191-0.0232. These results further indicated that the similarity between populations was higher and the genetic distance between populations was smaller. The UPGMA cluster analysis indicates that the geographical populations at Kuche, Kashi, Hetian were relatively independent Mendelian populations. Concurrently, there was also partial gene exchange between the populations. All the evidences indicated that the genetic diversity in Kuche population was the highest, suggesting that it could be a transition population from wild apricot to cultivated apricot. There were abundant genetic

  13. Conformation of a group 2 late embryogenesis abundant protein from soybean. Evidence of poly (L-proline)-type II structure.

    PubMed

    Soulages, Jose L; Kim, Kangmin; Arrese, Estela L; Walters, Christina; Cushman, John C

    2003-03-01

    Late embryogenesis abundant (LEA) proteins are members of a large group of hydrophilic, glycine-rich proteins found in plants, algae, fungi, and bacteria known collectively as hydrophilins that are preferentially expressed in response to dehydration or hyperosmotic stress. Group 2 LEA (dehydrins or responsive to abscisic acid) proteins are postulated to stabilize macromolecules against damage by freezing, dehydration, ionic, or osmotic stress. However, the structural and physicochemical properties of group 2 LEA proteins that account for such functions remain unknown. We have analyzed the structural properties of a recombinant form of a soybean (Glycine max) group 2 LEA (rGmDHN1). Differential scanning calorimetry of purified rGmDHN1 demonstrated that the protein does not display a cooperative unfolding transition upon heating. Ultraviolet absorption and circular dichroism spectroscopy revealed that the protein is in a largely hydrated and unstructured conformation in solution. However, ultraviolet absorption and circular dichroism measurements collected at different temperatures showed that the protein exists in equilibrium between two extended conf