A general population genetic framework for antagonistic selection that accounts for demography and recurrent mutation.

PubMed

Connallon, Tim; Clark, Andrew G

2012-04-01

Antagonistic selection--where alleles at a locus have opposing effects on male and female fitness ("sexual antagonism") or between components of fitness ("antagonistic pleiotropy")--might play an important role in maintaining population genetic variation and in driving phylogenetic and genomic patterns of sexual dimorphism and life-history evolution. While prior theory has thoroughly characterized the conditions necessary for antagonistic balancing selection to operate, we currently know little about the evolutionary interactions between antagonistic selection, recurrent mutation, and genetic drift, which should collectively shape empirical patterns of genetic variation. To fill this void, we developed and analyzed a series of population genetic models that simultaneously incorporate these processes. Our models identify two general properties of antagonistically selected loci. First, antagonistic selection inflates heterozygosity and fitness variance across a broad parameter range--a result that applies to alleles maintained by balancing selection and by recurrent mutation. Second, effective population size and genetic drift profoundly affect the statistical frequency distributions of antagonistically selected alleles. The "efficacy" of antagonistic selection (i.e., its tendency to dominate over genetic drift) is extremely weak relative to classical models, such as directional selection and overdominance. Alleles meeting traditional criteria for strong selection (N(e)s > 1, where N(e) is the effective population size, and s is a selection coefficient for a given sex or fitness component) may nevertheless evolve as if neutral. The effects of mutation and demography may generate population differences in overall levels of antagonistic fitness variation, as well as molecular population genetic signatures of balancing selection.

The effects of selection and genetic drift on the genomic distribution of sexually antagonistic alleles.

PubMed

Mullon, Charles; Pomiankowski, Andrew; Reuter, Max

2012-12-01

Sexual antagonism (SA) occurs when an allele that is beneficial to one sex, is detrimental to the other. This conflict can result in balancing, directional, or disruptive selection acting on SA alleles. A body of theory predicts the conditions under which sexually antagonistic mutants will invade and be maintained in stable polymorphism under balancing selection. There remains, however, considerable debate over the distribution of SA genetic variation across autosomes and sex chromosomes, with contradictory evidence coming from data and theory. In this article, we investigate how the interplay between selection and genetic drift will affect the genomic distribution of sexually antagonistic alleles. The effective population sizes can differ between the autosomes and the sex chromosomes due to a number of ecological factors and, consequently, the distribution of SA genetic variation in genomes. In general, we predict the interplay of SA selection and genetic drift should lead to the accumulation of SA alleles on the X in male heterogametic (XY) species and, on the autosomes in female heterogametic (ZW) species, especially when sexual competition is strong among males. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Disrupting evolutionary processes: the effect of habitat fragmentation on collared lizards in the Missouri Ozarks.

PubMed

Templeton, A R; Robertson, R J; Brisson, J; Strasburg, J

2001-05-08

Humans affect biodiversity at the genetic, species, community, and ecosystem levels. This impact on genetic diversity is critical, because genetic diversity is the raw material of evolutionary change, including adaptation and speciation. Two forces affecting genetic variation are genetic drift (which decreases genetic variation within but increases genetic differentiation among local populations) and gene flow (which increases variation within but decreases differentiation among local populations). Humans activities often augment drift and diminish gene flow for many species, which reduces genetic variation in local populations and prevents the spread of adaptive complexes outside their population of origin, thereby disrupting adaptive processes both locally and globally within a species. These impacts are illustrated with collared lizards (Crotaphytus collaris) in the Missouri Ozarks. Forest fire suppression has reduced habitat and disrupted gene flow in this lizard, thereby altering the balance toward drift and away from gene flow. This balance can be restored by managed landscape burns. Some have argued that, although human-induced fragmentation disrupts adaptation, it will also ultimately produce new species through founder effects. However, population genetic theory and experiments predict that most fragmentation events caused by human activities will facilitate not speciation, but local extinction. Founder events have played an important role in the macroevolution of certain groups, but only when ecological opportunities are expanding rather than contracting. The general impact of human activities on genetic diversity disrupts or diminishes the capacity for adaptation, speciation, and macroevolutionary change. This impact will ultimately diminish biodiversity at all levels.

Linking extinction-colonization dynamics to genetic structure in a salamander metapopulation.

PubMed

Cosentino, Bradley J; Phillips, Christopher A; Schooley, Robert L; Lowe, Winsor H; Douglas, Marlis R

2012-04-22

Theory predicts that founder effects have a primary role in determining metapopulation genetic structure. However, ecological factors that affect extinction-colonization dynamics may also create spatial variation in the strength of genetic drift and migration. We tested the hypothesis that ecological factors underlying extinction-colonization dynamics influenced the genetic structure of a tiger salamander (Ambystoma tigrinum) metapopulation. We used empirical data on metapopulation dynamics to make a priori predictions about the effects of population age and ecological factors on genetic diversity and divergence among 41 populations. Metapopulation dynamics of A. tigrinum depended on wetland area, connectivity and presence of predatory fish. We found that newly colonized populations were more genetically differentiated than established populations, suggesting that founder effects influenced genetic structure. However, ecological drivers of metapopulation dynamics were more important than age in predicting genetic structure. Consistent with demographic predictions from metapopulation theory, genetic diversity and divergence depended on wetland area and connectivity. Divergence was greatest in small, isolated wetlands where genetic diversity was low. Our results show that ecological factors underlying metapopulation dynamics can be key determinants of spatial genetic structure, and that habitat area and isolation may mediate the contributions of drift and migration to divergence and evolution in local populations.

Trapped within the city: integrating demography, time since isolation and population-specific traits to assess the genetic effects of urbanization.

PubMed

Lourenço, André; Álvarez, David; Wang, Ian J; Velo-Antón, Guillermo

2017-03-01

Urbanization is a severe form of habitat fragmentation that can cause many species to be locally extirpated and many others to become trapped and isolated within an urban matrix. The role of drift in reducing genetic diversity and increasing genetic differentiation is well recognized in urban populations. However, explicit incorporation and analysis of the demographic and temporal factors promoting drift in urban environments are poorly studied. Here, we genotyped 15 microsatellites in 320 fire salamanders from the historical city of Oviedo (Est. 8th century) to assess the effects of time since isolation, demographic history (historical effective population size; N e ) and patch size on genetic diversity, population structure and contemporary N e . Our results indicate that urban populations of fire salamanders are highly differentiated, most likely due to the recent N e declines, as calculated in coalescence analyses, concomitant with the urban development of Oviedo. However, urbanization only caused a small loss of genetic diversity. Regression modelling showed that patch size was positively associated with contemporary N e , while we found only moderate support for the effects of demographic history when excluding populations with unresolved history. This highlights the interplay between different factors in determining current genetic diversity and structure. Overall, the results of our study on urban populations of fire salamanders provide some of the very first insights into the mechanisms affecting changes in genetic diversity and population differentiation via drift in urban environments, a crucial subject in a world where increasing urbanization is forecasted. © 2017 John Wiley & Sons Ltd.

Change in genetic size of small-closed populations: Lessons from a domestic mammal population.

PubMed

Ghafouri-Kesbi, Farhad

2010-10-01

The aim of this study was to monitor changes in genetic size of a small-closed population of Iranian Zandi sheep, by using pedigree information from animals born between 1991 and 2005. The genetic size was assessed by using measures based on the probability of identity-by-descend of genes (coancestry, f, and effective population size, N(e) ), as well as measures based on probability of gene origin (effective number of founders, f(e) , effective number of founder genomes, f(g) , and effective number of non-founder genomes, f(ne) ). Average coancestry, or the degree of genetic similarity of individuals, increased from 0.81% to 1.44% during the period 1993 to 2005, at the same time that N(e) decreased from 263 to 93. The observed trend for f(e) was irregular throughout the experiment in a way that f(e) was 68, 87, 77, 92, and 80 in 1993, 1996, 1999, 2002, and 2005, respectively. Simultaneously, f(g) , the most informative effective number, decreased from 61 to 35. The index of genetic diversity (GD) which was obtained from estimates of f(g) , decreased about 2% throughout the period studied. In addition, a noticeable reduction was observed in the estimates of f(ne) from 595 in 1993 to 61 in 2005. The higher than 1 ratio of f(e) to f(g) indicated the presence of bottlenecks and genetic drift in the development of this population of Zandi sheep. From 1993 to 1999, f(ne) was much higher than f(e) , thereby indicating that with respect to loss of genetic diversity, the unequal contribution of founders was more important than the random genetic drift in non-founder generations. Subsequently, random genetic drift in non-founder generations was the major reason for f(e) > f(ne) . The minimization of average coancestry in new reproductive individuals was recommended as a means of preserving the population against a further loss in genetic diversity.

The influence of genetic drift and selection on quantitative traits in a plant pathogenic fungus.

PubMed

Stefansson, Tryggvi S; McDonald, Bruce A; Willi, Yvonne

2014-01-01

Genetic drift and selection are ubiquitous evolutionary forces acting to shape genetic variation in populations. While their relative importance has been well studied in plants and animals, less is known about their relative importance in fungal pathogens. Because agro-ecosystems are more homogeneous environments than natural ecosystems, stabilizing selection may play a stronger role than genetic drift or diversifying selection in shaping genetic variation among populations of fungal pathogens in agro-ecosystems. We tested this hypothesis by conducting a QST/FST analysis using agricultural populations of the barley pathogen Rhynchosporium commune. Population divergence for eight quantitative traits (QST) was compared with divergence at eight neutral microsatellite loci (FST) for 126 pathogen strains originating from nine globally distributed field populations to infer the effects of genetic drift and types of selection acting on each trait. Our analyses indicated that five of the eight traits had QST values significantly lower than FST, consistent with stabilizing selection, whereas one trait, growth under heat stress (22°C), showed evidence of diversifying selection and local adaptation (QST>FST). Estimates of heritability were high for all traits (means ranging between 0.55-0.84), and average heritability across traits was negatively correlated with microsatellite gene diversity. Some trait pairs were genetically correlated and there was significant evidence for a trade-off between spore size and spore number, and between melanization and growth under benign temperature. Our findings indicate that many ecologically and agriculturally important traits are under stabilizing selection in R. commune and that high within-population genetic variation is maintained for these traits.

Genetic and Morphometric Divergence of an Invasive Bird: The Introduced House Sparrow (Passer domesticus) in Brazil

PubMed Central

Lima, Marcos R.; Macedo, Regina H. F.; Martins, Thaís L. F.; Schrey, Aaron W.; Martin, Lynn B.; Bensch, Staffan

2012-01-01

Introduced species are interesting systems for the study of contemporary evolution in new environments because of their spatial and temporal scales. For this study we had three aims: (i) to determine how genetic diversity and genetic differentiation of introduced populations of the house sparrow (Passer domesticus) in Brazil varies with range expansion, (ii) to determine how genetic diversity and differentiation in Brazil compares to ancestral European populations; and (iii) to determine whether selection or genetic drift has been more influential on phenotypic divergence. We used six microsatellite markers to genotype six populations from Brazil and four populations from Europe. We found slightly reduced levels of genetic diversity in Brazilian compared to native European populations. However, among introduced populations of Brazil, we found no association between genetic diversity and time since introduction. Moreover, overall genetic differentiation among introduced populations was low indicating that the expansion took place from large populations in which genetic drift effects would likely have been weak. We found significant phenotypic divergence among sites in Brazil. Given the absence of a spatial genetic pattern, divergent selection and not genetic drift seems to be the main force behind most of the phenotypic divergence encountered. Unravelling whether microevolution (e.g., allele frequency change), phenotypic plasticity, or both mediated phenotypic divergence is challenging and will require experimental work (e.g., common garden experiments or breeding programs). PMID:23285283

Changes in variation at the MHC class II DQA locus during the final demise of the woolly mammoth

NASA Astrophysics Data System (ADS)

Pečnerová, Patrícia; Díez-Del-Molino, David; Vartanyan, Sergey; Dalén, Love

2016-05-01

According to the nearly-neutral theory of evolution, the relative strengths of selection and drift shift in favour of drift at small population sizes. Numerous studies have analysed the effect of bottlenecks and small population sizes on genetic diversity in the MHC, which plays a central role in pathogen recognition and immune defense and is thus considered a model example for the study of adaptive evolution. However, to understand changes in genetic diversity at loci under selection, it is necessary to compare the genetic diversity of a population before and after the bottleneck. In this study, we analyse three fragments of the MHC DQA gene in woolly mammoth samples radiocarbon dated to before and after a well-documented bottleneck that took place about ten thousand years ago. Our results indicate a decrease in observed heterozygosity and number of alleles, suggesting that genetic drift had an impact on the variation on MHC. Based on coalescent simulations, we found no evidence of balancing selection maintaining MHC diversity during the Holocene. However, strong trans-species polymorphism among mammoths and elephants points to historical effects of balancing selection on the woolly mammoth lineage.

Stochastic modelling of shifts in allele frequencies reveals a strongly polygynous mating system in the re-introduced Asiatic wild ass.

PubMed

Renan, Sharon; Greenbaum, Gili; Shahar, Naama; Templeton, Alan R; Bouskila, Amos; Bar-David, Shirli

2015-04-01

Small populations are prone to loss of genetic variation and hence to a reduction in their evolutionary potential. Therefore, studying the mating system of small populations and its potential effects on genetic drift and genetic diversity is of high importance for their viability assessments. The traditional method for studying genetic mating systems is paternity analysis. Yet, as small populations are often rare and elusive, the genetic data required for paternity analysis are frequently unavailable. The endangered Asiatic wild ass (Equus hemionus), like all equids, displays a behaviourally polygynous mating system; however, the level of polygyny has never been measured genetically in wild equids. Combining noninvasive genetic data with stochastic modelling of shifts in allele frequencies, we developed an alternative approach to paternity analysis for studying the genetic mating system of the re-introduced Asiatic wild ass in the Negev Desert, Israel. We compared the shifts in allele frequencies (as a measure of genetic drift) that have occurred in the wild ass population since re-introduction onset to simulated scenarios under different proportions of mating males. We revealed a strongly polygynous mating system in which less than 25% of all males participate in the mating process each generation. This strongly polygynous mating system and its potential effect on the re-introduced population's genetic diversity could have significant consequences for the long-term persistence of the population in the Negev. The stochastic modelling approach and the use of allele-frequency shifts can be further applied to systems that are affected by genetic drift and for which genetic data are limited. © 2015 John Wiley & Sons Ltd.

Effective size of density-dependent two-sex populations: the effect of mating systems.

PubMed

Myhre, A M; Engen, S; SAEther, B-E

2017-08-01

Density dependence in vital rates is a key feature affecting temporal fluctuations of natural populations. This has important implications for the rate of random genetic drift. Mating systems also greatly affect effective population sizes, but knowledge of how mating system and density regulation interact to affect random genetic drift is poor. Using theoretical models and simulations, we compare N e in short-lived, density-dependent animal populations with different mating systems. We study the impact of a fluctuating, density-dependent sex ratio and consider both a stable and a fluctuating environment. We find a negative relationship between annual N e /N and adult population size N due to density dependence, suggesting that loss of genetic variation is reduced at small densities. The magnitude of this decrease was affected by mating system and life history. A male-biased, density-dependent sex ratio reduces the rate of genetic drift compared to an equal, density-independent sex ratio, but a stochastic change towards male bias reduces the N e /N ratio. Environmental stochasticity amplifies temporal fluctuations in population size and is thus vital to consider in estimation of effective population sizes over longer time periods. Our results on the reduced loss of genetic variation at small densities, particularly in polygamous populations, indicate that density regulation may facilitate adaptive evolution at small population sizes. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Genetically distinct populations of northern shrimp, Pandalus borealis, in the North Atlantic: adaptation to different temperatures as an isolation factor.

PubMed

Jorde, Per Erik; Søvik, Guldborg; Westgaard, Jon-Ivar; Albretsen, Jon; André, Carl; Hvingel, Carsten; Johansen, Torild; Sandvik, Anne Dagrun; Kingsley, Michael; Jørstad, Knut Eirik

2015-04-01

The large-scale population genetic structure of northern shrimp, Pandalus borealis, was investigated over the species' range in the North Atlantic, identifying multiple genetically distinct groups. Genetic divergence among sample localities varied among 10 microsatellite loci (range: FST = -0.0002 to 0.0475) with a highly significant average (FST = 0.0149; P < 0.0001). In contrast, little or no genetic differences were observed among temporal replicates from the same localities (FST = 0.0004; P = 0.33). Spatial genetic patterns were compared to geographic distances, patterns of larval drift obtained through oceanographic modelling, and temperature differences, within a multiple linear regression framework. The best-fit model included all three factors and explained approximately 29% of all spatial genetic divergence. However, geographic distance and larval drift alone had only minor effects (2.5-4.7%) on large-scale genetic differentiation patterns, whereas bottom temperature differences explained most (26%). Larval drift was found to promote genetic homogeneity in parts of the study area with strong currents, but appeared ineffective across large temperature gradients. These findings highlight the breakdown of gene flow in a species with a long pelagic larval phase (up to 3 months) and indicate a role for local adaptation to temperature conditions in promoting evolutionary diversification and speciation in the marine environment. © 2015 John Wiley & Sons Ltd.

Genetic Diversity in Introduced Populations with an Allee Effect

PubMed Central

Wittmann, Meike J.; Gabriel, Wilfried; Metzler, Dirk

2014-01-01

A phenomenon that strongly influences the demography of small introduced populations and thereby potentially their genetic diversity is the demographic Allee effect, a reduction in population growth rates at small population sizes. We take a stochastic modeling approach to investigate levels of genetic diversity in populations that successfully overcame either a strong Allee effect, in which populations smaller than a certain critical size are expected to decline, or a weak Allee effect, in which the population growth rate is reduced at small sizes but not negative. Our results indicate that compared to successful populations without an Allee effect, successful populations with a strong Allee effect tend to (1) derive from larger founder population sizes and thus have a higher initial amount of genetic variation, (2) spend fewer generations at small population sizes where genetic drift is particularly strong, and (3) spend more time around the critical population size and thus experience more genetic drift there. In the case of multiple introduction events, there is an additional increase in diversity because Allee-effect populations tend to derive from a larger number of introduction events than other populations. Altogether, a strong Allee effect can either increase or decrease genetic diversity, depending on the average founder population size. By contrast, a weak Allee effect tends to decrease genetic diversity across the entire range of founder population sizes. Finally, we show that it is possible in principle to infer critical population sizes from genetic data, although this would require information from many independently introduced populations. PMID:25009147

A meta-analysis on the effects of 2,4-D and dicamba drift on soybean and cotton

USDA-ARS?s Scientific Manuscript database

Commercial introduction of cultivars of soybean and cotton genetically modified with resistance to the synthetic-auxin herbicides dicamba and 2,4-D will allow these compounds to be used with greater flexibility but may expose susceptible soybean and cotton cultivars to non-target herbicide drift. Fr...

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

PubMed Central

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

2011-01-01

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

Plant speciation in continental island floras as exemplified by Nigella in the Aegean Archipelago.

PubMed

Comes, Hans Peter; Tribsch, Andreas; Bittkau, Christiane

2008-09-27

Continental shelf island systems, created by rising sea levels, provide a premier setting for studying the effects of geographical isolation on non-adaptive radiation and allopatric speciation brought about by genetic drift. The Aegean Archipelago forms a highly fragmented complex of mostly continental shelf islands that have become disconnected from each other and the mainland in relatively recent geological times (ca <5.2 Ma). These ecologically fairly homogenous islands thus provide a suitable biogeographic context for assessing the relative influences of past range fragmentation, colonization, gene flow and drift on taxon diversification. Indeed, recent molecular biogeographic studies on the Aegean Nigella arvensis complex, combining phylogenetic, phylogeographic and population level approaches, exemplify the importance of allopatry and genetic drift coupled with restricted gene flow in driving plant speciation in this continental archipelago at different temporal and spatial scales. While the recent (Late Pleistocene) radiation of Aegean Nigella, as well as possible instances of incipient speciation (in the Cyclades), is shown to be strongly conditioned by (palaeo)geographic factors (including changes in sea level), shifts in breeding system (selfing) and associated isolating mechanisms have also contributed to this radiation. By contrast, founder event speciation has probably played only a minor role, perhaps reflecting a migratory situation typical for continental archipelagos characterized by niche pre-emption because of a long established resident flora. Overall, surveys of neutral molecular markers in Aegean Nigella have so far revealed population genetic processes that conform remarkably well to predictions raised by genetic drift theory. The challenge is now to gain more direct insights into the relative importance of the role of genetic drift, as opposed to natural selection, in the phenotypic and reproductive divergence among these Aegean plant species.

Narrow Bottlenecks Affect Pea Seedborne Mosaic Virus Populations during Vertical Seed Transmission but not during Leaf Colonization

PubMed Central

Johansen, Elisabeth Ida; Simon, Vincent; Jacquemond, Mireille; Senoussi, Rachid

2014-01-01

The effective size of populations (Ne) determines whether selection or genetic drift is the predominant force shaping their genetic structure and evolution. Populations having high Ne adapt faster, as selection acts more intensely, than populations having low Ne, where random effects of genetic drift dominate. Estimating Ne for various steps of plant virus life cycle has been the focus of several studies in the last decade, but no estimates are available for the vertical transmission of plant viruses, although virus seed transmission is economically significant in at least 18% of plant viruses in at least one plant species. Here we study the co-dynamics of two variants of Pea seedborne mosaic virus (PSbMV) colonizing leaves of pea plants (Pisum sativum L.) during the whole flowering period, and their subsequent transmission to plant progeny through seeds. Whereas classical estimators of Ne could be used for leaf infection at the systemic level, as virus variants were equally competitive, dedicated stochastic models were needed to estimate Ne during vertical transmission. Very little genetic drift was observed during the infection of apical leaves, with Ne values ranging from 59 to 216. In contrast, a very drastic genetic drift was observed during vertical transmission, with an average number of infectious virus particles contributing to the infection of a seedling from an infected mother plant close to one. A simple model of vertical transmission, assuming a cumulative action of virus infectious particles and a virus density threshold required for vertical transmission to occur fitted the experimental data very satisfactorily. This study reveals that vertically-transmitted viruses endure bottlenecks as narrow as those imposed by horizontal transmission. These bottlenecks are likely to slow down virus adaptation and could decrease virus fitness and virulence. PMID:24415934

HLA genetic diversity in Hungarians and Hungarian Gypsies: complementary differentiation patterns and demographic signals revealed by HLA-A, -B and -DRB1 in Central Europe.

PubMed

Inotai, D; Szilvasi, A; Benko, S; Boros-Major, A; Illes, Z; Bors, A; Kiss, K P; Rajczy, K; Gelle-Hossó, A; Buhler, S; Nunes, J M; Sanchez-Mazas, A; Tordai, A

2015-08-01

Systematic analyses of human leukocyte antigen (HLA) profiles in different populations may increase the efficiency of bone marrow donor selection and help reconstructing human peopling history. We typed HLA-A, -B, and -DRB1 allele groups in two bone marrow donor cohorts of 2402 Hungarians and 186 Hungarian Gypsies and compared them with several Central-European, Spanish Gypsy, and Indian populations. Our results indicate that different European Gypsy populations share a common origin but diverged genetically as a consequence of founder effect and rapid genetic drift, whereas other European populations are related genetically in relation to geography. This study also suggests that while HLA-A accurately depicts the effects of genetic drift, HLA-B, and -DRB1 conserve more signatures of ancient population relationships, as a result of balancing selection. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

The effects of historical fragmentation on major histocompatibility complex class II β and microsatellite variation in the Aegean island reptile, Podarcis erhardii.

PubMed

Santonastaso, Trent; Lighten, Jackie; van Oosterhout, Cock; Jones, Kenneth L; Foufopoulos, Johannes; Anthony, Nicola M

2017-07-01

The major histocompatibility complex (MHC) plays a key role in disease resistance and is the most polymorphic gene region in vertebrates. Although habitat fragmentation is predicted to lead to a loss in MHC variation through drift, the impact of other evolutionary forces may counter this effect. Here we assess the impact of selection, drift, migration, and recombination on MHC class II and microsatellite variability in 14 island populations of the Aegean wall lizard Podarcis erhardii . Lizards were sampled from islands within the Cyclades (Greece) formed by rising sea levels as the last glacial maximum approximately 20,000 before present. Bathymetric data were used to determine the area and age of each island, allowing us to infer the corresponding magnitude and timing of genetic bottlenecks associated with island formation. Both MHC and microsatellite variation were positively associated with island area, supporting the hypothesis that drift governs neutral and adaptive variation in this system. However, MHC but not microsatellite variability declined significantly with island age. This discrepancy is likely due to the fact that microsatellites attain mutation-drift equilibrium more rapidly than MHC. Although we detected signals of balancing selection, recombination and migration, the effects of these evolutionary processes appeared negligible relative to drift. This study demonstrates how land bridge islands can provide novel insights into the impact of historical fragmentation on genetic diversity as well as help disentangle the effects of different evolutionary forces on neutral and adaptive diversity.

Spatially-explicit estimation of Wright's neighborhood size in continuous populations

Treesearch

Andrew J. Shirk; Samuel A. Cushman

2014-01-01

Effective population size (Ne) is an important parameter in conservation genetics because it quantifies a population's capacity to resist loss of genetic diversity due to inbreeding and drift. The classical approach to estimate Ne from genetic data involves grouping sampled individuals into discretely defined subpopulations assumed to be panmictic. Importantly,...

Teaching Evolutionary Mechanisms: Genetic Drift and M&M's.

ERIC Educational Resources Information Center

Staub, Nancy L.

2002-01-01

Describes a classroom activity that teaches the mechanism of genetic drift to undergraduates. Illustrates a number of concepts that are critical in developing evolution literacy by sampling M&M milk chocolate candies. (MM)

Temporal genetic structure in a poecilogonous polychaete: the interplay of developmental mode and environmental stochasticity

PubMed Central

2014-01-01

Background Temporal variation in the genetic structure of populations can be caused by multiple factors, including natural selection, stochastic environmental variation, migration, or genetic drift. In benthic marine species, the developmental mode of larvae may indicate a possibility for temporal genetic variation: species with dispersive planktonic larvae are expected to be more likely to show temporal genetic variation than species with benthic or brooded non-dispersive larvae, due to differences in larval mortality and dispersal ability. We examined temporal genetic structure in populations of Pygospio elegans, a poecilogonous polychaete with within-species variation in developmental mode. P. elegans produces either planktonic, benthic, or intermediate larvae, varying both among and within populations, providing a within-species test of the generality of a relationship between temporal genetic variation and larval developmental mode. Results In contrast to our expectations, our microsatellite analyses of P. elegans revealed temporal genetic stability in the UK population with planktonic larvae, whereas there was variation indicative of drift in temporal samples of the populations from the Baltic Sea, which have predominantly benthic and intermediate larvae. We also detected temporal variation in relatedness within these populations. A large temporal shift in genetic structure was detected in a population from the Netherlands, having multiple developmental modes. This shift could have been caused by local extiction due to extreme environmental conditions and (re)colonization by planktonic larvae from neighboring populations. Conclusions In our study of P. elegans, temporal genetic variation appears to be due to not only larval developmental mode, but also the stochastic environment of adults. Large temporal genetic shifts may be more likely in marine intertidal habitats (e.g. North Sea and Wadden Sea) which are more prone to environmental stochasticity than the sub-tidal Baltic habitats. Sub-tidal and/or brackish (less saline) habitats may support smaller P. elegans populations and these may be more susceptible to the effects of random genetic drift. Moreover, higher frequencies of asexual reproduction and the benthic larval developmental mode in these populations leads to higher relatedness and contributes to drift. Our results indicate that a general relationship between larval developmental mode and temporal genetic variation may not exist. PMID:24447386

Temporal genetic structure in a poecilogonous polychaete: the interplay of developmental mode and environmental stochasticity.

PubMed

Kesäniemi, Jenni E; Mustonen, Marina; Boström, Christoffer; Hansen, Benni W; Knott, K Emily

2014-01-22

Temporal variation in the genetic structure of populations can be caused by multiple factors, including natural selection, stochastic environmental variation, migration, or genetic drift. In benthic marine species, the developmental mode of larvae may indicate a possibility for temporal genetic variation: species with dispersive planktonic larvae are expected to be more likely to show temporal genetic variation than species with benthic or brooded non-dispersive larvae, due to differences in larval mortality and dispersal ability. We examined temporal genetic structure in populations of Pygospio elegans, a poecilogonous polychaete with within-species variation in developmental mode. P. elegans produces either planktonic, benthic, or intermediate larvae, varying both among and within populations, providing a within-species test of the generality of a relationship between temporal genetic variation and larval developmental mode. In contrast to our expectations, our microsatellite analyses of P. elegans revealed temporal genetic stability in the UK population with planktonic larvae, whereas there was variation indicative of drift in temporal samples of the populations from the Baltic Sea, which have predominantly benthic and intermediate larvae. We also detected temporal variation in relatedness within these populations. A large temporal shift in genetic structure was detected in a population from the Netherlands, having multiple developmental modes. This shift could have been caused by local extiction due to extreme environmental conditions and (re)colonization by planktonic larvae from neighboring populations. In our study of P. elegans, temporal genetic variation appears to be due to not only larval developmental mode, but also the stochastic environment of adults. Large temporal genetic shifts may be more likely in marine intertidal habitats (e.g. North Sea and Wadden Sea) which are more prone to environmental stochasticity than the sub-tidal Baltic habitats. Sub-tidal and/or brackish (less saline) habitats may support smaller P. elegans populations and these may be more susceptible to the effects of random genetic drift. Moreover, higher frequencies of asexual reproduction and the benthic larval developmental mode in these populations leads to higher relatedness and contributes to drift. Our results indicate that a general relationship between larval developmental mode and temporal genetic variation may not exist.

A comparative study on genetic effects of artificial and natural habitat fragmentation on Loropetalum chinense (Hamamelidaceae) in Southeast China.

PubMed

Yuan, N; Comes, H P; Cao, Y N; Guo, R; Zhang, Y H; Qiu, Y X

2015-06-01

Elucidating the demographic and landscape features that determine the genetic effects of habitat fragmentation has become fundamental to research in conservation and evolutionary biology. Land-bridge islands provide ideal study areas for investigating the genetic effects of habitat fragmentation at different temporal and spatial scales. In this context, we compared patterns of nuclear microsatellite variation between insular populations of a shrub of evergreen broad-leaved forest, Loropetalum chinense, from the artificially created Thousand-Island Lake (TIL) and the Holocene-dated Zhoushan Archipelago of Southeast China. Populations from the TIL region harboured higher levels of genetic diversity than those from the Zhoushan Archipelago, but these differences were not significant. There was no correlation between genetic diversity and most island features, excepting a negative effect of mainland-island distance on allelic richness and expected heterozygosity in the Zhoushan Archipelago. In general, levels of gene flow among island populations were moderate to high, and tests of alternative models of population history strongly favoured a gene flow-drift model over a pure drift model in each region. In sum, our results showed no obvious genetic effects of habitat fragmentation due to recent (artificial) or past (natural) island formation. Rather, they highlight the importance of gene flow (most likely via seed) in maintaining genetic variation and preventing inter-population differentiation in the face of habitat 'insularization' at different temporal and spatial scales.

Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa

PubMed Central

Ramachandran, Sohini; Deshpande, Omkar; Roseman, Charles C.; Rosenberg, Noah A.; Feldman, Marcus W.; Cavalli-Sforza, L. Luca

2005-01-01

Equilibrium models of isolation by distance predict an increase in genetic differentiation with geographic distance. Here we find a linear relationship between genetic and geographic distance in a worldwide sample of human populations, with major deviations from the fitted line explicable by admixture or extreme isolation. A close relationship is shown to exist between the correlation of geographic distance and genetic differentiation (as measured by FST) and the geographic pattern of heterozygosity across populations. Considering a worldwide set of geographic locations as possible sources of the human expansion, we find that heterozygosities in the globally distributed populations of the data set are best explained by an expansion originating in Africa and that no geographic origin outside of Africa accounts as well for the observed patterns of genetic diversity. Although the relationship between FST and geographic distance has been interpreted in the past as the result of an equilibrium model of drift and dispersal, simulation shows that the geographic pattern of heterozygosities in this data set is consistent with a model of a serial founder effect starting at a single origin. Given this serial-founder scenario, the relationship between genetic and geographic distance allows us to derive bounds for the effects of drift and natural selection on human genetic variation. PMID:16243969

Radial Domany-Kinzel models with mutation and selection

NASA Astrophysics Data System (ADS)

Lavrentovich, Maxim O.; Korolev, Kirill S.; Nelson, David R.

2013-01-01

We study the effect of spatial structure, genetic drift, mutation, and selective pressure on the evolutionary dynamics in a simplified model of asexual organisms colonizing a new territory. Under an appropriate coarse-graining, the evolutionary dynamics is related to the directed percolation processes that arise in voter models, the Domany-Kinzel (DK) model, contact process, and so on. We explore the differences between linear (flat front) expansions and the much less familiar radial (curved front) range expansions. For the radial expansion, we develop a generalized, off-lattice DK model that minimizes otherwise persistent lattice artifacts. With both simulations and analytical techniques, we study the survival probability of advantageous mutants, the spatial correlations between domains of neutral strains, and the dynamics of populations with deleterious mutations. “Inflation” at the frontier leads to striking differences between radial and linear expansions. For a colony with initial radius R0 expanding at velocity v, significant genetic demixing, caused by local genetic drift, occurs only up to a finite time t*=R0/v, after which portions of the colony become causally disconnected due to the inflating perimeter of the expanding front. As a result, the effect of a selective advantage is amplified relative to genetic drift, increasing the survival probability of advantageous mutants. Inflation also modifies the underlying directed percolation transition, introducing novel scaling functions and modifications similar to a finite-size effect. Finally, we consider radial range expansions with deflating perimeters, as might arise from colonization initiated along the shores of an island.

The effect of pollen versus seed flow on the maintenance of nuclear-cytoplasmic gynodioecy.

PubMed

Dufay, Mathilde; Pannell, John R

2010-03-01

Gynodioecy, where females co-occur with hermaphrodites, is a relatively common sexual system in plants that is often the result of a genetic conflict between maternally inherited male sterility genes in the mitochondrial genome and the biparentally inherited male fertility restorer genes in the nucleus. Previous models have shown that nuclear-cytoplasmic gynodioecy can be maintained under certain conditions by negative frequency-dependent selection, but the effect of other evolutionary processes such as genetic drift and population subdivision is only partially understood. Here, we investigate the joint effects of frequency-dependent selection, drift, and migration through either pollen or seeds on the maintenance of nuclear-cytoplasmic gynodioecy in a subdivided population. We find that the combination of drift and selection causes the loss of gynodioecy under scenarios that would maintain it under the influence of selection alone, and that both seed and, more surprisingly, pollen flow can maintain the polymorphism. In particular, although pollen flow could not avoid the loss of cytoplasmic polymorphism within demes, it allowed the maintenance of nuclear-cytoplasmic polymorphism at the metapopulation level.

Wright's Shifting Balance Theory and the Diversification of Aposematic Signals

PubMed Central

Chouteau, Mathieu; Angers, Bernard

2012-01-01

Despite accumulating evidence for selection within natural systems, the importance of random genetic drift opposing Wright's and Fisher's views of evolution continue to be a subject of controversy. The geographical diversification of aposematic signals appears to be a suitable system to assess the factors involved in the process of adaptation since both theories were independently proposed to explain this phenomenon. In the present study, the effects of drift and selection were assessed from population genetics and predation experiments on poison-dart frogs, Ranitomaya imitator, of Northern Peru. We specifically focus on the transient zone between two distinct aposematic signals. In contrast to regions where high predation maintains a monomorphic aposematic signal, the transient zones are characterized by lowered selection and a high phenotypic diversity. As a result, the diversification of phenotypes may occur via genetic drift without a significant loss of fitness. These new phenotypes may then colonize alternative habitats if successfully recognized and avoided by predators. This study highlights the interplay between drift and selection as determinant processes in the adaptive diversification of aposematic signals. Results are consistent with the expectations of the Wright's shifting balance theory and represent, to our knowledge, the first empirical demonstration of this highly contested theory in a natural system. PMID:22470509

Temporal dynamics of genetic variability in a mountain goat (Oreamnos americanus) population.

PubMed

Ortego, Joaquín; Yannic, Glenn; Shafer, Aaron B A; Mainguy, Julien; Festa-Bianchet, Marco; Coltman, David W; Côté, Steeve D

2011-04-01

The association between population dynamics and genetic variability is of fundamental importance for both evolutionary and conservation biology. We combined long-term population monitoring and molecular genetic data from 123 offspring and their parents at 28 microsatellite loci to investigate changes in genetic diversity over 14 cohorts in a small and relatively isolated population of mountain goats (Oreamnos americanus) during a period of demographic increase. Offspring heterozygosity decreased while parental genetic similarity and inbreeding coefficients (F(IS) ) increased over the study period (1995-2008). Immigrants introduced three novel alleles into the population and matings between residents and immigrants produced more heterozygous offspring than local crosses, suggesting that immigration can increase population genetic variability. The population experienced genetic drift over the study period, reflected by a reduced allelic richness over time and an 'isolation-by-time' pattern of genetic structure. The temporal decline of individual genetic diversity despite increasing population size probably resulted from a combination of genetic drift due to small effective population size, inbreeding and insufficient counterbalancing by immigration. This study highlights the importance of long-term genetic monitoring to understand how demographic processes influence temporal changes of genetic diversity in long-lived organisms. © 2011 Blackwell Publishing Ltd.

Statistical aspects of evolution under natural selection, with implications for the advantage of sexual reproduction.

PubMed

Crouch, Daniel J M

2017-10-27

The prevalence of sexual reproduction remains mysterious, as it poses clear evolutionary drawbacks compared to reproducing asexually. Several possible explanations exist, with one of the most likely being that finite population size causes linkage disequilibria to randomly generate and impede the progress of natural selection, and that these are eroded by recombination via sexual reproduction. Previous investigations have either analysed this phenomenon in detail for small numbers of loci, or performed population simulations for many loci. Here we present a quantitative genetic model for fitness, based on the Price Equation, in order to examine the theoretical consequences of randomly generated linkage disequilibria when there are many loci. In addition, most previous work has been concerned with the long-term consequences of deleterious linkage disequilibria for population fitness. The expected change in mean fitness between consecutive generations, a measure of short-term evolutionary success, is shown under random environmental influences to be related to the autocovariance in mean fitness between the generations, capturing the effects of stochastic forces such as genetic drift. Interaction between genetic drift and natural selection, due to randomly generated linkage disequilibria, is demonstrated to be one possible source of mean fitness autocovariance. This suggests a possible role for sexual reproduction in reducing the negative effects of genetic drift, thereby improving the short-term efficacy of natural selection. Copyright © 2017 Elsevier Ltd. All rights reserved.

Population structure and genetic diversity of black redhorse (Moxostoma duquesnei) in a highly fragmented watershed

USGS Publications Warehouse

Reid, S.M.; Wilson, C.C.; Mandrak, N.E.; Carl, L.M.

2008-01-01

Dams have the potential to affect population size and connectivity, reduce genetic diversity, and increase genetic differences among isolated riverine fish populations. Previous research has reported adverse effects on the distribution and demographics of black redhorse (Moxostoma duquesnei), a threatened fish species in Canada. However, effects on genetic diversity and population structure are unknown. We used microsatellite DNA markers to assess the number of genetic populations in the Grand River (Ontario) and to test whether dams have resulted in a loss of genetic diversity and increased genetic differentiation among populations. Three hundred and seventy-seven individuals from eight Grand River sites were genotyped at eight microsatellite loci. Measures of genetic diversity were moderately high and not significantly different among populations; strong evidence of recent population bottlenecks was not detected. Pairwise FST and exact tests identified weak (global FST = 0.011) but statistically significant population structure, although little population structuring was detected using either genetic distances or an individual-based clustering method. Neither geographic distance nor the number of intervening dams were correlated with pairwise differences among populations. Tests for regional equilibrium indicate that Grand River populations were either in equilibrium between gene flow and genetic drift or that gene flow is more influential than drift. While studies on other species have identified strong dam-related effects on genetic diversity and population structure, this study suggests that barrier permeability, river fragment length and the ecological characteristics of affected species can counterbalance dam-related effects. ?? 2007 Springer Science+Business Media B.V.

[Genetic ecological monitoring in human populations: heterozygosity, mtDNA haplotype variation, and genetic load].

PubMed

Balanovskiĭ, O P; Koshel', S M; Zaporozhchenko, V V; Pshenichnov, A S; Frolova, S A; Kuznetsova, M A; Baranova, E E; Teuchezh, I E; Kuznetsova, A A; Romashkina, M V; Utevskaia, O M; Churnosov, M I; Villems, R; Balanovskaia, E V

2011-11-01

Yu. P. Altukhov suggested that heterozygosity is an indicator of the state of the gene pool. The idea and a linked concept of genetic ecological monitoring were applied to a new dataset on mtDNA variation in East European ethnic groups. Haplotype diversity (an analog of the average heterozygosity) was shown to gradually decrease northwards. Since a similar trend is known for population density, interlinked changes were assumed for a set of parameters, which were ordered to form a causative chain: latitude increases, land productivity decreases, population density decreases, effective population size decreases, isolation of subpopulations increases, genetic drift increases, and mtDNA haplotype diversity decreases. An increase in genetic drift increases the random inbreeding rate and, consequently, the genetic load. This was confirmed by a significant correlation observed between the incidence of autosomal recessive hereditary diseases and mtDNA haplotype diversity. Based on the findings, mtDNA was assumed to provide an informative genetic system for genetic ecological monitoring; e.g., analyzing the ecology-driven changes in the gene pool.

A Lab Exercise Explaining Hardy-Weinberg Equilibrium and Evolution Effectively.

ERIC Educational Resources Information Center

Winterer, Juliette

2001-01-01

Presents a set of six activities in population genetics for a college-level biology course that helps students understand the Hardy-Weinberg principle. Activities focus on characterizing a population, Hardy-Weinberg proportions, genetic drift, mutation and selection, population size and divergence, and secondary contact. The only materials…

Genetic consequences of sequential founder events by an island-colonizing bird.

PubMed

Clegg, Sonya M; Degnan, Sandie M; Kikkawa, Jiro; Moritz, Craig; Estoup, Arnaud; Owens, Ian P F

2002-06-11

The importance of founder events in promoting evolutionary changes on islands has been a subject of long-running controversy. Resolution of this debate has been hindered by a lack of empirical evidence from naturally founded island populations. Here we undertake a genetic analysis of a series of historically documented, natural colonization events by the silvereye species-complex (Zosterops lateralis), a group used to illustrate the process of island colonization in the original founder effect model. Our results indicate that single founder events do not affect levels of heterozygosity or allelic diversity, nor do they result in immediate genetic differentiation between populations. Instead, four to five successive founder events are required before indices of diversity and divergence approach that seen in evolutionarily old forms. A Bayesian analysis based on computer simulation allows inferences to be made on the number of effective founders and indicates that founder effects are weak because island populations are established from relatively large flocks. Indeed, statistical support for a founder event model was not significantly higher than for a gradual-drift model for all recently colonized islands. Taken together, these results suggest that single colonization events in this species complex are rarely accompanied by severe founder effects, and multiple founder events and/or long-term genetic drift have been of greater consequence for neutral genetic diversity.

The Effects of Population Size Histories on Estimates of Selection Coefficients from Time-Series Genetic Data

PubMed Central

Jewett, Ethan M.; Steinrücken, Matthias; Song, Yun S.

2016-01-01

Many approaches have been developed for inferring selection coefficients from time series data while accounting for genetic drift. These approaches have been motivated by the intuition that properly accounting for the population size history can significantly improve estimates of selective strengths. However, the improvement in inference accuracy that can be attained by modeling drift has not been characterized. Here, by comparing maximum likelihood estimates of selection coefficients that account for the true population size history with estimates that ignore drift by assuming allele frequencies evolve deterministically in a population of infinite size, we address the following questions: how much can modeling the population size history improve estimates of selection coefficients? How much can mis-inferred population sizes hurt inferences of selection coefficients? We conduct our analysis under the discrete Wright–Fisher model by deriving the exact probability of an allele frequency trajectory in a population of time-varying size and we replicate our results under the diffusion model. For both models, we find that ignoring drift leads to estimates of selection coefficients that are nearly as accurate as estimates that account for the true population history, even when population sizes are small and drift is high. This result is of interest because inference methods that ignore drift are widely used in evolutionary studies and can be many orders of magnitude faster than methods that account for population sizes. PMID:27550904

Genetic drift at expanding frontiers promotes gene segregation

PubMed Central

Hallatschek, Oskar; Hersen, Pascal; Ramanathan, Sharad; Nelson, David R.

2007-01-01

Competition between random genetic drift and natural selection play a central role in evolution: Whereas nonbeneficial mutations often prevail in small populations by chance, mutations that sweep through large populations typically confer a selective advantage. Here, however, we observe chance effects during range expansions that dramatically alter the gene pool even in large microbial populations. Initially well mixed populations of two fluorescently labeled strains of Escherichia coli develop well defined, sector-like regions with fractal boundaries in expanding colonies. The formation of these regions is driven by random fluctuations that originate in a thin band of pioneers at the expanding frontier. A comparison of bacterial and yeast colonies (Saccharomyces cerevisiae) suggests that this large-scale genetic sectoring is a generic phenomenon that may provide a detectable footprint of past range expansions. PMID:18056799

Blue Tigers, Black Tapirs, & the Pied Raven of the Faroe Islands: Teaching Genetic Drift Using Real-Life Animal Examples

ERIC Educational Resources Information Center

Robischon, Marcel

2015-01-01

Genetic drift is a concept of population genetics that is central to understanding evolutionary processes and aspects of conservation biology. It is frequently taught using rather abstract representations. I introduce three real-life zoological examples, based on historical and recent color morphs of tigers, tapirs, and ravens, that can complement…

Evolutionary processes in a continental island system: molecular phylogeography of the Aegean Nigella arvensis alliance (Ranunculaceae) inferred from chloroplast DNA.

PubMed

Bittkau, C; Comes, H P

2005-11-01

Continental shelf island systems, created by rising sea levels, provide a premier setting for studying the effects of past fragmentation, dispersal, and genetic drift on taxon diversification. We used phylogeographical (nested clade) and population genetic analyses to elucidate the relative roles of these processes in the evolutionary history of the Aegean Nigella arvensis alliance (= 'coenospecies'). We surveyed chloroplast DNA (cpDNA) variation in 455 individuals from 47 populations (nine taxa) of the alliance throughout its core range in the Aegean Archipelago and surrounding mainland areas of Greece and Turkey. The study revealed the presence of three major lineages, with largely nonoverlapping distributions in the Western, Central, and Eastern Aegean. There is evidence supporting the idea that these major lineages evolved in situ from a widespread (pan-Aegean) ancestral stock as a result of multiple fragmentation events, possibly due to the influence of post-Messinian sea flooding, Pleistocene eustatic changes and corresponding climate fluctuations. Over-sea dispersal and founder events appear to have played a rather insignificant role in the group's history. Rather, all analytical approaches identified the alliance as an organism group with poor seed dispersal capabilities and a susceptibility to genetic drift. In particular, we inferred that the observed level of cpDNA differentiation between Kikladian island populations of Nigella degenii largely reflects population history, (viz. Holocene island fragmentation) and genetic drift in the near absence of seed flow since their time of common ancestry. Overall, our cpDNA data for the N. arvensis alliance in general, and N. degenii in particular, indicate that historical events were important in determining the phylogeographical patterns seen, and that genetic drift has historically been relatively more influential on population structure than has cytoplasmic gene flow.

Demographic history of an elusive carnivore: using museums to inform management

PubMed Central

Holbrook, Joseph D; DeYoung, Randy W; Tewes, Michael E; Young, John H

2012-01-01

Elusive carnivores present a challenge to managers because traditional survey methods are not suitable. We applied a genetic approach using museum specimens to examine how historical and recent conditions influenced the demographic history of Puma concolor in western and southern Texas, USA. We used 10 microsatellite loci and indexed population trends by estimating historical and recent genetic diversity, genetic differentiation and effective population size. Mountain lions in southern Texas exhibited a 9% decline in genetic diversity, whereas diversity remained stable in western Texas. Genetic differentiation between western and southern Texas was minimal historically (FST = 0.04, P < 0.01), but increased 2–2.5 times in our recent sample. An index of genetic drift for southern Texas was seven to eight times that of western Texas, presumably contributing to the current differentiation between western and southern Texas. Furthermore, southern Texas exhibited a >50% temporal decline in effective population size, whereas western Texas showed no change. Our results illustrate that population declines and genetic drift have occurred in southern Texas, likely because of contemporary habitat loss and predator control. Population monitoring may be needed to ensure the persistence of mountain lions in the southern Texas region. This study highlights the utility of sampling museum collections to examine demographic histories and inform wildlife management. PMID:23028402

Drift, selection, or migration? Processes affecting genetic differentiation and variation along a latitudinal gradient in an amphibian.

PubMed

Cortázar-Chinarro, Maria; Lattenkamp, Ella Z; Meyer-Lucht, Yvonne; Luquet, Emilien; Laurila, Anssi; Höglund, Jacob

2017-08-14

Past events like fluctuations in population size and post-glacial colonization processes may influence the relative importance of genetic drift, migration and selection when determining the present day patterns of genetic variation. We disentangle how drift, selection and migration shape neutral and adaptive genetic variation in 12 moor frog populations along a 1700 km latitudinal gradient. We studied genetic differentiation and variation at a MHC exon II locus and a set of 18 microsatellites. Using outlier analyses, we identified the MHC II exon 2 (corresponding to the β-2 domain) locus and one microsatellite locus (RCO8640) to be subject to diversifying selection, while five microsatellite loci showed signals of stabilizing selection among populations. STRUCTURE and DAPC analyses on the neutral microsatellites assigned populations to a northern and a southern cluster, reflecting two different post-glacial colonization routes found in previous studies. Genetic variation overall was lower in the northern cluster. The signature of selection on MHC exon II was weaker in the northern cluster, possibly as a consequence of smaller and more fragmented populations. Our results show that historical demographic processes combined with selection and drift have led to a complex pattern of differentiation along the gradient where some loci are more divergent among populations than predicted from drift expectations due to diversifying selection, while other loci are more uniform among populations due to stabilizing selection. Importantly, both overall and MHC genetic variation are lower at northern latitudes. Due to lower evolutionary potential, the low genetic variation in northern populations may increase the risk of extinction when confronted with emerging pathogens and climate change.

Recent demography drives changes in linked selection across the maize genome

USDA-ARS?s Scientific Manuscript database

The interaction between genetic drift and selection in shaping genetic diversity is not fully understood. In particular, a population's propensity to drift is typically summarized by its long-term e_ective population size (Ne), but rapidly changing population demographics may complicate this relatio...

Evolution of the human immunodeficiency virus envelope gene is dominated by purifying selection.

PubMed

Edwards, C T T; Holmes, E C; Pybus, O G; Wilson, D J; Viscidi, R P; Abrams, E J; Phillips, R E; Drummond, A J

2006-11-01

The evolution of the human immunodeficiency virus (HIV-1) during chronic infection involves the rapid, continuous turnover of genetic diversity. However, the role of natural selection, relative to random genetic drift, in governing this process is unclear. We tested a stochastic model of genetic drift using partial envelope sequences sampled longitudinally in 28 infected children. In each case the Bayesian posterior (empirical) distribution of coalescent genealogies was estimated using Markov chain Monte Carlo methods. Posterior predictive simulation was then used to generate a null distribution of genealogies assuming neutrality, with the null and empirical distributions compared using four genealogy-based summary statistics sensitive to nonneutral evolution. Because both null and empirical distributions were generated within a coalescent framework, we were able to explicitly account for the confounding influence of demography. From the distribution of corrected P-values across patients, we conclude that empirical genealogies are more asymmetric than expected if evolution is driven by mutation and genetic drift only, with an excess of low-frequency polymorphisms in the population. This indicates that although drift may still play an important role, natural selection has a strong influence on the evolution of HIV-1 envelope. A negative relationship between effective population size and substitution rate indicates that as the efficacy of selection increases, a smaller proportion of mutations approach fixation in the population. This suggests the presence of deleterious mutations. We therefore conclude that intrahost HIV-1 evolution in envelope is dominated by purifying selection against low-frequency deleterious mutations that do not reach fixation.

The contribution of the mitochondrial genome to sex-specific fitness variance.

PubMed

Smith, Shane R T; Connallon, Tim

2017-05-01

Maternal inheritance of mitochondrial DNA (mtDNA) facilitates the evolutionary accumulation of mutations with sex-biased fitness effects. Whereas maternal inheritance closely aligns mtDNA evolution with natural selection in females, it makes it indifferent to evolutionary changes that exclusively benefit males. The constrained response of mtDNA to selection in males can lead to asymmetries in the relative contributions of mitochondrial genes to female versus male fitness variation. Here, we examine the impact of genetic drift and the distribution of fitness effects (DFE) among mutations-including the correlation of mutant fitness effects between the sexes-on mitochondrial genetic variation for fitness. We show how drift, genetic correlations, and skewness of the DFE determine the relative contributions of mitochondrial genes to male versus female fitness variance. When mutant fitness effects are weakly correlated between the sexes, and the effective population size is large, mitochondrial genes should contribute much more to male than to female fitness variance. In contrast, high fitness correlations and small population sizes tend to equalize the contributions of mitochondrial genes to female versus male variance. We discuss implications of these results for the evolution of mitochondrial genome diversity and the genetic architecture of female and male fitness. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

The Effects of Population Size Histories on Estimates of Selection Coefficients from Time-Series Genetic Data.

PubMed

Jewett, Ethan M; Steinrücken, Matthias; Song, Yun S

2016-11-01

Many approaches have been developed for inferring selection coefficients from time series data while accounting for genetic drift. These approaches have been motivated by the intuition that properly accounting for the population size history can significantly improve estimates of selective strengths. However, the improvement in inference accuracy that can be attained by modeling drift has not been characterized. Here, by comparing maximum likelihood estimates of selection coefficients that account for the true population size history with estimates that ignore drift by assuming allele frequencies evolve deterministically in a population of infinite size, we address the following questions: how much can modeling the population size history improve estimates of selection coefficients? How much can mis-inferred population sizes hurt inferences of selection coefficients? We conduct our analysis under the discrete Wright-Fisher model by deriving the exact probability of an allele frequency trajectory in a population of time-varying size and we replicate our results under the diffusion model. For both models, we find that ignoring drift leads to estimates of selection coefficients that are nearly as accurate as estimates that account for the true population history, even when population sizes are small and drift is high. This result is of interest because inference methods that ignore drift are widely used in evolutionary studies and can be many orders of magnitude faster than methods that account for population sizes. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Influence of drift and admixture on population structure of American black bears (Ursus americanus) in the Central Interior Highlands, USA, 50 years after translocation

USGS Publications Warehouse

Puckett, Emily E.; Kristensen, Thea V.; Wilton, Clay M.; Lyda, Sara B.; Noyce, Karen V.; Holahan, Paula M.; Leslie,, David M.; Beringer, J.; Belant, Jerrold L.; White, D.; Eggert, L.S.

2014-01-01

Bottlenecks, founder events, and genetic drift often result in decreased genetic diversity and increased population differentiation. These events may follow abundance declines due to natural or anthropogenic perturbations, where translocations may be an effective conservation strategy to increase population size. American black bears (Ursus americanus) were nearly extirpated from the Central Interior Highlands, USA by 1920. In an effort to restore bears, 254 individuals were translocated from Minnesota, USA, and Manitoba, Canada, into the Ouachita and Ozark Mountains from 1958 to 1968. Using 15 microsatellites and mitochondrial haplotypes, we observed contemporary genetic diversity and differentiation between the source and supplemented populations. We inferred four genetic clusters: Source, Ouachitas, Ozarks, and a cluster in Missouri where no individuals were translocated. Coalescent models using approximate Bayesian computation identified an admixture model as having the highest posterior probability (0.942) over models where the translocation was unsuccessful or acted as a founder event. Nuclear genetic diversity was highest in the source (AR = 9.11) and significantly lower in the translocated populations (AR = 7.07-7.34; P = 0.004). The Missouri cluster had the lowest genetic diversity (AR = 5.48) and served as a natural experiment showing the utility of translocations to increase genetic diversity following demographic bottlenecks. Differentiation was greater between the two admixed populations than either compared to the source, suggesting that genetic drift acted strongly over the eight generations since the translocation. The Ouachitas and Missouri were previously hypothesized to be remnant lineages. We observed a pretranslocation remnant signature in Missouri but not in the Ouachitas.

Dispersal ability and habitat requirements determine landscape-level genetic patterns in desert aquatic insects.

PubMed

Phillipsen, Ivan C; Kirk, Emily H; Bogan, Michael T; Mims, Meryl C; Olden, Julian D; Lytle, David A

2015-01-01

Species occupying the same geographic range can exhibit remarkably different population structures across the landscape, ranging from highly diversified to panmictic. Given limitations on collecting population-level data for large numbers of species, ecologists seek to identify proximate organismal traits-such as dispersal ability, habitat preference and life history-that are strong predictors of realized population structure. We examined how dispersal ability and habitat structure affect the regional balance of gene flow and genetic drift within three aquatic insects that represent the range of dispersal abilities and habitat requirements observed in desert stream insect communities. For each species, we tested for linear relationships between genetic distances and geographic distances using Euclidean and landscape-based metrics of resistance. We found that the moderate-disperser Mesocapnia arizonensis (Plecoptera: Capniidae) has a strong isolation-by-distance pattern, suggesting migration-drift equilibrium. By contrast, population structure in the flightless Abedus herberti (Hemiptera: Belostomatidae) is influenced by genetic drift, while gene flow is the dominant force in the strong-flying Boreonectes aequinoctialis (Coleoptera: Dytiscidae). The best-fitting landscape model for M. arizonensis was based on Euclidean distance. Analyses also identified a strong spatial scale-dependence, where landscape genetic methods only performed well for species that were intermediate in dispersal ability. Our results highlight the fact that when either gene flow or genetic drift dominates in shaping population structure, no detectable relationship between genetic and geographic distances is expected at certain spatial scales. This study provides insight into how gene flow and drift interact at the regional scale for these insects as well as the organisms that share similar habitats and dispersal abilities. © 2014 John Wiley & Sons Ltd.

Modern spandrels: the roles of genetic drift, gene flow and natural selection in the evolution of parallel clines.

PubMed

Santangelo, James S; Johnson, Marc T J; Ness, Rob W

2018-05-16

Urban environments offer the opportunity to study the role of adaptive and non-adaptive evolutionary processes on an unprecedented scale. While the presence of parallel clines in heritable phenotypic traits is often considered strong evidence for the role of natural selection, non-adaptive evolutionary processes can also generate clines, and this may be more likely when traits have a non-additive genetic basis due to epistasis. In this paper, we use spatially explicit simulations modelled according to the cyanogenesis (hydrogen cyanide, HCN) polymorphism in white clover ( Trifolium repens ) to examine the formation of phenotypic clines along urbanization gradients under varying levels of drift, gene flow and selection. HCN results from an epistatic interaction between two Mendelian-inherited loci. Our results demonstrate that the genetic architecture of this trait makes natural populations susceptible to decreases in HCN frequencies via drift. Gradients in the strength of drift across a landscape resulted in phenotypic clines with lower frequencies of HCN in strongly drifting populations, giving the misleading appearance of deterministic adaptive changes in the phenotype. Studies of heritable phenotypic change in urban populations should generate null models of phenotypic evolution based on the genetic architecture underlying focal traits prior to invoking selection's role in generating adaptive differentiation. © 2018 The Author(s).

Geographic variation in advertisement calls of a Microhylid frog - testing the role of drift and ecology.

PubMed

Lee, Ko-Huan; Shaner, Pei-Jen L; Lin, Yen-Po; Lin, Si-Min

2016-05-01

Acoustic signals for mating are important traits that could drive population differentiation and speciation. Ecology may play a role in acoustic divergence through direct selection (e.g., local adaptation to abiotic environment), constraint of correlated traits (e.g., acoustic traits linked to another trait under selection), and/or interspecific competition (e.g., character displacement). However, genetic drift alone can also drive acoustic divergence. It is not always easy to differentiate the role of ecology versus drift in acoustic divergence. In this study, we tested the role of ecology and drift in shaping geographic variation in the advertisement calls of Microhyla fissipes. We examined three predictions based on ecological processes: (1) the correlation between temperature and call properties across M. fissipes populations; (2) the correlation between call properties and body size across M. fissipes populations; and (3) reproductive character displacement (RCD) in call properties between M. fissipes populations that are sympatric with and allopatric to a congener M. heymonsi. To test genetic drift, we examined correlations among call divergence, geographic distance, and genetic distance across M. fissipes populations. We recorded the advertisement calls from 11 populations of M. fissipes in Taiwan, five of which are sympatrically distributed with M. heymonsi. We found geographic variation in both temporal and spectral properties of the advertisement calls of M. fissipes. However, the call properties were not correlated with local temperature or the callers' body size. Furthermore, we did not detect RCD. By contrast, call divergence, geographic distance, and genetic distance between M. fissipes populations were all positively correlated. The comparisons between phenotypic Q st (P st) and F st values did not show significant differences, suggesting a role of drift. We concluded that genetic drift, rather than ecological processes, is the more likely driver for the geographic variation in the advertisement calls of M. fissipes.

High genetic diversity in the endangered and narrowly distributed amphibian species Leptobrachium leishanense.

PubMed

Zhang, Wei; Luo, Zhenhua; Zhao, Mian; Wu, Hua

2015-09-01

Threatened species typically have a small or declining population size, which make them highly susceptible to loss of genetic diversity through genetic drift and inbreeding. Genetic diversity determines the evolutionary potential of a species; therefore, maintaining the genetic diversity of threatened species is essential for their conservation. In this study, we assessed the genetic diversity of the adaptive major histocompatibility complex (MHC) genes in an endangered and narrowly distributed amphibian species, Leptobrachium leishanense in Southwest China. We compared the genetic variation of MHC class I genes with that observed in neutral markers (5 microsatellite loci and cytochrome b gene) to elucidate the relative roles of genetic drift and natural selection in shaping the current MHC polymorphism in this species. We found a high level of genetic diversity in this population at both MHC and neutral markers compared with other threatened amphibian species. Historical positive selection was evident in the MHC class I genes. The higher allelic richness in MHC markers compared with that of microsatellite loci suggests that selection rather than genetic drift plays a prominent role in shaping the MHC variation pattern, as drift can affect all the genome in a similar way but selection directly targets MHC genes. Although demographic analysis revealed no recent bottleneck events in L. leishanense, additional population decline will accelerate the dangerous status for this species. We suggest that the conservation management of L. leishanense should concentrate on maximizing the retention of genetic diversity through preventing their continuous population decline. Protecting their living habitats and forbidding illegal hunting are the most important measures for conservation of L. leishanense. © 2015 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and Wiley Publishing Asia Pty Ltd.

Drift-driven evolution of electric signals in a Neotropical knifefish.

PubMed

Picq, Sophie; Alda, Fernando; Bermingham, Eldredge; Krahe, Rüdiger

2016-09-01

Communication signals are highly diverse traits. This diversity is usually assumed to be shaped by selective forces, whereas the null hypothesis of divergence through drift is often not considered. In Panama, the weakly electric fish Brachyhypopomus occidentalis is widely distributed in multiple independent drainage systems, which provide a natural evolutionary laboratory for the study of genetic and signal divergence in separate populations. We quantified geographic variation in the electric signals of 109 fish from five populations, and compared it to the neutral genetic variation estimated from cytochrome oxidase I (COI) sequences of the same individuals, to test whether drift may be driving divergence of their signals. Signal distances were highly correlated with genetic distances, even after controlling for geographic distances, suggesting that drift alone is sufficient to explain geographic variation in electric signals. Significant differences at smaller geographic scales (within drainages) showed, however, that electric signals may evolve at a faster rate than expected under drift, raising the possibility that additional adaptive forces may be contributing to their evolution. Overall, our data point to stochastic forces as main drivers of signal evolution in this species and extend the role of drift in the evolution of communication systems to fish and electrocommunication. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Foundational errors in the Neutral and Nearly-Neutral theories of evolution in relation to the Synthetic Theory: is a new evolutionary paradigm necessary?

PubMed

Valenzuela, Carlos Y

2013-01-01

The Neutral Theory of Evolution (NTE) proposes mutation and random genetic drift as the most important evolutionary factors. The most conspicuous feature of evolution is the genomic stability during paleontological eras and lack of variation among taxa; 98% or more of nucleotide sites are monomorphic within a species. NTE explains this homology by random fixation of neutral bases and negative selection (purifying selection) that does not contribute either to evolution or polymorphisms. Purifying selection is insufficient to account for this evolutionary feature and the Nearly-Neutral Theory of Evolution (N-NTE) included negative selection with coefficients as low as mutation rate. These NTE and N-NTE propositions are thermodynamically (tendency to random distributions, second law), biotically (recurrent mutation), logically and mathematically (resilient equilibria instead of fixation by drift) untenable. Recurrent forward and backward mutation and random fluctuations of base frequencies alone in a site make life organization and fixations impossible. Drift is not a directional evolutionary factor, but a directional tendency of matter-energy processes (second law) which threatens the biotic organization. Drift cannot drive evolution. In a site, the mutation rates among bases and selection coefficients determine the resilient equilibrium frequency of bases that genetic drift cannot change. The expected neutral random interaction among nucleotides is zero; however, huge interactions and periodicities were found between bases of dinucleotides separated by 1, 2... and more than 1,000 sites. Every base is co-adapted with the whole genome. Neutralists found that neutral evolution is independent of population size (N); thus neutral evolution should be independent of drift, because drift effect is dependent upon N. Also, chromosome size and shape as well as protein size are far from random.

Revealing life-history traits by contrasting genetic estimations with predictions of effective population size.

PubMed

Greenbaum, Gili; Renan, Sharon; Templeton, Alan R; Bouskila, Amos; Saltz, David; Rubenstein, Daniel I; Bar-David, Shirli

2017-12-22

Effective population size, a central concept in conservation biology, is now routinely estimated from genetic surveys and can also be theoretically predicted from demographic, life-history, and mating-system data. By evaluating the consistency of theoretical predictions with empirically estimated effective size, insights can be gained regarding life-history characteristics and the relative impact of different life-history traits on genetic drift. These insights can be used to design and inform management strategies aimed at increasing effective population size. We demonstrated this approach by addressing the conservation of a reintroduced population of Asiatic wild ass (Equus hemionus). We estimated the variance effective size (N ev ) from genetic data (N ev =24.3) and formulated predictions for the impacts on N ev of demography, polygyny, female variance in lifetime reproductive success (RS), and heritability of female RS. By contrasting the genetic estimation with theoretical predictions, we found that polygyny was the strongest factor affecting genetic drift because only when accounting for polygyny were predictions consistent with the genetically measured N ev . The comparison of effective-size estimation and predictions indicated that 10.6% of the males mated per generation when heritability of female RS was unaccounted for (polygyny responsible for 81% decrease in N ev ) and 19.5% mated when female RS was accounted for (polygyny responsible for 67% decrease in N ev ). Heritability of female RS also affected N ev ; hf2=0.91 (heritability responsible for 41% decrease in N ev ). The low effective size is of concern, and we suggest that management actions focus on factors identified as strongly affecting Nev, namely, increasing the availability of artificial water sources to increase number of dominant males contributing to the gene pool. This approach, evaluating life-history hypotheses in light of their impact on effective population size, and contrasting predictions with genetic measurements, is a general, applicable strategy that can be used to inform conservation practice. © 2017 Society for Conservation Biology.

Antigenic Drift in H5N1 Avian Influenza Virus in Poultry Is Driven by Mutations in Major Antigenic Sites of the Hemagglutinin Molecule Analogous to Those for Human Influenza Virus▿†

PubMed Central

Cattoli, Giovanni; Milani, Adelaide; Temperton, Nigel; Zecchin, Bianca; Buratin, Alessandra; Molesti, Eleonora; Aly, Mona Meherez; Arafa, Abdel; Capua, Ilaria

2011-01-01

H5N1 highly pathogenic avian influenza virus has been endemic in poultry in Egypt since 2008, notwithstanding the implementation of mass vaccination and culling of infected birds. Extensive circulation of the virus has resulted in a progressive genetic evolution and an antigenic drift. In poultry, the occurrence of antigenic drift in avian influenza viruses is less well documented and the mechanisms remain to be clarified. To test the hypothesis that H5N1 antigenic drift is driven by mechanisms similar to type A influenza viruses in humans, we generated reassortant viruses, by reverse genetics, that harbored molecular changes identified in genetically divergent viruses circulating in the vaccinated population. Parental and reassortant phenotype viruses were antigenically analyzed by hemagglutination inhibition (HI) test and microneutralization (MN) assay. The results of the study indicate that the antigenic drift of H5N1 in poultry is driven by multiple mutations primarily occurring in major antigenic sites at the receptor binding subdomain, similarly to what has been described for human influenza H1 and H3 subtype viruses. PMID:21734057

Founding events influence genetic population structure of sockeye salmon (Oncorhynchus nerka) in Lake Clark, Alaska

USGS Publications Warehouse

Ramstad, K.M.; Woody, C.A.; Sage, G.K.; Allendorf, F.W.

2004-01-01

Bottlenecks can have lasting effects on genetic population structure that obscure patterns of contemporary gene flow and drift. Sockeye salmon are vulnerable to bottleneck effects because they are a highly structured species with excellent colonizing abilities and often occupy geologically young habitats. We describe genetic divergence among and genetic variation within spawning populations of sockeye salmon throughout the Lake Clark area of Alaska. Fin tissue was collected from sockeye salmon representing 15 spawning populations of Lake Clark, Six-mile Lake, and Lake Iliamna. Allele frequencies differed significantly at 11 microsatellite loci in 96 of 105 pairwise population comparisons. Pairwise estimates of FST ranged from zero to 0.089. Six-mile Lake and Lake Clark populations have historically been grouped together for management purposes and are geographically proximate. However, Six-mile Lake populations are genetically similar to Lake Iliamna populations and are divergent from Lake Clark populations. The reduced allelic diversity and strong divergence of Lake Clark populations relative to Six-mile Lake and Lake Iliamna populations suggest a bottleneck associated with the colonization of Lake Clark by sockeye salmon. Geographic distance and spawning habitat differences apparently do not contribute to isolation and divergence among populations. However, temporal isolation based on spawning time and founder effects associated with ongoing glacial retreat and colonization of new spawning habitats contribute to the genetic population structure of Lake Clark sock-eye salmon. Nonequilibrium conditions and the strong influence of genetic drift caution against using estimates of divergence to estimate gene flow among populations of Lake Clark sockeye salmon.

African diversity from the HLA point of view: influence of genetic drift, geography, linguistics, and natural selection.

PubMed

Sanchez-Mazas, A

2001-09-01

This study investigates the influence of different evolutionary factors on the patterns of human leukocyte antigen (HLA) genetic diversity within sub-Saharan Africa, and between Africa, Europe, and East Asia. This is done by comparing the significance of several statistics computed on equivalent population data sets tested for two HLA class II loci, DRB1 and DPB1, which strongly differ from each other by the shape of their allelic distributions. Similar results are found for the two loci concerning highly significant correlations between geographic and genetic distances at the world scale, high levels of genetic diversity within sub-Saharan Africa and East Asia, and low within Europe, and low genetic differentiations among the three broad continental areas, with no special divergence of Africa. On the other hand, DPB1 behaves as a neutral polymorphism, although a significant excess of heterozygotes is often observed for DRB1. Whereas the pattern observed for DPB1 is explained by geographic differentiations and genetic drift in isolated populations, balancing selection is likely to have prevented genetic differentiations among populations at the DRB1 locus. However, this selective effect did not disrupt the high correlation found between DRB1 and geography at the world scale, nor between DRB1 and linguistic differentiations at the African level.

Conserving genomic variability in large mammals: Effect of population fluctuations and variance in male reproductive success on variability in Yellowstone bison

Treesearch

Andres Perez-Figueroa; Rick L. Wallen; Tiago Antao; Jason A. Coombs; Michael K. Schwartz; P. J. White; Gordon Luikart

2012-01-01

Loss of genetic variation through genetic drift can reduce population viability. However, relatively little is known about loss of variation caused by the combination of fluctuating population size and variance in reproductive success in age structured populations. We built an individual-based computer simulation model to examine how actual culling and hunting...

Quantitative Genetic Architecture at Latitudinal Range Boundaries: Reduced Variation but Higher Trait Independence.

PubMed

Paccard, Antoine; Van Buskirk, Josh; Willi, Yvonne

2016-05-01

Species distribution limits are hypothesized to be caused by small population size and limited genetic variation in ecologically relevant traits, but earlier studies have not evaluated genetic variation in multivariate phenotypes. We asked whether populations at the latitudinal edges of the distribution have altered quantitative genetic architecture of ecologically relevant traits compared with midlatitude populations. We calculated measures of evolutionary potential in nine Arabidopsis lyrata populations spanning the latitudinal range of the species in eastern and midwestern North America. Environments at the latitudinal extremes have reduced water availability, and therefore plants were assessed under wet and dry treatments. We estimated genetic variance-covariance (G-) matrices for 10 traits related to size, development, and water balance. Populations at southern and northern distribution edges had reduced levels of genetic variation across traits, but their G-matrices were more spherical; G-matrix orientation was unrelated to latitude. As a consequence, the predicted short-term response to selection was at least as strong in edge populations as in central populations. These results are consistent with genetic drift eroding variation and reducing the effectiveness of correlational selection at distribution margins. We conclude that genetic variation of isolated traits poorly predicts the capacity to evolve in response to multivariate selection and that the response to selection may frequently be greater than expected at species distribution margins because of genetic drift.

Loss of Mhc and Neutral Variation in Peary Caribou: Genetic Drift Is Not Mitigated by Balancing Selection or Exacerbated by Mhc Allele Distributions

PubMed Central

Taylor, Sabrina S.; Jenkins, Deborah A.; Arcese, Peter

2012-01-01

Theory and empirical results suggest that the rate of loss of variation at Mhc and neutral microsatellite loci may differ because selection influences Mhc genes, and because a high proportion of rare alleles at Mhc loci may result in high rates of loss via drift. Most published studies compare Mhc and microsatellite variation in various contemporary populations to infer the effects of population size on genetic variation, even though different populations are likely to have different demographic histories that may also affect contemporary genetic variation. We directly compared loss of variation at Mhc and microsatellite loci in Peary caribou by comparing historical and contemporary samples. We observed that similar proportions of genetic variation were lost over time at each type of marker despite strong evidence for selection at Mhc genes. These results suggest that microsatellites can be used to estimate genome-wide levels of variation, but also that adaptive potential is likely to be lost following population bottlenecks. However, gene conversion and recombination at Mhc loci may act to increase variation following bottlenecks. PMID:22655029

Evolution of the hemagglutinin gene of H3N8 canine influenza virus in dogs.

PubMed

Pecoraro, Heidi L; Bennett, Susi; Spindel, Miranda E; Landolt, Gabriele A

2014-12-01

With the widespread use of a recently developed canine influenza virus (CIV) H3N8 vaccine, continual molecular evaluation of circulating CIVs is necessary for monitoring antigenic drift. The aim of this project was to further describe the genetic evolution of CIV, as well as determine any genetic variation within potential antigenic regions that might result in antigenic drift. To this end, the hemagglutinin gene of 19 CIV isolates from dogs residing in Colorado, New York, and South Carolina humane shelters was sequenced and compared to CIV strains isolated during 2003-2012. Phylogenetic analysis suggests that CIV might be diverging into two geographically distinct lineages. Using a mixed-effects model for evolution and single likelihood ancestor counting methods, several amino acid sites were found to be undergoing selection pressure. Additionally, a total of six amino acid changes were observed in two possible antigenic sites for CIVs isolated from Colorado and New York humane shelters between 2009 and 2011. As CIV isolates might be diverging into geographically distinct lineages, further experiments are warranted to determine the extent of antigenic drift occurring within circulating CIV.

Alu polymorphisms in the Waorani tribe from the Ecuadorian Amazon reflect the effects of isolation and genetic drift.

PubMed

Gómez-Pérez, Luis; Alfonso-Sánchez, Miguel A; Sánchez, Dora; García-Obregón, Susana; Espinosa, Ibone; Martínez-Jarreta, Begoña; De Pancorbo, Marian M; Peña, José A

2011-01-01

The Amazon basin is inhabited by some of the most isolated human groups worldwide. Among them, the Waorani tribe is one of the most interesting Native American populations from the anthropological perspective. This study reports a genetic characterization of the Waorani based on autosomal genetic loci. We analyzed 12 polymorphic Alu insertions in 36 Waorani individuals from different communal longhouses settled in the Yasuní National Park. The most notable finding was the strikingly reduced genetic diversity detected in the Waorani, corroborated by the existence of four monomorphic loci (ACE, APO, FXIIIB, and HS4.65), and of other four Alu markers that were very close to the fixation for the presence (PV92 and D1) or the absence (A25 and HS4.32) of the insertion. Furthermore, results of the centroid analysis supported the notion of the Waorani being one of the Amerindian groups less impacted by gene flow processes. The prolonged isolation of the Waorani community, in conjunction with a historically low effective population size and high inbreeding levels, have resulted in the drastic reduction of their genetic diversity, because of the effects of severe genetic drift. Recurrent population bottlenecks most likely determined by certain deep-rooted sociocultural practices of the Waorani (characterized by violence, internal quarrels, and revenge killings until recent times) are likely responsible for this pattern of diversity. The findings of this study illustrate how sociocultural factors can shape the gene pool of human populations. Copyright © 2011 Wiley-Liss, Inc.

Distinct evolutionary strategies of human leucocyte antigen loci in pathogen-rich environments

PubMed Central

Sanchez-Mazas, Alicia; Lemaître, Jean-François; Currat, Mathias

2012-01-01

Human leucocyte antigen (HLA) loci have a complex evolution where both stochastic (e.g. genetic drift) and deterministic (natural selection) forces are involved. Owing to their extraordinary level of polymorphism, HLA genes are useful markers for reconstructing human settlement history. However, HLA variation often deviates significantly from neutral expectations towards an excess of genetic diversity. Because HLA molecules play a crucial role in immunity, this observation is generally explained by pathogen-driven-balancing selection (PDBS). In this study, we investigate the PDBS model by analysing HLA allelic diversity on a large database of 535 populations in relation to pathogen richness. Our results confirm that geographical distances are excellent predictors of HLA genetic differentiation worldwide. We also find a significant positive correlation between genetic diversity and pathogen richness at two HLA class I loci (HLA-A and -B), as predicted by PDBS, and a significant negative correlation at one HLA class II locus (HLA-DQB1). Although these effects are weak, as shown by a loss of significance when populations submitted to rapid genetic drift are removed from the analysis, the inverse relationship between genetic diversity and pathogen richness at different loci indicates that HLA genes have adopted distinct evolutionary strategies to provide immune protection in pathogen-rich environments. PMID:22312050

Genetic sex determination and extinction.

PubMed

Hedrick, Philip W; Gadau, Jürgen; Page, Robert E

2006-02-01

Genetic factors can affect the probability of extinction either by increasing the effect of detrimental variants or by decreasing the potential for future adaptive responses. In a recent paper, Zayed and Packer demonstrate that low variation at a specific locus, the complementary sex determination (csd) locus in Hymenoptera (ants, bees and wasps), can result in a sharply increased probability of extinction. Their findings illustrate situations in which there is a feedback process between decreased genetic variation at the csd locus owing to genetic drift and decreased population growth, resulting in an extreme type of extinction vortex for these ecologically important organisms.

The evolutionary dynamics of receptor binding avidity in influenza A: a mathematical model for a new antigenic drift hypothesis

PubMed Central

Yuan, Hsiang-Yu; Koelle, Katia

2013-01-01

The most salient feature of influenza evolution in humans is its antigenic drift. This process is characterized by structural changes in the virus's B-cell epitopes and ultimately results in the ability of the virus to evade immune recognition and thereby reinfect previously infected hosts. Until recently, amino acid substitutions in epitope regions of the viral haemagglutinin were thought to be positively selected for their ability to reduce antibody binding and therefore were thought to be responsible for driving antigenic drift. However, a recent hypothesis put forward by Hensley and co-workers posits that cellular receptor binding avidity is the dominant phenotype under selection, with antigenic drift being a side effect of these binding avidity changes. Here, we present a mathematical formulation of this new antigenic drift model and use it to show how rates of antigenic drift depend on epidemiological parameters. We further use the model to evaluate how two different vaccination strategies can impact antigenic drift rates and ultimately disease incidence levels. Finally, we discuss the assumptions present in the model formulation, predictions of the model, and future work that needs to be done to determine the consistency of this hypothesis with known patterns of influenza's genetic and antigenic evolution. PMID:23382426

Genetic drift of influenza A(H3N2) viruses during two consecutive seasons in 2011-2013 in Corsica, France.

PubMed

Fantoni, Anais; Arena, Christophe; Corrias, Laura; Salez, Nicolas; de Lamballerie, Xavier Nicolas; Amoros, Jean Pierre; Blanchon, Thierry; Varesi, Laurent; Falchi, Alessandra

2014-04-01

The 2011-2012 and 2012-2013 post-pandemic influenza outbreaks were characterized by variability in the A(H3N2) influenza viruses, resulting in low to moderate vaccine effectiveness (VE). The aim of this study was to investigate the molecular evolution and vaccine strain match of the A(H3N2) influenza viruses, having been circulated throughout the population of the French Corsica Island in 2011-2012 and again in 2012-2013. Clinical samples from 31 patients with confirmed A(H3N2) influenza viruses were collected by general practitioners (GPs) over these two consecutive seasons. An analysis of genetic distance and antigenic drift was conducted. Based on a hemagglutinin (HA) aminoacid sequence analysis, the Corsican A(H3N2) viruses fell into the A/Victoria/208/2009 genetic clade, group 3. All influenza viruses were characterized by at least four fixed amino acid mutations which were: N145S (epitope A); Q156H and V186G (epitope B) Y219S (epitope D), with respect to the A/Perth/16/2009 (reference vaccine strain for the 2011-2012) and the A/Victoria/361/2011 (reference vaccine strain for the 2012-2013). Using the p(epitope) model, the percentages of the perfect match VE estimated against circulated strains declined within and between seasons, with estimations of <50%. Overall, these results seem to indicate an antigenic drift of the A(H3N2) influenza viruses which were circulated in Corsica. These findings highlight the importance of the continuous and careful surveillance of genetic changes in the HA domain during seasonal influenza epidemics, in order to provide information on newly emerging genetic variants. © 2013 Wiley Periodicals, Inc.

Balancing selection and genetic drift at major histocompatibility complex class II genes in isolated populations of golden snub-nosed monkey (Rhinopithecus roxellana)

PubMed Central

2012-01-01

Background Small, isolated populations often experience loss of genetic variation due to random genetic drift. Unlike neutral or nearly neutral markers (such as mitochondrial genes or microsatellites), major histocompatibility complex (MHC) genes in these populations may retain high levels of polymorphism due to balancing selection. The relative roles of balancing selection and genetic drift in either small isolated or bottlenecked populations remain controversial. In this study, we examined the mechanisms maintaining polymorphisms of MHC genes in small isolated populations of the endangered golden snub-nosed monkey (Rhinopithecus roxellana) by comparing genetic variation found in MHC and microsatellite loci. There are few studies of this kind conducted on highly endangered primate species. Results Two MHC genes were sequenced and sixteen microsatellite loci were genotyped from samples representing three isolated populations. We isolated nine DQA1 alleles and sixteen DQB1 alleles and validated expression of the alleles. Lowest genetic variation for both MHC and microsatellites was found in the Shennongjia (SNJ) population. Historical balancing selection was revealed at both the DQA1 and DQB1 loci, as revealed by excess non-synonymous substitutions at antigen binding sites (ABS) and maximum-likelihood-based random-site models. Patterns of microsatellite variation revealed population structure. FST outlier analysis showed that population differentiation at the two MHC loci was similar to the microsatellite loci. Conclusions MHC genes and microsatellite loci showed the same allelic richness pattern with the lowest genetic variation occurring in SNJ, suggesting that genetic drift played a prominent role in these isolated populations. As MHC genes are subject to selective pressures, the maintenance of genetic variation is of particular interest in small, long-isolated populations. The results of this study may contribute to captive breeding and translocation programs for endangered species. PMID:23083308

Population size is weakly related to quantitative genetic variation and trait differentiation in a stream fish.

PubMed

Wood, Jacquelyn L A; Tezel, Defne; Joyal, Destin; Fraser, Dylan J

2015-09-01

How population size influences quantitative genetic variation and differentiation among natural, fragmented populations remains unresolved. Small, isolated populations might occupy poor quality habitats and lose genetic variation more rapidly due to genetic drift than large populations. Genetic drift might furthermore overcome selection as population size decreases. Collectively, this might result in directional changes in additive genetic variation (VA ) and trait differentiation (QST ) from small to large population size. Alternatively, small populations might exhibit larger variation in VA and QST if habitat fragmentation increases variability in habitat types. We explored these alternatives by investigating VA and QST using nine fragmented populations of brook trout varying 50-fold in census size N (179-8416) and 10-fold in effective number of breeders, Nb (18-135). Across 15 traits, no evidence was found for consistent differences in VA and QST with population size and almost no evidence for increased variability of VA or QST estimates at small population size. This suggests that (i) small populations of some species may retain adaptive potential according to commonly adopted quantitative genetic measures and (ii) populations of varying sizes experience a variety of environmental conditions in nature, however extremely large studies are likely required before any firm conclusions can be made. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

How does epistasis influence the response to selection?

PubMed Central

Barton, N H

2017-01-01

Much of quantitative genetics is based on the ‘infinitesimal model', under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load', and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects. PMID:27901509

How does epistasis influence the response to selection?

PubMed

Barton, N H

2017-01-01

Much of quantitative genetics is based on the 'infinitesimal model', under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4N e by the 'drift load', and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large N e s, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects.

Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans.

PubMed

Keinan, Alon; Mullikin, James C; Patterson, Nick; Reich, David

2007-10-01

Large data sets on human genetic variation have been collected recently, but their usefulness for learning about history and natural selection has been limited by biases in the ways polymorphisms were chosen. We report large subsets of SNPs from the International HapMap Project that allow us to overcome these biases and to provide accurate measurement of a quantity of crucial importance for understanding genetic variation: the allele frequency spectrum. Our analysis shows that East Asian and northern European ancestors shared the same population bottleneck expanding out of Africa but that both also experienced more recent genetic drift, which was greater in East Asians.

Genetic drift and mutational hazard in the evolution of salamander genomic gigantism.

PubMed

Mohlhenrich, Erik Roger; Mueller, Rachel Lockridge

2016-12-01

Salamanders have the largest nuclear genomes among tetrapods and, excepting lungfishes, among vertebrates as a whole. Lynch and Conery (2003) have proposed the mutational-hazard hypothesis to explain variation in genome size and complexity. Under this hypothesis, noncoding DNA imposes a selective cost by increasing the target for degenerative mutations (i.e., the mutational hazard). Expansion of noncoding DNA, and thus genome size, is driven by increased levels of genetic drift and/or decreased mutation rates; the former determines the efficiency with which purifying selection can remove excess DNA, whereas the latter determines the level of mutational hazard. Here, we test the hypothesis that salamanders have experienced stronger long-term, persistent genetic drift than frogs, a related clade with more typically sized vertebrate genomes. To test this hypothesis, we compared dN/dS and Kr/Kc values of protein-coding genes between these clades. Our results do not support this hypothesis; we find that salamanders have not experienced stronger genetic drift than frogs. Additionally, we find evidence consistent with a lower nucleotide substitution rate in salamanders. This result, along with previous work showing lower rates of small deletion and ectopic recombination in salamanders, suggests that a lower mutational hazard may contribute to genomic gigantism in this clade. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

The colours of humanity: the evolution of pigmentation in the human lineage.

PubMed

Jablonski, Nina G; Chaplin, George

2017-07-05

Humans are a colourful species of primate, with human skin, hair and eye coloration having been influenced by a great variety of evolutionary forces throughout prehistory. Functionally naked skin has been the physical interface between the physical environment and the human body for most of the history of the genus Homo , and hence skin coloration has been under intense natural selection. From an original condition of protective, dark, eumelanin-enriched coloration in early tropical-dwelling Homo and Homo sapiens , loss of melanin pigmentation occurred under natural selection as Homo sapiens dispersed into non-tropical latitudes of Africa and Eurasia. Genes responsible for skin, hair and eye coloration appear to have been affected significantly by population bottlenecks in the course of Homo sapiens dispersals. Because specific skin colour phenotypes can be created by different combinations of skin colour-associated genetic markers, loss of genetic variability due to genetic drift appears to have had negligible effects on the highly redundant genetic 'palette' for the skin colour. This does not appear to have been the case for hair and eye coloration, however, and these traits appear to have been more strongly influenced by genetic drift and, possibly, sexual selection.This article is part of the themed issue 'Animal coloration: production, perception, function and application'. © 2017 The Author(s).

Spatial and temporal patterns of neutral and adaptive genetic variation in the endangered African wild dog (Lycaon pictus).

PubMed

Marsden, Clare D; Woodroffe, Rosie; Mills, Michael G L; McNutt, J Weldon; Creel, Scott; Groom, Rosemary; Emmanuel, Masenga; Cleaveland, Sarah; Kat, Pieter; Rasmussen, Gregory S A; Ginsberg, Joshua; Lines, Robin; André, Jean-Marc; Begg, Colleen; Wayne, Robert K; Mable, Barbara K

2012-03-01

Deciphering patterns of genetic variation within a species is essential for understanding population structure, local adaptation and differences in diversity between populations. Whilst neutrally evolving genetic markers can be used to elucidate demographic processes and genetic structure, they are not subject to selection and therefore are not informative about patterns of adaptive variation. As such, assessments of pertinent adaptive loci, such as the immunity genes of the major histocompatibility complex (MHC), are increasingly being incorporated into genetic studies. In this study, we combined neutral (microsatellite, mtDNA) and adaptive (MHC class II DLA-DRB1 locus) markers to elucidate the factors influencing patterns of genetic variation in the African wild dog (Lycaon pictus); an endangered canid that has suffered extensive declines in distribution and abundance. Our genetic analyses found all extant wild dog populations to be relatively small (N(e)  < 30). Furthermore, through coalescent modelling, we detected a genetic signature of a recent and substantial demographic decline, which correlates with human expansion, but contrasts with findings in some other African mammals. We found strong structuring of wild dog populations, indicating the negative influence of extensive habitat fragmentation and loss of gene flow between habitat patches. Across populations, we found that the spatial and temporal structure of microsatellite diversity and MHC diversity were correlated and strongly influenced by demographic stability and population size, indicating the effects of genetic drift in these small populations. Despite this correlation, we detected signatures of selection at the MHC, implying that selection has not been completely overwhelmed by genetic drift. © 2012 Blackwell Publishing Ltd.

Variation of genetic diversity in a rapidly expanding population of the greater long-tailed hamster (Tscherskia triton) as revealed by microsatellites.

PubMed

Xu, Laixiang; Xue, Huiliang; Song, Mingjing; Zhao, Qinghua; Dong, Jingping; Liu, Juan; Guo, Yu; Xu, Tongqin; Cao, Xiaoping; Wang, Fusheng; Wang, Shuqing; Hao, Shushen; Yang, Hefang; Zhang, Zhibin

2013-01-01

Genetic diversity is essential for persistence of animal populations over both the short- and long-term. Previous studies suggest that genetic diversity may decrease with population decline due to genetic drift or inbreeding of small populations. For oscillating populations, there are some studies on the relationship between population density and genetic diversity, but these studies were based on short-term observation or in low-density phases. Evidence from rapidly expanding populations is lacking. In this study, genetic diversity of a rapidly expanding population of the Greater long-tailed hamsters during 1984-1990, in the Raoyang County of the North China Plain was studied using DNA microsatellite markers. Results show that genetic diversity was positively correlated with population density (as measured by % trap success), and the increase in population density was correlated with a decrease of genetic differentiation between the sub-population A and B. The genetic diversity tended to be higher in spring than in autumn. Variation in population density and genetic diversity are consistent between sub-population A and B. Such results suggest that dispersal is density- and season-dependent in a rapidly expanding population of the Greater long-tailed hamster. For typically solitary species, increasing population density can increase intra-specific attack, which is a driving force for dispersal. This situation is counterbalanced by decreasing population density caused by genetic drift or inbreeding as the result of small population size. Season is a major factor influencing population density and genetic diversity. Meanwhile, roads, used to be considered as geographical isolation, have less effect on genetic differentiation in a rapidly expanding population. Evidences suggest that gene flow (Nm) is positively correlated with population density, and it is significant higher in spring than that in autumn.

Reduction of Genetic Diversity of the Harpy Eagle in Brazilian Tropical Forests.

PubMed

Banhos, Aureo; Hrbek, Tomas; Sanaiotti, Tânia M; Farias, Izeni Pires

2016-01-01

Habitat loss and fragmentation intensify the effects of genetic drift and endogamy, reducing genetic variability of populations with serious consequences for wildlife conservation. The Harpy Eagle (Harpia harpyja) is a forest dwelling species that is considered near threatened and suffers from habitat loss in the forests of the Neotropical region. In this study, 72 historical and current samples were assessed using eight autosomal microsatellite markers to investigate the distribution of genetic diversity of the Harpy Eagle of the Amazonian and Atlantic forests in Brazil. The results showed that the genetic diversity of Harpy Eagle decreased in the regions where deforestation is intense in the southern Amazon and Atlantic Forest.

Reduction of Genetic Diversity of the Harpy Eagle in Brazilian Tropical Forests

PubMed Central

2016-01-01

Habitat loss and fragmentation intensify the effects of genetic drift and endogamy, reducing genetic variability of populations with serious consequences for wildlife conservation. The Harpy Eagle (Harpia harpyja) is a forest dwelling species that is considered near threatened and suffers from habitat loss in the forests of the Neotropical region. In this study, 72 historical and current samples were assessed using eight autosomal microsatellite markers to investigate the distribution of genetic diversity of the Harpy Eagle of the Amazonian and Atlantic forests in Brazil. The results showed that the genetic diversity of Harpy Eagle decreased in the regions where deforestation is intense in the southern Amazon and Atlantic Forest. PMID:26871719

Structural drift: the population dynamics of sequential learning.

PubMed

Crutchfield, James P; Whalen, Sean

2012-01-01

We introduce a theory of sequential causal inference in which learners in a chain estimate a structural model from their upstream "teacher" and then pass samples from the model to their downstream "student". It extends the population dynamics of genetic drift, recasting Kimura's selectively neutral theory as a special case of a generalized drift process using structured populations with memory. We examine the diffusion and fixation properties of several drift processes and propose applications to learning, inference, and evolution. We also demonstrate how the organization of drift process space controls fidelity, facilitates innovations, and leads to information loss in sequential learning with and without memory.

Time-Sampled Population Sequencing Reveals the Interplay of Selection and Genetic Drift in Experimental Evolution of Potato Virus Y

PubMed Central

2017-01-01

ABSTRACT RNA viruses are one of the fastest-evolving biological entities. Within their hosts, they exist as genetically diverse populations (i.e., viral mutant swarms), which are sculpted by different evolutionary mechanisms, such as mutation, natural selection, and genetic drift, and also the interactions between genetic variants within the mutant swarms. To elucidate the mechanisms that modulate the population diversity of an important plant-pathogenic virus, we performed evolution experiments with Potato virus Y (PVY) in potato genotypes that differ in their defense response against the virus. Using deep sequencing of small RNAs, we followed the temporal dynamics of standing and newly generated variations in the evolving viral lineages. A time-sampled approach allowed us to (i) reconstruct theoretical haplotypes in the starting population by using clustering of single nucleotide polymorphisms' trajectories and (ii) use quantitative population genetics approaches to estimate the contribution of selection and genetic drift, and their interplay, to the evolution of the virus. We detected imprints of strong selective sweeps and narrow genetic bottlenecks, followed by the shift in frequency of selected haplotypes. Comparison of patterns of viral evolution in differently susceptible host genotypes indicated possible diversifying evolution of PVY in the less-susceptible host (efficient in the accumulation of salicylic acid). IMPORTANCE High diversity of within-host populations of RNA viruses is an important aspect of their biology, since they represent a reservoir of genetic variants, which can enable quick adaptation of viruses to a changing environment. This study focuses on an important plant virus, Potato virus Y, and describes, at high resolution, temporal changes in the structure of viral populations within different potato genotypes. A novel and easy-to-implement computational approach was established to cluster single nucleotide polymorphisms into viral haplotypes from very short sequencing reads. During the experiment, a shift in the frequency of selected viral haplotypes was observed after a narrow genetic bottleneck, indicating an important role of the genetic drift in the evolution of the virus. On the other hand, a possible case of diversifying selection of the virus was observed in less susceptible host genotypes. PMID:28592544

Chance and necessity in the genome evolution of endosymbiotic bacteria of insects.

PubMed

Sabater-Muñoz, Beatriz; Toft, Christina; Alvarez-Ponce, David; Fares, Mario A

2017-06-01

An open question in evolutionary biology is how does the selection-drift balance determine the fates of biological interactions. We searched for signatures of selection and drift in genomes of five endosymbiotic bacterial groups known to evolve under strong genetic drift. Although most genes in endosymbiotic bacteria showed evidence of relaxed purifying selection, many genes in these bacteria exhibited stronger selective constraints than their orthologs in free-living bacterial relatives. Remarkably, most of these highly constrained genes had no role in the host-symbiont interactions but were involved in either buffering the deleterious consequences of drift or other host-unrelated functions, suggesting that they have either acquired new roles or their role became more central in endosymbiotic bacteria. Experimental evolution of Escherichia coli under strong genetic drift revealed remarkable similarities in the mutational spectrum, genome reduction patterns and gene losses to endosymbiotic bacteria of insects. Interestingly, the transcriptome of the experimentally evolved lines showed a generalized deregulation of the genome that affected genes encoding proteins involved in mutational buffering, regulation and amino acid biosynthesis, patterns identical to those found in endosymbiotic bacteria. Our results indicate that drift has shaped endosymbiotic associations through a change in the functional landscape of bacterial genes and that the host had only a small role in such a shift.

Implications of long tails in the distribution of mutant effects

NASA Astrophysics Data System (ADS)

Waxman, D.; Feng, J.

2005-07-01

Long-tailed distributions possess an infinite variance, yet a finite sample that is drawn from such a distribution has a finite variance. In this work we consider a model of a population subject to mutation, selection and drift. We investigate the implications of a long-tailed distribution of mutant allelic effects on the distribution of genotypic effects in a model with a continuum of allelic effects. While the analysis is confined to asexual populations, it does also have implications for sexual populations. We obtain analytical results for a selectively neutral population as well as one subject to selection. We supplement these analytical results with numerical simulations, to take into account genetic drift. We find that a long-tailed distribution of mutant effects may affect both the equilibrium and the evolutionary adaptive behaviour of a population.

Connectivity in a pond system influences migration and genetic structure in threespine stickleback.

PubMed

Seymour, Mathew; Räsänen, Katja; Holderegger, Rolf; Kristjánsson, Bjarni K

2013-03-01

Neutral genetic structure of natural populations is primarily influenced by migration (the movement of individuals and, subsequently, their genes) and drift (the statistical chance of losing genetic diversity over time). Migration between populations is influenced by several factors, including individual behavior, physical barriers, and environmental heterogeneity among populations. However, drift is expected to be stronger in populations with low immigration rate and small effective population size. With the technological advancement in geological information systems and spatial analysis tools, landscape genetics now allows the development of realistic migration models and increased insight to important processes influencing diversity of natural populations. In this study, we investigated the relationship between landscape connectivity and genetic distance of threespine stickleback (Gasterosteus aculeatus) inhabiting a pond complex in Belgjarskógur, Northeast Iceland. We used two landscape genetic approaches (i.e., least-cost-path and isolation-by-resistance) and asked whether gene flow, as measured by genetic distance, was more strongly associated with Euclidean distance (isolation-by-distance) or with landscape connectivity provided by areas prone to flooding (as indicated by Carex sp. cover)? We found substantial genetic structure across the study area, with pairwise genetic distances among populations (DPS) ranging from 0.118 to 0.488. Genetic distances among populations were more strongly correlated with least-cost-path and isolation-by-resistance than with Euclidean distance, whereas the relative contribution of isolation-by-resistance and Euclidian distance could not be disentangled. These results indicate that migration among stickleback populations occurs via periodically flooded areas. Overall, this study highlights the importance of transient landscape elements influencing migration and genetic structure of populations at small spatial scales.

A latitudinal diversity gradient in terrestrial bacteria of the genus Streptomyces

DOE PAGES

Andam, Cheryl P.; Doroghazi, James R.; Campbell, Ashley N.; ...

2016-04-12

We show that Streptomyces biogeography in soils across North America is influenced by the regional diversification of microorganisms due to dispersal limitation and genetic drift. Streptomyces spp. form desiccation-resistant spores, which can be dispersed on the wind, allowing for a strong test of whether dispersal limitation governs patterns of terrestrial microbial diversity. We employed an approach that has high sensitivity for determining the effects of genetic drift. Specifically, we examined the genetic diversity and phylogeography of physiologically similar Streptomyces strains isolated from geographically distributed yet ecologically similar habitats. We found that Streptomyces beta diversity scales with geographic distance and bothmore » beta diversity and phylogenetic diversity manifest in a latitudinal diversity gradient. This pattern of Streptomyces biogeography resembles patterns seen for diverse species of plants and animals, and we therefore evaluated these data in the context of ecological and evolutionary hypotheses proposed to explain latitudinal diversity gradients. The data are consistent with the hypothesis that niche conservatism limits dispersal, and historical patterns of glaciation have limited the time for speciation in higher-latitude sites. Most notably, higher-latitude sites have lower phylogenetic diversity, higher phylogenetic clustering, and evidence of range expansion from lower latitudes. In addition, patterns of beta diversity partition with respect to the glacial history of sites. Furthermore, the data support the hypothesis that extant patterns of Streptomyces biogeography have been driven by historical patterns of glaciation and are the result of demographic range expansion, dispersal limitation, and regional diversification due to drift.« less

The Kalash Genetic Isolate: Ancient Divergence, Drift, and Selection

PubMed Central

Ayub, Qasim; Mezzavilla, Massimo; Pagani, Luca; Haber, Marc; Mohyuddin, Aisha; Khaliq, Shagufta; Mehdi, Syed Qasim; Tyler-Smith, Chris

2015-01-01

The Kalash represent an enigmatic isolated population of Indo-European speakers who have been living for centuries in the Hindu Kush mountain ranges of present-day Pakistan. Previous Y chromosome and mitochondrial DNA markers provided no support for their claimed Greek descent following Alexander III of Macedon's invasion of this region, and analysis of autosomal loci provided evidence of a strong genetic bottleneck. To understand their origins and demography further, we genotyped 23 unrelated Kalash samples on the Illumina HumanOmni2.5M-8 BeadChip and sequenced one male individual at high coverage on an Illumina HiSeq 2000. Comparison with published data from ancient hunter-gatherers and European farmers showed that the Kalash share genetic drift with the Paleolithic Siberian hunter-gatherers and might represent an extremely drifted ancient northern Eurasian population that also contributed to European and Near Eastern ancestry. Since the split from other South Asian populations, the Kalash have maintained a low long-term effective population size (2,319–2,603) and experienced no detectable gene flow from their geographic neighbors in Pakistan or from other extant Eurasian populations. The mean time of divergence between the Kalash and other populations currently residing in this region was estimated to be 11,800 (95% confidence interval = 10,600−12,600) years ago, and thus they represent present-day descendants of some of the earliest migrants into the Indian sub-continent from West Asia. PMID:25937445

The Kalash genetic isolate: ancient divergence, drift, and selection.

PubMed

Ayub, Qasim; Mezzavilla, Massimo; Pagani, Luca; Haber, Marc; Mohyuddin, Aisha; Khaliq, Shagufta; Mehdi, Syed Qasim; Tyler-Smith, Chris

2015-05-07

The Kalash represent an enigmatic isolated population of Indo-European speakers who have been living for centuries in the Hindu Kush mountain ranges of present-day Pakistan. Previous Y chromosome and mitochondrial DNA markers provided no support for their claimed Greek descent following Alexander III of Macedon's invasion of this region, and analysis of autosomal loci provided evidence of a strong genetic bottleneck. To understand their origins and demography further, we genotyped 23 unrelated Kalash samples on the Illumina HumanOmni2.5M-8 BeadChip and sequenced one male individual at high coverage on an Illumina HiSeq 2000. Comparison with published data from ancient hunter-gatherers and European farmers showed that the Kalash share genetic drift with the Paleolithic Siberian hunter-gatherers and might represent an extremely drifted ancient northern Eurasian population that also contributed to European and Near Eastern ancestry. Since the split from other South Asian populations, the Kalash have maintained a low long-term effective population size (2,319-2,603) and experienced no detectable gene flow from their geographic neighbors in Pakistan or from other extant Eurasian populations. The mean time of divergence between the Kalash and other populations currently residing in this region was estimated to be 11,800 (95% confidence interval = 10,600-12,600) years ago, and thus they represent present-day descendants of some of the earliest migrants into the Indian sub-continent from West Asia. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

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

Andam, Cheryl P.; Doroghazi, James R.; Campbell, Ashley N.

We show that Streptomyces biogeography in soils across North America is influenced by the regional diversification of microorganisms due to dispersal limitation and genetic drift. Streptomyces spp. form desiccation-resistant spores, which can be dispersed on the wind, allowing for a strong test of whether dispersal limitation governs patterns of terrestrial microbial diversity. We employed an approach that has high sensitivity for determining the effects of genetic drift. Specifically, we examined the genetic diversity and phylogeography of physiologically similar Streptomyces strains isolated from geographically distributed yet ecologically similar habitats. We found that Streptomyces beta diversity scales with geographic distance and bothmore » beta diversity and phylogenetic diversity manifest in a latitudinal diversity gradient. This pattern of Streptomyces biogeography resembles patterns seen for diverse species of plants and animals, and we therefore evaluated these data in the context of ecological and evolutionary hypotheses proposed to explain latitudinal diversity gradients. The data are consistent with the hypothesis that niche conservatism limits dispersal, and historical patterns of glaciation have limited the time for speciation in higher-latitude sites. Most notably, higher-latitude sites have lower phylogenetic diversity, higher phylogenetic clustering, and evidence of range expansion from lower latitudes. In addition, patterns of beta diversity partition with respect to the glacial history of sites. Furthermore, the data support the hypothesis that extant patterns of Streptomyces biogeography have been driven by historical patterns of glaciation and are the result of demographic range expansion, dispersal limitation, and regional diversification due to drift.« less

A Latitudinal Diversity Gradient in Terrestrial Bacteria of the Genus Streptomyces

PubMed Central

Andam, Cheryl P.; Doroghazi, James R.; Campbell, Ashley N.; Kelly, Peter J.; Choudoir, Mallory J.

2016-01-01

ABSTRACT We show that Streptomyces biogeography in soils across North America is influenced by the regional diversification of microorganisms due to dispersal limitation and genetic drift. Streptomyces spp. form desiccation-resistant spores, which can be dispersed on the wind, allowing for a strong test of whether dispersal limitation governs patterns of terrestrial microbial diversity. We employed an approach that has high sensitivity for determining the effects of genetic drift. Specifically, we examined the genetic diversity and phylogeography of physiologically similar Streptomyces strains isolated from geographically distributed yet ecologically similar habitats. We found that Streptomyces beta diversity scales with geographic distance and both beta diversity and phylogenetic diversity manifest in a latitudinal diversity gradient. This pattern of Streptomyces biogeography resembles patterns seen for diverse species of plants and animals, and we therefore evaluated these data in the context of ecological and evolutionary hypotheses proposed to explain latitudinal diversity gradients. The data are consistent with the hypothesis that niche conservatism limits dispersal, and historical patterns of glaciation have limited the time for speciation in higher-latitude sites. Most notably, higher-latitude sites have lower phylogenetic diversity, higher phylogenetic clustering, and evidence of range expansion from lower latitudes. In addition, patterns of beta diversity partition with respect to the glacial history of sites. Hence, the data support the hypothesis that extant patterns of Streptomyces biogeography have been driven by historical patterns of glaciation and are the result of demographic range expansion, dispersal limitation, and regional diversification due to drift. PMID:27073097

The interplay between local ecology, divergent selection, and genetic drift in population divergence of a sexually antagonistic female trait.

PubMed

Green, Kristina Karlsson; Svensson, Erik I; Bergsten, Johannes; Härdling, Roger; Hansson, Bengt

2014-07-01

Genetically polymorphic species offer the possibility to study maintenance of genetic variation and the potential role for genetic drift in population divergence. Indirect inference of the selection regimes operating on polymorphic traits can be achieved by comparing population divergence in neutral genetic markers with population divergence in trait frequencies. Such an approach could further be combined with ecological data to better understand agents of selection. Here, we infer the selective regimes acting on a polymorphic mating trait in an insect group; the dorsal structures (either rough or smooth) of female diving beetles. Our recent work suggests that the rough structures have a sexually antagonistic function in reducing male mating attempts. For two species (Dytiscus lapponicus and Graphoderus zonatus), we could not reject genetic drift as an explanation for population divergence in morph frequencies, whereas for the third (Hygrotus impressopunctatus) we found that divergent selection pulls morph frequencies apart across populations. Furthermore, population morph frequencies in H. impressopunctatus were significantly related to local bioclimatic factors, providing an additional line of evidence for local adaptation in this species. These data, therefore, suggest that local ecological factors and sexual conflict interact over larger spatial scales to shape population divergence in the polymorphism. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

The influence of gene flow and drift on genetic and phenotypic divergence in two species of Zosterops in Vanuatu

PubMed Central

Clegg, Sonya M.; Phillimore, Albert B.

2010-01-01

Colonization of an archipelago sets the stage for adaptive radiation. However, some archipelagos are home to spectacular radiations, while others have much lower levels of diversification. The amount of gene flow among allopatric populations is one factor proposed to contribute to this variation. In island colonizing birds, selection for reduced dispersal ability is predicted to produce changing patterns of regional population genetic structure as gene flow-dominated systems give way to drift-mediated divergence. If this transition is important in facilitating phenotypic divergence, levels of genetic and phenotypic divergence should be associated. We consider population genetic structure and phenotypic divergence among two co-distributed, congeneric (Genus: Zosterops) bird species inhabiting the Vanuatu archipelago. The more recent colonist, Z. lateralis, exhibits genetic patterns consistent with a strong influence of distance-mediated gene flow. However, complex patterns of asymmetrical gene flow indicate variation in dispersal ability or inclination among populations. The endemic species, Z. flavifrons, shows only a partial transition towards a drift-mediated system, despite a long evolutionary history on the archipelago. We find no strong evidence that gene flow constrains phenotypic divergence in either species, suggesting that levels of inter-island gene flow do not explain the absence of a radiation across this archipelago. PMID:20194170

A comparison of worldwide phonemic and genetic variation in human populations

PubMed Central

Creanza, Nicole; Ruhlen, Merritt; Pemberton, Trevor J.; Rosenberg, Noah A.; Feldman, Marcus W.; Ramachandran, Sohini

2015-01-01

Worldwide patterns of genetic variation are driven by human demographic history. Here, we test whether this demographic history has left similar signatures on phonemes—sound units that distinguish meaning between words in languages—to those it has left on genes. We analyze, jointly and in parallel, phoneme inventories from 2,082 worldwide languages and microsatellite polymorphisms from 246 worldwide populations. On a global scale, both genetic distance and phonemic distance between populations are significantly correlated with geographic distance. Geographically close language pairs share significantly more phonemes than distant language pairs, whether or not the languages are closely related. The regional geographic axes of greatest phonemic differentiation correspond to axes of genetic differentiation, suggesting that there is a relationship between human dispersal and linguistic variation. However, the geographic distribution of phoneme inventory sizes does not follow the predictions of a serial founder effect during human expansion out of Africa. Furthermore, although geographically isolated populations lose genetic diversity via genetic drift, phonemes are not subject to drift in the same way: within a given geographic radius, languages that are relatively isolated exhibit more variance in number of phonemes than languages with many neighbors. This finding suggests that relatively isolated languages are more susceptible to phonemic change than languages with many neighbors. Within a language family, phoneme evolution along genetic, geographic, or cognate-based linguistic trees predicts similar ancestral phoneme states to those predicted from ancient sources. More genetic sampling could further elucidate the relative roles of vertical and horizontal transmission in phoneme evolution. PMID:25605893

DRIFTSEL: an R package for detecting signals of natural selection in quantitative traits.

PubMed

Karhunen, M; Merilä, J; Leinonen, T; Cano, J M; Ovaskainen, O

2013-07-01

Approaches and tools to differentiate between natural selection and genetic drift as causes of population differentiation are of frequent demand in evolutionary biology. Based on the approach of Ovaskainen et al. (2011), we have developed an R package (DRIFTSEL) that can be used to differentiate between stabilizing selection, diversifying selection and random genetic drift as causes of population differentiation in quantitative traits when neutral marker and quantitative genetic data are available. Apart from illustrating the use of this method and the interpretation of results using simulated data, we apply the package on data from three-spined sticklebacks (Gasterosteus aculeatus) to highlight its virtues. DRIFTSEL can also be used to perform usual quantitative genetic analyses in common-garden study designs. © 2013 John Wiley & Sons Ltd.

How Obstacles Perturb Population Fronts and Alter Their Genetic Structure.

PubMed

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

2015-12-01

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 expected from complex environments with many obstacles.

Recombination Processes and Nonlinear Markov Chains.

PubMed

Pirogov, Sergey; Rybko, Alexander; Kalinina, Anastasia; Gelfand, Mikhail

2016-09-01

Bacteria are known to exchange genetic information by horizontal gene transfer. Since the frequency of homologous recombination depends on the similarity between the recombining segments, several studies examined whether this could lead to the emergence of subspecies. Most of them simulated fixed-size Wright-Fisher populations, in which the genetic drift should be taken into account. Here, we use nonlinear Markov processes to describe a bacterial population evolving under mutation and recombination. We consider a population structure as a probability measure on the space of genomes. This approach implies the infinite population size limit, and thus, the genetic drift is not assumed. We prove that under these conditions, the emergence of subspecies is impossible.

Ecological, morphological, genetic and life history characteristics of two sockeye salmon populations, Tustumena Lake, Alaska

USGS Publications Warehouse

Woody, Carol Ann

1998-01-01

Populations can differ in both phenotypic and molecular genetic traits. Phenotypic differences likely result from differential selection pressures in the environment, whereas differences in neutral molecular markers result from genetic drift associated with some degree of reproductive isolation. Two sockeye salmon, Oncorhynchus nerka, populations were compared using both phenotypic and genotypic characters, and causal factors were examined. Salmon spawning in a short (<3 km), shallow (<21 cm), clear, homogenous spring-fed study site spawned later, were younger, smaller, and produced fewer and smaller eggs than salmon spawning in a longer (∼80 km), deeper, stained, diverse, precipitation-dominated stream. Run timing differences were associated with differences in stream thermal regimes. Age and size at maturity differences are likely due to differences in age-specific mortality rates. Fish in the shallow spring-fed system suffered higher adult predation rates and exhibited greater egg to fry survival compared to fish in the precipitation-fed system. Salmon in both streams exhibited non-random nest site selection for deeper habitats and smaller substrates (≥2 to <64 mm mean diameter) relative to available habitat; fish from the precipitation system avoided low velocity habitats containing fine (<2 mm) substrates. Genetic comparisons of six microsatellite loci indicated that run time was a more effective reproductive isolating mechanism than geographical distance. Differences between and within the tributary spawning populations are discussed in terms of selection, genetic drift, and the homogenizing effects of gene flow. This study indicates important adaptive differences may exist between proximate spawning groups of salmon which should be considered when characterizing populations for conservation or management purposes.

Small Ne of the Isolated and Unmanaged Horse Population on Sable Island.

PubMed

Uzans, Andrea J; Lucas, Zoe; McLeod, Brenna A; Frasier, Timothy R

2015-01-01

For small, isolated populations 2 common conservation concerns relate to genetic threats: inbreeding and negative consequences associated with loss of genetic diversity due to drift. Mitigating these threats often involves conservation actions that can be controversial, such as translocations or captive breeding programs. Although such actions have been successful in some situations, in others they have had undesirable outcomes. Here, we estimated the effective population size (N e ) of the Sable Island horses to assess the risk to this population of these genetic threats. We found surprising consistency of N e estimates across the 5 different methods used, with a mean of 48 effective individuals. This estimate falls below the 50 criterion of the "50/500 rule," below which inbreeding depression is a concern for population viability. However, simulations and knowledge of population history indicate that this population is still in its early stages of approaching equilibrium between mutation, drift, and genetic diversity; and no negative consequences have been identified that could be associated with inbreeding depression. Therefore, we do not recommend taking management action (such as translocations) at this stage. Rather, we propose continued monitoring of genetic diversity and fitness over time so that trends and any substantial changes can be detected. This represents one of the few unmanaged horse populations in the world, and therefore these data will not only alert us to serious concerns regarding their conservation status, but will also provide a wealth of information about how natural processes drive patterns of reproduction, mortality, and population growth over time. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

AFLPs and Mitochondrial Haplotypes Reveal Local Adaptation to Extreme Thermal Environments in a Freshwater Gastropod

PubMed Central

Quintela, María; Johansson, Magnus P.; Kristjánsson, Bjarni K.; Barreiro, Rodolfo; Laurila, Anssi

2014-01-01

The way environmental variation shapes neutral and adaptive genetic variation in natural populations is a key issue in evolutionary biology. Genome scans allow the identification of the genetic basis of local adaptation without previous knowledge of genetic variation or traits under selection. Candidate loci for divergent adaptation are expected to show higher FST than neutral loci influenced solely by random genetic drift, migration and mutation. The comparison of spatial patterns of neutral markers and loci under selection may help disentangle the effects of gene flow, genetic drift and selection among populations living in contrasting environments. Using the gastropod Radix balthica as a system, we analyzed 376 AFLP markers and 25 mtDNA COI haplotypes for candidate loci and associations with local adaptation among contrasting thermal environments in Lake Mývatn, a volcanic lake in northern Iceland. We found that 2% of the analysed AFLP markers were under directional selection and 12% of the mitochondrial haplotypes correlated with differing thermal habitats. The genetic networks were concordant for AFLP markers and mitochondrial haplotypes, depicting distinct topologies at neutral and candidate loci. Neutral topologies were characterized by intense gene flow revealed by dense nets with edges connecting contrasting thermal habitats, whereas the connections at candidate loci were mostly restricted to populations within each thermal habitat and the number of edges decreased with temperature. Our results suggest microgeographic adaptation within Lake Mývatn and highlight the utility of genome scans in detecting adaptive divergence. PMID:25007329

Drift-Induced Selection Between Male and Female Heterogamety.

PubMed

Veller, Carl; Muralidhar, Pavitra; Constable, George W A; Nowak, Martin A

2017-10-01

Evolutionary transitions between male and female heterogamety are common in both vertebrates and invertebrates. Theoretical studies of these transitions have found that, when all genotypes are equally fit, continuous paths of intermediate equilibria link the two sex chromosome systems. This observation has led to a belief that neutral evolution along these paths can drive transitions, and that arbitrarily small fitness differences among sex chromosome genotypes can determine the system to which evolution leads. Here, we study stochastic evolutionary dynamics along these equilibrium paths. We find non-neutrality, both in transitions retaining the ancestral pair of sex chromosomes, and in those creating a new pair. In fact, substitution rates are biased in favor of dominant sex determining chromosomes, which fix with higher probabilities than mutations of no effect. Using diffusion approximations, we show that this non-neutrality is a result of "drift-induced selection" operating at every point along the equilibrium paths: stochastic jumps off the paths return with, on average, a directional bias in favor of the dominant segregating sex chromosome. Our results offer a novel explanation for the observed preponderance of dominant sex determining genes, and hint that drift-induced selection may be a common force in standard population genetic systems. Copyright © 2017 by the Genetics Society of America.

The effect of gene interactions on the long-term response to selection.

PubMed

Paixão, Tiago; Barton, Nicholas H

2016-04-19

The role of gene interactions in the evolutionary process has long been controversial. Although some argue that they are not of importance, because most variation is additive, others claim that their effect in the long term can be substantial. Here, we focus on the long-term effects of genetic interactions under directional selection assuming no mutation or dominance, and that epistasis is symmetrical overall. We ask by how much the mean of a complex trait can be increased by selection and analyze two extreme regimes, in which either drift or selection dominate the dynamics of allele frequencies. In both scenarios, epistatic interactions affect the long-term response to selection by modulating the additive genetic variance. When drift dominates, we extend Robertson's [Robertson A (1960)Proc R Soc Lond B Biol Sci153(951):234-249] argument to show that, for any form of epistasis, the total response of a haploid population is proportional to the initial total genotypic variance. In contrast, the total response of a diploid population is increased by epistasis, for a given initial genotypic variance. When selection dominates, we show that the total selection response can only be increased by epistasis when some initially deleterious alleles become favored as the genetic background changes. We find a simple approximation for this effect and show that, in this regime, it is the structure of the genotype-phenotype map that matters and not the variance components of the population.

Genetic divergence and signatures of natural selection in marginal populations of a keystone, long-lived conifer, Eastern White Pine (Pinus strobus) from Northern Ontario.

PubMed

Chhatre, Vikram E; Rajora, Om P

2014-01-01

Marginal populations are expected to provide the frontiers for adaptation, evolution and range shifts of plant species under the anticipated climate change conditions. Marginal populations are predicted to show genetic divergence from central populations due to their isolation, and divergent natural selection and genetic drift operating therein. Marginal populations are also expected to have lower genetic diversity and effective population size (Ne) and higher genetic differentiation than central populations. We tested these hypotheses using eastern white pine (Pinus strobus) as a model for keystone, long-lived widely-distributed plants. All 614 eastern white pine trees, in a complete census of two populations each of marginal old-growth, central old-growth, and central second-growth, were genotyped at 11 microsatellite loci. The central populations had significantly higher allelic and genotypic diversity, latent genetic potential (LGP) and Ne than the marginal populations. However, heterozygosity and fixation index were similar between them. The marginal populations were genetically diverged from the central populations. Model testing suggested predominant north to south gene flow in the study area with curtailed gene flow to northern marginal populations. Signatures of natural selection were detected at three loci in the marginal populations; two showing divergent selection with directional change in allele frequencies, and one balancing selection. Contrary to the general belief, no significant differences were observed in genetic diversity, differentiation, LGP, and Ne between old-growth and second-growth populations. Our study provides information on the dynamics of migration, genetic drift and selection in central versus marginal populations of a keystone long-lived plant species and has broad evolutionary, conservation and adaptation significance.

Genetic Divergence and Signatures of Natural Selection in Marginal Populations of a Keystone, Long-Lived Conifer, Eastern White Pine (Pinus strobus) from Northern Ontario

PubMed Central

Chhatre, Vikram E.; Rajora, Om P.

2014-01-01

Marginal populations are expected to provide the frontiers for adaptation, evolution and range shifts of plant species under the anticipated climate change conditions. Marginal populations are predicted to show genetic divergence from central populations due to their isolation, and divergent natural selection and genetic drift operating therein. Marginal populations are also expected to have lower genetic diversity and effective population size (N e) and higher genetic differentiation than central populations. We tested these hypotheses using eastern white pine (Pinus strobus) as a model for keystone, long-lived widely-distributed plants. All 614 eastern white pine trees, in a complete census of two populations each of marginal old-growth, central old-growth, and central second-growth, were genotyped at 11 microsatellite loci. The central populations had significantly higher allelic and genotypic diversity, latent genetic potential (LGP) and N e than the marginal populations. However, heterozygosity and fixation index were similar between them. The marginal populations were genetically diverged from the central populations. Model testing suggested predominant north to south gene flow in the study area with curtailed gene flow to northern marginal populations. Signatures of natural selection were detected at three loci in the marginal populations; two showing divergent selection with directional change in allele frequencies, and one balancing selection. Contrary to the general belief, no significant differences were observed in genetic diversity, differentiation, LGP, and N e between old-growth and second-growth populations. Our study provides information on the dynamics of migration, genetic drift and selection in central versus marginal populations of a keystone long-lived plant species and has broad evolutionary, conservation and adaptation significance. PMID:24859159

Serial Founder Effects During Range Expansion: A Spatial Analog of Genetic Drift

PubMed Central

Slatkin, Montgomery; Excoffier, Laurent

2012-01-01

Range expansions cause a series of founder events. We show that, in a one-dimensional habitat, these founder events are the spatial analog of genetic drift in a randomly mating population. The spatial series of allele frequencies created by successive founder events is equivalent to the time series of allele frequencies in a population of effective size ke, the effective number of founders. We derive an expression for ke in a discrete-population model that allows for local population growth and migration among established populations. If there is selection, the net effect is determined approximately by the product of the selection coefficients and the number of generations between successive founding events. We use the model of a single population to compute analytically several quantities for an allele present in the source population: (i) the probability that it survives the series of colonization events, (ii) the probability that it reaches a specified threshold frequency in the last population, and (iii) the mean and variance of the frequencies in each population. We show that the analytic theory provides a good approximation to simulation results. A consequence of our approximation is that the average heterozygosity of neutral alleles decreases by a factor of 1 – 1/(2ke) in each new population. Therefore, the population genetic consequences of surfing can be predicted approximately by the effective number of founders and the effective selection coefficients, even in the presence of migration among populations. We also show that our analytic results are applicable to a model of range expansion in a continuously distributed population. PMID:22367031

Serial founder effects during range expansion: a spatial analog of genetic drift.

PubMed

Slatkin, Montgomery; Excoffier, Laurent

2012-05-01

Range expansions cause a series of founder events. We show that, in a one-dimensional habitat, these founder events are the spatial analog of genetic drift in a randomly mating population. The spatial series of allele frequencies created by successive founder events is equivalent to the time series of allele frequencies in a population of effective size ke, the effective number of founders. We derive an expression for ke in a discrete-population model that allows for local population growth and migration among established populations. If there is selection, the net effect is determined approximately by the product of the selection coefficients and the number of generations between successive founding events. We use the model of a single population to compute analytically several quantities for an allele present in the source population: (i) the probability that it survives the series of colonization events, (ii) the probability that it reaches a specified threshold frequency in the last population, and (iii) the mean and variance of the frequencies in each population. We show that the analytic theory provides a good approximation to simulation results. A consequence of our approximation is that the average heterozygosity of neutral alleles decreases by a factor of 1-1/(2ke) in each new population. Therefore, the population genetic consequences of surfing can be predicted approximately by the effective number of founders and the effective selection coefficients, even in the presence of migration among populations. We also show that our analytic results are applicable to a model of range expansion in a continuously distributed population.

Changes in composition of cuticular biochemicals of the facultatively polygynous ant Petalomyrmex phylax during range expansion in Cameroon with respect to social, spatial and genetic variation.

PubMed

Dalecky, Ambroise; Renucci, Marielle; Tirard, Alain; Debout, Gabriel; Roux, Maurice; Kjellberg, Finn; Provost, Erick

2007-09-01

In social insects, biochemicals found at the surface of the cuticle are involved in the recognition process and in protection against desiccation and pathogens. However, the relative contribution of evolutionary forces in shaping diversity of these biochemicals remains largely unresolved in ants. We determined the composition of epicuticular biochemicals for workers sampled in 12 populations of the ant Petalomyrmex phylax from Cameroon. Genetic variation at 12 microsatellite markers was used to infer population history and to provide null expectations under the neutrality hypothesis. Genetic data suggest a recent southward range expansion of this ant species. Furthermore, there is a decline southward in the numbers of queens present in mature colonies. Here, we contrast the pattern of biochemical variation against genetic, social and spatial parameters. We thus provide the first estimates of the relative contribution of neutral and selective processes on variation of ant cuticular profile. Populations in migration-drift disequilibrium showed reduction of within-population variation for genetic markers as well as for cuticular profiles. In these populations, the cuticular profile became biased towards a limited number of high molecular weight molecules. Within- and among-population biochemical variation was explained by both genetic and social variation and by the spatial distribution of populations. We therefore propose that during range expansion of P. phylax, the composition of epicuticular compounds has been affected by a combination of neutral processes - genetic drift and spatially limited dispersal - and spatially varying selection, social organization and environmental effects.

Local selection modifies phenotypic divergence among Rana temporaria populations in the presence of gene flow.

PubMed

Richter-Boix, Alex; Teplitsky, Céline; Rogell, Björn; Laurila, Anssi

2010-02-01

In ectotherms, variation in life history traits among populations is common and suggests local adaptation. However, geographic variation itself is not a proof for local adaptation, as genetic drift and gene flow may also shape patterns of quantitative variation. We studied local and regional variation in means and phenotypic plasticity of larval life history traits in the common frog Rana temporaria using six populations from central Sweden, breeding in either open-canopy or partially closed-canopy ponds. To separate local adaptation from genetic drift, we compared differentiation in quantitative genetic traits (Q(ST)) obtained from a common garden experiment with differentiation in presumably neutral microsatellite markers (F(ST)). We found that R. temporaria populations differ in means and plasticities of life history traits in different temperatures at local, and in F(ST) at regional scale. Comparisons of differentiation in quantitative traits and in molecular markers suggested that natural selection was responsible for the divergence in growth and development rates as well as in temperature-induced plasticity, indicating local adaptation. However, at low temperature, the role of genetic drift could not be separated from selection. Phenotypes were correlated with forest canopy closure, but not with geographical or genetic distance. These results indicate that local adaptation can evolve in the presence of ongoing gene flow among the populations, and that natural selection is strong in this system.

Phylogeny of Fomitopsis pinicola: A species complex

Treesearch

John Haight; Gary A. Laursen; Jessie A. Glaeser; D. Lee Taylor

2016-01-01

Fungal species with a broad distribution may exhibit considerable genetic variation over their geographic ranges. Variation may develop among populations based on geographic isolation, lack of migration, and genetic drift, though this genetic variation may not always be evident when examining phenotypic characters. Fomitopsis pinicola is an...

Natural history of Ashkenazi intelligence.

PubMed

Cochran, Gregory; Hardy, Jason; Harpending, Henry

2006-09-01

This paper elaborates the hypothesis that the unique demography and sociology of Ashkenazim in medieval Europe selected for intelligence. Ashkenazi literacy, economic specialization, and closure to inward gene flow led to a social environment in which there was high fitness payoff to intelligence, specifically verbal and mathematical intelligence but not spatial ability. As with any regime of strong directional selection on a quantitative trait, genetic variants that were otherwise fitness reducing rose in frequency. In particular we propose that the well-known clusters of Ashkenazi genetic diseases, the sphingolipid cluster and the DNA repair cluster in particular, increase intelligence in heterozygotes. Other Ashkenazi disorders are known to increase intelligence. Although these disorders have been attributed to a bottleneck in Ashkenazi history and consequent genetic drift, there is no evidence of any bottleneck. Gene frequencies at a large number of autosomal loci show that if there was a bottleneck then subsequent gene flow from Europeans must have been very large, obliterating the effects of any bottleneck. The clustering of the disorders in only a few pathways and the presence at elevated frequency of more than one deleterious allele at many of them could not have been produced by drift. Instead these are signatures of strong and recent natural selection.

Unconstrained cranial evolution in Neandertals and modern humans compared to common chimpanzees

PubMed Central

Weaver, Timothy D.; Stringer, Chris B.

2015-01-01

A variety of lines of evidence support the idea that neutral evolutionary processes (genetic drift, mutation) have been important in generating cranial differences between Neandertals and modern humans. But how do Neandertals and modern humans compare with other species? And how do these comparisons illuminate the evolutionary processes underlying cranial diversification? To address these questions, we used 27 standard cranial measurements collected on 2524 recent modern humans, 20 Neandertals and 237 common chimpanzees to estimate split times between Neandertals and modern humans, and between Pan troglodytes verus and two other subspecies of common chimpanzee. Consistent with a neutral divergence, the Neandertal versus modern human split-time estimates based on cranial measurements are similar to those based on DNA sequences. By contrast, the common chimpanzee cranial estimates are much lower than DNA-sequence estimates. Apparently, cranial evolution has been unconstrained in Neandertals and modern humans compared with common chimpanzees. Based on these and additional analyses, it appears that cranial differentiation in common chimpanzees has been restricted by stabilizing natural selection. Alternatively, this restriction could be due to genetic and/or developmental constraints on the amount of within-group variance (relative to effective population size) available for genetic drift to act on. PMID:26468243

Microgeographic and temporal genetic variation in populations of the bluetongue virus vector Culicoides variipennis (Diptera: Ceratopogonidae).

PubMed

Tabachnick, W J

1992-05-01

Seven Colorado populations of the bluetongue virus vector Culicoides varipennis (Coquillett) were analyzed for genetic variation at 19-21 isozyme loci. Permanent populations, which overwinter as larvae, showed little temporal genetic change at 19 loci. PGD and MDH showed seasonal changes in gene frequencies, attributable to selection at two permanent populations. Two temporary populations showed low heterozygosity compared with permanent populations. Independent estimates of gene flow, calculated using FST and the private allele method, were Nm* = 2.15 and 6.95, respectively. Colorado C. variipennis permanent populations showed high levels of gene flow which prevented significant genetic differentiation due to genetic drift. Temporary populations showed significant gene frequency differences from nearby permanent populations due to the "founder effect" associated with chance colonization.

Holocene re-colonisation, central-marginal distribution and habitat specialisation shape population genetic patterns within an Atlantic European grass species.

PubMed

Harter, D E V; Jentsch, A; Durka, W

2015-05-01

Corynephorus canescens (L.) P.Beauv. is an outbreeding, short-lived and wind-dispersed grass species, highly specialised on scattered and disturbance-dependent habitats of open sandy sites. Its distribution ranges from the Iberian Peninsula over Atlantic regions of Western and Central Europe, but excludes the two other classical European glacial refuge regions on the Apennine and Balkan Peninsulas. To investigate genetic patterns of this uncommon combination of ecological and biogeographic species characteristics, we analysed AFLP variation among 49 populations throughout the European distribution range, expecting (i) patterns of SW European glacial refugia and post-glacial expansion to the NE; (ii) decreasing genetic diversity from central to marginal populations; and (iii) interacting effects of high gene flow and disturbance-driven genetic drift. Decreasing genetic diversity from SW to NE and distinct gene pool clustering imply refugia on the Iberian Peninsula and in western France, from where range expansion originated towards the NE. High genetic diversity within and moderate genetic differentiation among populations, and a significant pattern of isolation-by-distance indicate a gene flow drift equilibrium within C. canescens, probably due to its restriction to scattered and dynamic habitats and limited dispersal distances. These features, as well as the re-colonisation history, were found to affect genetic diversity gradients from central to marginal populations. Our study emphasises the need for including the specific ecology into analyses of species (re-)colonisation histories and range centre-margin analyses. To account for discontinuous distributions, new indices of marginality were tested for their suitability in studies of centre-periphery gradients. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

Genetics and evolution: an iOS application to supplement introductory courses in transmission and evolutionary genetics.

PubMed

Myers, Russell B; Millman, Brandon; Noor, Mohamed A F

2014-04-11

Students in college courses struggle to understand many concepts fundamental to transmission and evolutionary genetics, including multilocus inheritance, recombination, Hardy-Weinberg, and genetic drift. These students consistently ask for more demonstrations and more practice problems. With this demand in mind, the "Genetics and Evolution" app was designed to help students (and their instructors) by providing a suite of tools granting them the ability to: (1) simulate genetic crosses with varying numbers of genes and patterns of inheritance, (2) simulate allele frequency changes under natural selection and/ or genetic drift, (3) quiz themselves to reinforce terminology (customizable by any instructor for their whole classroom), *4) solve various problems (recombination fractions, Hardy-Weinberg, heritability, population growth), and (5) generate literally an infinite number of practice problems in all of these areas to try on their own. Although some of these functions are available elsewhere, the alternatives do not have the ability to instantly generate new practice problems or achieve these diverse functions in devices that students carry in their pockets every day. Copyright © 2014 Myers et al.

Population Genetics of Three Dimensional Range Expansions

NASA Astrophysics Data System (ADS)

Lavrentovich, Maxim; Nelson, David

2014-03-01

We develop a simple model of genetic diversity in growing spherical cell clusters, where the growth is confined to the cluster surface. This kind of growth occurs in cells growing in soft agar, and can also serve as a simple model of avascular tumors. Mutation-selection balance in these radial expansions is strongly influenced by scaling near a neutral, voter model critical point and by the inflating frontier. We develop a scaling theory to describe how the dynamics of mutation-selection balance is cut off by inflation. Genetic drift, i.e., local fluctuations in the genetic diversity, also plays an important role, and can lead to the extinction even of selectively advantageous strains. We calculate this extinction probability, taking into account the effect of rough population frontiers.

The paradox of forest fragmentation genetics

Treesearch

Andrea T. Kramer; Jennifer L. Ison; Mary V. Ashley; Henry F. Howe

2008-01-01

Theory predicts widespread loss of genetic diversity from drift and inbreeding in trees subjected to habitat fragmentation, yet empirical support of this theory is scarce. We argue that population genetics theory may be misapplied in light of ecological realities that, when recognized, require scrutiny of underlying evolutionary assumptions. One ecological reality is...

Distance, dams and drift: What structures populations of an endangered, benthic stream fish?

USGS Publications Warehouse

Roberts, James H.; Angermeier, Paul; Hallerman, Eric M.

2013-01-01

Spatial population structure plays an important role in species persistence, evolution and conservation. Benthic stream fishes are diverse and frequently imperilled, yet the determinants and spatial scaling of their population structure are understudied. We investigated the range-wide population genetic structure of Roanoke logperch (Percina rex), an endangered, benthic stream fish of the eastern United States. Fish were sampled from 35 sites and analysed at 11 microsatellite DNA loci. Clustering models were used to sort individuals into genetically cohesive groups and thereby estimate the spatial scaling of population structure. We then used Bayesian generalized linear mixed models (BGLMMs) to test alternative hypotheses about the environmental factors most responsible for generating structure, as measured by the differentiation statistic FST. Clustering models delineated seven discrete populations, whose boundaries coincided with agents of fragmentation, including hydroelectric dams and tailwaters. In the absence of hydrological barriers, gene flow was extensive throughout catchments, whereas there was no evidence for contemporary dispersal between catchments across barriers. In the best-supported BGLMM, FST was positively related to the spatial distance and degree of hydrological alteration between sites and negatively related to genetic diversity within sites. Whereas the effect of tailwaters was equivocal, dams strongly influenced differentiation: the effect of a dam on FST was comparable to that of a between-site distance of over 1200 km of unimpounded river. Overall, the effect of distance-mediated dispersal was negligible compared to the combined effects of fragmentation and genetic drift. The contemporary population structure of P. rex comprises a few geographically extensive ‘islands’ that are fragmented by hydroelectric projects. This information clarifies the importance of a catchment-scale perspective on conserving the species and suggests that its recovery may require genetic and/or demographic reconnection of presently isolated populations.

Task 1.5 Genomic Shift and Drift Trends of Emerging Pathogens

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

Borucki, M

2010-01-05

The Lawrence Livermore National Laboratory (LLNL) Bioinformatics group has recently taken on a role in DTRA's Transformation Medical Technologies Initiative (TMTI). The high-level goal of TMTI is to accelerate the development of broad-spectrum countermeasures. To achieve those goals, TMTI has a near term need to conduct analyses of genomic shift and drift trends of emerging pathogens, with a focused eye on select agent pathogens, as well as antibiotic and virulence markers. Most emerging human pathogens are zoonotic viruses with a genome composed of RNA. The high mutation rate of the replication enzymes of RNA viruses contributes to sequence drift andmore » provides one mechanism for these viruses to adapt to diverse hosts (interspecies transmission events) and cause new human and zoonotic diseases. Additionally, new viral pathogens frequently emerge due to genetic shift (recombination and segment reassortment) which allows for dramatic genotypic and phenotypic changes to occur rapidly. Bacterial pathogens also evolve via genetic drift and shift, although sequence drift generally occurs at a much slower rate for bacteria as compared to RNA viruses. However, genetic shift such as lateral gene transfer and inter- and intragenomic recombination enables bacteria to rapidly acquire new mechanisms of survival and antibiotic resistance. New technologies such as rapid whole genome sequencing of bacterial genomes, ultra-deep sequencing of RNA virus populations, metagenomic studies of environments rich in antibiotic resistance genes, and the use of microarrays for the detection and characterization of emerging pathogens provide mechanisms to address the challenges posed by the rapid emergence of pathogens. Bioinformatic algorithms that enable efficient analysis of the massive amounts of data generated by these technologies as well computational modeling of protein structures and evolutionary processes need to be developed to allow the technology to fulfill its potential.« less

Genetic perspectives on northern population cycles: bridging the gap between theory and empirical studies.

PubMed

Norén, Karin; Angerbjörn, Anders

2014-05-01

Many key species in northern ecosystems are characterised by high-amplitude cyclic population demography. In 1924, Charles Elton described the ecology and evolution of cyclic populations in a classic paper and, since then, a major focus has been the underlying causes of population cycles. Elton hypothesised that fluctuations reduced population genetic variation and influenced the direction of selection pressures. In concordance with Elton, present theories concern the direct consequences of population cycles for genetic structure due to the processes of genetic drift and selection, but also include feedback models of genetic composition on population dynamics. Most of these theories gained mathematical support during the 1970s and onwards, but due to methodological drawbacks, difficulties in long-term sampling and a complex interplay between microevolutionary processes, clear empirical data allowing the testing of these predictions are still scarce. Current genetic tools allow for estimates of genetic variation and identification of adaptive genomic regions, making this an ideal time to revisit this subject. Herein, we attempt to contribute towards a consensus regarding the enigma described by Elton almost 90 years ago. We present nine predictions covering the direct and genetic feedback consequences of population cycles on genetic variation and population structure, and review the empirical evidence. Generally, empirical support for the predictions was low and scattered, with obvious gaps in the understanding of basic population processes. We conclude that genetic variation in northern cyclic populations generally is high and that the geographic distribution and amount of diversity are usually suggested to be determined by various forms of context- and density-dependent dispersal exceeding the impact of genetic drift. Furthermore, we found few clear signatures of selection determining genetic composition in cyclic populations. Dispersal is assumed to have a strong impact on genetic structuring and we suggest that the signatures of other microevolutionary processes such as genetic drift and selection are weaker and have been over-shadowed by density-dependent dispersal. We emphasise that basic biological and demographical questions still need to be answered and stress the importance of extensive sampling, appropriate choice of tools and the value of standardised protocols. © 2013 The Authors. Biological Reviews © 2013 Cambridge Philosophical Society.

Toll-like receptor variation in the bottlenecked population of the Seychelles warbler: computer simulations see the 'ghost of selection past' and quantify the 'drift debt'.

PubMed

Gilroy, D L; Phillips, K P; Richardson, D S; van Oosterhout, C

2017-07-01

Balancing selection can maintain immunogenetic variation within host populations, but detecting its signal in a postbottlenecked population is challenging due to the potentially overriding effects of drift. Toll-like receptor genes (TLRs) play a fundamental role in vertebrate immune defence and are predicted to be under balancing selection. We previously characterized variation at TLR loci in the Seychelles warbler (Acrocephalus sechellensis), an endemic passerine that has undergone a historical bottleneck. Five of seven TLR loci were polymorphic, which is in sharp contrast to the low genomewide variation observed. However, standard population genetic statistical methods failed to detect a contemporary signature of selection at any TLR locus. We examined whether the observed TLR polymorphism could be explained by neutral evolution, simulating the population's demography in the software DIYABC. This showed that the posterior distributions of mutation rates had to be unrealistically high to explain the observed genetic variation. We then conducted simulations with an agent-based model using typical values for the mutation rate, which indicated that weak balancing selection has acted on the three TLR genes. The model was able to detect evidence of past selection elevating TLR polymorphism in the prebottleneck populations, but was unable to discern any effects of balancing selection in the contemporary population. Our results show drift is the overriding evolutionary force that has shaped TLR variation in the contemporary Seychelles warbler population, and the observed TLR polymorphisms might be merely the 'ghost of selection past'. Forecast models predict immunogenetic variation in this species will continue to be eroded in the absence of contemporary balancing selection. Such 'drift debt' occurs when a gene pool has not yet reached its new equilibrium level of polymorphism, and this loss could be an important threat to many recently bottlenecked populations. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Contradictory genetic make-up of Dutch harbour porpoises: Response to van der Plas-Duivesteijn et al.

NASA Astrophysics Data System (ADS)

Kopps, Anna M.; Palsbøll, Per J.

2016-02-01

The assessment of the status of endangered species or populations typically draw generously on the plethora of population genetic software available to detect population genetic structuring. However, despite the many available analytical approaches, population genetic inference methods [of neutral genetic variation] essentially capture three basic processes; migration, random genetic drift and mutation. Consequently, different analytical approaches essentially capture the same basic process, and should yield consistent results.

Mitochondrial genetic codes evolve to match amino acid requirements of proteins.

PubMed

Swire, Jonathan; Judson, Olivia P; Burt, Austin

2005-01-01

Mitochondria often use genetic codes different from the standard genetic code. Now that many mitochondrial genomes have been sequenced, these variant codes provide the first opportunity to examine empirically the processes that produce new genetic codes. The key question is: Are codon reassignments the sole result of mutation and genetic drift? Or are they the result of natural selection? Here we present an analysis of 24 phylogenetically independent codon reassignments in mitochondria. Although the mutation-drift hypothesis can explain reassignments from stop to an amino acid, we found that it cannot explain reassignments from one amino acid to another. In particular--and contrary to the predictions of the mutation-drift hypothesis--the codon involved in such a reassignment was not rare in the ancestral genome. Instead, such reassignments appear to take place while the codon is in use at an appreciable frequency. Moreover, the comparison of inferred amino acid usage in the ancestral genome with the neutral expectation shows that the amino acid gaining the codon was selectively favored over the amino acid losing the codon. These results are consistent with a simple model of weak selection on the amino acid composition of proteins in which codon reassignments are selected because they compensate for multiple slightly deleterious mutations throughout the mitochondrial genome. We propose that the selection pressure is for reduced protein synthesis cost: most reassignments give amino acids that are less expensive to synthesize. Taken together, our results strongly suggest that mitochondrial genetic codes evolve to match the amino acid requirements of proteins.

The Effects of Both Recent and Long-Term Selection and Genetic Drift Are Readily Evident in North American Barley Breeding Populations

PubMed Central

Poets, Ana M.; Mohammadi, Mohsen; Seth, Kiran; Wang, Hongyun; Kono, Thomas J. Y.; Fang, Zhou; Muehlbauer, Gary J.; Smith, Kevin P.; Morrell, Peter L.

2015-01-01

Barley was introduced to North America ∼400 yr ago but adaptation to modern production environments is more recent. Comparisons of allele frequencies among growth habits and spike (inflorescence) types in North America indicate that significant genetic differentiation has accumulated in a relatively short evolutionary time span. Allele frequency differentiation is greatest among barley with two-row vs. six-row spikes, followed by spring vs. winter growth habit. Large changes in allele frequency among breeding programs suggest a major contribution of genetic drift and linked selection on genetic variation. Despite this, comparisons of 3613 modern North American cultivated barley breeding lines that differ for spike-type and growth habit permit the discovery of 142 single nucleotide polymorphism (SNP) outliers putatively linked to targets of selection. For example, SNPs within the Cbf4, Ppd-H1, and Vrn-H1 loci, which have previously been associated with agronomically adaptive phenotypes, are identified as outliers. Analysis of extended haplotype sharing identifies genomic regions shared within and among breeding populations, suggestive of a number of genomic regions subject to recent selection. Finally, we are able to identify recent bouts of gene flow between breeding populations that could point to the sharing of agronomically adaptive variation. These results are supported by pedigrees and breeders’ understanding of germplasm sharing. PMID:26715093

Clinal variation at microsatellite loci reveals historical secondary intergradation between glacial races of Coregonus artedi (Teleostei: Coregoninae).

PubMed

Turgeon, J; Bernatchez, L

2001-11-11

Classical models of the spatial structure of population genetics rely on the assumption of migration-drift equilibrium, which is seldom met in natural populations having only recently colonized their current range (e.g., postglacial). Population structure then depicts historical events, and counfounding effects due to recent secondary contact between recently differentiated lineages can further counfound analyses of association between geographic and genetic distances. Mitochondrial polymorphisms have revealed the existence of two closely related lineages of the lake cisco, Coregonus artedi, whose significantly different but overlaping geographical distributions provided a weak signal of past range fragmentation blurred by putative subsequent extensive secondary contacts. In this study, we analyzed geographical patterns of genetic variation at seven microsatellite loci among 22 populations of lake cisco located along the axis of an area covered by proglacial lakes 12,000-8,000 years ago in North America. The results clearly confirmed the existence of two genetically distinct races characterized by different sets of microsatellite alleles whose frequencies varied clinally across some 3000 km. Equilibrium and nonequilibrium analyses of isolation by distance revealed historical signal of gene flow resulting from the nearly complete admixture of these races following neutral secondary contacts in their historical habitat and indicated that the colonization process occurred by a stepwise expansion of an eastern (Atlantic) race into a previously established Mississippian race. This historical signal of equilibrium contrasted with the current migration-drift disequilibrium within major extant watersheds and was apparently maintained by high effective population sizes and low migration regimes.

Experimental evolution: Assortative mating and sexual selection, independent of local adaptation, lead to reproductive isolation in the nematode Caenorhabditis remanei.

PubMed

Castillo, Dean M; Burger, Melissa K; Lively, Curtis M; Delph, Lynda F

2015-12-01

Using experimental evolution, we investigated the contributions of ecological divergence, sexual selection, and genetic drift to the evolution of reproductive isolation in Caenorhabditis remanei. The nematodes were reared on two different environments for 100 generations. They were assayed for fitness on both environments after 30, 64, and 100 generations, and hybrid fitness were analyzed after 64 and 100 generations. Mating propensity within and between populations was also analyzed. The design allowed us to determine whether local adaptation was synchronous with pre- and postzygotic reproductive isolation. Prezygotic isolation evolved quickly but was unconnected with adaptation to the divergent environments. Instead, prezygotic isolation was driven by mate preferences favoring individuals from the same replicate population. A bottleneck treatment, meant to enhance the opportunity for genetic drift, had no effect on prezygotic isolation. Postzygotic isolation occurred in crosses where at least one population had a large fitness advantage in its "home" environment. Taken together, our results suggest that prezygotic isolation did not depend on drift or adaptation to divergent environments, but instead resulted from differences in sexual interactions within individual replicates. Furthermore, our results suggest that postzygotic isolation can occur between populations even when only one population has greater fitness in its home environment. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Genetic and morphological divergence among Cooper's Hawk (Accipiter cooperii) populations breeding in north-central and western North America

USGS Publications Warehouse

Sonsthagen, Sarah A.; Rosenfield, Robert N.; Bielefeldt, John; Murphy, Robert K.; Stewart, Andrew C.; Stout, William C.; Driscoll, Timothy G.; Bozek, Michael A.; Sloss, Brian L.; Talbot, Sandra L.

2012-01-01

Cooper's Hawk (Accipiter cooperii) populations breeding in the northern portion of the species' range exhibit variation in morphological traits that conforms to predictions based on differences in prey size, tree stand density, and migratory behavior. We examined genetic structure and gene flow and compared divergence at morphological traits (PST) and genetic markers (FST) to elucidate mechanisms (selection or genetic drift) that promote morphological diversification among Cooper's Hawk populations. Cooper's Hawks appear to conform to the genetic pattern of an east-west divide. Populations in British Columbia are genetically differentiated from north-central populations (Wisconsin, Minnesota, and North Dakota; pairwise microsatellite FST= 0.031-0.050; mitochondrial DNA ΦST = 0.177-0.204), which suggests that Cooper's Hawks were restricted to at least two Pleistocene glacial refugia. The strength of the Rocky Mountains—Great Plains area as a barrier to dispersal is further supported by restricted gene-flow rates between British Columbia and other sampled breeding populations. Divergence in morphological traits (PST) was also observed across study areas, but with British Columbia and North Dakota differentiated from Wisconsin and Minnesota, a pattern not predicted on the basis of FST and ΦST interpopulation estimates. Comparison of PSTand FSTestimates suggests that heterogeneous selection may be acting on Cooper's Hawks in the northern portion of their distribution, which is consistent with hypotheses that variation in prey mass and migratory behavior among populations may be influencing overall body size and wing chord. We were unable to distinguish between the effects of genetic drift and selection on tail length in the study populations.

RATES OF FITNESS DECLINE AND REBOUND SUGGEST PERVASIVE EPISTASIS

PubMed Central

Perfeito, L; Sousa, A; Bataillon, T; Gordo, I

2014-01-01

Unraveling the factors that determine the rate of adaptation is a major question in evolutionary biology. One key parameter is the effect of a new mutation on fitness, which invariably depends on the environment and genetic background. The fate of a mutation also depends on population size, which determines the amount of drift it will experience. Here, we manipulate both population size and genotype composition and follow adaptation of 23 distinct Escherichia coli genotypes. These have previously accumulated mutations under intense genetic drift and encompass a substantial fitness variation. A simple rule is uncovered: the net fitness change is negatively correlated with the fitness of the genotype in which new mutations appear—a signature of epistasis. We find that Fisher's geometrical model can account for the observed patterns of fitness change and infer the parameters of this model that best fit the data, using Approximate Bayesian Computation. We estimate a genomic mutation rate of 0.01 per generation for fitness altering mutations, albeit with a large confidence interval, a mean fitness effect of mutations of −0.01, and an effective number of traits nine in mutS− E. coli. This framework can be extended to confront a broader range of models with data and test different classes of fitness landscape models. PMID:24372601

Evolution of branched regulatory genetic pathways: directional selection on pleiotropic loci accelerates developmental system drift.

PubMed

Johnson, Norman A; Porter, Adam H

2007-01-01

Developmental systems are regulated by a web of interacting loci. One common and useful approach in studying the evolution of development is to focus on classes of interacting elements within these systems. Here, we use individual-based simulations to study the evolution of traits controlled by branched developmental pathways involving three loci, where one locus regulates two different traits. We examined the system under a variety of selective regimes. In the case where one branch was under stabilizing selection and the other under directional selection, we observed "developmental system drift": the trait under stabilizing selection showed little phenotypic change even though the loci underlying that trait showed considerable evolutionary divergence. This occurs because the pleiotropic locus responds to directional selection and compensatory mutants are then favored in the pathway under stabilizing selection. Though developmental system drift may be caused by other mechanisms, it seems likely that it is accelerated by the same underlying genetic mechanism as that producing the Dobzhansky-Muller incompatibilities that lead to speciation in both linear and branched pathways. We also discuss predictions of our model for developmental system drift and how different selective regimes affect probabilities of speciation in the branched pathway system.

Current status, future opportunities, and remaining challenges in landscape genetics [Chapter 14

Treesearch

Niko Balkenhol; Samuel A. Cushman; Lisette P. Waits; Andrew Storfer

2016-01-01

Landscape genetics has advanced the field of evolutionary ecology by providing a direct focus on relationships between landscape patterns and population processes, such as gene flow, selection, and genetic drift. This chapter discusses the current and emerging challenges and opportunities, which focus and facilitate future progress in the field. It presents ten...

An invasive social insect overcomes genetic load at the sex locus.

PubMed

Gloag, Rosalyn; Ding, Guiling; Christie, Joshua R; Buchmann, Gabriele; Beekman, Madeleine; Oldroyd, Benjamin P

2016-11-07

Some invasive hymenopteran social insects found new populations with very few reproductive individuals. This is despite the high cost of founder effects for such insects, which generally require heterozygosity at a single locus-the complementary sex determiner, csd-to develop as females. Individuals that are homozygous at csd develop as either infertile or subfertile diploid males or not at all. Furthermore, diploid males replace the female workers that are essential for colony function. Here we document how the Asian honey bee (Apis cerana) overcame the diploid male problem during its invasion of Australia. Natural selection prevented the loss of rare csd alleles due to genetic drift and corrected the skew in allele frequencies caused by founder effects to restore high average heterozygosity. Thus, balancing selection can alleviate the genetic load at csd imposed by severe bottlenecks, and so facilitate invasiveness.

Societies drifting apart? Behavioural, genetic and chemical differentiation between supercolonies in the yellow crazy ant Anoplolepis gracilipes.

PubMed

Drescher, Jochen; Blüthgen, Nico; Schmitt, Thomas; Bühler, Jana; Feldhaar, Heike

2010-10-22

In populations of most social insects, gene flow is maintained through mating between reproductive individuals from different colonies in periodic nuptial flights followed by dispersal of the fertilized foundresses. Some ant species, however, form large polygynous supercolonies, in which mating takes place within the maternal nest (intranidal mating) and fertilized queens disperse within or along the boundary of the supercolony, leading to supercolony growth (colony budding). As a consequence, gene flow is largely confined within supercolonies. Over time, such supercolonies may diverge genetically and, thus, also in recognition cues (cuticular hydrocarbons, CHC's) by a combination of genetic drift and accumulation of colony-specific, neutral mutations. We tested this hypothesis for six supercolonies of the invasive ant Anoplolepis gracilipes in north-east Borneo. Within supercolonies, workers from different nests tolerated each other, were closely related and showed highly similar CHC profiles. Between supercolonies, aggression ranged from tolerance to mortal encounters and was negatively correlated with relatedness and CHC profile similarity. Supercolonies were genetically and chemically distinct, with mutually aggressive supercolony pairs sharing only 33.1%±17.5% (mean ± SD) of their alleles across six microsatellite loci and 73.8%±11.6% of the compounds in their CHC profile. Moreover, the proportion of alleles that differed between supercolony pairs was positively correlated to the proportion of qualitatively different CHC compounds. These qualitatively differing CHC compounds were found across various substance classes including alkanes, alkenes and mono-, di- and trimethyl-branched alkanes. We conclude that positive feedback between genetic, chemical and behavioural traits may further enhance supercolony differentiation through genetic drift and neutral evolution, and may drive colonies towards different evolutionary pathways, possibly including speciation.

Digest: Local adaptation at close quarters.

PubMed

Schmidt, Chloé; Garroway, Colin

2018-06-19

Although the theory of how gene flow and genetic drift interact with local adaptation is well understood, few empirical studies have examined this process. Hämälä et al. (2018) present evidence that adaptive divergence between populations of Arabidopsis lyrata can persist in the face of relatively high levels of gene flow and drift. Maintaining divergence despite gene flow and drift has important implications for understanding adaptive responses of populations in response to human-driven environmental change. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Schizophrenia and subsequent neighborhood deprivation: revisiting the social drift hypothesis using population, twin and molecular genetic data.

PubMed

Sariaslan, A; Fazel, S; D'Onofrio, B M; Långström, N; Larsson, H; Bergen, S E; Kuja-Halkola, R; Lichtenstein, P

2016-05-03

Neighborhood influences in the etiology of schizophrenia have been emphasized in a number of systematic reviews, but causality remains uncertain. To test the social drift hypothesis, we used three complementary genetically informed Swedish cohorts. First, we used nationwide Swedish data on approximately 760 000 full- and half-sibling pairs born between 1951 and 1974 and quantitative genetic models to study genetic and environmental influences on the overlap between schizophrenia in young adulthood and subsequent residence in socioeconomically deprived neighborhoods. Schizophrenia diagnoses were ascertained using the National Patient Registry. Second, we tested the overlap between childhood psychotic experiences and neighborhood deprivation in early adulthood in the longitudinal Twin Study of Child and Adolescent Development (TCHAD; n=2960). Third, we investigated to what extent polygenic risk scores for schizophrenia predicted residence in deprived neighborhoods during late adulthood using the TwinGene sample (n=6796). Sibling data suggested that living in deprived neighborhoods was substantially heritable; 65% (95% confidence interval (95% CI): 60-71%) of the variance was attributed to genetic influences. Although the correlation between schizophrenia and neighborhood deprivation was moderate in magnitude (r=0.22; 95% CI: 0.20-0.24), it was entirely explained by genetic influences. We replicated these findings in the TCHAD sample. Moreover, the association between polygenic risk for schizophrenia and neighborhood deprivation was statistically significant (R(2)=0.15%, P=0.002). Our findings are primarily consistent with a genetic selection interpretation where genetic liability for schizophrenia also predicts subsequent residence in socioeconomically deprived neighborhoods. Previous studies may have overemphasized the relative importance of environmental influences in the social drift of schizophrenia patients. Clinical and policy interventions will therefore benefit from the future identification of potentially causal pathways between different dimensions of cognitive functions and socioeconomic trajectories derived from studies adopting family-based research designs.

The split of the Arara population: comparison of genetic drift and founder effect.

PubMed

Ribeiro-dos-Santos, A K; Guerreiro, J F; Santos, S E; Zago, M A

2001-01-01

The total genetic diversity of the Amerindian population is as high as that observed for other continental human populations because a large contribution from variation among tribes makes up for the low variation within tribes. This is attributed mainly to genetic drift acting on small isolated populations. However, a small founder population with a low genetic diversity is another factor that may contribute to the low intratribal diversity. Small founder populations seem to be a frequent event in the formation of new tribes among the Amerindians, but this event is usually not well recorded. In this paper, we analyze the genetic diversity of the Arara of Laranjal village and the Arara of Iriri village, with respect to seven tandem repeat autosomic segments (D1S80, ApoB, D4S43, vW1, vW2, F13A1 and D12S67), two Y-chromosome-specific polymorphisms (DYS19 and DYS199), and mitochondrial DNA (mtDNA) markers (restriction fragment length polymorphisms and sequencing of a segment of the D loop region). The occurrence of a single Y chromosome and mtDNA haplotype, and only 1-4 alleles of the autosomic loci investigated, corroborates historic and demographic records that the Arara of Iriri were founded by a single couple of siblings who came from the Arara of Laranjal, the largest group. Notwithstanding this fact, the genetic distance and the molecular variance between the two Arara villages were greater than those observed between them and other Amazonian tribes, suggesting that the microevolutionary process among Brazilian Amerindians may be misinterpreted if historic demographic data are not considered. Copyright 2000 S. Karger AG, Basel.

Microsatellite variation and rare alleles in a bottlenecked Hawaiian Islands endemic: implications for reintroductions

USGS Publications Warehouse

Reynolds, Michelle H.; Pearce, John M.; Lavretsky, Philip; Seixas, Pedro P.; Courtot, Karen

2015-01-01

Conservation of genetic biodiversity in endangered wildlife populations is an important challenge to address since the loss of alleles and genetic drift may influence future adaptability. Reintroduction aims to re-establish species to restored or protected ecosystems; however, moving a subset of individuals may result in loss of gene variants during the management-induced bottleneck (i.e. translocation). The endangered Laysan teal Anas laysanensis was once widespread across the Hawaiian archipelago, but became isolated on Laysan Island (415 ha) from the mid-1800s until 2004 when a translocation to Midway Atoll (596 ha) was undertaken to reduce extinction risks. We compared genetic diversity and quantified variation at microsatellite loci sampled from 230 individuals from the wild populations at Laysan (1999 to 2009) and Midway (2007 to 2010; n = 133 Laysan, n = 96 Midway birds). We identified polymorphic markers by screening nuclear microsatellites (N = 83). Low nuclear variation was detected, consistent with the species’ insular isolation and historical bottleneck. Six of 83 microsatellites were polymorphic. We found limited but similar estimates of allelic richness (2.58 alleles per locus) and heterozygosity within populations. However, 2 rare alleles found in the Laysan source population were not present in Midway’s reintroduced population, and a unique allele was discovered in an individual on Midway. Differentiation between island populations was low (FST = 0.6%), but statistically significant. Our results indicate that genetic drift had little effect on offspring generations 3 to 6 yr post-release and demonstrate the utility of using known founder events to help quantify genetic capture during translocations and to inform management decisions.

Spatiotemporal Dynamics of Genetic Variation in the Iberian Lynx along Its Path to Extinction Reconstructed with Ancient DNA

PubMed Central

Casas-Marce, Mireia; Marmesat, Elena; Soriano, Laura; Martínez-Cruz, Begoña; Lucena-Perez, Maria; Nocete, Francisco; Rodríguez-Hidalgo, Antonio; Canals, Antoni; Nadal, Jordi; Detry, Cleia; Bernáldez-Sánchez, Eloísa; Fernández-Rodríguez, Carlos; Pérez-Ripoll, Manuel; Stiller, Mathias; Hofreiter, Michael; Rodríguez, Alejandro; Revilla, Eloy; Delibes, Miguel; Godoy, José A.

2017-01-01

Abstract There is the tendency to assume that endangered species have been both genetically and demographically healthier in the past, so that any genetic erosion observed today was caused by their recent decline. The Iberian lynx (Lynx pardinus) suffered a dramatic and continuous decline during the 20th century, and now shows extremely low genome- and species-wide genetic diversity among other signs of genomic erosion. We analyze ancient (N = 10), historical (N = 245), and contemporary (N = 172) samples with microsatellite and mitogenome data to reconstruct the species' demography and investigate patterns of genetic variation across space and time. Iberian lynx populations transitioned from low but significantly higher genetic diversity than today and shallow geographical differentiation millennia ago, through a structured metapopulation with varying levels of diversity during the last centuries, to two extremely genetically depauperate and differentiated remnant populations by 2002. The historical subpopulations show varying extents of genetic drift in relation to their recent size and time in isolation, but these do not predict whether the populations persisted or went finally extinct. In conclusion, current genetic patterns were mainly shaped by genetic drift, supporting the current admixture of the two genetic pools and calling for a comprehensive genetic management of the ongoing conservation program. This study illustrates how a retrospective analysis of demographic and genetic patterns of endangered species can shed light onto their evolutionary history and this, in turn, can inform conservation actions. PMID:28962023

The peopling of Greenland: further insights from the analysis of genetic diversity using autosomal and X-chromosomal markers

PubMed Central

Pereira, Vania; Tomas, Carmen; Sanchez, Juan J; Syndercombe-Court, Denise; Amorim, António; Gusmão, Leonor; Prata, Maria João; Morling, Niels

2015-01-01

The peopling of Greenland has a complex history shaped by population migrations, isolation and genetic drift. The Greenlanders present a genetic heritage with components of European and Inuit groups; previous studies using uniparentally inherited markers in Greenlanders have reported evidence of a sex-biased, admixed genetic background. This work further explores the genetics of the Greenlanders by analysing autosomal and X-chromosomal data to obtain deeper insights into the factors that shaped the genetic diversity in Greenlanders. Fourteen Greenlandic subsamples from multiple geographical settlements were compared to assess the level of genetic substructure in the Greenlandic population. The results showed low levels of genetic diversity in all sets of the genetic markers studied, together with an increased number of X-chromosomal loci in linkage disequilibrium in relation to the Danish population. In the broader context of worldwide populations, Greenlanders are remarkably different from most populations, but they are genetically closer to some Inuit groups from Alaska. Admixture analyses identified an Inuit component in the Greenlandic population of approximately 80%. The sub-populations of Ammassalik and Nanortalik are the least diverse, presenting the lowest levels of European admixture. Isolation-by-distance analyses showed that only 16% of the genetic substructure of Greenlanders is most likely to be explained by geographic barriers. We suggest that genetic drift and a differentiated settlement history around the island explain most of the genetic substructure of the population in Greenland. PMID:24801759

The peopling of Greenland: further insights from the analysis of genetic diversity using autosomal and X-chromosomal markers.

PubMed

Pereira, Vania; Tomas, Carmen; Sanchez, Juan J; Syndercombe-Court, Denise; Amorim, António; Gusmão, Leonor; Prata, Maria João; Morling, Niels

2015-02-01

The peopling of Greenland has a complex history shaped by population migrations, isolation and genetic drift. The Greenlanders present a genetic heritage with components of European and Inuit groups; previous studies using uniparentally inherited markers in Greenlanders have reported evidence of a sex-biased, admixed genetic background. This work further explores the genetics of the Greenlanders by analysing autosomal and X-chromosomal data to obtain deeper insights into the factors that shaped the genetic diversity in Greenlanders. Fourteen Greenlandic subsamples from multiple geographical settlements were compared to assess the level of genetic substructure in the Greenlandic population. The results showed low levels of genetic diversity in all sets of the genetic markers studied, together with an increased number of X-chromosomal loci in linkage disequilibrium in relation to the Danish population. In the broader context of worldwide populations, Greenlanders are remarkably different from most populations, but they are genetically closer to some Inuit groups from Alaska. Admixture analyses identified an Inuit component in the Greenlandic population of approximately 80%. The sub-populations of Ammassalik and Nanortalik are the least diverse, presenting the lowest levels of European admixture. Isolation-by-distance analyses showed that only 16% of the genetic substructure of Greenlanders is most likely to be explained by geographic barriers. We suggest that genetic drift and a differentiated settlement history around the island explain most of the genetic substructure of the population in Greenland.

River network architecture, genetic effective size and distributional patterns predict differences in genetic structure across species in a dryland stream fish community.

PubMed

Pilger, Tyler J; Gido, Keith B; Propst, David L; Whitney, James E; Turner, Thomas F

2017-05-01

Dendritic ecological network (DEN) architecture can be a strong predictor of spatial genetic patterns in theoretical and simulation studies. Yet, interspecific differences in dispersal capabilities and distribution within the network may equally affect species' genetic structuring. We characterized patterns of genetic variation from up to ten microsatellite loci for nine numerically dominant members of the upper Gila River fish community, New Mexico, USA. Using comparative landscape genetics, we evaluated the role of network architecture for structuring populations within species (pairwise F ST ) while explicitly accounting for intraspecific demographic influences on effective population size (N e ). Five species exhibited patterns of connectivity and/or genetic diversity gradients that were predicted by network structure. These species were generally considered to be small-bodied or habitat specialists. Spatial variation of N e was a strong predictor of pairwise F ST for two species, suggesting patterns of connectivity may also be influenced by genetic drift independent of network properties. Finally, two study species exhibited genetic patterns that were unexplained by network properties and appeared to be related to nonequilibrium processes. Properties of DENs shape community-wide genetic structure but effects are modified by intrinsic traits and nonequilibrium processes. Further theoretical development of the DEN framework should account for such cases. © 2017 John Wiley & Sons Ltd.

Testing natural selection vs. genetic drift in phenotypic evolution using quantitative trait locus data.

PubMed Central

Orr, H A

1998-01-01

Evolutionary biologists have long sought a way to determine whether a phenotypic difference between two taxa was caused by natural selection or random genetic drift. Here I argue that data from quantitative trait locus (QTL) analyses can be used to test the null hypothesis of neutral phenotypic evolution. I propose a sign test that compares the observed number of plus and minus alleles in the "high line" with that expected under neutrality, conditioning on the known phenotypic difference between the taxa. Rejection of the null hypothesis implies a role for directional natural selection. This test is applicable to any character in any organism in which QTL analysis can be performed. PMID:9691061

The effect of climatic forcing on population synchrony and genetic structuring of the Canadian lynx

PubMed Central

Stenseth, Nils Chr.; Ehrich, Dorothee; Rueness, Eli Knispel; Lingjærde, Ole Chr.; Chan, Kung-Sik; Boutin, Stan; O'Donoghue, Mark; Robinson, David A.; Viljugrein, Hildegunn; Jakobsen, Kjetill S.

2004-01-01

The abundance of Canadian lynx follows 10-year density fluctuations across the Canadian subcontinent. These cyclic fluctuations have earlier been shown to be geographically structured into three climatic regions: the Atlantic, Continental, and Pacific zones. Recent genetic evidence revealed an essentially similar spatial structuring. Introducing a new population model, the “climate forcing of ecological and evolutionary patterns” model, we link the observed ecological and evolutionary patterns. Specifically, we demonstrate that there is greater phase synchrony within climatic zones than between them and show that external climatic forcing may act as a synchronizer. We simulated genetic drift by using data on population dynamics generated by the climate forcing of ecological and evolutionary patterns model, and we demonstrate that the observed genetic structuring can be seen as an emerging property of the spatiotemporal ecological dynamics. PMID:15067131

Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity

PubMed Central

Nana-Djeunga, Hugues C.; Kengne-Ouafo, Jonas A.; Pion, Sébastien D. S.; Bopda, Jean; Kamgno, Joseph; Wanji, Samuel; Che, Hua; Kuesel, Annette C.; Walker, Martin; Basáñez, Maria-Gloria; Boakye, Daniel A.; Osei-Atweneboana, Mike Y.; Boussinesq, Michel; Prichard, Roger K.; Grant, Warwick N.

2017-01-01

Background Treatment of onchocerciasis using mass ivermectin administration has reduced morbidity and transmission throughout Africa and Central/South America. Mass drug administration is likely to exert selection pressure on parasites, and phenotypic and genetic changes in several Onchocerca volvulus populations from Cameroon and Ghana—exposed to more than a decade of regular ivermectin treatment—have raised concern that sub-optimal responses to ivermectin's anti-fecundity effect are becoming more frequent and may spread. Methodology/Principal findings Pooled next generation sequencing (Pool-seq) was used to characterise genetic diversity within and between 108 adult female worms differing in ivermectin treatment history and response. Genome-wide analyses revealed genetic variation that significantly differentiated good responder (GR) and sub-optimal responder (SOR) parasites. These variants were not randomly distributed but clustered in ~31 quantitative trait loci (QTLs), with little overlap in putative QTL position and gene content between the two countries. Published candidate ivermectin SOR genes were largely absent in these regions; QTLs differentiating GR and SOR worms were enriched for genes in molecular pathways associated with neurotransmission, development, and stress responses. Finally, single worm genotyping demonstrated that geographic isolation and genetic change over time (in the presence of drug exposure) had a significantly greater role in shaping genetic diversity than the evolution of SOR. Conclusions/Significance This study is one of the first genome-wide association analyses in a parasitic nematode, and provides insight into the genomics of ivermectin response and population structure of O. volvulus. We argue that ivermectin response is a polygenically-determined quantitative trait (QT) whereby identical or related molecular pathways but not necessarily individual genes are likely to determine the extent of ivermectin response in different parasite populations. Furthermore, we propose that genetic drift rather than genetic selection of SOR is the underlying driver of population differentiation, which has significant implications for the emergence and potential spread of SOR within and between these parasite populations. PMID:28746337

Ecological correlates of population genetic structure: a comparative approach using a vertebrate metacommunity.

PubMed

Manier, Mollie K; Arnold, Stevan J

2006-12-07

Identifying ecological factors associated with population genetic differentiation is important for understanding microevolutionary processes and guiding the management of threatened populations. We identified ecological correlates of several population genetic parameters for three interacting species (two garter snakes and an anuran) that occupy a common landscape. Using multiple regression analysis, we found that species interactions were more important in explaining variation in population genetic parameters than habitat and nearest-neighbour characteristics. Effective population size was best explained by census size, while migration was associated with differences in species abundance. In contrast, genetic distance was poorly explained by the ecological correlates that we tested, but geographical distance was prominent in models for all species. We found substantially different population dynamics for the prey species relative to the two predators, characterized by larger effective sizes, lower gene flow and a state of migration-drift equilibrium. We also identified an escarpment formed by a series of block faults that serves as a barrier to dispersal for the predators. Our results suggest that successful landscape-level management should incorporate genetic and ecological data for all relevant species, because even closely associated species can exhibit very different population genetic dynamics on the same landscape.

Comparative genetic diversity in a sample of pony breeds from the U.K. and North America: a case study in the conservation of global genetic resources.

PubMed

Winton, Clare L; Plante, Yves; Hind, Pamela; McMahon, Robert; Hegarty, Matthew J; McEwan, Neil R; Davies-Morel, Mina C G; Morgan, Charly M; Powell, Wayne; Nash, Deborah M

2015-08-01

Most species exist as subdivided ex situ daughter population(s) derived from a single original group of individuals. Such subdivision occurs for many reasons both natural and manmade. Traditional British and Irish pony breeds were introduced to North America (U.S.A. and Canada) within the last 150 years, and subsequently equivalent breed societies were established. We have analyzed selected U.K. and North American equivalent pony populations as a case study for understanding the relationship between putative source and derived subpopulations. Diversity was measured using mitochondrial DNA and a panel of microsatellite markers. Genetic signatures differed between the North American subpopulations according to historical management processes. Founder effect and stochastic drift was apparent, particularly pronounced in some breeds, with evidence of admixture of imported mares of different North American breeds. This demonstrates the importance of analysis of subpopulations to facilitate understanding the genetic effects of past management practices and to lead to informed future conservation strategies.

Novel population genetics in ciliates due to life cycle and nuclear dimorphism.

PubMed

Morgens, David W; Stutz, Timothy C; Cavalcanti, Andre R O

2014-08-01

Our understanding of population genetics comes primarily from studies of organisms with canonical life cycles and nuclear organization, either haploid or diploid, sexual, or asexual. Although this template yields satisfactory results for the study of animals and plants, the wide variety of genomic organizations and life cycles of unicellular eukaryotes can make these organisms behave differently in response to mutation, selection, and drift than predicted by traditional population genetic models. In this study, we show how each of these unique features of ciliates affects their evolutionary parameters in mutation-selection, selection-drift, and mutation-selection-drift situations. In general, ciliates are less efficient in eliminating deleterious mutations-these mutations linger longer and at higher frequencies in ciliate populations than in sexual populations--and more efficient in selecting beneficial mutations. Approaching this problem via analytical techniques and simulation allows us to make specific predictions about the nature of ciliate evolution, and we discuss the implications of these results with respect to the high levels of polymorphism and high rate of protein evolution reported for ciliates. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The reality and importance of founder speciation in evolution.

PubMed

Templeton, Alan R

2008-05-01

A founder event occurs when a new population is established from a small number of individuals drawn from a large ancestral population. Mayr proposed that genetic drift in an isolated founder population could alter the selective forces in an epistatic system, an observation supported by recent studies. Carson argued that a period of relaxed selection could occur when a founder population is in an open ecological niche, allowing rapid population growth after the founder event. Selectable genetic variation can actually increase during this founder-flush phase due to recombination, enhanced survival of advantageous mutations, and the conversion of non-additive genetic variance into additive variance in an epistatic system, another empirically confirmed prediction. Templeton combined the theories of Mayr and Carson with population genetic models to predict the conditions under which founder events can contribute to speciation, and these predictions are strongly confirmed by the empirical literature. Much of the criticism of founder speciation is based upon equating founder speciation to an adaptive peak shift opposed by selection. However, Mayr, Carson and Templeton all modeled a positive interaction of selection and drift, and Templeton showed that founder speciation is incompatible with peak-shift conditions. Although rare, founder speciation can have a disproportionate importance in adaptive innovation and radiation, and examples are given to show that "rare" does not mean "unimportant" in evolution. Founder speciation also interacts with other speciation mechanisms such that a speciation event is not a one-dimensional process due to either selection alone or drift alone. (c) 2008 Wiley Periodicals, Inc.

Genetic drift and rapid evolution of viviparity in insular fire salamanders (Salamandra salamandra)

PubMed Central

Velo-Antón, G; Zamudio, K R; Cordero-Rivera, A

2012-01-01

Continental islands offer an excellent opportunity to investigate adaptive processes and to time microevolutionary changes that precede macroevolutionary events. We performed a population genetic study of the fire salamander (Salamandra salamandra), a species that displays unique intraspecific diversity of reproductive strategies, to address the microevolutionary processes leading to phenotypic and genetic differentiation of island, coastal and interior populations. We used eight microsatellite markers to estimate genetic diversity, population structure and demographic parameters in viviparous insular populations and ovoviviparous coastal and interior populations. Our results show considerable genetic differentiation (FST range: 0.06–0.27), and no clear signs of gene flow among populations, except between the large and admixed interior populations. We find no support for island colonization by rafting or intentional/accidental anthropogenic introductions, indicating that rising sea levels were responsible for isolation of the island populations approximately 9000 years ago. Our study provides evidence of rapid genetic differentiation between island and coastal populations, and rapid evolution of viviparity driven by climatic selective pressures on island populations, geographic isolation with genetic drift, or a combination of these factors. Studies of these viviparous island populations in early stages of divergence help us better understand the microevolutionary processes involved in rapid phenotypic shifts. PMID:22086081

Genetic drift and rapid evolution of viviparity in insular fire salamanders (Salamandra salamandra).

PubMed

Velo-Antón, G; Zamudio, K R; Cordero-Rivera, A

2012-04-01

Continental islands offer an excellent opportunity to investigate adaptive processes and to time microevolutionary changes that precede macroevolutionary events. We performed a population genetic study of the fire salamander (Salamandra salamandra), a species that displays unique intraspecific diversity of reproductive strategies, to address the microevolutionary processes leading to phenotypic and genetic differentiation of island, coastal and interior populations. We used eight microsatellite markers to estimate genetic diversity, population structure and demographic parameters in viviparous insular populations and ovoviviparous coastal and interior populations. Our results show considerable genetic differentiation (F(ST) range: 0.06-0.27), and no clear signs of gene flow among populations, except between the large and admixed interior populations. We find no support for island colonization by rafting or intentional/accidental anthropogenic introductions, indicating that rising sea levels were responsible for isolation of the island populations approximately 9000 years ago. Our study provides evidence of rapid genetic differentiation between island and coastal populations, and rapid evolution of viviparity driven by climatic selective pressures on island populations, geographic isolation with genetic drift, or a combination of these factors. Studies of these viviparous island populations in early stages of divergence help us better understand the microevolutionary processes involved in rapid phenotypic shifts.

Y-chromosomal insights into the genetic impact of the caste system in India.

PubMed

Zerjal, Tatiana; Pandya, Arpita; Thangaraj, Kumarasamy; Ling, Edmund Y S; Kearley, Jennifer; Bertoneri, Stefania; Paracchini, Silvia; Singh, Lalji; Tyler-Smith, Chris

2007-03-01

The caste system has persisted in Indian Hindu society for around 3,500 years. Like the Y chromosome, caste is defined at birth, and males cannot change their caste. In order to investigate the genetic consequences of this system, we have analysed male-lineage variation in a sample of 227 Indian men of known caste, 141 from the Jaunpur district of Uttar Pradesh and 86 from the rest of India. We typed 131 Y-chromosomal binary markers and 16 microsatellites. We find striking evidence for male substructure: in particular, Brahmins and Kshatriyas (but not other castes) from Jaunpur each show low diversity and the predominance of a single distinct cluster of haplotypes. These findings confirm the genetic isolation and drift within the Jaunpur upper castes, which are likely to result from founder effects and social factors. In the other castes, there may be either larger effective population sizes, or less strict isolation, or both.

Dispersal responses override density effects on genetic diversity during post-disturbance succession

PubMed Central

Landguth, Erin L.; Bull, C. Michael; Banks, Sam C.; Gardner, Michael G.; Driscoll, Don A.

2016-01-01

Dispersal fundamentally influences spatial population dynamics but little is known about dispersal variation in landscapes where spatial heterogeneity is generated predominantly by disturbance and succession. We tested the hypothesis that habitat succession following fire inhibits dispersal, leading to declines over time in genetic diversity in the early successional gecko Nephrurus stellatus. We combined a landscape genetics field study with a spatially explicit simulation experiment to determine whether successional patterns in genetic diversity were driven by habitat-mediated dispersal or demographic effects (declines in population density leading to genetic drift). Initial increases in genetic structure following fire were likely driven by direct mortality and rapid population expansion. Subsequent habitat succession increased resistance to gene flow and decreased dispersal and genetic diversity in N. stellatus. Simulated changes in population density alone did not reproduce these results. Habitat-mediated reductions in dispersal, combined with changes in population density, were essential to drive the field-observed patterns. Our study provides a framework for combining demographic, movement and genetic data with simulations to discover the relative influence of demography and dispersal on patterns of landscape genetic structure. Our results suggest that succession can inhibit connectivity among individuals, opening new avenues for understanding how disturbance regimes influence spatial population dynamics. PMID:27009225

Genetic Divergence and signatures of natural election in marginal populations of a Keystone, long-lived conifer, Eastern White Pine (Pinus strobus) from Northern Ontario

Treesearch

Vikram E. Chhatre; Om P. Rajora

2014-01-01

Marginal populations are expected to provide the frontiers for adaptation, evolution and range shifts of plant species under the anticipated climate change conditions. Marginal populations are predicted to show genetic divergence from central populations due to their isolation, and divergent natural selection and genetic drift operating therein. Marginal populations...

Contemporary and historic factors influence differently genetic differentiation and diversity in a tropical palm

PubMed Central

da Silva Carvalho, C; Ribeiro, M C; Côrtes, M C; Galetti, M; Collevatti, R G

2015-01-01

Population genetics theory predicts loss in genetic variability because of drift and inbreeding in isolated plant populations; however, it has been argued that long-distance pollination and seed dispersal may be able to maintain gene flow, even in highly fragmented landscapes. We tested how historical effective population size, historical migration and contemporary landscape structure, such as forest cover, patch isolation and matrix resistance, affect genetic variability and differentiation of seedlings in a tropical palm (Euterpe edulis) in a human-modified rainforest. We sampled 16 sites within five landscapes in the Brazilian Atlantic forest and assessed genetic variability and differentiation using eight microsatellite loci. Using a model selection approach, none of the covariates explained the variation observed in inbreeding coefficients among populations. The variation in genetic diversity among sites was best explained by historical effective population size. Allelic richness was best explained by historical effective population size and matrix resistance, whereas genetic differentiation was explained by matrix resistance. Coalescence analysis revealed high historical migration between sites within landscapes and constant historical population sizes, showing that the genetic differentiation is most likely due to recent changes caused by habitat loss and fragmentation. Overall, recent landscape changes have a greater influence on among-population genetic variation than historical gene flow process. As immediate restoration actions in landscapes with low forest amount, the development of more permeable matrices to allow the movement of pollinators and seed dispersers may be an effective strategy to maintain microevolutionary processes. PMID:25873150

Calculating expected DNA remnants from ancient founding events in human population genetics

PubMed Central

Stacey, Andrew; Sheffield, Nathan C; Crandall, Keith A

2008-01-01

Background Recent advancements in sequencing and computational technologies have led to rapid generation and analysis of high quality genetic data. Such genetic data have achieved wide acceptance in studies of historic human population origins and admixture. However, in studies relating to small, recent admixture events, genetic factors such as historic population sizes, genetic drift, and mutation can have pronounced effects on data reliability and utility. To address these issues we conducted genetic simulations targeting influential genetic parameters in admixed populations. Results We performed a series of simulations, adjusting variable values to assess the affect of these genetic parameters on current human population studies and what these studies infer about past population structure. Final mean allele frequencies varied from 0.0005 to over 0.50, depending on the parameters. Conclusion The results of the simulations illustrate that, while genetic data may be sensitive and powerful in large genetic studies, caution must be used when applying genetic information to small, recent admixture events. For some parameter sets, genetic data will not be adequate to detect historic admixture. In such cases, studies should consider anthropologic, archeological, and linguistic data where possible. PMID:18928554

Spatiotemporal Dynamics of Genetic Variation in the Iberian Lynx along Its Path to Extinction Reconstructed with Ancient DNA.

PubMed

Casas-Marce, Mireia; Marmesat, Elena; Soriano, Laura; Martínez-Cruz, Begoña; Lucena-Perez, Maria; Nocete, Francisco; Rodríguez-Hidalgo, Antonio; Canals, Antoni; Nadal, Jordi; Detry, Cleia; Bernáldez-Sánchez, Eloísa; Fernández-Rodríguez, Carlos; Pérez-Ripoll, Manuel; Stiller, Mathias; Hofreiter, Michael; Rodríguez, Alejandro; Revilla, Eloy; Delibes, Miguel; Godoy, José A

2017-11-01

There is the tendency to assume that endangered species have been both genetically and demographically healthier in the past, so that any genetic erosion observed today was caused by their recent decline. The Iberian lynx (Lynx pardinus) suffered a dramatic and continuous decline during the 20th century, and now shows extremely low genome- and species-wide genetic diversity among other signs of genomic erosion. We analyze ancient (N = 10), historical (N = 245), and contemporary (N = 172) samples with microsatellite and mitogenome data to reconstruct the species' demography and investigate patterns of genetic variation across space and time. Iberian lynx populations transitioned from low but significantly higher genetic diversity than today and shallow geographical differentiation millennia ago, through a structured metapopulation with varying levels of diversity during the last centuries, to two extremely genetically depauperate and differentiated remnant populations by 2002. The historical subpopulations show varying extents of genetic drift in relation to their recent size and time in isolation, but these do not predict whether the populations persisted or went finally extinct. In conclusion, current genetic patterns were mainly shaped by genetic drift, supporting the current admixture of the two genetic pools and calling for a comprehensive genetic management of the ongoing conservation program. This study illustrates how a retrospective analysis of demographic and genetic patterns of endangered species can shed light onto their evolutionary history and this, in turn, can inform conservation actions. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Turtle groups or turtle soup: dispersal patterns of hawksbill turtles in the Caribbean.

PubMed

Blumenthal, J M; Abreu-Grobois, F A; Austin, T J; Broderick, A C; Bruford, M W; Coyne, M S; Ebanks-Petrie, G; Formia, A; Meylan, P A; Meylan, A B; Godley, B J

2009-12-01

Despite intense interest in conservation of marine turtles, spatial ecology during the oceanic juvenile phase remains relatively unknown. Here, we used mixed stock analysis and examination of oceanic drift to elucidate movements of hawksbill turtles (Eretmochelys imbricata) and address management implications within the Caribbean. Among samples collected from 92 neritic juvenile hawksbills in the Cayman Islands we detected 11 mtDNA control region haplotypes. To estimate contributions to the aggregation, we performed 'many-to-many' mixed stock analysis, incorporating published hawksbill genetic and population data. The Cayman Islands aggregation represents a diverse mixed stock: potentially contributing source rookeries spanned the Caribbean basin, delineating a scale of recruitment of 200-2500 km. As hawksbills undergo an extended phase of oceanic dispersal, ocean currents may drive patterns of genetic diversity observed on foraging aggregations. Therefore, using high-resolution Aviso ocean current data, we modelled movement of particles representing passively drifting oceanic juvenile hawksbills. Putative distribution patterns varied markedly by origin: particles from many rookeries were broadly distributed across the region, while others would appear to become entrained in local gyres. Overall, we detected a significant correlation between genetic profiles of foraging aggregations and patterns of particle distribution produced by a hatchling drift model (Mantel test, r = 0.77, P < 0.001; linear regression, r = 0.83, P < 0.001). Our results indicate that although there is a high degree of mixing across the Caribbean (a 'turtle soup'), current patterns play a substantial role in determining genetic structure of foraging aggregations (forming turtle groups). Thus, for marine turtles and other widely distributed marine species, integration of genetic and oceanographic data may enhance understanding of population connectivity and management requirements.

Temporal genetic analysis of the endangered tidewater goby: extinction-colonization dynamics or drift in isolation?

PubMed

Kinziger, Andrew P; Hellmair, Michael; McCraney, W Tyler; Jacobs, David K; Goldsmith, Greg

2015-11-01

Extinction and colonization dynamics are critical to understanding the evolution and conservation of metapopulations. However, traditional field studies of extinction-colonization are potentially fraught with detection bias and have rarely been validated. Here, we provide a comparison of molecular and field-based approaches for assessment of the extinction-colonization dynamics of tidewater goby (Eucyclogobius newberryi) in northern California. Our analysis of temporal genetic variation across 14 northern California tidewater goby populations failed to recover genetic change expected with extinction-colonization cycles. Similarly, analysis of site occupancy data from field studies (94 sites) indicated that extinction and colonization are very infrequent for our study populations. Comparison of the approaches indicated field data were subject to imperfect detection, and falsely implied extinction-colonization cycles in several instances. For northern California populations of tidewater goby, we interpret the strong genetic differentiation between populations and high degree of within-site temporal stability as consistent with a model of drift in the absence of migration, at least over the past 20-30 years. Our findings show that tidewater goby exhibit different population structures across their geographic range (extinction-colonization dynamics in the south vs. drift in isolation in the north). For northern populations, natural dispersal is too infrequent to be considered a viable approach for recolonizing extirpated populations, suggesting that species recovery will likely depend on artificial translocation in this region. More broadly, this work illustrates that temporal genetic analysis can be used in combination with field data to strengthen inference of extinction-colonization dynamics or as a stand-alone tool when field data are lacking. © 2015 John Wiley & Sons Ltd.

Determinants of genetic structure in a nonequilibrium metapopulation of the plant Silene latifolia.

PubMed

Fields, Peter D; Taylor, Douglas R

2014-01-01

Population genetic differentiation will be influenced by the demographic history of populations, opportunities for migration among neighboring demes and founder effects associated with repeated extinction and recolonization. In natural populations, these factors are expected to interact with each other and their magnitudes will vary depending on the spatial distribution and age structure of local demes. Although each of these effects has been individually identified as important in structuring genetic variance, their relative magnitude is seldom estimated in nature. We conducted a population genetic analysis in a metapopulation of the angiosperm, Silene latifolia, from which we had more than 20 years of data on the spatial distribution, demographic history, and extinction and colonization of demes. We used hierarchical Bayesian methods to disentangle which features of the populations contributed to among population variation in allele frequencies, including the magnitude and direction of their effects. We show that population age, long-term size and degree of connectivity all combine to affect the distribution of genetic variance; small, recently-founded, isolated populations contributed most to increase FST in the metapopulation. However, the effects of population size and population age are best understood as being modulated through the effects of connectivity to other extant populations, i.e. FST diminishes as populations age, but at a rate that depends how isolated the population is. These spatial and temporal correlates of population structure give insight into how migration, founder effect and within-deme genetic drift have combined to enhance and restrict genetic divergence in a natural metapopulation.

Destiny of a transgene escape from Brassica napus into Brassica rapa.

PubMed

Lu, M.; Kato, M.; Kakihara, F.

2002-07-01

Transgenic Brassica napus can be easily crossed with wild Brassica rapa. The spread of the transgene to wild species has aroused the general concern about its effect on ecological and agricultural systems. This paper was designated, by means of population genetics, to study the fate of a transgene escape from B. napus to B. rapa. Three models were proposed to survey the change in gene frequency during successive backcross processes by considering selection pressures against aneuploids, against herbicide-susceptible individuals, and by considering A-C intergenomic recombination and the effect of genetic drift. The transmission rate of an A-chromosome gene through an individual to the next generation was 50%, irrespective of the chromosome number; while that of a C-chromosome transgene varied from 8.7% to 39.9%, depending on the chromosome number of the individual used in the backcross. Without spraying herbicide, the frequency of an A-chromosome gene was 50% in the BC(1) generation, and decreased by 50% with the advance of each backcross generation; that of a C-chromosome gene was around 39.9% in BC(1), 7.7% in BC(2), 1.2% in BC(3) and 0.1% in the BC(4) generation. Under the selection pressure against herbicide-susceptible individuals, the frequency of a transgene reached a stable value of about 5.5% within six generations of successive backcrossings. The effect of genetic drift and intergenomic exchange on gene transmission rate was discussed. It is suggested that the transgene integrated on a C-chromosome (or better on a cytoplasm genome) is safer than that on an A-chromosome. The transgenic cultivars should be cultivated rotationally by year(s) with other non-transgenic varieties in order to reduce the transfer of the transgene to wild B. rapa species.

When three traits make a line: evolution of phenotypic plasticity and genetic assimilation through linear reaction norms in stochastic environments.

PubMed

Ergon, T; Ergon, R

2017-03-01

Genetic assimilation emerges from selection on phenotypic plasticity. Yet, commonly used quantitative genetics models of linear reaction norms considering intercept and slope as traits do not mimic the full process of genetic assimilation. We argue that intercept-slope reaction norm models are insufficient representations of genetic effects on linear reaction norms and that considering reaction norm intercept as a trait is unfortunate because the definition of this trait relates to a specific environmental value (zero) and confounds genetic effects on reaction norm elevation with genetic effects on environmental perception. Instead, we suggest a model with three traits representing genetic effects that, respectively, (i) are independent of the environment, (ii) alter the sensitivity of the phenotype to the environment and (iii) determine how the organism perceives the environment. The model predicts that, given sufficient additive genetic variation in environmental perception, the environmental value at which reaction norms tend to cross will respond rapidly to selection after an abrupt environmental change, and eventually becomes equal to the new mean environment. This readjustment of the zone of canalization becomes completed without changes in genetic correlations, genetic drift or imposing any fitness costs of maintaining plasticity. The asymptotic evolutionary outcome of this three-trait linear reaction norm generally entails a lower degree of phenotypic plasticity than the two-trait model, and maximum expected fitness does not occur at the mean trait values in the population. © 2016 The Authors. Journal of Evolutionary Biology published by John Wiley & Sons Ltd on behalf of European Society for Evolutionary Biology.

Flexible social organization and high incidence of drifting in the sweat bee, Halictus scabiosae.

PubMed

Ulrich, Yuko; Perrin, Nicolas; Chapuisat, Michel

2009-04-01

The very diverse social systems of sweat bees make them interesting models to study social evolution. Here we focus on the dispersal behaviour and social organization of Halictus scabiosae, a common yet poorly known species of Europe. By combining field observations and genetic data, we show that females have multiple reproductive strategies, which generates a large diversity in the social structure of nests. A detailed microsatellite analysis of 60 nests revealed that 55% of the nests contained the offspring of a single female, whereas the rest had more complex social structures, with three clear cases of multiple females reproducing in the same nest and frequent occurrence of unrelated individuals. Drifting among nests was surprisingly common, as 16% of the 122 nests in the overall sample and 44% of the nests with complex social structure contained females that had genotypes consistent with being full-sisters of females sampled in other nests of the population. Drifters originated from nests with an above-average productivity and were unrelated to their nestmates, suggesting that drifting might be a strategy to avoid competition among related females. The sex-specific comparison of genetic differentiation indicated that dispersal was male-biased, which would reinforce local resource competition among females. The pattern of genetic differentiation among populations was consistent with a dynamic process of patch colonization and extinction, as expected from the unstable, anthropogenic habitat of this species. Overall, our data show that H. scabiosae varies greatly in dispersal behaviour and social organization. The surprisingly high frequency of drifters echoes recent findings in wasps and bees, calling for further investigation of the adaptive basis of drifting in the social insects.

Population genetic structure and demographic history of the black fly vector, Simulium nodosum in Thailand.

PubMed

Chaiyasan, P; Pramual, P

2016-09-01

An understanding of the genetic structure and diversity of vector species is crucial for effective control and management. In this study, mitochondrial DNA sequences were used to examine the genetic structure, diversity and demographic history of a black fly vector, Simulium nodosum Puri (Diptera: Simuliidae), in Thailand. A total of 145 sequences were obtained from 10 sampling locations collected across geographical ranges in the country. Low genetic diversity was found in populations of S. nodosum that could be explained by the recent population history of this species. Demographic history analysis revealed a signature of demographic expansion dating back to only 2600-5200 years ago. Recent population expansion in S. nodosum possibly followed an increase in agriculture that enabled its hosts', humans and domestic animals, densities to increase. Alternatively, the Thai populations could be a derivative of an older expansion event in the more northern populations. Mitochondrial DNA genealogy revealed no genetically divergent lineages, which agrees with the previous cytogenetic study. Genetic structure analyses found that only 27% of the pairwise comparisons were significantly different. The most likely explanation for the pattern of genetic structuring is the effect of genetic drift because of recent colonization. © 2016 The Royal Entomological Society.

The genetic tale of a recovering lion population (Panthera leo) in the Savé Valley region (Zimbabwe): A better understanding of the history and managing the future

PubMed Central

Groom, Rosemary J.; Khuzwayo, Joy; Jansen van Vuuren, Bettine

2018-01-01

The rapid decline of the African lion (Panthera leo) has raised conservation concerns. In the Savé Valley Conservancy (SVC), in the Lowveld of Zimbabwe, lions were presumably reduced to approximately 5 to 10 individuals. After ten lions were reintroduced in 2005, the population has recovered to over 200 lions in 2016. Although the increase of lions in the SVC seems promising, a question remains whether the population is genetically viable, considering their small founding population. In this study, we document the genetic diversity in the SVC lion population using both mitochondrial and nuclear genetic markers, and compare our results to literature from other lion populations across Africa. We also tested whether genetic diversity is spatially structured between lion populations residing on several reserves in the Lowveld of Zimbabwe. A total of 42 lions were genotyped successfully for 11 microsatellite loci. We confirmed that the loss of allelic richness (probably resulting from genetic drift and small number of founders) has resulted in low genetic diversity and inbreeding. The SVC lion population was also found to be genetically differentiated from surrounding population, as a result of genetic drift and restricted natural dispersal due to anthropogenic barriers. From a conservation perspective, it is important to avoid further loss of genetic variability in the SVC lion population and maintain evolutionary potential required for future survival. Genetic restoration through the introduction of unrelated individuals is recommended, as this will increase genetic heterozygosity and improve survival and reproductive fitness in populations. PMID:29415031

The genetic tale of a recovering lion population (Panthera leo) in the Savé Valley region (Zimbabwe): A better understanding of the history and managing the future.

PubMed

Tensen, Laura; Groom, Rosemary J; Khuzwayo, Joy; Jansen van Vuuren, Bettine

2018-01-01

The rapid decline of the African lion (Panthera leo) has raised conservation concerns. In the Savé Valley Conservancy (SVC), in the Lowveld of Zimbabwe, lions were presumably reduced to approximately 5 to 10 individuals. After ten lions were reintroduced in 2005, the population has recovered to over 200 lions in 2016. Although the increase of lions in the SVC seems promising, a question remains whether the population is genetically viable, considering their small founding population. In this study, we document the genetic diversity in the SVC lion population using both mitochondrial and nuclear genetic markers, and compare our results to literature from other lion populations across Africa. We also tested whether genetic diversity is spatially structured between lion populations residing on several reserves in the Lowveld of Zimbabwe. A total of 42 lions were genotyped successfully for 11 microsatellite loci. We confirmed that the loss of allelic richness (probably resulting from genetic drift and small number of founders) has resulted in low genetic diversity and inbreeding. The SVC lion population was also found to be genetically differentiated from surrounding population, as a result of genetic drift and restricted natural dispersal due to anthropogenic barriers. From a conservation perspective, it is important to avoid further loss of genetic variability in the SVC lion population and maintain evolutionary potential required for future survival. Genetic restoration through the introduction of unrelated individuals is recommended, as this will increase genetic heterozygosity and improve survival and reproductive fitness in populations.

The Grandest Genetic Experiment Ever Performed on Man? - A Y-Chromosomal Perspective on Genetic Variation in India.

PubMed

Carvalho-Silva, Denise R; Tyler-Smith, Chris

2008-05-01

We have analysed Y-chromosomal data from Indian caste, Indian tribal and East Asian populations in order to investigate the impact of the caste system on male genetic variation. We find that variation within populations is lower in India than in East Asia, while variation between populations is overall higher. This observation can be explained by greater subdivision within the Indian population, leading to more genetic drift. However, the effect is most marked in the tribal populations, and the level of variation between caste populations is similar to the level between Chinese populations. The caste system has therefore had a detectable impact on Y-chromosomal variation, but this has been less strong than the influence of the tribal system, perhaps because of larger population sizes in the castes, more gene flow or a shorter period of time.

Genetic homogeneity of Fascioloides magna in Austria.

PubMed

Husch, Christian; Sattmann, Helmut; Hörweg, Christoph; Ursprung, Josef; Walochnik, Julia

2017-08-30

The large American liver fluke, Fascioloides magna, is an economically relevant parasite of both domestic and wild ungulates. F. magna was repeatedly introduced into Europe, for the first time already in the 19th century. In Austria, a stable population of F. magna has established in the Danube floodplain forests southeast of Vienna. The aim of this study was to determine the genetic diversity of F. magna in Austria. A total of 26 individuals from various regions within the known area of distribution were investigated for their cytochrome oxidase subunit 1 (cox1) and nicotinamide dehydrogenase subunit 1 (nad1) gene haplotypes. Interestingly, all 26 individuals revealed one and the same haplotype, namely concatenated haplotype Ha5. This indicates a homogenous population of F. magna in Austria and may argue for a single introduction. Alternatively, genetic homogeneity might also be explained by a bottleneck effect and/or genetic drift. Copyright © 2017 Elsevier B.V. All rights reserved.

Gene flow among established Puerto Rican populations of the exotic tree species, Albizia lebbeck.

PubMed

Dunphy, B K; Hamrick, J L

2005-04-01

We estimate gene flow and patterns of genetic diversity in Albizia lebbeck, an invasive leguminous tree in the dry forest of southwestern Puerto Rico. Genetic diversity estimates calculated for 10 populations of 24 trees each indicated that these populations may have been formed from multiple introductions. The presence of unique genotypes in the northernmost populations suggests that novel genotypes are still immigrating into the area. This combination of individuals from disparate locations led to high estimates of genetic diversity (He = 0.266, P = 0.67). Indirect estimates of gene flow indicate that only 0.69 migrants per generation move between populations, suggesting that genetic diversity within populations should decrease due to genetic drift. Since migration-drift equilibrium was not found, however, this estimate needs to be viewed with caution. The regular production of pods in this outcrossing species (tm = 0.979) indicates that sufficient outcross pollen is received to insure successful reproduction. Direct estimates of gene flow indicate that between 44 and 100% of pollen received by trees in four small stands of trees (n < 11) was foreign. The role of gene flow in facilitating the spread of this invasive plant species is discussed.

Population structure and cultural geography of a folktale in Europe

PubMed Central

Ross, Robert M.; Greenhill, Simon J.; Atkinson, Quentin D.

2013-01-01

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. PMID:23390109

Scale-dependent genetic structure of the Idaho giant salamander (Dicamptodon aterrimus) in stream networks.

PubMed

Mullen, Lindy B; Arthur Woods, H; Schwartz, Michael K; Sepulveda, Adam J; Lowe, Winsor H

2010-03-01

The network architecture of streams and rivers constrains evolutionary, demographic and ecological processes of freshwater organisms. This consistent architecture also makes stream networks useful for testing general models of population genetic structure and the scaling of gene flow. We examined genetic structure and gene flow in the facultatively paedomorphic Idaho giant salamander, Dicamptodon aterrimus, in stream networks of Idaho and Montana, USA. We used microsatellite data to test population structure models by (i) examining hierarchical partitioning of genetic variation in stream networks; and (ii) testing for genetic isolation by distance along stream corridors vs. overland pathways. Replicated sampling of streams within catchments within three river basins revealed that hierarchical scale had strong effects on genetic structure and gene flow. amova identified significant structure at all hierarchical scales (among streams, among catchments, among basins), but divergence among catchments had the greatest structural influence. Isolation by distance was detected within catchments, and in-stream distance was a strong predictor of genetic divergence. Patterns of genetic divergence suggest that differentiation among streams within catchments was driven by limited migration, consistent with a stream hierarchy model of population structure. However, there was no evidence of migration among catchments within basins, or among basins, indicating that gene flow only counters the effects of genetic drift at smaller scales (within rather than among catchments). These results show the strong influence of stream networks on population structure and genetic divergence of a salamander, with contrasting effects at different hierarchical scales.

Antigenic and genetic evolution of contemporary swine H1 influenza viruses in the United States

USDA-ARS?s Scientific Manuscript database

Several lineages of influenza A viruses (IAV) currently circulate in North American pigs. Genetic diversity is further increased by the bidirectional transmission of IAV between swine and humans and the subsequent processes of antigenic shift and drift. Such evolution can be the basis for changes in...

Relationships among walleye population characteristics and genetic diversity in northern Wisconsin Lakes

USGS Publications Warehouse

Waterhouse, Matthew D.; Sloss, Brian L.; Isermann, Daniel A.

2014-01-01

The maintenance of genetic integrity is an important goal of fisheries management, yet little is known regarding the effects of management actions (e.g., stocking, harvest regulations) on the genetic diversity of many important fish species. Furthermore, relationships between population characteristics and genetic diversity remain poorly understood. We examined relationships among population demographics (abundance, recruitment, sex ratio, and mean age of the breeding population), stocking intensity, and genetic characteristics (heterozygosity, effective number of alleles, allelic richness, Wright's inbreeding coefficient, effective population size [Ne], mean d2 [a measure of inbreeding], mean relatedness, and pairwise population ΦST estimates) for 15 populations of Walleye Sander vitreus in northern Wisconsin. We also tested for potential demographic and genetic influences on Walleye body condition and early growth. Combinations of demographic variables explained 47.1–79.8% of the variation in genetic diversity. Skewed sex ratios contributed to a reduction in Ne and subsequent increases in genetic drift and relatedness among individuals within populations; these factors were correlated to reductions in allelic richness and early growth rate. Levels of inbreeding were negatively related to both age-0 abundance and mean age, suggesting Ne was influenced by recruitment and generational overlap. A negative relationship between the effective number of alleles and body condition suggests stocking affected underlying genetic diversity of recipient populations and the overall productivity of the population. These relationships may result from poor performance of stocked fish, outbreeding depression, or density-dependent factors. An isolation-by-distance pattern of genetic diversity was apparent in nonstocked populations, but was disrupted in stocked populations, suggesting that stocking affected genetic structure. Overall, demographic factors were related to genetic diversity and stocking appeared to alter allelic frequencies and the genetic structure of Walleye populations in Wisconsin, possibly resulting in disruption of local adaptation.

Cytonuclear disequilibrium and genetic drift in a natural population of ponderosa pine.

PubMed Central

Latta, R G; Linhart, Y B; Mitton, J B

2001-01-01

We measured the cytonuclear disequilibrium between 11 nuclear allozyme loci and both mitochondrial and chloroplast DNA haplotypes in a natural population of ponderosa pine (Pinus ponderosa, Laws). Three allozyme loci showed significant associations with mtDNA variation, while two other loci showed significant association with cpDNA. However, the absolute number of individuals involved in any of the associations was small, such that in none of the nuclear-organellar combinations was the difference between observed and expected numbers >11 individuals. Patterns of association were not consistent across loci or organellar genomes, suggesting that they are not the result of mating patterns, which would act uniformly on all loci. This pattern of disequilibria is consistent with the action of genetic drift and with existing knowledge of the structure of this population and thus does not imply the action of other evolutionary processes. The overall magnitude (normalized disequilibrium) of associations was greater for maternally inherited mtDNA than for paternally inherited cpDNA, though this difference was neither large nor significant. Such significant disequilibria involving the paternally inherited organelle indicate that not only are there a limited number of seed parents, but the effective number of pollen parents is also limited. PMID:11404345

Adaptive Differentiation of Quantitative Traits in the Globally Distributed Weed, Wild Radish (Raphanus raphanistrum)

PubMed Central

Sahli, Heather F.; Conner, Jeffrey K.; Shaw, Frank H.; Howe, Stephen; Lale, Allison

2008-01-01

Weedy species with wide geographical distributions may face strong selection to adapt to new environments, which can lead to adaptive genetic differentiation among populations. However, genetic drift, particularly due to founder effects, will also commonly result in differentiation in colonizing species. To test whether selection has contributed to trait divergence, we compared differentiation at eight microsatellite loci (measured as FST) to differentiation of quantitative floral and phenological traits (measured as QST) of wild radish (Raphanus raphanistrum) across populations from three continents. We sampled eight populations: seven naturalized populations and one from its native range. By comparing estimates of QST and FST, we found that petal size was the only floral trait that may have diverged more than expected due to drift alone, but inflorescence height, flowering time, and rosette formation have greatly diverged between the native and nonnative populations. Our results suggest the loss of a rosette and the evolution of early flowering time may have been the key adaptations enabling wild radish to become a major agricultural weed. Floral adaptation to different pollinators does not seem to have been as necessary for the success of wild radish in new environments. PMID:18854585

Allele frequency changes due to hitch-hiking in genomic selection programs

PubMed Central

2014-01-01

Background Genomic selection makes it possible to reduce pedigree-based inbreeding over best linear unbiased prediction (BLUP) by increasing emphasis on own rather than family information. However, pedigree inbreeding might not accurately reflect loss of genetic variation and the true level of inbreeding due to changes in allele frequencies and hitch-hiking. This study aimed at understanding the impact of using long-term genomic selection on changes in allele frequencies, genetic variation and level of inbreeding. Methods Selection was performed in simulated scenarios with a population of 400 animals for 25 consecutive generations. Six genetic models were considered with different heritabilities and numbers of QTL (quantitative trait loci) affecting the trait. Four selection criteria were used, including selection on own phenotype and on estimated breeding values (EBV) derived using phenotype-BLUP, genomic BLUP and Bayesian Lasso. Changes in allele frequencies at QTL, markers and linked neutral loci were investigated for the different selection criteria and different scenarios, along with the loss of favourable alleles and the rate of inbreeding measured by pedigree and runs of homozygosity. Results For each selection criterion, hitch-hiking in the vicinity of the QTL appeared more extensive when accuracy of selection was higher and the number of QTL was lower. When inbreeding was measured by pedigree information, selection on genomic BLUP EBV resulted in lower levels of inbreeding than selection on phenotype BLUP EBV, but this did not always apply when inbreeding was measured by runs of homozygosity. Compared to genomic BLUP, selection on EBV from Bayesian Lasso led to less genetic drift, reduced loss of favourable alleles and more effectively controlled the rate of both pedigree and genomic inbreeding in all simulated scenarios. In addition, selection on EBV from Bayesian Lasso showed a higher selection differential for mendelian sampling terms than selection on genomic BLUP EBV. Conclusions Neutral variation can be shaped to a great extent by the hitch-hiking effects associated with selection, rather than just by genetic drift. When implementing long-term genomic selection, strategies for genomic control of inbreeding are essential, due to a considerable hitch-hiking effect, regardless of the method that is used for prediction of EBV. PMID:24495634

Systems Thinking Versus Population Thinking: Genotype Integration and Chromosomal Organization 1930s-1950s.

PubMed

Lamm, Ehud

2015-11-01

This article describes how empirical discoveries in the 1930s-1950s regarding population variation for chromosomal inversions affected Theodosius Dobzhansky and Richard Goldschmidt. A significant fraction of the empirical work I discuss was done by Dobzhansky and his coworkers; Goldschmidt was an astute interpreter, with strong and unusual commitments. I argue that both belong to a mechanistic tradition in genetics, concerned with the effects of chromosomal organization and systems on the inheritance patterns of species. Their different trajectories illustrate how scientists' commitments affect how they interpret new evidence and adjust to it. Dobzhansky was moved to revised views about selection, while Goldschmidt moved his attention to different genetic phenomena. However different, there are significant connections between the two that enrich our understanding of their views. I focus on two: the role of developmental considerations in Dobzhansky's thought and the role of neutrality and drift in Goldschmidt's evolutionary account. Dobzhansky's struggle with chromosomal variation is not solely about competing schools of thought within the selectionist camp, as insightfully articulated by John Beatty, but also a story of competition between selectionist thinking and developmental perspectives. In contraposition, Goldschmidt emphasized the role of low penetrance mutations that spread neutrally and pointed out that drift could result from developmental canalization. This account adds to the dominant story about Goldschmidt's resistance to the splitting of development from genetics, as told by Garland Allen and Michael Dietrich. The story I tell illustrates how developmental thinking and genetic thinking conflicted and influenced researchers with different convictions about the significance of chromosomal organization.

Genetic variation and genetic structure of the endangered species Sinowilsonia henryi Hemsi. (Hamamelidaceae) revealed by amplified fragment length polymorphism (AFLP) markers.

PubMed

Zhang, H; Ji, W L; Li, M; Zhou, L Y

2015-10-14

Comprehensive research of genetic variation is crucial in designing conservation strategies for endangered and threatened species. Sinowilsonia henryi Hemsi. is a tertiary relic with a limited geographical distribution in the central and western areas of China. It is endangered because of climate change and habitat fragmentation over the last thousands of years. In this study, amplified fragment length polymorphism markers were utilized to estimate genetic diversity and genetic structure in and among S. henryi. In this study, Nei's genetic diversity and Shannon's information index were found to be 0.192 and 0.325 respectively, indicating a moderate-to-high genetic diversity in species. According to analysis of molecular variation results, 32% of the genetic variation was shown to be partitioned among populations, demonstrating a relatively high genetic divergence; this was supported by principal coordinate analysis and unweighted pair-group method with arithmetic average analysis. Moreover, the Mantel test showed that there was no significant correlation between genetic and geographical distances. The above results can be explained by the effects of habitat fragmentation, history traits, and gene drift. Based on the results, several implications were indicated and suggestions proposed for preservation strategies for this species.

Neutral theory, microbial practice: challenges in bacterial population genetics.

PubMed

Rocha, Eduardo P C

2018-04-19

Kimura's outstanding contributions to population genetics included many elegant theoretical results on the vagaries of alleles in populations. Once polymorphism data showed extensive variation in natural populations, these results led naturally to the Neutral Theory. In this article, I'll depart from some of these results to focus on four major open problems in microbial population genetics with direct implications to the study of molecular evolution: the lack of neutral polymorphism, the modeling of genetic exchanges, the population genetics of ill-defined populations, and the difficulty of untangling selection and demography in the light of the previous issues. Whilst studies in population genetics usually focus on single nucleotide polymorphism and allelic recombination, ignoring even small indels, a large fraction of genetic diversification in Bacteria results from horizontal gene transfer. Ignoring this fact defeats the purpose of population genetics: to characterize the genetic variation in populations and their adaptive effects. I'll argue that, following on Kimura's life work, one may need to develop new approaches to study microbes that reproduce asexually but are able to engage in gene exchanges with very distantly related organisms in a context where random sampling is often unachievable, populations are ill-defined, genetic linkage is strong, and random drift is rare.

Hubby and Lewontin on Protein Variation in Natural Populations: When Molecular Genetics Came to the Rescue of Population Genetics.

PubMed

Charlesworth, Brian; Charlesworth, Deborah; Coyne, Jerry A; Langley, Charles H

2016-08-01

The 1966 GENETICS papers by John Hubby and Richard Lewontin were a landmark in the study of genome-wide levels of variability. They used the technique of gel electrophoresis of enzymes and proteins to study variation in natural populations of Drosophila pseudoobscura, at a set of loci that had been chosen purely for technical convenience, without prior knowledge of their levels of variability. Together with the independent study of human populations by Harry Harris, this seminal study provided the first relatively unbiased picture of the extent of genetic variability in protein sequences within populations, revealing that many genes had surprisingly high levels of diversity. These papers stimulated a large research program that found similarly high electrophoretic variability in many different species and led to statistical tools for interpreting the data in terms of population genetics processes such as genetic drift, balancing and purifying selection, and the effects of selection on linked variants. The current use of whole-genome sequences in studies of variation is the direct descendant of this pioneering work. Copyright © 2016 by the Genetics Society of America.

Pronounced fixation, strong population differentiation and complex population history in the Canary Islands blue tit subspecies complex.

PubMed

Hansson, Bengt; Ljungqvist, Marcus; Illera, Juan-Carlos; Kvist, Laura

2014-01-01

Evolutionary molecular studies of island radiations may lead to insights in the role of vicariance, founder events, population size and drift in the processes of population differentiation. We evaluate the degree of population genetic differentiation and fixation of the Canary Islands blue tit subspecies complex using microsatellite markers and aim to get insights in the population history using coalescence based methods. The Canary Island populations were strongly genetically differentiated and had reduced diversity with pronounced fixation including many private alleles. In population structure models, the relationship between the central island populations (La Gomera, Tenerife and Gran Canaria) and El Hierro was difficult to disentangle whereas the two European populations showed consistent clustering, the two eastern islands (Fuerteventura and Lanzarote) and Morocco weak clustering, and La Palma a consistent unique lineage. Coalescence based models suggested that the European mainland forms an outgroup to the Afrocanarian population, a split between the western island group (La Palma and El Hierro) and the central island group, and recent splits between the three central islands, and between the two eastern islands and Morocco, respectively. It is clear that strong genetic drift and low level of concurrent gene flow among populations have shaped complex allelic patterns of fixation and skewed frequencies over the archipelago. However, understanding the population history remains challenging; in particular, the pattern of extreme divergence with low genetic diversity and yet unique genetic material in the Canary Island system requires an explanation. A potential scenario is population contractions of a historically large and genetically variable Afrocanarian population, with vicariance and drift following in the wake. The suggestion from sequence-based analyses of a Pleistocene extinction of a substantial part of North Africa and a Pleistocene/Holocene eastward re-colonisation of western North Africa from the Canaries remains possible.

Pronounced Fixation, Strong Population Differentiation and Complex Population History in the Canary Islands Blue Tit Subspecies Complex

PubMed Central

Hansson, Bengt; Ljungqvist, Marcus; Illera, Juan-Carlos; Kvist, Laura

2014-01-01

Evolutionary molecular studies of island radiations may lead to insights in the role of vicariance, founder events, population size and drift in the processes of population differentiation. We evaluate the degree of population genetic differentiation and fixation of the Canary Islands blue tit subspecies complex using microsatellite markers and aim to get insights in the population history using coalescence based methods. The Canary Island populations were strongly genetically differentiated and had reduced diversity with pronounced fixation including many private alleles. In population structure models, the relationship between the central island populations (La Gomera, Tenerife and Gran Canaria) and El Hierro was difficult to disentangle whereas the two European populations showed consistent clustering, the two eastern islands (Fuerteventura and Lanzarote) and Morocco weak clustering, and La Palma a consistent unique lineage. Coalescence based models suggested that the European mainland forms an outgroup to the Afrocanarian population, a split between the western island group (La Palma and El Hierro) and the central island group, and recent splits between the three central islands, and between the two eastern islands and Morocco, respectively. It is clear that strong genetic drift and low level of concurrent gene flow among populations have shaped complex allelic patterns of fixation and skewed frequencies over the archipelago. However, understanding the population history remains challenging; in particular, the pattern of extreme divergence with low genetic diversity and yet unique genetic material in the Canary Island system requires an explanation. A potential scenario is population contractions of a historically large and genetically variable Afrocanarian population, with vicariance and drift following in the wake. The suggestion from sequence-based analyses of a Pleistocene extinction of a substantial part of North Africa and a Pleistocene/Holocene eastward re-colonisation of western North Africa from the Canaries remains possible. PMID:24587269

The roles of genetic drift and natural selection in quantitative trait divergence along an altitudinal gradient in Arabidopsis thaliana

PubMed Central

Luo, Y; Widmer, A; Karrenberg, S

2015-01-01

Understanding how natural selection and genetic drift shape biological variation is a central topic in biology, yet our understanding of the agents of natural selection and their target traits is limited. We investigated to what extent selection along an altitudinal gradient or genetic drift contributed to variation in ecologically relevant traits in Arabidopsis thaliana. We collected seeds from 8 to 14 individuals from each of 14 A. thaliana populations originating from sites between 800 and 2700 m above sea level in the Swiss Alps. Seed families were grown with and without vernalization, corresponding to winter-annual and summer-annual life histories, respectively. We analyzed putatively neutral genetic divergence between these populations using 24 simple sequence repeat markers. We measured seven traits related to growth, phenology and leaf morphology that are rarely reported in A. thaliana and performed analyses of altitudinal clines, as well as overall QST-FST comparisons and correlation analyses among pair-wise QST, FST and altitude of origin differences. Multivariate analyses suggested adaptive differentiation along altitude in the entire suite of traits, particularly when expressed in the summer-annual life history. Of the individual traits, a decrease in rosette leaf number in the vegetative state and an increase in leaf succulence with increasing altitude could be attributed to adaptive divergence. Interestingly, these patterns relate well to common within- and between-species trends of smaller plant size and thicker leaves at high altitude. Our results thus offer exciting possibilities to unravel the underlying mechanisms for these conspicuous trends using the model species A. thaliana. PMID:25293874

The devil is in the details: genetic variation in introduced populations and its contributions to invasion.

PubMed

Dlugosch, Katrina M; Anderson, Samantha R; Braasch, Joseph; Cang, F Alice; Gillette, Heather D

2015-05-01

The influence of genetic variation on invasion success has captivated researchers since the start of the field of invasion genetics 50 years ago. We review the history of work on this question and conclude that genetic variation-as surveyed with molecular markers-appears to shape invasion rarely. Instead, there is a significant disconnect between marker assays and ecologically relevant genetic variation in introductions. We argue that the potential for adaptation to facilitate invasion will be shaped by the details of genotypes affecting phenotypes, and we highlight three areas in which we see opportunities to make powerful new insights. (i) The genetic architecture of adaptive variation. Traits shaped by large-effect alleles may be strongly impacted by founder events yet more likely to respond to selection when genetic drift is strong. Large-effect loci may be especially relevant for traits involved in biotic interactions. (ii) Cryptic genetic variation exposed during invasion. Introductions have strong potential to uncover masked variation due to alterations in genetic and ecological environments. (iii) Genetic interactions during admixture of multiple source populations. As divergence among sources increases, positive followed by increasingly negative effects of admixture should be expected. Although generally hypothesized to be beneficial during invasion, admixture is most often reported among sources of intermediate divergence, supporting the possibility that incompatibilities among divergent source populations might be limiting their introgression. Finally, we note that these details of invasion genetics can be coupled with comparative demographic analyses to link genetic changes to the evolution of invasiveness itself. © 2015 John Wiley & Sons Ltd.

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

PubMed Central

Rico, Y; Wagner, H H

2016-01-01

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

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

PubMed

Rico, Y; Wagner, H H

2016-11-01

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

Complete Numerical Solution of the Diffusion Equation of Random Genetic Drift

PubMed Central

Zhao, Lei; Yue, Xingye; Waxman, David

2013-01-01

A numerical method is presented to solve the diffusion equation for the random genetic drift that occurs at a single unlinked locus with two alleles. The method was designed to conserve probability, and the resulting numerical solution represents a probability distribution whose total probability is unity. We describe solutions of the diffusion equation whose total probability is unity as complete. Thus the numerical method introduced in this work produces complete solutions, and such solutions have the property that whenever fixation and loss can occur, they are automatically included within the solution. This feature demonstrates that the diffusion approximation can describe not only internal allele frequencies, but also the boundary frequencies zero and one. The numerical approach presented here constitutes a single inclusive framework from which to perform calculations for random genetic drift. It has a straightforward implementation, allowing it to be applied to a wide variety of problems, including those with time-dependent parameters, such as changing population sizes. As tests and illustrations of the numerical method, it is used to determine: (i) the probability density and time-dependent probability of fixation for a neutral locus in a population of constant size; (ii) the probability of fixation in the presence of selection; and (iii) the probability of fixation in the presence of selection and demographic change, the latter in the form of a changing population size. PMID:23749318

Does population size affect genetic diversity? A test with sympatric lizard species.

PubMed

Hague, M T J; Routman, E J

2016-01-01

Genetic diversity is a fundamental requirement for evolution and adaptation. Nonetheless, the forces that maintain patterns of genetic variation in wild populations are not completely understood. Neutral theory posits that genetic diversity will increase with a larger effective population size and the decreasing effects of drift. However, the lack of compelling evidence for a relationship between genetic diversity and population size in comparative studies has generated some skepticism over the degree that neutral sequence evolution drives overall patterns of diversity. The goal of this study was to measure genetic diversity among sympatric populations of related lizard species that differ in population size and other ecological factors. By sampling related species from a single geographic location, we aimed to reduce nuisance variance in genetic diversity owing to species differences, for example, in mutation rates or historical biogeography. We compared populations of zebra-tailed lizards and western banded geckos, which are abundant and short-lived, to chuckwallas and desert iguanas, which are less common and long-lived. We assessed population genetic diversity at three protein-coding loci for each species. Our results were consistent with the predictions of neutral theory, as the abundant species almost always had higher levels of haplotype diversity than the less common species. Higher population genetic diversity in the abundant species is likely due to a combination of demographic factors, including larger local population sizes (and presumably effective population sizes), faster generation times and high rates of gene flow with other populations.

Spatial genetic structure in wild cardoon, the ancestor of cultivated globe artichoke: Limited gene flow, fragmentation and population history.

PubMed

Rau, D; Rodriguez, M; Rapposelli, E; Murgia, M L; Papa, R; Brown, A H D; Attene, G

2016-12-01

Nuclear and chloroplast markers and phenotypic characters were integrated to analyse the population genetic structure of wild cardoon, Cynara cardunculus var. sylvestris, the ancestor of cultivated globe artichoke, Cynara cardunculus var. scolymus on the island of Sardinia, Italy. The spatial scale ranged from a few metres to ∼200km. Wild cardoon appears to be genetically fragmented, with significant genetic divergence at various scales, indicating that gene flow is insufficient to counterbalance the effects of genetic drift or founder effects. Divergence between populations was higher for chloroplast (40%) than for nuclear markers (15%), suggesting that gene flow via seed was lower than via pollen. Two main genetic groups were detected; these correlated with differences in flowering time, capitula size, glossiness, and anthocyanin pigmentation. A complex population structure of wild cardoon emerged over small spatial scales, likely resulting from the interplay between gene dispersal, colonisation history and selective forces. Indeed, Sardinia appears to be a 'hybrid zone' of different gene pools. The island has unique diverse germplasm that has originated from hybridisation among different gene pools. The sampling of seeds from a few plants but from many sites is suggested as the best strategy to harvest the genetic diversity of wild cardoon. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Negative self-referential processing is associated with genetic variation in the serotonin transporter-linked polymorphic region (5-HTTLPR): Evidence from two independent studies.

PubMed

Dainer-Best, Justin; Disner, Seth G; McGeary, John E; Hamilton, Bethany J; Beevers, Christopher G

2018-01-01

The current research examined whether carriers of the short 5-HTTLPR allele (in SLC6A4), who have been shown to selectively attend to negative information, exhibit a bias towards negative self-referent processing. The self-referent encoding task (SRET) was used to measure self-referential processing of positive and negative adjectives. Ratcliff's diffusion model isolated and extracted decision-making components from SRET responses and reaction times. Across the initial (N = 183) and replication (N = 137) studies, results indicated that short 5-HTTLPR allele carriers more easily categorized negative adjectives as self-referential (i.e., higher drift rate). Further, drift rate was associated with recall of negative self-referential stimuli. Findings across both studies provide further evidence that genetic variation may contribute to the etiology of negatively biased processing of self-referent information. Large scale studies examining the genetic contributions to negative self-referent processing may be warranted.

Genetic hitchhiking can promote the initial spread of strong altruism

PubMed Central

2008-01-01

Background The evolutionary origin of strong altruism (where the altruist pays an absolute cost in terms of fitness) towards non-kin has never been satisfactorily explained since no mechanism (except genetic drift) seems to be able to overcome the fitness disadvantage of the individual who practiced altruism in the first place. Results Here we consider a multilocus, single-generation random group model and demonstrate that with low, but realistic levels of recombination and social heterosis (selecting for allelic diversity within groups) altruism can evolve without invoking kin selection, because sampling effects in the formation of temporary groups and selection for complementary haplotypes generate nonrandom associations between alleles at polymorphic loci. Conclusion By letting altruism get off the ground, selection on other genes favourably interferes with the eventual fate of the altruistic trait due to genetic hitchhiking. PMID:18847475

Evolution of Fitness in Experimental Populations of Vesicular Stomatitis Virus

PubMed Central

Elena, S. F.; Gonzalez-Candelas, F.; Novella, I. S.; Duarte, E. A.; Clarke, D. K.; Domingo, E.; Holland, J. J.; Moya, A.

1996-01-01

The evolution of fitness in experimental clonal populations of vesicular stomatitis virus (VSV) has been compared under different genetic (fitness of initial clone) and demographic (population dynamics) regimes. In spite of the high genetic heterogeneity among replicates within experiments, there is a clear effect of population dynamics on the evolution of fitness. Those populations that went through strong periodic bottlenecks showed a decreased fitness in competition experiments with wild type. Conversely, mutant populations that were transferred under the dynamics of continuous population expansions increased their fitness when compared with the same wild type. The magnitude of the observed effect depended on the fitness of the original viral clone. Thus, high fitness clones showed a larger reduction in fitness than low fitness clones under dynamics with included periodic bottleneck. In contrast, the gain in fitness was larger the lower the initial fitness of the viral clone. The quantitative genetic analysis of the trait ``fitness'' in the resulting populations shows that genetic variation for the trait is positively correlated with the magnitude of the change in the same trait. The results are interpreted in terms of the operation of MULLER's ratchet and genetic drift as opposed to the appearance of beneficial mutations. PMID:8849878

Genetic Structure and Diversity of the Endangered Fir Tree of Lebanon (Abies cilicica Carr.): Implications for Conservation

PubMed Central

Awad, Lara; Fady, Bruno; Khater, Carla; Roig, Anne; Cheddadi, Rachid

2014-01-01

The threatened conifer Abies cilicica currently persists in Lebanon in geographically isolated forest patches. The impact of demographic and evolutionary processes on population genetic diversity and structure were assessed using 10 nuclear microsatellite loci. All remnant 15 local populations revealed a low genetic variation but a high recent effective population size. FST-based measures of population genetic differentiation revealed a low spatial genetic structure, but Bayesian analysis of population structure identified a significant Northeast-Southwest population structure. Populations showed significant but weak isolation-by-distance, indicating non-equilibrium conditions between dispersal and genetic drift. Bayesian assignment tests detected an asymmetric Northeast-Southwest migration involving some long-distance dispersal events. We suggest that the persistence and Northeast-Southwest geographic structure of Abies cilicica in Lebanon is the result of at least two demographic processes during its recent evolutionary history: (1) recent migration to currently marginal populations and (2) local persistence through altitudinal shifts along a mountainous topography. These results might help us better understand the mechanisms involved in the species response to expected climate change. PMID:24587219

Variation in male courtship song traits in Drosophila virilis: the effects of selection and drift on song divergence at the intraspecific level.

PubMed

Huttunen, Susanna; Aspi, Jouni; Schlötterer, Christian; Routtu, Jarkko; Hoikkala, Anneli

2008-01-01

Genetic and phenotypic divergence of Drosophila virilis laboratory strains originating from different parts of the species range were studied with the aid of microsatellite markers and by analysing male courtship songs. The strains from America, Europe, continental Asia and Japan showed moderate geographic clustering both at the genetic level and in several traits of the male song. The genetic distances and the song divergence of the strains did not show significant association, which suggests that the songs have not diverged solely as a side-effect of genetic divergence. Comparison of the songs of the laboratory strains to those of freshly collected strains showed that pulse characters of the song are quite sensitive to culture conditions. While laboratory rearing of the flies had no effect on the number of pulses in a pulse train or the pulse train length, the tendency of the sound pulses to become longer during laboratory maintenance could explain the lack of geographic variation in pulse length and inter pulse interval. Sensitivity of songs to culturing conditions should be taken in account in studies on song divergence.

Sylvatic plague reduces genetic variability in black-tailed prairie dogs.

PubMed

Trudeau, Kristie M; Britten, Hugh B; Restani, Marco

2004-04-01

Small, isolated populations are vulnerable to loss of genetic diversity through in-breeding and genetic drift. Sylvatic plague due to infection by the bacterium Yersinia pestis caused an epizootic in the early 1990s resullting in declines and extirpations of many black-tailed prairie dog (Cynomys ludovicianus) colonies in north-central Montana, USA. Plague-induced population bottlenecks may contribute to significant reductions in genetic variability. In contrast, gene flow maintains genetic variability within colonies. We investigated the impacts of the plague epizootic and distance to nearest colony on levels of genetic variability in six prairie dog colonies sampled between June 1999 and July 2001 using 24 variable randomly amplified polymorphic DNA (RAPD) markers. Number of effective alleles per locus (n(e)) and gene diversity (h) were significantly decreased in the three colonies affected by plague that were recovering from the resulting bottlenecks compared with the three colonies that did not experience plague. Genetic variability was not significantly affected by geographic distance between colonies. The majority of variance in gene fieqnencies was found within prairie clog colonies. Conservation of genetic variability in black-tailed prairie dogs will require the preservation of both large and small colony complexes and the gene flow amonog them.

Population size, center-periphery, and seed dispersers' effects on the genetic diversity and population structure of the Mediterranean relict shrub Cneorum tricoccon.

PubMed

Lázaro-Nogal, Ana; Matesanz, Silvia; García-Fernández, Alfredo; Traveset, Anna; Valladares, Fernando

2017-09-01

The effect of population size on population genetic diversity and structure has rarely been studied jointly with other factors such as the position of a population within the species' distribution range or the presence of mutualistic partners influencing dispersal. Understanding these determining factors for genetic variation is critical for conservation of relict plants that are generally suffering from genetic deterioration. Working with 16 populations of the vulnerable relict shrub Cneorum tricoccon throughout the majority of its western Mediterranean distribution range, and using nine polymorphic microsatellite markers, we examined the effects of periphery (peripheral vs. central), population size (large vs. small), and seed disperser (introduced carnivores vs. endemic lizards) on the genetic diversity and population structure of the species. Contrasting genetic variation ( H E : 0.04-0.476) was found across populations. Peripheral populations showed lower genetic diversity, but this was dependent on population size. Large peripheral populations showed high levels of genetic diversity, whereas small central populations were less diverse. Significant isolation by distance was detected, indicating that the effect of long-distance gene flow is limited relative to that of genetic drift, probably due to high selfing rates ( F IS  = 0.155-0.887), restricted pollen flow, and ineffective seed dispersal. Bayesian clustering also supported the strong population differentiation and highly fragmented structure. Contrary to expectations, the type of disperser showed no significant effect on either population genetic diversity or structure. Our results challenge the idea of an effect of periphery per se that can be mainly explained by population size, drawing attention to the need of integrative approaches considering different determinants of genetic variation. Furthermore, the very low genetic diversity observed in several small populations and the strong among-population differentiation highlight the conservation value of large populations throughout the species' range, particularly in light of climate change and direct human threats.

Y-chromosomal insights into the genetic impact of the caste system in India

PubMed Central

Zerjal, Tatiana; Pandya, Arpita; Thangaraj, Kumarasamy; Ling, Edmund Y. S.; Kearley, Jennifer; Bertoneri, Stefania; Paracchini, Silvia; Singh, Lalji; Tyler-Smith, Chris

2008-01-01

The caste system has persisted in Indian Hindu society for around 3,500 years. Like the Y chromosome, caste is defined at birth, and males cannot change their caste. In order to investigate the genetic consequences of this system, we have analysed male-lineage variation in a sample of 227 Indian men of known caste, 141 from the Jaunpur district of Uttar Pradesh and 86 from the rest of India. We typed 131 Y-chromosomal binary markers and 16 microsatellites. We find striking evidence for male substructure: in particular, Brahmins and Kshatriyas (but not other castes) from Jaunpur each show low diversity and the predominance of a single distinct cluster of haplotypes. These findings confirm the genetic isolation and drift within the Jaunpur upper castes, which are likely to result from founder effects and social factors. In the other castes, there may be either larger effective population sizes, or less strict isolation, or both. PMID:17075717

Reduced MHC and neutral variation in the Galápagos hawk, an island endemic

PubMed Central

2011-01-01

Background Genes at the major histocompatibility complex (MHC) are known for high levels of polymorphism maintained by balancing selection. In small or bottlenecked populations, however, genetic drift may be strong enough to overwhelm the effect of balancing selection, resulting in reduced MHC variability. In this study we investigated MHC evolution in two recently diverged bird species: the endemic Galápagos hawk (Buteo galapagoensis), which occurs in small, isolated island populations, and its widespread mainland relative, the Swainson's hawk (B. swainsoni). Results We amplified at least two MHC class II B gene copies in each species. We recovered only three different sequences from 32 Galápagos hawks, while we amplified 20 unique sequences in 20 Swainson's hawks. Most of the sequences clustered into two groups in a phylogenetic network, with one group likely representing pseudogenes or nonclassical loci. Neutral genetic diversity at 17 microsatellite loci was also reduced in the Galápagos hawk compared to the Swainson's hawk. Conclusions The corresponding loss in neutral diversity suggests that the reduced variability present at Galápagos hawk MHC class II B genes compared to the Swainson's hawk is primarily due to a founder event followed by ongoing genetic drift in small populations. However, purifying selection could also explain the low number of MHC alleles present. This lack of variation at genes involved in the adaptive immune response could be cause for concern should novel diseases reach the archipelago. PMID:21612651

Leptokurtic pollen-flow, non-leptokurtic gene-flow in a wind-pollinated herb, Plantago lanceolata L.

PubMed

Tonsor, Stephen J

1985-10-01

The purpose of this study was to simultaneously measure pollen dispersal distance and actual pollen-mediated gene-flow distance in a wind-pollinated herb, Plantago lanceolata. The pollen dispersal distribution, measured as pollen deposition in a wind tunnel, is leptokurtic, as expected from previous studies of wind-pollinated plants. Gene-flow, measured as seeds produced on rows of male-sterile inflorescences in the wind tunnel, is non-leptokurtic, peaking at an intermediate distance. The difference between the two distributions results from the tendency of the pollen grains to cluster. These pollen clusters are the units of gene dispersal, with clusters of intermediate and large size contributing disproportionately to gene-flow. Since many wind-pollinated species show pollen clustering (see text), the common assumption for wind-pollinated plants that gene-flow is leptokurtic requires re-examination. Gene-flow was also measured in an artifical outdoor population of male-steriles, containing a single pollen source plant in the center of the array. The gene flow distribution is significantly platykurtic, and has the same general properties outdoors, where wind speed and turbulence are uncontrolled, as it does in the wind tunnel. I estimated genetic neighborhood size based on my measure of gene-flow in the outdoor population. The estimate shows that populations of Plantago lanceolata will vary in effective number from a few tens of plants to more than five hundred plants, depending on the density of the population in question. Thus, the measured pollen-mediated gene-flow distribution and population density will interact to produce effective population sizes ranging from those in which there is no random genetic drift to those in which random genetic drift plays an important role in determining gene frequencies within and among populations. Despite the platykurtosis in the distribution, pollen-mediated gene dispersal distances are still quite limited, and considerable within and among-population genetic differentiation is to be expected in this species.

Life-stage differences in spatial genetic structure in an irruptive forest insect: implications for dispersal and spatial synchrony

Treesearch

Patrick M.A. James; Barry Cooke; Bryan M.T. Brunet; Lisa M. Lumley; Felix A.H. Sperling; Marie-Josee Fortin; Vanessa S. Quinn; Brian R. Sturtevant

2015-01-01

Dispersal determines the flux of individuals, energy and information and is therefore a key determinant of ecological and evolutionary dynamics. Yet, it remains difficult to quantify its importance relative to other factors. This is particularly true in cyclic populations in which demography, drift and dispersal contribute to spatio-temporal variability in genetic...

Genetic drift and selection in many-allele range expansions.

PubMed

Weinstein, Bryan T; Lavrentovich, Maxim O; Möbius, Wolfram; Murray, Andrew W; Nelson, David R

2017-12-01

We experimentally and numerically investigate the evolutionary dynamics of four competing strains of E. coli with differing expansion velocities in radially expanding colonies. We compare experimental measurements of the average fraction, correlation functions between strains, and the relative rates of genetic domain wall annihilations and coalescences to simulations modeling the population as a one-dimensional ring of annihilating and coalescing random walkers with deterministic biases due to selection. The simulations reveal that the evolutionary dynamics can be collapsed onto master curves governed by three essential parameters: (1) an expansion length beyond which selection dominates over genetic drift; (2) a characteristic angular correlation describing the size of genetic domains; and (3) a dimensionless constant quantifying the interplay between a colony's curvature at the frontier and its selection length scale. We measure these parameters with a new technique that precisely measures small selective differences between spatially competing strains and show that our simulations accurately predict the dynamics without additional fitting. Our results suggest that the random walk model can act as a useful predictive tool for describing the evolutionary dynamics of range expansions composed of an arbitrary number of genotypes with different fitnesses.

R2d2 Drives Selfish Sweeps in the House Mouse.

PubMed

Didion, John P; Morgan, Andrew P; Yadgary, Liran; Bell, Timothy A; McMullan, Rachel C; Ortiz de Solorzano, Lydia; Britton-Davidian, Janice; Bult, Carol J; Campbell, Karl J; Castiglia, Riccardo; Ching, Yung-Hao; Chunco, Amanda J; Crowley, James J; Chesler, Elissa J; Förster, Daniel W; French, John E; Gabriel, Sofia I; Gatti, Daniel M; Garland, Theodore; Giagia-Athanasopoulou, Eva B; Giménez, Mabel D; Grize, Sofia A; Gündüz, İslam; Holmes, Andrew; Hauffe, Heidi C; Herman, Jeremy S; Holt, James M; Hua, Kunjie; Jolley, Wesley J; Lindholm, Anna K; López-Fuster, María J; Mitsainas, George; da Luz Mathias, Maria; McMillan, Leonard; Ramalhinho, Maria da Graça Morgado; Rehermann, Barbara; Rosshart, Stephan P; Searle, Jeremy B; Shiao, Meng-Shin; Solano, Emanuela; Svenson, Karen L; Thomas-Laemont, Patricia; Threadgill, David W; Ventura, Jacint; Weinstock, George M; Pomp, Daniel; Churchill, Gary A; Pardo-Manuel de Villena, Fernando

2016-06-01

A selective sweep is the result of strong positive selection driving newly occurring or standing genetic variants to fixation, and can dramatically alter the pattern and distribution of allelic diversity in a population. Population-level sequencing data have enabled discoveries of selective sweeps associated with genes involved in recent adaptations in many species. In contrast, much debate but little evidence addresses whether "selfish" genes are capable of fixation-thereby leaving signatures identical to classical selective sweeps-despite being neutral or deleterious to organismal fitness. We previously described R2d2, a large copy-number variant that causes nonrandom segregation of mouse Chromosome 2 in females due to meiotic drive. Here we show population-genetic data consistent with a selfish sweep driven by alleles of R2d2 with high copy number (R2d2(HC)) in natural populations. We replicate this finding in multiple closed breeding populations from six outbred backgrounds segregating for R2d2 alleles. We find that R2d2(HC) rapidly increases in frequency, and in most cases becomes fixed in significantly fewer generations than can be explained by genetic drift. R2d2(HC) is also associated with significantly reduced litter sizes in heterozygous mothers, making it a true selfish allele. Our data provide direct evidence of populations actively undergoing selfish sweeps, and demonstrate that meiotic drive can rapidly alter the genomic landscape in favor of mutations with neutral or even negative effects on overall Darwinian fitness. Further study will reveal the incidence of selfish sweeps, and will elucidate the relative contributions of selfish genes, adaptation and genetic drift to evolution. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

R2d2 Drives Selfish Sweeps in the House Mouse

PubMed Central

Didion, John P.; Morgan, Andrew P.; Yadgary, Liran; Bell, Timothy A.; McMullan, Rachel C.; Ortiz de Solorzano, Lydia; Britton-Davidian, Janice; Bult, Carol J.; Campbell, Karl J.; Castiglia, Riccardo; Ching, Yung-Hao; Chunco, Amanda J.; Crowley, James J.; Chesler, Elissa J.; Förster, Daniel W.; French, John E.; Gabriel, Sofia I.; Gatti, Daniel M.; Garland, Theodore; Giagia-Athanasopoulou, Eva B.; Giménez, Mabel D.; Grize, Sofia A.; Gündüz, İslam; Holmes, Andrew; Hauffe, Heidi C.; Herman, Jeremy S.; Holt, James M.; Hua, Kunjie; Jolley, Wesley J.; Lindholm, Anna K.; López-Fuster, María J.; Mitsainas, George; da Luz Mathias, Maria; McMillan, Leonard; Ramalhinho, Maria da Graça Morgado; Rehermann, Barbara; Rosshart, Stephan P.; Searle, Jeremy B.; Shiao, Meng-Shin; Solano, Emanuela; Svenson, Karen L.; Thomas-Laemont, Patricia; Threadgill, David W.; Ventura, Jacint; Weinstock, George M.; Pomp, Daniel; Churchill, Gary A.; Pardo-Manuel de Villena, Fernando

2016-01-01

A selective sweep is the result of strong positive selection driving newly occurring or standing genetic variants to fixation, and can dramatically alter the pattern and distribution of allelic diversity in a population. Population-level sequencing data have enabled discoveries of selective sweeps associated with genes involved in recent adaptations in many species. In contrast, much debate but little evidence addresses whether “selfish” genes are capable of fixation—thereby leaving signatures identical to classical selective sweeps—despite being neutral or deleterious to organismal fitness. We previously described R2d2, a large copy-number variant that causes nonrandom segregation of mouse Chromosome 2 in females due to meiotic drive. Here we show population-genetic data consistent with a selfish sweep driven by alleles of R2d2 with high copy number (R2d2HC) in natural populations. We replicate this finding in multiple closed breeding populations from six outbred backgrounds segregating for R2d2 alleles. We find that R2d2HC rapidly increases in frequency, and in most cases becomes fixed in significantly fewer generations than can be explained by genetic drift. R2d2HC is also associated with significantly reduced litter sizes in heterozygous mothers, making it a true selfish allele. Our data provide direct evidence of populations actively undergoing selfish sweeps, and demonstrate that meiotic drive can rapidly alter the genomic landscape in favor of mutations with neutral or even negative effects on overall Darwinian fitness. Further study will reveal the incidence of selfish sweeps, and will elucidate the relative contributions of selfish genes, adaptation and genetic drift to evolution. PMID:26882987

Evolution of advertisement calls in African clawed frogs

PubMed Central

Tobias, Martha L.; Evans, Ben J.; Kelley, Darcy B.

2014-01-01

Summary For most frogs, advertisement calls are essential for reproductive success, conveying information on species identity, male quality, sexual state and location. While the evolutionary divergence of call characters has been examined in a number of species, the relative impacts of genetic drift or natural and sexual selection remain unclear. Insights into the evolutionary trajectory of vocal signals can be gained by examining how advertisement calls vary in a phylogenetic context. Evolution by genetic drift would be supported if more closely related species express more similar songs. Conversely, a poor correlation between evolutionary history and song expression would suggest evolution shaped by natural or sexual selection. Here, we measure seven song characters in 20 described and two undescribed species of African clawed frogs (genera Xenopus and Silurana) and four populations of X. laevis. We identify three call types — click, burst and trill — that can be distinguished by click number, call rate and intensity modulation. A fourth type is biphasic, consisting of two of the above. Call types vary in complexity from the simplest, a click, to the most complex, a biphasic call. Maximum parsimony analysis of variation in call type suggests that the ancestral type was of intermediate complexity. Each call type evolved independently more than once and call type is typically not shared by closely related species. These results indicate that call type is homoplasious and has low phylogenetic signal. We conclude that the evolution of call type is not due to genetic drift, but is under selective pressure. PMID:24723737

Regressive Evolution in the Mexican Cave Tetra, Astyanax mexicanus

PubMed Central

Protas, Meredith; Conrad, Melissa; Gross, Joshua B.; Tabin, Clifford; Borowsky, Richard

2007-01-01

Summary Cave adapted animals generally have reduced pigmentation and eyes, but the evolutionary forces driving the reductions are unknown; Darwin famously questioned the role of natural selection in eye loss in cave fishes; “As it is difficult to imagine that eyes, although useless, could be in any way injurious to animals living in darkness, I attribute their loss wholly to disuse” [1]. We studied the genetic basis of this phenomenon in the Mexican cave tetra, Astyanax mexicanus, by mapping the quantitative trait loci (QTL) determining differences in eye/lens sizes and melanophore number between cave and surface fish. In addition, we mapped QTL for the putatively constructive traits of jaw size, tooth number, and numbers of taste buds. The data suggest that eyes and pigmentation regressed through different mechanisms. Cave alleles at each eye/lens QTL we detected caused size reductions. This uniform negative polarity is consistent with evolution by natural selection and inconsistent with evolution by drift. In contrast, QTL polarities for melanophore number were mixed, consistent with evolution by genetic drift or indirect selection through pleiotropy. Past arguments against a role for selection in regression of cave fish eyes cited the insignificant cost of their development [2, 3], but we argue that the energetic cost of their maintenance is sufficiently high for eyes to be detrimental in the cave environment. Regression, a ubiquitous aspect of all evolutionary change, can be caused either by selection or genetic drift/pleiotropy. PMID:17306543

Understanding the genetic effects of recent habitat fragmentation in the context of evolutionary history: Phylogeography and landscape genetics of a southern California endemic Jerusalem cricket (Orthoptera: Stenopelmatidae: Stenopelmatus)

USGS Publications Warehouse

Vandergast, A.G.; Bohonak, A.J.; Weissman, D.B.; Fisher, R.N.

2007-01-01

Habitat loss and fragmentation due to urbanization are the most pervasive threats to biodiversity in southern California. Loss of habitat and fragmentation can lower migration rates and genetic connectivity among remaining populations of native species, reducing genetic variability and increasing extinction risk. However, it may be difficult to separate the effects of recent anthropogenic fragmentation from the genetic signature of prehistoric fragmentation due to previous natural geological and climatic changes. To address these challenges, we examined the phylogenetic and population genetic structure of a flightless insect endemic to cismontane southern California, Stenopelmatus 'mahogani' (Orthoptera: Stenopelmatidae). Analyses of mitochondrial DNA sequence data suggest that diversification across southern California began during the Pleistocene, with most haplotypes currently restricted to a single population. Patterns of genetic divergence correlate with contemporary urbanization, even after correcting for (geographical information system) GIS-based reconstructions of fragmentation during the Pleistocene. Theoretical simulations confirm that contemporary patterns of genetic structure could be produced by recent urban fragmentation using biologically reasonable assumptions about model parameters. Diversity within populations was positively correlated with current fragment size, but not prehistoric fragment size, suggesting that the effects of increased drift following anthropogenic fragmentation are already being seen. Loss of genetic connectivity and diversity can hinder a population's ability to adapt to ecological perturbations commonly associated with urbanization, such as habitat degradation, climatic changes and introduced species. Consequently, our results underscore the importance of preserving and restoring landscape connectivity for long-term persistence of low vagility native species. Journal compilation ?? 2006 Blackwell Publishing Ltd.

Spatial and temporal genetic diversity of lake whitefish (Coregonus clupeaformis (Mitchill)) from Lake Huron and Lake Erie

USGS Publications Warehouse

Stott, Wendylee; Ebener, Mark P.; Mohr, Lloyd; Hartman, Travis; Johnson, Jim; Roseman, Edward F.

2013-01-01

Lake whitefish (Coregonus clupeaformis (Mitchill)) are important commercially, culturally, and ecologically in the Laurentian Great Lakes. Stocks of lake whitefish in the Great Lakes have recovered from low levels of abundance in the 1960s. Reductions in abundance, loss of habitat and environmental degradation can be accompanied by losses of genetic diversity and overall fitness that may persist even as populations recover demographically. Therefore, it is important to be able to identify stocks that have reduced levels of genetic diversity. In this study, we investigated patterns of genetic diversity at microsatellite DNA loci in lake whitefish collected between 1927 and 1929 (historical period) and between 1997 and 2005 (contemporary period) from Lake Huron and Lake Erie. Genetic analysis of lake whitefish from Lakes Huron and Erie shows that the amount of population structuring varies from lake to lake. Greater genetic divergences among collections from Lake Huron may be the result of sampling scale, migration patterns and demographic processes. Fluctuations in abundance of lake whitefish populations may have resulted in periods of increased genetic drift that have resulted in changes in allele frequencies over time, but periodic genetic drift was not severe enough to result in a significant loss of genetic diversity. Migration among stocks may have decreased levels of genetic differentiation while not completely obscuring stock boundaries. Recent changes in spatial boundaries to stocks, the number of stocks and life history characteristics of stocks further demonstrate the potential of coregonids for a swift and varied response to environmental change and emphasise the importance of incorporating both spatial and temporal considerations into management plans to ensure that diversity is preserved.

Genetic and phenotypic divergence in an island bird: isolation by distance, by colonization or by adaptation?

PubMed

Spurgin, Lewis G; Illera, Juan Carlos; Jorgensen, Tove H; Dawson, Deborah A; Richardson, David S

2014-03-01

Discerning the relative roles of adaptive and nonadaptive processes in generating differences among populations and species, as well as how these processes interact, is a fundamental aim in biology. Both genetic and phenotypic divergence across populations can be the product of limited dispersal and gradual genetic drift across populations (isolation by distance), of colonization history and founder effects (isolation by colonization) or of adaptation to different environments preventing migration between populations (isolation by adaptation). Here, we attempt to differentiate between these processes using island populations of Berthelot's pipit (Anthus berthelotii), a passerine bird endemic to three Atlantic archipelagos. Using microsatellite markers and approximate Bayesian computation, we reveal that the northward colonization of this species ca. 8500 years ago resulted in genetic bottlenecks in the colonized archipelagos. We then show that high levels of genetic structure exist across archipelagos and that these are consistent with a pattern of isolation by colonization, but not with isolation by distance or adaptation. Finally, we show that substantial morphological divergence also exists and that this is strongly concordant with patterns of genetic structure and bottleneck history, but not with environmental differences or geographic distance. Overall, our data suggest that founder effects are responsible for both genetic and phenotypic changes across archipelagos. Our findings provide a rare example of how founder effects can persist over evolutionary timescales and suggest that they may play an important role in the early stages of speciation. © 2014 John Wiley & Sons Ltd.

Spatial structure of morphological and neutral genetic variation in Brook Trout

USGS Publications Warehouse

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

2015-01-01

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

Rock outcrop orchids reveal the genetic connectivity and diversity of inselbergs of northeastern Brazil.

PubMed

Pinheiro, Fábio; Cozzolino, Salvatore; Draper, David; de Barros, Fábio; Félix, Leonardo P; Fay, Michael F; Palma-Silva, Clarisse

2014-03-15

Because of their fragmented nature, inselberg species are interesting biological models for studying the genetic consequences of disjoint populations. Inselbergs are commonly compared with oceanic islands, as most of them display a marked ecological isolation from the surrounding area. The isolation of these rock outcrops is reflected in the high number of recorded endemic species and the strong floristic differences between individual inselbergs and adjacent habitats. We examined the genetic connectivity of orchids Epidendrum cinnabarinum and E. secundum adapted to Neotropical inselbergs of northeastern Brazil. Our goals were to identify major genetic divergences or disjunctions across the range of the species and to investigate potential demographic and evolutionary mechanisms leading to lineage divergence in Neotropical mountain ecosystems. Based on plastid markers, high genetic differentiation was found for E. cinnabarinum (FST = 0.644) and E. secundum (FST = 0.636). Haplotypes were not geographically structured in either taxon, suggesting that restricted gene flow and genetic drift may be significant factors influencing the diversification of these inselberg populations. Moreover, strong differentiation was found between populations over short spatial scales, indicating substantial periods of isolation among populations. For E. secundum, nuclear markers indicated higher gene flow by pollen than by seeds. The comparative approach adopted in this study contributed to the elucidation of patterns in both species. Our results confirm the ancient and highly isolated nature of inselberg populations. Both species showed similar patterns of genetic diversity and structure, highlighting the importance of seed-restricted gene flow and genetic drift as drivers of plant diversification in terrestrial islands such as inselbergs.

Virus fitness differences observed between two naturally occurring isolates of Ebola virus Makona variant using a reverse genetics approach.

PubMed

Albariño, César G; Guerrero, Lisa Wiggleton; Chakrabarti, Ayan K; Kainulainen, Markus H; Whitmer, Shannon L M; Welch, Stephen R; Nichol, Stuart T

2016-09-01

During the large outbreak of Ebola virus disease that occurred in Western Africa from late 2013 to early 2016, several hundred Ebola virus (EBOV) genomes have been sequenced and the virus genetic drift analyzed. In a previous report, we described an efficient reverse genetics system designed to generate recombinant EBOV based on a Makona variant isolate obtained in 2014. Using this system, we characterized the replication and fitness of 2 isolates of the Makona variant. These virus isolates are nearly identical at the genetic level, but have single amino acid differences in the VP30 and L proteins. The potential effects of these differences were tested using minigenomes and recombinant viruses. The results obtained with this approach are consistent with the role of VP30 and L as components of the EBOV RNA replication machinery. Moreover, the 2 isolates exhibited clear fitness differences in competitive growth assays. Published by Elsevier Inc.

Allee effect: the story behind the stabilization or extinction of microbial ecosystem.

PubMed

Goswami, Madhurankhi; Bhattacharyya, Purnita; Tribedi, Prosun

2017-03-01

A population exhibiting Allee effect shows a positive correlation between population fitness and population size or density. Allee effect decides the extinction or conservation of a microbial population and thus appears to be an important criterion in population ecology. The underlying factor of Allee effect that decides the stabilization and extinction of a particular population density is the threshold or the critical density of their abundance. According to Allee, microbial populations exhibit a definite, critical or threshold density, beyond which the population fitness of a particular population increases with the rise in population density and below it, the population fitness goes down with the decrease in population density. In particular, microbial population displays advantageous traits such as biofilm formation, expression of virulence genes, spore formation and many more only at a high population density. It has also been observed that microorganisms exhibiting a lower population density undergo complete extinction from the residual microbial ecosystem. In reference to Allee effect, decrease in population density or size introduces deleterious mutations among the population density through genetic drift. Mutations are carried forward to successive generations resulting in its accumulation among the population density thus reducing its microbial fitness and thereby increasing the risk of extinction of a particular microbial population. However, when the microbial load is high, the chance of genetic drift is less, and through the process of biofilm formation, the cooperation existing among the microbial population increases that increases the microbial fitness. Thus, the high microbial population through the formation of microbial biofilm stabilizes the ecosystem by increasing fitness. Taken together, microbial fitness shows positive correlation with the ecosystem conservation and negative correlation with ecosystem extinction.

Quantification of the genetic change in the transition of Rhodnius pallescens Barber, 1932 (Hemiptera: Reduviidae) from field to laboratory.

PubMed

Gómez-Sucerquia, Leysa Jackeline; Triana-Chávez, Omar; Jaramillo-Ocampo, Nicolás

2009-09-01

Previous studies have reported genetic differences between wild-caught sylvatic, domestic and laboratory pop-ulations of several Triatominae species. The differences between sylvatic and laboratory colonies parallel are similar to the differences observed between sylvatic and domestic populations. Laboratory colonies are frequently used as references for field populations, but the consequences of founder events on the genetic makeup of laboratory or domestic populations are rarely quantified. Our goal was to quantify the genetic change in Rhodnius pallescens populations artificially submitted to founder effects via laboratory colonization. We compared the genetic makeup of two sylvatic populations and their laboratory descendants using a panel of 10 microsatellite markers. Both sylvatic populations were initially collected from palm trees, but the colonies differed in the number of founder insects and amount of time kept in the laboratory. We evaluated allelic polymorphism, differences between expected and observed heterozygosity, estimates of population differentiation (Fst) and inbreeding (Fis, Fit) and cluster analyses based on Nei's distances. We found a unique genetic structure for each sample population, with significant differentiation between the field insects and each of the laboratory generations. These analyses showed strong founder effects and showed that genetic drift had led to a genetic equilibrium over several generations of isolation. Our results suggest that laboratory colonies of R. pallescens have a different genetic structure than their wild relatives and similar processes likely affect other Triatominae laboratory stocks.

How Ebola impacts genetics of Western lowland gorilla populations.

PubMed

Le Gouar, Pascaline J; Vallet, Dominique; David, Laetitia; Bermejo, Magdalena; Gatti, Sylvain; Levréro, Florence; Petit, Eric J; Ménard, Nelly

2009-12-18

Emerging infectious diseases in wildlife are major threats for both human health and biodiversity conservation. Infectious diseases can have serious consequences for the genetic diversity of populations, which could enhance the species' extinction probability. The Ebola epizootic in western and central Africa induced more than 90% mortality in Western lowland gorilla population. Although mortality rates are very high, the impacts of Ebola on genetic diversity of Western lowland gorilla have never been assessed. We carried out long term studies of three populations of Western lowland gorilla in the Republic of the Congo (Odzala-Kokoua National Park, Lossi gorilla sanctuary both affected by Ebola and Lossi's periphery not affected). Using 17 microsatellite loci, we compared genetic diversity and structure of the populations and estimate their effective size before and after Ebola outbreaks. Despite the effective size decline in both populations, we did not detect loss in genetic diversity after the epizootic. We revealed temporal changes in allele frequencies in the smallest population. Immigration and short time elapsed since outbreaks could explain the conservation of genetic diversity after the demographic crash. Temporal changes in allele frequencies could not be explained by genetic drift or random sampling. Immigration from genetically differentiated populations and a non random mortality induced by Ebola, i.e., selective pressure and cost of sociality, are alternative hypotheses. Understanding the influence of Ebola on gorilla genetic dynamics is of paramount importance for human health, primate evolution and conservation biology.

Genetic consequences of polygyny and social structure in an Indian fruit bat, Cynopterus sphinx. II. Variance in male mating success and effective population size.

PubMed

Storz, J F; Bhat, H R; Kunz, T H

2001-06-01

Variance in reproductive success is a primary determinant of genetically effective population size (Ne), and thus has important implications for the role of genetic drift in the evolutionary dynamics of animal taxa characterized by polygynous mating systems. Here we report the results of a study designed to test the hypothesis that polygynous mating results in significantly reduced Ne in an age-structured population. This hypothesis was tested in a natural population of a harem-forming fruit bat, Cynopterus sphinx (Chiroptera: Pteropodidae), in western India. The influence of the mating system on the ratio of variance Ne to adult census number (N) was assessed using a mathematical model designed for age-structured populations that incorporated demographic and genetic data. Male mating success was assessed by means of direct and indirect paternity analysis using 10-locus microsatellite genotypes of adults and progeny from two consecutive breeding periods (n = 431 individually marked bats). Combined results from both analyses were used to infer the effective number of male parents in each breeding period. The relative proportion of successfully reproducing males and the size distribution of paternal sibships comprising each offspring cohort revealed an extremely high within-season variance in male mating success (up to 9.2 times higher than Poisson expectation). The resultant estimate of Ne/N for the C. sphinx study population was 0.42. As a result of polygynous mating, the predicted rate of drift (1/2Ne per generation) was 17.6% higher than expected from a Poisson distribution of male mating success. However, the estimated Ne/N was well within the 0.25-0.75 range expected for age-structured populations under normal demographic conditions. The life-history schedule of C. sphinx is characterized by a disproportionately short sexual maturation period scaled to adult life span. Consequently, the influence of polygynous mating on Ne/N is mitigated by the extensive overlap of generations. In C. sphinx, turnover of breeding males between seasons ensures a broader sampling of the adult male gamete pool than expected from the variance in mating success within a single breeding period.

Great influence of geographic isolation on the genetic differentiation of Myriophyllum spicatum under a steep environmental gradient

PubMed Central

Wu, Zhigang; Yu, Dan; Wang, Zhong; Li, Xing; Xu, Xinwei

2015-01-01

Understanding how natural processes affect population genetic structures is an important issue in evolutionary biology. One effective method is to assess the relative importance of environmental and geographical factors in the genetic structure of populations. In this study, we examined the spatial genetic variation of thirteen Myriophyllum spicatum populations from the Qinghai-Tibetan Plateau (QTP) and adjacent highlands (Yunnan-Guizhou Plateau, YGP) by using microsatellite loci and environmental and geographical factors. Bioclim layers, hydrological properties and elevation were considered as environmental variables and reduced by principal component analysis. The genetic isolation by geographic distance (IBD) was tested by Mantel tests and the relative importance of environmental variables on population genetic differentiation was determined by a partial Mantel test and multiple matrix regression with randomization (MMRR). Two genetic clusters corresponding to the QTP and YGP were identified. Both tests and MMRR revealed a significant and strong correlation between genetic divergence and geographic isolation under the influence of environmental heterogeneity at the overall and finer spatial scales. Our findings suggested the dominant role of geography on the evolution of M. spicatum under a steep environmental gradient in the alpine landscape as a result of dispersal limitation and genetic drift. PMID:26494202

Genetic demixing and evolution in linear stepping stone models

NASA Astrophysics Data System (ADS)

Korolev, K. S.; Avlund, Mikkel; Hallatschek, Oskar; Nelson, David R.

2010-04-01

Results for mutation, selection, genetic drift, and migration in a one-dimensional continuous population are reviewed and extended. The population is described by a continuous limit of the stepping stone model, which leads to the stochastic Fisher-Kolmogorov-Petrovsky-Piscounov equation with additional terms describing mutations. Although the stepping stone model was first proposed for population genetics, it is closely related to “voter models” of interest in nonequilibrium statistical mechanics. The stepping stone model can also be regarded as an approximation to the dynamics of a thin layer of actively growing pioneers at the frontier of a colony of micro-organisms undergoing a range expansion on a Petri dish. The population tends to segregate into monoallelic domains. This segregation slows down genetic drift and selection because these two evolutionary forces can only act at the boundaries between the domains; the effects of mutation, however, are not significantly affected by the segregation. Although fixation in the neutral well-mixed (or “zero-dimensional”) model occurs exponentially in time, it occurs only algebraically fast in the one-dimensional model. An unusual sublinear increase is also found in the variance of the spatially averaged allele frequency with time. If selection is weak, selective sweeps occur exponentially fast in both well-mixed and one-dimensional populations, but the time constants are different. The relatively unexplored problem of evolutionary dynamics at the edge of an expanding circular colony is studied as well. Also reviewed are how the observed patterns of genetic diversity can be used for statistical inference and the differences are highlighted between the well-mixed and one-dimensional models. Although the focus is on two alleles or variants, q -allele Potts-like models of gene segregation are considered as well. Most of the analytical results are checked with simulations and could be tested against recent spatial experiments on range expansions of inoculations of Escherichia coli and Saccharomyces cerevisiae.

Genetic Structure in a Small Pelagic Fish Coincides with a Marine Protected Area: Seascape Genetics in Patagonian Fjords.

PubMed

Canales-Aguirre, Cristian B; Ferrada-Fuentes, Sandra; Galleguillos, Ricardo; Hernández, Cristián E

2016-01-01

Marine environmental variables can play an important role in promoting population genetic differentiation in marine organisms. Although fjord ecosystems have attracted much attention due to the great oscillation of environmental variables that produce heterogeneous habitats, species inhabiting this kind of ecosystem have received less attention. In this study, we used Sprattus fuegensis, a small pelagic species that populates the inner waters of the continental shelf, channels and fjords of Chilean Patagonia and Argentina, as a model species to test whether environmental variables of fjords relate to population genetic structure. A total of 282 individuals were analyzed from Chilean Patagonia with eight microsatellite loci. Bayesian and non-Bayesian analyses were conducted to describe the genetic variability of S. fuegensis and whether it shows spatial genetic structure. Results showed two well-differentiated genetic clusters along the Chilean Patagonia distribution (i.e. inside the embayment area called TicToc, and the rest of the fjords), but no spatial isolation by distance (IBD) pattern was found with a Mantel test analysis. Temperature and nitrate were correlated to the expected heterozygosities and explained the allelic frequency variation of data in the redundancy analyses. These results suggest that the singular genetic differences found in S. fuegensis from inside TicToc Bay (East of the Corcovado Gulf) are the result of larvae retention bya combination of oceanographic mesoscale processes (i.e. the west wind drift current reaches the continental shelf exactly in this zone), and the local geographical configuration (i.e. embayment area, islands, archipelagos). We propose that these features generated an isolated area in the Patagonian fjords that promoted genetic differentiation by drift and a singular biodiversity, adding support to the existence of the largest marine protected area (MPA) of continental Chile, which is the Tic-Toc MPA.

Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes

PubMed Central

Fierst, Janna L.; Willis, John H.; Thomas, Cristel G.; Wang, Wei; Reynolds, Rose M.; Ahearne, Timothy E.; Cutter, Asher D.; Phillips, Patrick C.

2015-01-01

The self-fertile nematode worms Caenorhabditis elegans, C. briggsae, and C. tropicalis evolved independently from outcrossing male-female ancestors and have genomes 20-40% smaller than closely related outcrossing relatives. This pattern of smaller genomes for selfing species and larger genomes for closely related outcrossing species is also seen in plants. We use comparative genomics, including the first high quality genome assembly for an outcrossing member of the genus (C. remanei) to test several hypotheses for the evolution of genome reduction under a change in mating system. Unlike plants, it does not appear that reductions in the number of repetitive elements, such as transposable elements, are an important contributor to the change in genome size. Instead, all functional genomic categories are lost in approximately equal proportions. Theory predicts that self-fertilization should equalize the effective population size, as well as the resulting effects of genetic drift, between the X chromosome and autosomes. Contrary to this, we find that the self-fertile C. briggsae and C. elegans have larger intergenic spaces and larger protein-coding genes on the X chromosome when compared to autosomes, while C. remanei actually has smaller introns on the X chromosome than either self-reproducing species. Rather than being driven by mutational biases and/or genetic drift caused by a reduction in effective population size under self reproduction, changes in genome size in this group of nematodes appear to be caused by genome-wide patterns of gene loss, most likely generated by genomic adaptation to self reproduction per se. PMID:26114425

Genetic Drift, Not Life History or RNAi, Determine Long-Term Evolution of Transposable Elements

PubMed Central

Szitenberg, Amir; Cha, Soyeon; Opperman, Charles H.; Bird, David M.; Blaxter, Mark L.; Lunt, David H.

2016-01-01

Abstract Transposable elements (TEs) are a major source of genome variation across the branches of life. Although TEs may play an adaptive role in their host’s genome, they are more often deleterious, and purifying selection is an important factor controlling their genomic loads. In contrast, life history, mating system, GC content, and RNAi pathways have been suggested to account for the disparity of TE loads in different species. Previous studies of fungal, plant, and animal genomes have reported conflicting results regarding the direction in which these genomic features drive TE evolution. Many of these studies have had limited power, however, because they studied taxonomically narrow systems, comparing only a limited number of phylogenetically independent contrasts, and did not address long-term effects on TE evolution. Here, we test the long-term determinants of TE evolution by comparing 42 nematode genomes spanning over 500 million years of diversification. This analysis includes numerous transitions between life history states, and RNAi pathways, and evaluates if these forces are sufficiently persistent to affect the long-term evolution of TE loads in eukaryotic genomes. Although we demonstrate statistical power to detect selection, we find no evidence that variation in these factors influence genomic TE loads across extended periods of time. In contrast, the effects of genetic drift appear to persist and control TE variation among species. We suggest that variation in the tested factors are largely inconsequential to the large differences in TE content observed between genomes, and only by these large-scale comparisons can we distinguish long-term and persistent effects from transient or random changes. PMID:27566762

Genetic characterization of Greek population isolates reveals strong genetic drift at missense and trait-associated variants

PubMed Central

Panoutsopoulou, Kalliope; Hatzikotoulas, Konstantinos; Xifara, Dionysia Kiara; Colonna, Vincenza; Farmaki, Aliki-Eleni; Ritchie, Graham R. S.; Southam, Lorraine; Gilly, Arthur; Tachmazidou, Ioanna; Fatumo, Segun; Matchan, Angela; Rayner, Nigel W.; Ntalla, Ioanna; Mezzavilla, Massimo; Chen, Yuan; Kiagiadaki, Chrysoula; Zengini, Eleni; Mamakou, Vasiliki; Athanasiadis, Antonis; Giannakopoulou, Margarita; Kariakli, Vassiliki-Eirini; Nsubuga, Rebecca N.; Karabarinde, Alex; Sandhu, Manjinder; McVean, Gil; Tyler-Smith, Chris; Tsafantakis, Emmanouil; Karaleftheri, Maria; Xue, Yali; Dedoussis, George; Zeggini, Eleftheria

2014-01-01

Isolated populations are emerging as a powerful study design in the search for low-frequency and rare variant associations with complex phenotypes. Here we genotype 2,296 samples from two isolated Greek populations, the Pomak villages (HELIC-Pomak) in the North of Greece and the Mylopotamos villages (HELIC-MANOLIS) in Crete. We compare their genomic characteristics to the general Greek population and establish them as genetic isolates. In the MANOLIS cohort, we observe an enrichment of missense variants among the variants that have drifted up in frequency by more than fivefold. In the Pomak cohort, we find novel associations at variants on chr11p15.4 showing large allele frequency increases (from 0.2% in the general Greek population to 4.6% in the isolate) with haematological traits, for example, with mean corpuscular volume (rs7116019, P=2.3 × 10−26). We replicate this association in a second set of Pomak samples (combined P=2.0 × 10−36). We demonstrate significant power gains in detecting medical trait associations. PMID:25373335

Electromagnetic drift waves dispersion for arbitrarily collisional plasmas

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

Lee, Wonjae, E-mail: wol023@ucsd.edu; Krasheninnikov, Sergei I., E-mail: skrash@mae.ucsd.edu; Angus, J. R.

2015-07-15

The impacts of the electromagnetic effects on resistive and collisionless drift waves are studied. A local linear analysis on an electromagnetic drift-kinetic equation with Bhatnagar-Gross-Krook-like collision operator demonstrates that the model is valid for describing linear growth rates of drift wave instabilities in a wide range of plasma parameters showing convergence to reference models for limiting cases. The wave-particle interactions drive collisionless drift-Alfvén wave instability in low collisionality and high beta plasma regime. The Landau resonance effects not only excite collisionless drift wave modes but also suppress high frequency electron inertia modes observed from an electromagnetic fluid model in collisionlessmore » and low beta regime. Considering ion temperature effects, it is found that the impact of finite Larmor radius effects significantly reduces the growth rate of the drift-Alfvén wave instability with synergistic effects of high beta stabilization and Landau resonance.« less

A portrait of a sucker using landscape genetics: how colonization and life history undermine the idealized dendritic metapopulation.

PubMed

Salisbury, Sarah J; McCracken, Gregory R; Keefe, Donald; Perry, Robert; Ruzzante, Daniel E

2016-09-01

Dendritic metapopulations have been attributed unique properties by in silico studies, including an elevated genetic diversity relative to a panmictic population of equal total size. These predictions have not been rigorously tested in nature, nor has there been full consideration of the interacting effects among contemporary landscape features, colonization history and life history traits of the target species. We tested for the effects of dendritic structure as well as the relative importance of life history, environmental barriers and historical colonization on the neutral genetic structure of a longnose sucker (Catostomus catostomus) metapopulation in the Kogaluk watershed of northern Labrador, Canada. Samples were collected from eight lakes, genotyped with 17 microsatellites, and aged using opercula. Lakes varied in differentiation, historical and contemporary connectivity, and life history traits. Isolation by distance was detected only by removing two highly genetically differentiated lakes, suggesting a lack of migration-drift equilibrium and the lingering influence of historical factors on genetic structure. Bayesian analyses supported colonization via the Kogaluk's headwaters. The historical concentration of genetic diversity in headwaters inferred by this result was supported by high historical and contemporary effective sizes of the headwater lake, T-Bone. Alternatively, reduced allelic richness in headwaters confirmed the dendritic structure's influence on gene flow, but this did not translate to an elevated metapopulation effective size. A lack of equilibrium and upstream migration may have dampened the effects of dendritic structure. We suggest that interacting historical and contemporary factors prevent the achievement of the idealized traits of a dendritic metapopulation in nature. © 2016 John Wiley & Sons Ltd.

Genomic diversity is similar between Atlantic Forest restorations and natural remnants for the native tree Casearia sylvestris Sw.

PubMed

Gomes Viana, João Paulo; Bohrer Monteiro Siqueira, Marcos Vinícius; Araujo, Fabiano Lucas; Grando, Carolina; Sanae Sujii, Patricia; Silvestre, Ellida de Aguiar; Novello, Mariana; Pinheiro, José Baldin; Cavallari, Marcelo Mattos; Brancalion, Pedro H S; Rodrigues, Ricardo Ribeiro; Pereira de Souza, Anete; Catchen, Julian; Zucchi, Maria I

2018-01-01

The primary focus of tropical forest restoration has been the recovery of forest structure and tree taxonomic diversity, with limited attention given to genetic conservation. Populations reintroduced through restoration plantings may have low genetic diversity and be genetically structured due to founder effects and genetic drift, which limit the potential of restoration to recover ecologically resilient plant communities. Here, we studied the genetic diversity, genetic structure and differentiation using single nucleotide polymorphisms (SNP) markers between restored and natural populations of the native tree Casearia sylvestris in the Atlantic Forest of Brazil. We sampled leaves from approximately 24 adult individuals in each of the study sites: two restoration plantations (27 and 62 years old) and two forest remnants. We prepared and sequenced a genotyping-by-sequencing library, SNP markers were identified de novo using Stacks pipeline, and genetic parameters and structure analyses were then estimated for populations. The sequencing step was successful for 80 sampled individuals. Neutral genetic diversity was similar among restored and natural populations (AR = 1.72 ± 0.005; HO = 0.135 ± 0.005; HE = 0.167 ± 0.005; FIS = 0.16 ± 0.022), which were not genetically structured by population subdivision. In spite of this absence of genetic structure by population we found genetic structure within populations but even so there is not spatial genetic structure in any population studied. Less than 1% of the neutral alleles were exclusive to a population. In general, contrary to our expectations, restoration plantations were then effective for conserving tree genetic diversity in human-modified tropical landscapes. Furthermore, we demonstrate that genotyping-by-sequencing can be a useful tool in restoration genetics.

Population genetic structure of the African elephant in Uganda based on variation at mitochondrial and nuclear loci: evidence for male-biased gene flow.

PubMed

Nyakaana, S; Arctander, P

1999-07-01

A drastic decline has occurred in the size of the Uganda elephant population in the last 40 years, exacerbated by two main factors; an increase in the size of the human population and poaching for ivory. One of the attendant consequences of such a decline is a reduction in the amount of genetic diversity in the surviving populations due to increased effects of random genetic drift. Information about the amount of genetic variation within and between the remaining populations is vital for their future conservation and management. The genetic structure of the African elephant in Uganda was examined using nucleotide variation of mitochondrial control region sequences and four nuclear microsatellite loci in 72 individuals from three localities. Eleven mitochondrial DNA (mtDNA) haplotypes were observed, nine of which were geographically localized. We found significant genetic differentiation between the three populations at the mitochondrial locus while three out of the four microsatellite loci differentiated KV and QE, one locus differentiated KV and MF and no loci differentiated MF and QE. Expected heterozygosity at the four loci varied between 0.51 and 0.84 while nucleotide diversity at the mitochondrial locus was 1.4%. Incongruent patterns of genetic variation within and between populations were revealed by the two genetic systems, and we have explained these in terms of the differences in the effective population sizes of the two genomes and male-biased gene flow between populations.

Geographic isolation drives divergence of uncorrelated genetic and song variation in the Ruddy-capped Nightingale-Thrush (Catharus frantzii; Aves: Turdidae).

PubMed

Ortiz-Ramírez, Marco F; Andersen, Michael J; Zaldívar-Riverón, Alejandro; Ornelas, Juan Francisco; Navarro-Sigüenza, Adolfo G

2016-01-01

Montane barriers influence the evolutionary history of lineages by promoting isolation of populations. The effects of these historical processes are evident in patterns of differentiation among extant populations, which are often expressed as genetic and behavioral variation between populations. We investigated the effects of geographic barriers on the evolutionary history of a Mesoamerican bird by studying patterns of genetic and vocal variation in the Ruddy-capped Nightingale-Thrush (Turdidae: Catharus frantzii), a non-migratory oscine bird that inhabits montane forests from central Mexico to Panama. We reconstructed the phylogeographic history and estimated divergence times between populations using Bayesian and maximum likelihood methods. We found strong support for the existence of four mitochondrial lineages of C. frantzii corresponding to isolated mountain ranges: Sierra Madre Oriental; Sierra Madre del Sur; the highlands of Chiapas, Guatemala, and El Salvador; and the Talamanca Cordillera. Vocal features in C. frantzii were highly variable among the four observed clades, but vocal variation and genetic variation were uncorrelated. Song variation in C. frantzii suggests that sexual selection and cultural drift could be important factors driving song differentiation in C. frantzii. Copyright © 2015 Elsevier Inc. All rights reserved.

Influenza virus sequence feature variant type analysis: evidence of a role for NS1 in influenza virus host range restriction.

PubMed

Noronha, Jyothi M; Liu, Mengya; Squires, R Burke; Pickett, Brett E; Hale, Benjamin G; Air, Gillian M; Galloway, Summer E; Takimoto, Toru; Schmolke, Mirco; Hunt, Victoria; Klem, Edward; García-Sastre, Adolfo; McGee, Monnie; Scheuermann, Richard H

2012-05-01

Genetic drift of influenza virus genomic sequences occurs through the combined effects of sequence alterations introduced by a low-fidelity polymerase and the varying selective pressures experienced as the virus migrates through different host environments. While traditional phylogenetic analysis is useful in tracking the evolutionary heritage of these viruses, the specific genetic determinants that dictate important phenotypic characteristics are often difficult to discern within the complex genetic background arising through evolution. Here we describe a novel influenza virus sequence feature variant type (Flu-SFVT) approach, made available through the public Influenza Research Database resource (www.fludb.org), in which variant types (VTs) identified in defined influenza virus protein sequence features (SFs) are used for genotype-phenotype association studies. Since SFs have been defined for all influenza virus proteins based on known structural, functional, and immune epitope recognition properties, the Flu-SFVT approach allows the rapid identification of the molecular genetic determinants of important influenza virus characteristics and their connection to underlying biological functions. We demonstrate the use of the SFVT approach to obtain statistical evidence for effects of NS1 protein sequence variations in dictating influenza virus host range restriction.

Genetic Drift Linked to Heterogeneous Landscape and Ecological Specialization Drives Diversification in the Alpine Endemic Columbine Aquilegia thalictrifolia.

PubMed

Lega, Margherita; Fior, Simone; Li, Mingai; Leonardi, Stefano; Varotto, Claudio

2014-01-01

The European Alpine system is an extensive mountain range, whose heterogeneous landscape together with Quaternary climatic oscillations significantly affected organismal diversity and distribution in Europe. The model genus Aquilegia represents a textbook example of a rapid and recent radiation through the Northern hemisphere, with the majority of the European taxa occuring in the Alpine system. However, the processes governing genetic differentiation of the genus in this complex geographic area are still widely unexplored. In this work, we used 9 microsatellite loci to study the genetic structure and diversity of 11 populations of Aquilegia thalictrifolia Schott & Kotschy, an alpine taxon characterized by a marked ecological specificity. We found that, despite the endemic and fragmented distribution, A. thalictrifolia has overall high levels of heterozygosity, which is consistent to the substantial inbreeding depression that characterizes the genus. Strong spatial genetic structuring of populations suggests a historical prevalence of genetic drift over gene flow, with natural barriers and ecological niche hindering migration. An analytical comparison of fixation and population differentiation indexes allowed us to infer hypotheses of the postglacial history and more recent demographic events that have influenced the genetics of the species. Overall, our results indicate allopatry as a major force of differentiation in the European scenario, likely to underlie the development of taxonomic boundaries in a broader geographic context. This adds to previous notions on the primary evolutionary forces shaping the Aquilegia radiation in Europe. © The American Genetic Association 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Effects of Isolation by Continental Islands in the Seto Inland Sea, Japan, on Genetic Diversity of the Large Japanese Field Mouse, Apodemus speciosus (Rodentia: Muridae), Inferred from the Mitochondrial Dloop Region.

PubMed

Sato, Jun J; Tasaka, Yurina; Tasaka, Ryoya; Gunji, Kentaro; Yamamoto, Yuya; Takada, Yasushi; Uematsu, Yasushi; Sakai, Eiichi; Tateishi, Takashi; Yamaguchi, Yasunori

2017-04-01

To study the effects of post-glacial isolation by islands on population genetic diversity and differentiation of the large Japanese field mouse, Apodemus speciosus, we examined partial nucleotide sequences of the mitochondrial Dloop region (ca. 300 bp) in 231 individuals collected from islands in the Seto Inland Sea and adjacent regions on Honshu and Shikoku Islands in the western part of the Japanese archipelago. Molecular phylogenetic and network analyses showed that haplotypes in each island tended to form monophyletic groups, while those in Honshu and Shikoku (the major Japanese islands) showed scattered relationships and were connected with island haplotypes. These observations suggest that a set of Honshu and Shikoku haplotypes became the ancestral lineages of the island population. No gene flow was detected among island populations, indicating that independent evolution occurred on each island, without the influence of human activities, since the establishment of the islands in the Holocene. Population genetic diversities on each island were lower than those on Honshu and Shikoku. Comparison between genetic diversity and island area size showed positive correlations and supported the suggestion that genetic drift is a major factor that shaped the current haplotype constitution of the islands in the Seto Inland Sea.

Individual and population-level responses to ocean acidification.

PubMed

Harvey, Ben P; McKeown, Niall J; Rastrick, Samuel P S; Bertolini, Camilla; Foggo, Andy; Graham, Helen; Hall-Spencer, Jason M; Milazzo, Marco; Shaw, Paul W; Small, Daniel P; Moore, Pippa J

2016-01-29

Ocean acidification is predicted to have detrimental effects on many marine organisms and ecological processes. Despite growing evidence for direct impacts on specific species, few studies have simultaneously considered the effects of ocean acidification on individuals (e.g. consequences for energy budgets and resource partitioning) and population level demographic processes. Here we show that ocean acidification increases energetic demands on gastropods resulting in altered energy allocation, i.e. reduced shell size but increased body mass. When scaled up to the population level, long-term exposure to ocean acidification altered population demography, with evidence of a reduction in the proportion of females in the population and genetic signatures of increased variance in reproductive success among individuals. Such increased variance enhances levels of short-term genetic drift which is predicted to inhibit adaptation. Our study indicates that even against a background of high gene flow, ocean acidification is driving individual- and population-level changes that will impact eco-evolutionary trajectories.

Spatial and temporal genetic variation of Echinostoma revolutum (Trematoda: Echinostomatidae) from Thailand and the Lao PDR.

PubMed

Saijuntha, Weerachai; Tantrawatpan, Chairat; Sithithaworn, Paiboon; Andrews, Ross H; Petney, Trevor N

2011-05-01

A total of 314 individual Echinostoma revolutum were collected at different locations and times from domestic ducks from Khon Kaen Province, Thailand and Vientiane Province, the Lao People's Democratic Republic (PDR). Genetic variation of these parasites was analyzed using multilocus enzyme electrophoresis at three polymorphic loci namely, glucose-6-phosphate dehydrogenase (G6pd), malic enzyme (Me) and peptidase valine-leucine (PepA). High levels of genetic variability were found within and between populations. Significant heterozygote deficiencies compared with the predictions under Hardy-Weinberg equilibrium were detected in populations from Thailand and the Lao PDR for all loci except G6pd-1. Significant genetic differentiation was observed between spatially separated populations from Thailand and the Lao PDR. This as also true for some samples collected at different times in Thailand. The variability found may be consistent with a Wahlund effect, genetic drift and/or other factors such as the population structure of snail hosts. Our data provide further insight into the process of genetic divergence within and among geographically and temporally isolated populations of E. revolutum, and potentially other medically important echinostomes in Southeast Asia. Copyright © 2011 Elsevier B.V. All rights reserved.

Population demographics and genetic diversity in remnant and translocated populations of sea otters

USGS Publications Warehouse

Bodkin, James L.; Ballachey, Brenda E.; Cronin, M.A.; Scribner, K.T.

1999-01-01

The effects of small population size on genetic diversity and subsequent population recovery are theoretically predicted, but few empirical data are available to describe those relations. We use data from four remnant and three translocated sea otter (Enhydra lutris) populations to examine relations among magnitude and duration of minimum population size, population growth rates, and genetic variation. Metochondrial (mt)DNA haplotype diversity was correlated with the number of years at minimum population size (r = -0.741, p = 0.038) and minimum population size (r = 0.709, p = 0.054). We found no relation between population growth and haplotype diversity, altough growth was significantly greater in translocated than in remnant populations. Haplotype diversity in populations established from two sources was higher than in a population established from a single source and was higher than in the respective source populations. Haplotype frequencies in translocated populations of founding sizes of 4 and 28 differed from expected, indicating genetic drift and differential reproduction between source populations, whereas haplotype frequencies in a translocated population with a founding size of 150 did not. Relations between population demographics and genetic characteristics suggest that genetic sampling of source and translocated populations can provide valuable inferences about translocations.

Effects of magnetic drift tangential to magnetic surfaces on neoclassical transport in non-axisymmetric plasmas

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

Matsuoka, Seikichi, E-mail: matsuoka@rist.or.jp; Satake, Shinsuke; Kanno, Ryutaro

2015-07-15

In evaluating neoclassical transport by radially local simulations, the magnetic drift tangential to a flux surface is usually ignored in order to keep the phase-space volume conservation. In this paper, effect of the tangential magnetic drift on the local neoclassical transport is investigated. To retain the effect of the tangential magnetic drift in the local treatment of neoclassical transport, a new local formulation for the drift kinetic simulation is developed. The compressibility of the phase-space volume caused by the tangential magnetic drift is regarded as a source term for the drift kinetic equation, which is solved by using a two-weightmore » δf Monte Carlo method for non-Hamiltonian system [G. Hu and J. A. Krommes, Phys. Plasmas 1, 863 (1994)]. It is demonstrated that the effect of the drift is negligible for the neoclassical transport in tokamaks. In non-axisymmetric systems, however, the tangential magnetic drift substantially changes the dependence of the neoclassical transport on the radial electric field E{sub r}. The peaked behavior of the neoclassical radial fluxes around E{sub r }={sub  }0 observed in conventional local neoclassical transport simulations is removed by taking the tangential magnetic drift into account.« less

EPA and States' Collective Efforts Lead to Regulatory Action on Dicamba

EPA Pesticide Factsheets

Agreement with Monsanto, BASF and DuPont on measures to further minimize the potential for drift to damage neighboring crops from the use of dicamba formulations used to control weeds in genetically modified cotton and soybeans.

Positive selection drives faster-Z evolution in silkmoths

PubMed Central

Sackton, Timothy B.; Corbett-Detig, Russell B.; Nagaraju, Javaregowda; Vaishna, R. Lakshmi; Arunkumar, Kallare P.; Hartl, Daniel L.

2014-01-01

Genes linked to X or Z chromosomes, which are hemizygous in the heterogametic sex, are predicted to evolve at different rates than those on autosomes. This “faster-X effect” can arise either as a consequence of hemizygosity, which leads to more efficient selection for recessive beneficial mutations in the heterogametic sex, or as a consequence of reduced effective population size of the hemizygous chromosome, which leads to increased fixation of weakly deleterious mutations due to genetic drift. Empirical results to date suggest that, while the overall pattern across taxa is complicated, systems with male-heterogamy show a faster-X effect attributable to more efficient selection, while the faster-Z effect in female-heterogametic taxa is attributable to increased drift. To test the generality of the faster-Z pattern seen in birds and snakes, we sequenced the genome of the Lepidopteran silkmoth Bombyx huttoni. We show that silkmoths experience faster-Z evolution, but unlike in birds and snakes, the faster-Z effect appears to be attributable to more efficient positive selection. These results suggest that female-heterogamy alone is unlikely to explain the reduced efficacy of selection on the bird Z chromosome. It is likely that many factors, including differences in overall effective population size, influence Z chromosome evolution. PMID:24826901

Effects of particle drifts on the solar modulation of galactic cosmic rays

NASA Technical Reports Server (NTRS)

Jokipii, J. R.; Levy, E. H.

1977-01-01

Gradient and curvature drifts in an Archimedean-spiral magnetic field are shown to produce a significant effect on the modulation of galactic cosmic rays by the solar wind. The net modulation, heliocentric radial gradient, and average energy change of particles which reach the inner solar system are significantly reduced. The effects of drifts are due to the fact that cosmic rays for which the drift velocity is comparable to the wind velocity or larger, have more rapid access to the inner solar system than in the absence of drifts.

Gene networks, occlusal clocks, and functional patches: new understanding of pattern and process in the evolution of the dentition.

PubMed

Polly, P David

2015-05-01

Our understanding of the evolution of the dentition has been transformed by advances in the developmental biology, genetics, and functional morphology of teeth, as well as the methods available for studying tooth form and function. The hierarchical complexity of dental developmental genetics combined with dynamic effects of cells and tissues during development allow for substantial, rapid, and potentially non-linear evolutionary changes. Studies of selection on tooth function in the wild and evolutionary functional comparisons both suggest that tooth function and adaptation to diets are the most important factors guiding the evolution of teeth, yet selection against random changes that produce malocclusions (selectional drift) may be an equally important factor in groups with tribosphenic dentitions. These advances are critically reviewed here.

Bottlenecks drive temporal and spatial genetic changes in alpine caddisfly metapopulations.

PubMed

Shama, Lisa N S; Kubow, Karen B; Jokela, Jukka; Robinson, Christopher T

2011-09-27

Extinction and re-colonisation of local populations is common in ephemeral habitats such as temporary streams. In most cases, such population turnover leads to reduced genetic diversity within populations and increased genetic differentiation among populations due to stochastic founder events, genetic drift, and bottlenecks associated with re-colonisation. Here, we examined the spatio-temporal genetic structure of 8 alpine caddisfly populations inhabiting permanent and temporary streams from four valleys in two regions of the Swiss Alps in years before and after a major stream drying event, the European heat wave in summer 2003. We found that population turnover after 2003 led to a loss of allelic richness and gene diversity but not to significant changes in observed heterozygosity. Within all valleys, permanent and temporary streams in any given year were not differentiated, suggesting considerable gene flow and admixture between streams with differing hydroperiods. Large changes in allele frequencies after 2003 resulted in a substantial increase in genetic differentiation among valleys within one to two years (1-2 generations) driven primarily by drift and immigration. Signatures of genetic bottlenecks were detected in all 8 populations after 2003 using the M-ratio method, but in no populations when using a heterozygosity excess method, indicating differential sensitivity of bottleneck detection methods. We conclude that genetic differentiation among A. uncatus populations changed markedly both temporally and spatially in response to the extreme climate event in 2003. Our results highlight the magnitude of temporal population genetic changes in response to extreme events. More specifically, our results show that extreme events can cause rapid genetic divergence in metapopulations. Further studies are needed to determine if recovery from this perturbation through gradual mixing of diverged populations by migration and gene flow leads to the pre-climate event state, or whether the observed changes represent a new genetic equilibrium.

Inbred or Outbred? Genetic Diversity in Laboratory Rodent Colonies

PubMed Central

Brekke, Thomas D.; Steele, Katherine A.; Mulley, John F.

2017-01-01

Nonmodel rodents are widely used as subjects for both basic and applied biological research, but the genetic diversity of the study individuals is rarely quantified. University-housed colonies tend to be small and subject to founder effects and genetic drift; so they may be highly inbred or show substantial genetic divergence from other colonies, even those derived from the same source. Disregard for the levels of genetic diversity in an animal colony may result in a failure to replicate results if a different colony is used to repeat an experiment, as different colonies may have fixed alternative variants. Here we use high throughput sequencing to demonstrate genetic divergence in three isolated colonies of Mongolian gerbil (Meriones unguiculatus) even though they were all established recently from the same source. We also show that genetic diversity in allegedly “outbred” colonies of nonmodel rodents (gerbils, hamsters, house mice, deer mice, and rats) varies considerably from nearly no segregating diversity to very high levels of polymorphism. We conclude that genetic divergence in isolated colonies may play an important role in the “replication crisis.” In a more positive light, divergent rodent colonies represent an opportunity to leverage genetically distinct individuals in genetic crossing experiments. In sum, awareness of the genetic diversity of an animal colony is paramount as it allows researchers to properly replicate experiments and also to capitalize on other genetically distinct individuals to explore the genetic basis of a trait. PMID:29242387

Influence of tungsten fiber’s slow drift on the measurement of G with angular acceleration method

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

Luo, Jie; Wu, Wei-Huang; Zhan, Wen-Ze

In the measurement of the gravitational constant G with angular acceleration method, the equilibrium position of torsion pendulum with tungsten fiber undergoes a linear slow drift, which results in a quadratic slow drift on the angular velocity of the torsion balance turntable under feedback control unit. The accurate amplitude determination of the useful angular acceleration signal with known frequency is biased by the linear slow drift and the coupling effect of the drifting equilibrium position and the room fixed gravitational background signal. We calculate the influences of the linear slow drift and the complex coupling effect on the value ofmore » G, respectively. The result shows that the bias of the linear slow drift on G is 7 ppm, and the influence of the coupling effect is less than 1 ppm.« less

Influence of tungsten fiber's slow drift on the measurement of G with angular acceleration method.

PubMed

Luo, Jie; Wu, Wei-Huang; Xue, Chao; Shao, Cheng-Gang; Zhan, Wen-Ze; Wu, Jun-Fei; Milyukov, Vadim

2016-08-01

In the measurement of the gravitational constant G with angular acceleration method, the equilibrium position of torsion pendulum with tungsten fiber undergoes a linear slow drift, which results in a quadratic slow drift on the angular velocity of the torsion balance turntable under feedback control unit. The accurate amplitude determination of the useful angular acceleration signal with known frequency is biased by the linear slow drift and the coupling effect of the drifting equilibrium position and the room fixed gravitational background signal. We calculate the influences of the linear slow drift and the complex coupling effect on the value of G, respectively. The result shows that the bias of the linear slow drift on G is 7 ppm, and the influence of the coupling effect is less than 1 ppm.

Influence of tungsten fiber's slow drift on the measurement of G with angular acceleration method

NASA Astrophysics Data System (ADS)

Luo, Jie; Wu, Wei-Huang; Xue, Chao; Shao, Cheng-Gang; Zhan, Wen-Ze; Wu, Jun-Fei; Milyukov, Vadim

2016-08-01

In the measurement of the gravitational constant G with angular acceleration method, the equilibrium position of torsion pendulum with tungsten fiber undergoes a linear slow drift, which results in a quadratic slow drift on the angular velocity of the torsion balance turntable under feedback control unit. The accurate amplitude determination of the useful angular acceleration signal with known frequency is biased by the linear slow drift and the coupling effect of the drifting equilibrium position and the room fixed gravitational background signal. We calculate the influences of the linear slow drift and the complex coupling effect on the value of G, respectively. The result shows that the bias of the linear slow drift on G is 7 ppm, and the influence of the coupling effect is less than 1 ppm.

Intracellular population genetics: evidence for random drift of mitochondrial allele frequencies in Saccharomyces cerevisiae and Schizosaccharomyces pombe.

PubMed

Thrailkill, K M; Birky, C W

1980-09-01

We report evidence for random drift of mitochondrial allele frequencies in zygote clones of Saccharomyces cerevisiae and Schizosaccharomyces pombe. Monofactorial and bifactorial crosses were done, using strains resistant or sensitive to erythromycin (alleles Er, Es), oligomycin (Or, Os), or diuron (Dr, Ds). The frequencies of resistant and sensitive cells (and thus the frequencies of the resistant and sensitive alleles) were determined for each of a number of clones of diploid cells arising from individual zygotes. Allele frequencies were extremely variable among these zygote clones; some clones were "uniparental," with mitochondrial alleles from only one parent present. These observations suggest random drift of the allele frequencies in the population of mitochondrial genes within an individual zygote and its diploid progeny. Drift would cease when all the cells in a clone become homoplasmic, due to segregation of the mitochondrial genomes during vegetative cell divisions. To test this, we delayed cell division (and hence segregation) for varying times by starving zygotes in order to give drift more time to operate. As predicted, delaying cell division resulted in an increase in the variance of allele frequencies among the zygote clones and an increase in the proportion of uniparental zygote clones. The changes in form of the allele frequency distributions resembled those seen during random drift in finite Mendelian populations. In bifactorial crosses, genotypes as well as individual alleles were fixed or lost in some zygote clones. However, the mean recombination frequency for a large number of clones did not increase when cell division was delayed. Several possible molecular mechanisms for intracellular random drift are discussed.

Estimating black bear population density and genetic diversity at Tensas River, Louisiana using microsatellite DNA markers

USGS Publications Warehouse

Boersen, Mark R.; Clark, Joseph D.; King, Tim L.

2003-01-01

The Recovery Plan for the federally threatened Louisiana black bear (Ursus americanus luteolus) mandates that remnant populations be estimated and monitored. In 1999 we obtained genetic material with barbed-wire hair traps to estimate bear population size and genetic diversity at the 329-km2 Tensas River Tract, Louisiana. We constructed and monitored 122 hair traps, which produced 1,939 hair samples. Of those, we randomly selected 116 subsamples for genetic analysis and used up to 12 microsatellite DNA markers to obtain multilocus genotypes for 58 individuals. We used Program CAPTURE to compute estimates of population size using multiple mark-recapture models. The area of study was almost entirely circumscribed by agricultural land, thus the population was geographically closed. Also, study-area boundaries were biologically discreet, enabling us to accurately estimate population density. Using model Chao Mh to account for possible effects of individual heterogeneity in capture probabilities, we estimated the population size to be 119 (SE=29.4) bears, or 0.36 bears/km2. We were forced to examine a substantial number of loci to differentiate between some individuals because of low genetic variation. Despite the probable introduction of genes from Minnesota bears in the 1960s, the isolated population at Tensas exhibited characteristics consistent with inbreeding and genetic drift. Consequently, the effective population size at Tensas may be as few as 32, which warrants continued monitoring or possibly genetic augmentation.

Conflicts in maintaining biodiversity at multiple scales.

PubMed

Lankau, Richard A

2011-05-01

Biodiversity consists of multiple scales, including functional diversity in ecological traits, species diversity and genetic diversity within species, and is declining across the globe, largely in response to human activities. While species extinctions are the most obvious aspect of this, there has also been a more insidious loss of genetic diversity within species. While a vast literature concerns each of these scales of biodiversity, less is known about how different scales affect one another. In particular, genetic and species diversity may influence each other in numerous ways, both positively and negatively. However, we know little about the mechanism behind these patterns. In this issue of Molecular Ecology, Nestmann et al. (2011) experimentally explore the effect of species and functional diversity and composition of grassland plant communities on the genetic structure of one of the component species. Increasing species richness led to greater changes in the genetic composition of the focal populations over 4 years, primarily because of genetic drift in smaller population sizes. However, there were also genetic changes in response to particular plant functional groups, indicating selective differences driven by plant community composition. These results suggest that different levels of biodiversity can trade-off in communities, which may prove a challenge for conservation biologists seeking to preserve all aspects of biodiversity.

[Helgoland (Germany): hemogenetic study of an island population].

PubMed

Schmidt, H D; Scheil, H G; Winkelbauer, S

2001-03-01

24 haemogenetic markers (5 erythrocyte antigenes, 6 polymorphisms of serum proteins, 12 polymorphisms of red cell enzymes) had been studied in up to 80 individuals from the island of Helgoland (Germany). The cluster analysis separates clearly the Helgoland sample from the neighbouring populations as well as from European standard data. This special position is interpreted partly by genetic peculiarities developed in the course of time, partly as a consequence of genetic drift.

Environmental heterogeneity explains the genetic structure of Continental and Mediterranean populations of Fraxinus angustifolia Vahl.

PubMed

Temunović, Martina; Franjić, Jozo; Satovic, Zlatko; Grgurev, Marin; Frascaria-Lacoste, Nathalie; Fernández-Manjarrés, Juan F

2012-01-01

Tree species with wide distributions often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in a wind-pollinated Mediterranean tree species, Fraxinus angustifolia Vahl, within a recognised glacial refugium in Croatia. We sampled 11 populations from environmentally divergent habitats within the Continental and Mediterranean biogeographical regions. We combined genetic data analyses based on nuclear microsatellite loci, multivariate statistics on environmental data and ecological niche modelling (ENM). We identified a geographic structure with a high genetic diversity and low differentiation in the Continental region, which contrasted with the significantly lower genetic diversity and higher population divergence in the Mediterranean region. The positive and significant correlation between environmental and genetic distances after controlling for geographic distance suggests an important influence of ecological divergence of the sites in shaping genetic variation. The ENM provided support for niche differentiation between the populations from the Continental and Mediterranean regions, suggesting that contemporary populations may represent two divergent ecotypes. Ecotype differentiation was also supported by multivariate environmental and genetic distance analyses. Our results suggest that despite extensive gene flow in continental areas, long-term stability of heterogeneous environments have likely promoted genetic divergence of ashes in this region and can explain the present-day genetic variation patterns of these ancient populations.

Environmental Heterogeneity Explains the Genetic Structure of Continental and Mediterranean Populations of Fraxinus angustifolia Vahl

PubMed Central

Temunović, Martina; Franjić, Jozo; Satovic, Zlatko; Grgurev, Marin; Frascaria-Lacoste, Nathalie; Fernández-Manjarrés, Juan F.

2012-01-01

Tree species with wide distributions often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in a wind-pollinated Mediterranean tree species, Fraxinus angustifolia Vahl, within a recognised glacial refugium in Croatia. We sampled 11 populations from environmentally divergent habitats within the Continental and Mediterranean biogeographical regions. We combined genetic data analyses based on nuclear microsatellite loci, multivariate statistics on environmental data and ecological niche modelling (ENM). We identified a geographic structure with a high genetic diversity and low differentiation in the Continental region, which contrasted with the significantly lower genetic diversity and higher population divergence in the Mediterranean region. The positive and significant correlation between environmental and genetic distances after controlling for geographic distance suggests an important influence of ecological divergence of the sites in shaping genetic variation. The ENM provided support for niche differentiation between the populations from the Continental and Mediterranean regions, suggesting that contemporary populations may represent two divergent ecotypes. Ecotype differentiation was also supported by multivariate environmental and genetic distance analyses. Our results suggest that despite extensive gene flow in continental areas, long-term stability of heterogeneous environments have likely promoted genetic divergence of ashes in this region and can explain the present-day genetic variation patterns of these ancient populations. PMID:22905171

Detecting evolutionary forces in language change.

PubMed

Newberry, Mitchell G; Ahern, Christopher A; Clark, Robin; Plotkin, Joshua B

2017-11-09

Both language and genes evolve by transmission over generations with opportunity for differential replication of forms. The understanding that gene frequencies change at random by genetic drift, even in the absence of natural selection, was a seminal advance in evolutionary biology. Stochastic drift must also occur in language as a result of randomness in how linguistic forms are copied between speakers. Here we quantify the strength of selection relative to stochastic drift in language evolution. We use time series derived from large corpora of annotated texts dating from the 12th to 21st centuries to analyse three well-known grammatical changes in English: the regularization of past-tense verbs, the introduction of the periphrastic 'do', and variation in verbal negation. We reject stochastic drift in favour of selection in some cases but not in others. In particular, we infer selection towards the irregular forms of some past-tense verbs, which is likely driven by changing frequencies of rhyming patterns over time. We show that stochastic drift is stronger for rare words, which may explain why rare forms are more prone to replacement than common ones. This work provides a method for testing selective theories of language change against a null model and reveals an underappreciated role for stochasticity in language evolution.

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

PubMed

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

2017-01-01

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

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

PubMed Central

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

2017-01-01

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

Testing evolutionary hypotheses for phenotypic divergence using landscape genetics.

PubMed

Funk, W Chris; Murphy, Melanie A

2010-02-01

Understanding the evolutionary causes of phenotypic variation among populations has long been a central theme in evolutionary biology. Several factors can influence phenotypic divergence, including geographic isolation, genetic drift, divergent natural or sexual selection, and phenotypic plasticity. But the relative importance of these factors in generating phenotypic divergence in nature is still a tantalizing and unresolved problem in evolutionary biology. The origin and maintenance of phenotypic divergence is also at the root of many ongoing debates in evolutionary biology, such as the extent to which gene flow constrains adaptive divergence (Garant et al. 2007) and the relative importance of genetic drift, natural selection, and sexual selection in initiating reproductive isolation and speciation (Coyne & Orr 2004). In this issue, Wang & Summers (2010) test the causes of one of the most fantastic examples of phenotypic divergence in nature: colour pattern divergence among populations of the strawberry poison frog (Dendrobates pumilio) in Panama and Costa Rica (Fig. 1). This study provides a beautiful example of the use of the emerging field of landscape genetics to differentiate among hypotheses for phenotypic divergence. Using landscape genetic analyses, Wang & Summers were able to reject the hypotheses that colour pattern divergence is due to isolation-by-distance (IBD) or landscape resistance. Instead, the hypothesis left standing is that colour divergence is due to divergent selection, in turn driving reproductive isolation among populations with different colour morphs. More generally, this study provides a wonderful example of how the emerging field of landscape genetics, which has primarily been applied to questions in conservation and ecology, now plays an essential role in evolutionary research.

Heterozygosity-fitness correlations among wild populations of European tree frog (Hyla arborea) detect fixation load.

PubMed

Luquet, E; David, P; Lena, J-P; Joly, P; Konecny, L; Dufresnes, C; Perrin, N; Plenet, S

2011-05-01

Quantifying the impacts of inbreeding and genetic drift on fitness traits in fragmented populations is becoming a major goal in conservation biology. Such impacts occur at different levels and involve different sets of loci. Genetic drift randomly fixes slightly deleterious alleles leading to different fixation load among populations. By contrast, inbreeding depression arises from highly deleterious alleles in segregation within a population and creates variation among individuals. A popular approach is to measure correlations between molecular variation and phenotypic performances. This approach has been mainly used at the individual level to detect inbreeding depression within populations and sometimes at the population level but without consideration about the genetic processes measured. For the first time, we used in this study a molecular approach considering both the interpopulation and intrapopulation level to discriminate the relative importance of inbreeding depression vs. fixation load in isolated and non-fragmented populations of European tree frog (Hyla arborea), complemented with interpopulational crosses. We demonstrated that the positive correlations observed between genetic heterozygosity and larval performances on merged data were mainly caused by co-variations in genetic diversity and fixation load among populations rather than by inbreeding depression and segregating deleterious alleles within populations. Such a method is highly relevant in a conservation perspective because, depending on how populations lose fitness (inbreeding vs. fixation load), specific management actions may be designed to improve the persistence of populations. © 2011 Blackwell Publishing Ltd.

Exploring the biomechanics of taurodontism.

PubMed

Benazzi, Stefano; Nguyen, Huynh N; Kullmer, Ottmar; Hublin, Jean-Jacques

2015-02-01

Taurodontism (i.e. enlarged pulp chamber with concomitant apical displacement of the root bi/trifurcation) is considered a dental anomaly with relatively low incidence in contemporary societies, but it represents a typical trait frequently found in Neandertal teeth. Four hypotheses can be envisioned to explain the high frequency in Neandertals: adaptation to a specific occlusal loading regime (biomechanical advantage), adaptation to a high attrition diet, pleiotropic or genetic drift effects. In this contribution we used finite element analysis (FEA) and advanced loading concepts based on macrowear information to evaluate whether taurodontism supplies some dental biomechanical advantages. Loads were applied to the digital model of the lower right first molar (RM1 ) of the Neandertal specimen Le Moustier 1, as well as to the digital models of both a shortened and a hyper-taurodontic version of Le Moustier RM1 . Moreover, we simulated a scenario where an object is held between teeth and pulled in different directions to investigate whether taurodontism might be useful for para-masticatory activities. Our results do not show any meaningful difference among all the simulations, pointing out that taurodontism does not improve the functional biomechanics of the tooth and does not favour para-masticatory pulling activities. Therefore, taurodontism should be considered either an adaptation to a high attrition diet or most likely the result of pleiotropic or genetic drift effects. Finally, our results have important implications for modern dentistry during endodontic treatments, as we observed that filling the pulp chamber with dentine-like material increases tooth stiffness, and ultimately tensile stresses in the crown, thus favouring tooth failure. © 2014 Anatomical Society.

Space charge effect in spectrometers of ion mobility increment with planar drift chamber.

PubMed

Elistratov, A A; Sherbakov, L A

2007-01-01

The effect of space charge on the ion beam in a spectrometer of ion mobility increment with the planar drift chamber has been investigated. A model for the drift of ions under a non-uniform high-frequency electric field(1-3) has been developed recently. We have amplified this model by taking space charge effect into account. The ion peak shape taking into consideration the space charge effect is obtained. The output current saturation effect limiting the rise of the ion peak with increasing ion density at the input of the drift chamber of a spectrometer is observed. We show that the saturation effect is caused by the following phenomenon. The maximum possible output ion density exists, depending on the ion type (constant ion mobility, k(0)) and the time of the motion of ions through the drift chamber. At the same time, the ion density does not depend on the parameters of the drift chamber.

A rapid, strong, and convergent genetic response to urban habitat fragmentation in four divergent and widespread vertebrates

USGS Publications Warehouse

Delaney, Kathleen Semple; Riley, Seth P.D.; Fisher, Robert N.

2010-01-01

Background: Urbanization is a major cause of habitat fragmentation worldwide. Ecological and conservation theory predicts many potential impacts of habitat fragmentation on natural populations, including genetic impacts. Habitat fragmentation by urbanization causes populations of animals and plants to be isolated in patches of suitable habitat that are surrounded by non-native vegetation or severely altered vegetation, asphalt, concrete, and human structures. This can lead to genetic divergence between patches and in turn to decreased genetic diversity within patches through genetic drift and inbreeding. Methodology/Principal Findings: We examined population genetic patterns using microsatellites in four common vertebrate species, three lizards and one bird, in highly fragmented urban southern California. Despite significant phylogenetic, ecological, and mobility differences between these species, all four showed similar and significant reductions in gene flow over relatively short geographic and temporal scales. For all four species, the greatest genetic divergence was found where development was oldest and most intensive. All four animals also showed significant reduction in gene flow associated with intervening roads and freeways, the degree of patch isolation, and the time since isolation. Conclusions/Significance: Despite wide acceptance of the idea in principle, evidence of significant population genetic changes associated with fragmentation at small spatial and temporal scales has been rare, even in smaller terrestrial vertebrates, and especially for birds. Given the striking pattern of similar and rapid effects across four common and widespread species, including a volant bird, intense urbanization may represent the most severe form of fragmentation, with minimal effective movement through the urban matrix.

Development of genetic diversity, differentiation and structure over 500 years in four ponderosa pine populations.

PubMed

Lesser, M R; Parchman, T L; Jackson, S T

2013-05-01

Population history plays an important role in shaping contemporary levels of genetic variation and geographic structure. This is especially true in small, isolated range-margin populations, where effects of inbreeding, genetic drift and gene flow may be more pronounced than in large continuous populations. Effects of landscape fragmentation and isolation distance may have implications for persistence of range-margin populations if they are demographic sinks. We studied four small, disjunct populations of ponderosa pine over a 500-year period. We coupled demographic data obtained through dendroecological methods with microsatellite data to discern how and when contemporary levels of allelic diversity, among and within-population levels of differentiation, and geographic structure, arose. Alleles accumulated rapidly following initial colonization, demonstrating proportionally high levels of gene flow into the populations. At population sizes of approximately 100 individuals, allele accumulation saturated. Levels of genetic differentiation among populations (F(ST) and Jost's D(est)) and diversity within populations (F(IS)) remained stable through time. There was no evidence of geographic genetic structure at any time in the populations' history. Proportionally, high gene flow in the early stages of population growth resulted in rapid accumulation of alleles and quickly created relatively homogenous genetic patterns among populations. Our study demonstrates that contemporary levels of genetic diversity were formed quickly and early in population development. How contemporary genetic diversity accumulates over time is a key facet of understanding population growth and development. This is especially relevant given the extent and speed at which species ranges are predicted to shift in the coming century. © 2013 Blackwell Publishing Ltd.

A Rapid, Strong, and Convergent Genetic Response to Urban Habitat Fragmentation in Four Divergent and Widespread Vertebrates

PubMed Central

Delaney, Kathleen Semple; Riley, Seth P. D.; Fisher, Robert N.

2010-01-01

Background Urbanization is a major cause of habitat fragmentation worldwide. Ecological and conservation theory predicts many potential impacts of habitat fragmentation on natural populations, including genetic impacts. Habitat fragmentation by urbanization causes populations of animals and plants to be isolated in patches of suitable habitat that are surrounded by non-native vegetation or severely altered vegetation, asphalt, concrete, and human structures. This can lead to genetic divergence between patches and in turn to decreased genetic diversity within patches through genetic drift and inbreeding. Methodology/Principal Findings We examined population genetic patterns using microsatellites in four common vertebrate species, three lizards and one bird, in highly fragmented urban southern California. Despite significant phylogenetic, ecological, and mobility differences between these species, all four showed similar and significant reductions in gene flow over relatively short geographic and temporal scales. For all four species, the greatest genetic divergence was found where development was oldest and most intensive. All four animals also showed significant reduction in gene flow associated with intervening roads and freeways, the degree of patch isolation, and the time since isolation. Conclusions/Significance Despite wide acceptance of the idea in principle, evidence of significant population genetic changes associated with fragmentation at small spatial and temporal scales has been rare, even in smaller terrestrial vertebrates, and especially for birds. Given the striking pattern of similar and rapid effects across four common and widespread species, including a volant bird, intense urbanization may represent the most severe form of fragmentation, with minimal effective movement through the urban matrix. PMID:20862274

TEMPLE: analysing population genetic variation at transcription factor binding sites.

PubMed

Litovchenko, Maria; Laurent, Stefan

2016-11-01

Genetic variation occurring at the level of regulatory sequences can affect phenotypes and fitness in natural populations. This variation can be analysed in a population genetic framework to study how genetic drift and selection affect the evolution of these functional elements. However, doing this requires a good understanding of the location and nature of regulatory regions and has long been a major hurdle. The current proliferation of genomewide profiling experiments of transcription factor occupancies greatly improves our ability to identify genomic regions involved in specific DNA-protein interactions. Although software exists for predicting transcription factor binding sites (TFBS), and the effects of genetic variants on TFBS specificity, there are no tools currently available for inferring this information jointly with the genetic variation at TFBS in natural populations. We developed the software Transcription Elements Mapping at the Population LEvel (TEMPLE), which predicts TFBS, evaluates the effects of genetic variants on TFBS specificity and summarizes the genetic variation occurring at TFBS in intraspecific sequence alignments. We demonstrate that TEMPLE's TFBS prediction algorithms gives identical results to PATSER, a software distribution commonly used in the field. We also illustrate the unique features of TEMPLE by analysing TFBS diversity for the TF Senseless (SENS) in one ancestral and one cosmopolitan population of the fruit fly Drosophila melanogaster. TEMPLE can be used to localize TFBS that are characterized by strong genetic differentiation across natural populations. This will be particularly useful for studies aiming to identify adaptive mutations. TEMPLE is a java-based cross-platform software that easily maps the genetic diversity at predicted TFBSs using a graphical interface, or from the Unix command line. © 2016 John Wiley & Sons Ltd.

Complete mitochondrial genomes of Thai and Lao populations indicate an ancient origin of Austroasiatic groups and demic diffusion in the spread of Tai-Kadai languages.

PubMed

Kutanan, Wibhu; Kampuansai, Jatupol; Srikummool, Metawee; Kangwanpong, Daoroong; Ghirotto, Silvia; Brunelli, Andrea; Stoneking, Mark

2017-01-01

The Tai-Kadai (TK) language family is thought to have originated in southern China and spread to Thailand and Laos, but it is not clear if TK languages spread by demic diffusion (i.e., a migration of people from southern China) or by cultural diffusion, with native Austroasiatic (AA) speakers switching to TK languages. To address this and other questions, we obtained 1234 complete mtDNA genome sequences from 51 TK and AA groups from Thailand and Laos. We find high genetic heterogeneity across the region, with 212 different haplogroups, and significant genetic differentiation among different samples from the same ethnolinguistic group. TK groups are more genetically homogeneous than AA groups, with the latter exhibiting more ancient/basal mtDNA lineages, and showing more drift effects. Modeling of demic diffusion, cultural diffusion, and admixture scenarios consistently supports the spread of TK languages by demic diffusion.

Tempest in a tea pot: How did the public conversation on genetically modified crops drift so far from the facts?

PubMed

Goldstein, Daniel A

2014-06-01

The debate over genetically modified (GM) crops has raged in Europe since 1996, but had barely risen above a whisper in the USA until recent labeling debates raised public attention. This article will explain GM crops and traits discuss safety assessment provide a view on safety from authoritative organizations discuss selected issues of current debate, and provide the author's perspective as to why the public debate has drifted so far from scientific reality. The economic and environmental benefits of GM crops are beyond scope, but references are provided. GM food and feed undergo comprehensive assessments using recognized approaches to assure they are as safe as the conventional congener. Issues of food safety and nutrition, unrelated to the GM process, may arise when GM foods display novel components or composition. Unanticipated genetic effects in GM crops appear to be limited in contrast to existing variations among conventional varieties resulting from breeding, mutation, and natural mobile genetic elements. Allergenic potential is assessed when selecting genes for introduction into GM crops and remains a theoretical risk to date. Emerging weed and insect resistance is not unique to GM technology and will require the use of integrated pest management/best practices for pest control. Gene flow from GM crops to wild relatives is limited by existing biological barriers but can at time be a relevant consideration in gene selection and planting practices. Insect-resistant GM crops have significantly reduced use of chemical insecticides and appear to have reduced the incidence of pesticide poisoning in areas where small scale farming and hand application are common. Changes in herbicide patterns are more complex and are evolving over time in response to weed resistance management needs. Recent public debate is driven by a combination of unfounded allegations about the technology and purveyors, pseudoscience, and attempts to apply a strict precautionary principle.

Purifying selection and genetic drift shaped Pleistocene evolution of the mitochondrial genome in an endangered Australian freshwater fish.

PubMed

Pavlova, A; Gan, H M; Lee, Y P; Austin, C M; Gilligan, D M; Lintermans, M; Sunnucks, P

2017-05-01

Genetic variation in mitochondrial genes could underlie metabolic adaptations because mitochondrially encoded proteins are directly involved in a pathway supplying energy to metabolism. Macquarie perch from river basins exposed to different climates differ in size and growth rate, suggesting potential presence of adaptive metabolic differences. We used complete mitochondrial genome sequences to build a phylogeny, estimate lineage divergence times and identify signatures of purifying and positive selection acting on mitochondrial genes for 25 Macquarie perch from three basins: Murray-Darling Basin (MDB), Hawkesbury-Nepean Basin (HNB) and Shoalhaven Basin (SB). Phylogenetic analysis resolved basin-level clades, supporting incipient speciation previously inferred from differentiation in allozymes, microsatellites and mitochondrial control region. The estimated time of lineage divergence suggested an early- to mid-Pleistocene split between SB and the common ancestor of HNB+MDB, followed by mid-to-late Pleistocene splitting between HNB and MDB. These divergence estimates are more recent than previous ones. Our analyses suggested that evolutionary drivers differed between inland MDB and coastal HNB. In the cooler and more climatically variable MDB, mitogenomes evolved under strong purifying selection, whereas in the warmer and more climatically stable HNB, purifying selection was relaxed. Evidence for relaxed selection in the HNB includes elevated transfer RNA and 16S ribosomal RNA polymorphism, presence of potentially mildly deleterious mutations and a codon (ATP6 113 ) displaying signatures of positive selection (ratio of nonsynonymous to synonymous substitution rates (dN/dS) >1, radical change of an amino-acid property and phylogenetic conservation across the Percichthyidae). In addition, the difference could be because of stronger genetic drift in the smaller and historically more subdivided HNB with low per-population effective population sizes.

Predicting nuclear gene coalescence from mitochondrial data: the three-times rule.

PubMed

Palumbi, S R; Cipriano, F; Hare, M P

2001-05-01

Coalescence theory predicts when genetic drift at nuclear loci will result in fixation of sequence differences to produce monophyletic gene trees. However, the theory is difficult to apply to particular taxa because it hinges on genetically effective population size, which is generally unknown. Neutral theory also predicts that evolution of monophyly will be four times slower in nuclear than in mitochondrial genes primarily because genetic drift is slower at nuclear loci. Variation in mitochondrial DNA (mtDNA) within and between species has been studied extensively, but can these mtDNA data be used to predict coalescence in nuclear loci? Comparison of neutral theories of coalescence of mitochondrial and nuclear loci suggests a simple rule of thumb. The "three-times rule" states that, on average, most nuclear loci will be monophyletic when the branch length leading to the mtDNA sequences of a species is three times longer than the average mtDNA sequence diversity observed within that species. A test using mitochondrial and nuclear intron data from seven species of whales and dolphins suggests general agreement with predictions of the three-times rule. We define the coalescence ratio as the mitochondrial branch length for a species divided by intraspecific mtDNA diversity. We show that species with high coalescence ratios show nuclear monophyly, whereas species with low ratios have polyphyletic nuclear gene trees. As expected, species with intermediate coalescence ratios show a variety of patterns. Especially at very high or low coalescence ratios, the three-times rule predicts nuclear gene patterns that can help detect the action of selection. The three-times rule may be useful as an empirical benchmark for evaluating evolutionary processes occurring at multiple loci.

Characterization of the genetic profile of five Danish dog breeds.

PubMed

Pertoldi, C; Kristensen, T N; Loeschcke, V; Berg, P; Praebel, A; Stronen, A V; Proschowsky, H F; Fredholm, M

2013-11-01

This investigation presents results from a genetic characterization of 5 Danish dog breeds genotyped on the CanineHD BeadChip microarray with 170,000 SNP. The breeds investigated were 1) Danish Spitz (DS; n=8), 2) Danish-Swedish Farm Dog (DSF; n=18), 3) Broholmer (BR; n=22), 4) Old Danish Pointing Dog (ODP; n=24), and 5) Greenland Dog (GD; n=23). The aims of the investigation were to characterize the genetic profile of the abovementioned dog breeds by quantifying the genetic differentiation among them and the degree of genetic homogeneity within breeds. The genetic profile was determined by means of principal component analysis (PCA) and through a Bayesian clustering method. Both the PCA and the Bayesian clustering method revealed a clear genetic separation of the 5 breeds. The level of genetic variation within the breeds varied. The expected heterozygosity (HE) as well as the degree of polymorphism (P%) ranked the dog breeds in the order DS>DSF>BR>ODP>GD. Interestingly, the breed with a tenfold higher census population size compared to the other breeds, the Greenland Dog, had the lowest within-breed genetic variation, emphasizing that census size is a poor predictor of genetic variation. The observed differences in variation among and within dog breeds may be related to factors such as genetic drift, founder effects, genetic admixture, and population bottlenecks. We further examined whether the observed genetic patterns in the 5 dog breeds can be used to design breeding strategies for the preservation of the genetic pool of these dog breeds.

Redshift drift in an inhomogeneous universe: averaging and the backreaction conjecture

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

Koksbang, S.M.; Hannestad, S., E-mail: koksbang@phys.au.dk, E-mail: sth@phys.au.dk

2016-01-01

An expression for the average redshift drift in a statistically homogeneous and isotropic dust universe is given. The expression takes the same form as the expression for the redshift drift in FLRW models. It is used for a proof-of-principle study of the effects of backreaction on redshift drift measurements by combining the expression with two-region models. The study shows that backreaction can lead to positive redshift drift at low redshifts, exemplifying that a positive redshift drift at low redshifts does not require dark energy. Moreover, the study illustrates that models without a dark energy component can have an average redshiftmore » drift observationally indistinguishable from that of the standard model according to the currently expected precision of ELT measurements. In an appendix, spherically symmetric solutions to Einstein's equations with inhomogeneous dark energy and matter are used to study deviations from the average redshift drift and effects of local voids.« less

Measuring genetic distances between breeds: use of some distances in various short term evolution models

PubMed Central

Laval, Guillaume; SanCristobal, Magali; Chevalet, Claude

2002-01-01

Many works demonstrate the benefits of using highly polymorphic markers such as microsatellites in order to measure the genetic diversity between closely related breeds. But it is sometimes difficult to decide which genetic distance should be used. In this paper we review the behaviour of the main distances encountered in the literature in various divergence models. In the first part, we consider that breeds are populations in which the assumption of equilibrium between drift and mutation is verified. In this case some interesting distances can be expressed as a function of divergence time, t, and therefore can be used to construct phylogenies. Distances based on allele size distribution (such as (δμ)2 and derived distances), taking a mutation model of microsatellites, the Stepwise Mutation Model, specifically into account, exhibit large variance and therefore should not be used to accurately infer phylogeny of closely related breeds. In the last section, we will consider that breeds are small populations and that the divergence times between them are too small to consider that the observed diversity is due to mutations: divergence is mainly due to genetic drift. Expectation and variance of distances were calculated as a function of the Wright-Malécot inbreeding coefficient, F. Computer simulations performed under this divergence model show that the Reynolds distance [57]is the best method for very closely related breeds. PMID:12270106

Identifying Loci Under Selection Against Gene Flow in Isolation-with-Migration Models

PubMed Central

Sousa, Vitor C.; Carneiro, Miguel; Ferrand, Nuno; Hey, Jody

2013-01-01

When divergence occurs in the presence of gene flow, there can arise an interesting dynamic in which selection against gene flow, at sites associated with population-specific adaptations or genetic incompatibilities, can cause net gene flow to vary across the genome. Loci linked to sites under selection may experience reduced gene flow and may experience genetic bottlenecks by the action of nearby selective sweeps. Data from histories such as these may be poorly fitted by conventional neutral model approaches to demographic inference, which treat all loci as equally subject to forces of genetic drift and gene flow. To allow for demographic inference in the face of such histories, as well as the identification of loci affected by selection, we developed an isolation-with-migration model that explicitly provides for variation among genomic regions in migration rates and/or rates of genetic drift. The method allows for loci to fall into any of multiple groups, each characterized by a different set of parameters, thus relaxing the assumption that all loci share the same demography. By grouping loci, the method can be applied to data with multiple loci and still have tractable dimensionality and statistical power. We studied the performance of the method using simulated data, and we applied the method to study the divergence of two subspecies of European rabbits (Oryctolagus cuniculus). PMID:23457232

Genetic Structure in a Small Pelagic Fish Coincides with a Marine Protected Area: Seascape Genetics in Patagonian Fjords

PubMed Central

Ferrada-Fuentes, Sandra; Galleguillos, Ricardo; Hernández, Cristián E.

2016-01-01

Marine environmental variables can play an important role in promoting population genetic differentiation in marine organisms. Although fjord ecosystems have attracted much attention due to the great oscillation of environmental variables that produce heterogeneous habitats, species inhabiting this kind of ecosystem have received less attention. In this study, we used Sprattus fuegensis, a small pelagic species that populates the inner waters of the continental shelf, channels and fjords of Chilean Patagonia and Argentina, as a model species to test whether environmental variables of fjords relate to population genetic structure. A total of 282 individuals were analyzed from Chilean Patagonia with eight microsatellite loci. Bayesian and non-Bayesian analyses were conducted to describe the genetic variability of S. fuegensis and whether it shows spatial genetic structure. Results showed two well-differentiated genetic clusters along the Chilean Patagonia distribution (i.e. inside the embayment area called TicToc, and the rest of the fjords), but no spatial isolation by distance (IBD) pattern was found with a Mantel test analysis. Temperature and nitrate were correlated to the expected heterozygosities and explained the allelic frequency variation of data in the redundancy analyses. These results suggest that the singular genetic differences found in S. fuegensis from inside TicToc Bay (East of the Corcovado Gulf) are the result of larvae retention bya combination of oceanographic mesoscale processes (i.e. the west wind drift current reaches the continental shelf exactly in this zone), and the local geographical configuration (i.e. embayment area, islands, archipelagos). We propose that these features generated an isolated area in the Patagonian fjords that promoted genetic differentiation by drift and a singular biodiversity, adding support to the existence of the largest marine protected area (MPA) of continental Chile, which is the Tic-Toc MPA. PMID:27505009

The effect of stimulus strength on binocular rivalry rate in healthy individuals: Implications for genetic, clinical and individual differences studies.

PubMed

Law, Phillip C F; Miller, Steven M; Ngo, Trung T

2017-11-01

Binocular rivalry (BR) occurs when conflicting images concurrently presented to corresponding retinal locations of each eye stochastically alternate in perception. Anomalies of BR rate have been examined in a range of clinical psychiatric conditions. In particular, slow BR rate has been proposed as an endophenotype for bipolar disorder (BD) to improve power in large-scale genome-wide association studies. Examining the validity of BR rate as a BD endophenotype however requires large-scale datasets (n=1000s to 10,000s), a standardized testing protocol, and optimization of stimulus parameters to maximize separation between BD and healthy groups. Such requirements are indeed relevant to all clinical psychiatric BR studies. Here we address the issue of stimulus optimization by examining the effect of stimulus parameter variation on BR rate and mixed-percept duration (MPD) in healthy individuals. We aimed to identify the stimulus parameters that induced the fastest BR rates with the least MPD. Employing a repeated-measures within-subjects design, 40 healthy adults completed four BR tasks using orthogonally drifting grating stimuli that varied in drift speed and aperture size. Pairwise comparisons were performed to determine modulation of BR rate and MPD by these stimulus parameters, and individual variation of such modulation was also assessed. From amongst the stimulus parameters examined, we found that 8cycles/s drift speed in a 1.5° aperture induced the fastest BR rate without increasing MPD, but that BR rate with this stimulus configuration was not substantially different to BR rate with stimulus parameters we have used in previous studies (i.e., 4cycles/s drift speed in a 1.5° aperture). In addition to contributing to stimulus optimization issues, the findings have implications for Levelt's Proposition IV of binocular rivalry dynamics and individual differences in such dynamics. Copyright © 2017 Elsevier Inc. All rights reserved.

MHC class II diversity of koala (Phascolarctos cinereus) populations across their range

PubMed Central

Lau, Q; Jaratlerdsiri, W; Griffith, J E; Gongora, J; Higgins, D P

2014-01-01

Major histocompatibility complex class II (MHCII) genes code for proteins that bind and present antigenic peptides and trigger the adaptive immune response. We present a broad geographical study of MHCII DA β1 (DAB) and DB β1 (DBB) variants of the koala (Phascolarctos cinereus; n=191) from 12 populations across eastern Australia, with a total of 13 DAB and 7 DBB variants found. We identified greater MHCII variation and, possibly, additional gene copies in koala populations in the north (Queensland and New South Wales) relative to the south (Victoria), confirmed by STRUCTURE analyses and genetic differentiation using analysis of molecular variance. The higher MHCII diversity in the north relative to south could potentially be attributed to (i) significant founder effect in Victorian populations linked to historical translocation of bottlenecked koala populations and (ii) increased pathogen-driven balancing selection and/or local genetic drift in the north. Low MHCII genetic diversity in koalas from the south could reduce their potential response to disease, although the three DAB variants found in the south had substantial sequence divergence between variants. This study assessing MHCII diversity in the koala with historical translocations in some populations contributes to understanding the effects of population translocations on functional genetic diversity. PMID:24690756

The episode of genetic drift defining the migration of humans out of Africa is derived from a large east African population size.

PubMed

Elhassan, Nuha; Gebremeskel, Eyoab Iyasu; Elnour, Mohamed Ali; Isabirye, Dan; Okello, John; Hussien, Ayman; Kwiatksowski, Dominic; Hirbo, Jibril; Tishkoff, Sara; Ibrahim, Muntaser E

2014-01-01

Human genetic variation particularly in Africa is still poorly understood. This is despite a consensus on the large African effective population size compared to populations from other continents. Based on sequencing of the mitochondrial Cytochrome C Oxidase subunit II (MT-CO2), and genome wide microsatellite data we observe evidence suggesting the effective size (Ne) of humans to be larger than the current estimates, with a foci of increased genetic diversity in east Africa, and a population size of east Africans being at least 2-6 fold larger than other populations. Both phylogenetic and network analysis indicate that east Africans possess more ancestral lineages in comparison to various continental populations placing them at the root of the human evolutionary tree. Our results also affirm east Africa as the likely spot from which migration towards Asia has taken place. The study reflects the spectacular level of sequence variation within east Africans in comparison to the global sample, and appeals for further studies that may contribute towards filling the existing gaps in the database. The implication of these data to current genomic research, as well as the need to carry out defined studies of human genetic variation that includes more African populations; particularly east Africans is paramount.

The Role of Genetic Drift in Shaping Modern Human Cranial Evolution: A Test Using Microevolutionary Modeling

PubMed Central

Smith, Heather F.

2011-01-01

The means by which various microevolutionary processes have acted in the past to produce patterns of cranial variation that characterize modern humans is not thoroughly understood. Applying a microevolutionary framework, within- and among-population variance/covariance (V/CV) structure was compared for several functional and developmental modules of the skull across a worldwide sample of modern humans. V/CV patterns in the basicranium, temporal bone, and face are proportional within and among groups, which is consistent with a hypothesis of neutral evolution; however, mandibular morphology deviated from this pattern. Degree of intergroup similarity in facial, temporal bone, and mandibular morphology is significantly correlated with geographic distance; however, much of the variance remains unexplained. These findings provide insight into the evolutionary history of modern human cranial variation by identifying signatures of genetic drift, gene flow, and migration and set the stage for inferences regarding selective pressures that early humans encountered since their initial migrations around the world. PMID:21461369

The Effect of Recurrent Floods on Genetic Composition of Marble Trout Populations

PubMed Central

Pujolar, José Martin; Vincenzi, Simone; Zane, Lorenzo; Jesensek, Dusan; De Leo, Giulio A.; Crivelli, Alain J.

2011-01-01

A changing global climate can threaten the diversity of species and ecosystems. We explore the consequences of catastrophic disturbances in determining the evolutionary and demographic histories of secluded marble trout populations in Slovenian streams subjected to weather extremes, in particular recurrent flash floods and debris flows causing massive mortalities. Using microsatellite data, a pattern of extreme genetic differentiation was found among populations (global F ST of 0.716), which exceeds the highest values reported in freshwater fish. All locations showed low levels of genetic diversity as evidenced by low heterozygosities and a mean of only 2 alleles per locus, with few or no rare alleles. Many loci showed a discontinuous allele distribution, with missing alleles across the allele size range, suggestive of a population contraction. Accordingly, bottleneck episodes were inferred for all samples with a reduction in population size of 3–4 orders of magnitude. The reduced level of genetic diversity observed in all populations implies a strong impact of genetic drift, and suggests that along with limited gene flow, genetic differentiation might have been exacerbated by recurrent mortalities likely caused by flash flood and debris flows. Due to its low evolutionary potential the species might fail to cope with an intensification and altered frequency of flash flood events predicted to occur with climate change. PMID:21931617

Selection and geographic isolation influence hummingbird speciation: genetic, acoustic and morphological divergence in the wedge-tailed sabrewing (Campylopterus curvipennis).

PubMed

González, Clementina; Ornelas, Juan Francisco; Gutiérrez-Rodríguez, Carla

2011-02-08

Mesoamerica is one of the most threatened biodiversity hotspots in the world, yet we are far from understanding the geologic history and the processes driving population divergence and speciation for most endemic taxa. In species with highly differentiated populations selective and/or neutral factors can induce rapid changes to traits involved in mate choice, promoting reproductive isolation between allopatric populations that can eventually lead to speciation. We present the results of genetic differentiation, and explore drift and selection effects in promoting acoustic and morphological divergence among populations of Campylopterus curvipennis, a lekking hummingbird with an extraordinary vocal variability across Mesoamerica. Analyses of two mitochondrial genes and ten microsatellite loci genotyped for 160 individuals revealed the presence of three lineages with no contemporary gene flow: C. c. curvipennis, C. c. excellens, and C. c. pampa disjunctly distributed in the Sierra Madre Oriental, the Tuxtlas region and the Yucatan Peninsula, respectively. Sequence mtDNA and microsatellite data were congruent with two diversification events: an old vicariance event at the Isthmus of Tehuantepec (c. 1.4 Ma), and a more recent Pleistocene split, isolating populations in the Tuxtlas region. Hummingbirds of the excellens group were larger, and those of the pampa group had shorter bills, and lineages that have been isolated the longest shared fewer syllables and differed in spectral and temporal traits of a shared syllable. Coalescent simulations showed that fixation of song types has occurred faster than expected under neutrality but the null hypothesis that morphological divergence resulted from drift was not rejected. Our phylogeographic analyses uncovered the presence of three Mesoamerican wedge-tailed sabrewing lineages, which diverged at different time scales. These results highlight the importance of the Isthmus of Tehuantepec and more recent Pleistocene climatic events in driving isolation and population divergence. Coalescent analyses of the evolution of phenotypic traits suggest that selection is driving song evolution in wedge-tailed sabrewings but drift could not be rejected as a possibility for morphological divergence.

Effect of natural windbreaks on drift reduction in orchard spraying.

PubMed

Wenneker, M; Heijne, B; van de Zande, J C

2005-01-01

In the Netherlands windbreaks are commonly grown to protect orchards against wind damage and to improve micro-climate. Natural windbreaks of broad-leaved trees can also reduce the risk of surface water contamination caused by spray drift during orchard spraying. Spray drift from pesticide applications is a major concern in the Netherlands, especially drift into water courses. So far, several drift reducing measures have been accepted by water quality control organisations and the Board for the Authorization of Pesticides (CTB), e.g. presence of a windbreak (i.e. 70% drift reduction at early season and 90% drift reduction at full leaf, respectively before and after first of May). From the experiments it was concluded that the risk of drift contamination is high during the early developmental stages of the growing season. The 70% drift reduction at early season as determined in previous experiments, appears to be valid only for windbreaks with a certain degree of developed leaves. At full leaf stage 80-90% drift reduction by the windbreak was measured. The use of evergreen windbreaks or wind-break species that develop in early season can reduce the risk of drift contamination considerably. Also, the combination of drift reducing methods, such as one-sided spraying of the last tree row and a windbreak is an effective method to reduce spray drift in the Netherlands in early season.

Genetic structure of the Mon-Khmer speaking groups and their affinity to the neighbouring Tai populations in Northern Thailand

PubMed Central

2011-01-01

Background The Mon-Khmer speaking peoples inhabited northern Thailand before the arrival of the Tai speaking people from southern China in the thirteenth century A.D. Historical and anthropological evidence suggests a close relationship between the Mon-Khmer groups and the present day majority northern Thai groups. In this study, mitochondrial and Y-chromosomal DNA polymorphisms in more than 800 volunteers from eight Mon-Khmer and ten Tai speaking populations were investigated to estimate the degree of genetic divergence between these major linguistic groups and their internal structure. Results A large fraction of genetic variation is observed within populations (about 80% and 90% for mtDNA and the Y-chromosome, respectively). The genetic divergence between populations is much higher in Mon-Khmer than in Tai speaking groups, especially at the paternally inherited markers. The two major linguistic groups are genetically distinct, but only for a marginal fraction (1 to 2%) of the total genetic variation. Genetic distances between populations correlate with their linguistic differences, whereas the geographic distance does not explain the genetic divergence pattern. Conclusions The Mon-Khmer speaking populations in northern Thailand exhibited the genetic divergence among each other and also when compared to Tai speaking peoples. The different drift effects and the post-marital residence patterns between the two linguistic groups are the explanation for a small but significant fraction of the genetic variation pattern within and between them. PMID:21672265

Genetic depletion at adaptive but not neutral loci in an endangered bird species.

PubMed

Hartmann, Stefanie A; Schaefer, H Martin; Segelbacher, Gernot

2014-12-01

Many endangered species suffer from the loss of genetic diversity, but some populations may be able to thrive even if genetically depleted. To investigate the underlying genetic processes of population bottlenecks, we apply an innovative approach for assessing genetic diversity in the last known population of the endangered Pale-headed Brushfinch (Atlapetes pallidiceps) in Ecuador. First, we measure genetic diversity at eleven neutral microsatellite loci and adaptive SNP variation in five Toll-like receptor (TLR) immune system genes. Bottleneck tests confirm genetic drift as the main force shaping genetic diversity in this species and indicate a 99 % reduction in population size dating back several hundred years. Second, we compare contemporary microsatellite diversity with historic museum samples of A. pallidiceps, finding no change in genetic diversity. Third, we compare genetic diversity in the Pale-headed Brushfinch with two co-occurring-related brushfinch species (Atlapetes latinuchus, Buarremon torquatus), finding a reduction of up to 91% diversity in the immune system genes but not in microsatellites. High TLR diversity is linked to decreased survival probabilities in A. pallidiceps. Low TLR diversity is thus probably an adaptation to the specific selection regime within its currently very restricted distribution (approximately 200 ha), but could severely restrict the adaptive potential of the species in the long run. Our study illustrates the importance of investigating both neutral and adaptive markers to assess the effect of population bottlenecks and for recommending specific management plans in endangered species. © 2014 John Wiley & Sons Ltd.

Genetic structure of the Mon-Khmer speaking groups and their affinity to the neighbouring Tai populations in Northern Thailand.

PubMed

Kutanan, Wibhu; Kampuansai, Jatupol; Fuselli, Silvia; Nakbunlung, Supaporn; Seielstad, Mark; Bertorelle, Giorgio; Kangwanpong, Daoroong

2011-06-15

The Mon-Khmer speaking peoples inhabited northern Thailand before the arrival of the Tai speaking people from southern China in the thirteenth century A.D. Historical and anthropological evidence suggests a close relationship between the Mon-Khmer groups and the present day majority northern Thai groups. In this study, mitochondrial and Y-chromosomal DNA polymorphisms in more than 800 volunteers from eight Mon-Khmer and ten Tai speaking populations were investigated to estimate the degree of genetic divergence between these major linguistic groups and their internal structure. A large fraction of genetic variation is observed within populations (about 80% and 90% for mtDNA and the Y-chromosome, respectively). The genetic divergence between populations is much higher in Mon-Khmer than in Tai speaking groups, especially at the paternally inherited markers. The two major linguistic groups are genetically distinct, but only for a marginal fraction (1 to 2%) of the total genetic variation. Genetic distances between populations correlate with their linguistic differences, whereas the geographic distance does not explain the genetic divergence pattern. The Mon-Khmer speaking populations in northern Thailand exhibited the genetic divergence among each other and also when compared to Tai speaking peoples. The different drift effects and the post-marital residence patterns between the two linguistic groups are the explanation for a small but significant fraction of the genetic variation pattern within and between them. © 2011 Kutanan et al; licensee BioMed Central Ltd.

Environmental Variables Explain Genetic Structure in a Beetle-Associated Nematode

PubMed Central

McGaughran, Angela; Morgan, Katy; Sommer, Ralf J.

2014-01-01

The distribution of a species is a complex expression of its ecological and evolutionary history and integrating population genetic, environmental, and ecological data can provide new insights into the effects of the environment on the population structure of species. Previous work demonstrated strong patterns of genetic differentiation in natural populations of the hermaphroditic nematode Pristionchus pacificus in its La Réunion Island habitat, but gave no clear understanding of the role of the environment in structuring this variation. Here, we present what is to our knowledge the first study to statistically evaluate the role of the environment in shaping the structure and distribution of nematode populations. We test the hypothesis that genetic structure in P. pacificus is influenced by environmental variables, by combining population genetic analyses of microsatellite data from 18 populations and 370 strains, with multivariate statistics on environmental data, and species distribution modelling. We assess and quantify the relative importance of environmental factors (geographic distance, altitude, temperature, precipitation, and beetle host) on genetic variation among populations. Despite the fact that geographic populations of P. pacificus comprise vast genetic diversity sourced from multiple ancestral lineages, we find strong evidence for local associations between environment and genetic variation. Further, we show that significantly more genetic variation in P. pacificus populations is explained by environmental variation than by geographic distances. This supports a strong role for environmental heterogeneity vs. genetic drift in the divergence of populations, which we suggest may be influenced by adaptive forces. PMID:24498073

Genetic structure of nomadic Bedouin from Kuwait

PubMed Central

Mohammad, T.; Xue, Yali; Evison, M.; Tyler-Smith, Chris

2009-01-01

Bedouin are traditionally nomadic inhabitants of the Persian Gulf who claim descent from two male lineages: Adnani and Qahtani. We have investigated whether or not this tradition is reflected in the current genetic structure of a sample of 153 Bedouin males from six Kuwaiti tribes, including three tribes from each traditional lineage. Volunteers were genotyped using a panel of autosomal and Y-STRs, and Y-SNPs. The samples clustered with their geographical neighbours in both the autosomal and Y-chromosomal analyses, and showed strong evidence of genetic isolation and drift. Whilst there was no evidence of segregation into the two male lineages, other aspects of genetic structure were in accord with tradition. PMID:19639002

What's in a name? Y chromosomes, surnames and the genetic genealogy revolution.

PubMed

King, Turi E; Jobling, Mark A

2009-08-01

Heritable surnames are highly diverse cultural markers of coancestry in human populations. A patrilineal surname is inherited in the same way as the non-recombining region of the Y chromosome and there should, therefore, be a correlation between the two. Studies of Y haplotypes within surnames, mostly of the British Isles, reveal high levels of coancestry among surname cohorts and the influence of confounding factors, including multiple founders for names, non-paternities and genetic drift. Combining molecular genetics and surname analysis illuminates population structure and history, has potential applications in forensic studies and, in the form of 'genetic genealogy', is an area of rapidly growing interest for the public.

Plant reproduction is altered by simulated herbicide drift to constructed plant communities

EPA Science Inventory

Herbicide drift may have unintended impacts on native vegetation, adversely affecting structure and function of plant communities. However, these potential effects have been rarely studied or quantified. To determine potential ecological effects of herbicide drift, we construct...

Conservation Genetics of Threatened Hippocampus guttulatus in Vulnerable Habitats in NW Spain: Temporal and Spatial Stability of Wild Populations with Flexible Polygamous Mating System in Captivity

PubMed Central

López, Almudena; Vera, Manuel; Planas, Miquel; Bouza, Carmen

2015-01-01

This study was focused on conservation genetics of threatened Hippocampus guttulatus on the Atlantic coast of NW Iberian Peninsula. Information about spatial structure and temporal stability of wild populations was obtained based on microsatellite markers, and used for monitoring a captive breeding program firstly initiated in this zone at the facilities of the Institute of Marine Research (Vigo, Spain). No significant major genetic structure was observed regarding the biogeographical barrier of Cape Finisterre. However, two management units under continuous gene flow are proposed based on the allelic differentiation between South-Atlantic and Cantabrian subpopulations, with small to moderate contemporary effective size based on single-sample methods. Temporal stability was observed in South-Atlantic population samples of H. guttulatus for the six-year period studied, suggesting large enough effective population size to buffer the effects of genetic drift within the time frame of three generations. Genetic analysis of wild breeders and offspring in captivity since 2009 allowed us to monitor the breeding program founded in 2006 in NW Spain for this species. Similar genetic diversity in the renewed and founder broodstock, regarding the wild population of origin, supports suitable renewal and rearing processes to maintain genetic variation in captivity. Genetic parentage proved single-brood monogamy in the wild and in captivity, but flexible short- and long-term mating system under captive conditions, from strict monogamy to polygamy within and/or among breeding seasons. Family analysis showed high reproductive success in captivity under genetic management assisted by molecular relatedness estimates to avoid inbreeding. This study provides genetic information about H. guttulatus in the wild and captivity within an uncovered geographical range for this data deficient species, to be taken into account for management and conservation purposes. PMID:25646777

Effects of spray drift of glyphosate on nontarget terrestrial plants-A critical review.

PubMed

Cederlund, Harald

2017-11-01

Glyphosate is a widely used broad-spectrum postemergent herbicide used for weed control in both agricultural and nonagricultural settings. Spray drift of glyphosate can pose a risk to nontarget terrestrial plants and plant communities outside the intended area of application, but the lack of a well-established predicted-no-effect drift rate makes properly assessing such risk difficult. For this reason, a literature review and meta-analysis was carried out with the aim to determine the level of drift that is likely to cause harm to plants and to explore what spray-reducing targets would be sufficiently protective. No-observed-adverse effect rates, lowest-observed-adverse effect rates, and effect rates giving 10, 25, and 50% effects were extracted from a total of 39 different publications. The data were combined per species, and species sensitivity distributions were constructed and fitted with a log-logistic model to assess protectiveness. No systematic differences were detected between the responses of monocotyledons or dicotyledons, but wild plants were found to be generally less sensitive to glyphosate drift than domesticated plants. The results indicate that restricting spray drift to a level below 5 g a.e./ha would protect approximately 95% of all higher plant species against minor adverse effects of glyphosate drift and that rates below 1 to 2 g a.e./ha would be almost completely protective. No studies were encountered that evaluated effects of spray drift against nonvascular plants, and therefore, the conclusions are only valid for vascular plants. Environ Toxicol Chem 2017;36:2879-2886. © 2017 SETAC. © 2017 SETAC.

Development of novel DNA markers for genetic analysis of grey hamsters by cross-species amplification of microsatellites.

PubMed

Wang, C; Zhang, S J; Du, X Y; Xu, Y M; Huo, X Y; Liao, L F; Chen, Z W

2015-11-13

The grey hamster has been used in biomedical research for decades. However, effective molecular methods for evaluating the genetic structure of this species are lacking, which hinders its wider usage. In this study, we employed cross-amplification of microsatellite loci of species within the same genus by polymerase chain reaction. Loci screened included 107 from the Mongolian gerbil (MG) and 60 from the Chinese hamster (CH); of these, 15 polymorphic loci were identified for the grey hamster. Of the 167 loci screened, 95 (56.9%) with clear bands on agarose gel were initially identified. After sequencing, 74 (77.9%) of these matched the criteria for microsatellite characteristics, including 41 from MG and 33 from CH. Lastly, 15 (20.3%) loci with more than two alleles for each locus were identified through capillary electrophoresis scanning. To justify the applicability of the 15 grey hamster loci, genetic indexes of grey hamsters were evaluated using 46 generations of outbred stock, established 20 years ago, from Xinjiang, China. Mean effective allele numbers and expected heterozygosity of stock were as low as, respectively, 1.2 and 0.14; these were 2.8 and 4.0 times inferior, respectively, to wild grey hamsters. This finding suggests that the genetic structure of the stock-bred population is too weak to resist artificial and natural selection, mutation and genetic drifting. In conclusion, we have developed de novo microsatellite markers for genetic analysis of the grey hamster, providing data and methodology for the enrichment of a genetic library for this species.

Phylogeography and genetic effects of habitat fragmentation on endemic Urophysa (Ranunculaceae) in Yungui Plateau and adjacent regions

PubMed Central

Li, Min-Jie; Tan, Jin-Bo; Price, Megan; Xiao, Qun-Ying; Zhou, Song-Dong; Yu, Yan; He, Xing-Jin

2017-01-01

Urophysa is a Chinese endemic genus with only two species (U. rockii and U. henryi) distributed in Yungui Plateau (Guizhou Province) and adjacent regions (i.e., Provinces of Hunan, Hubei, Chongqing and Sichuan). The aim of this study was to determine the genetic diversity and population differentiation within Urophysa and investigate the effect of the Yungui Plateau uplift and climate oscillations on evolution of Urophysa. In this study, micro-morphological characteristics, nine microsatellite loci (SSR), two nuclear loci (ITS and ETS) and two chloroplast fragments (psbA-trnH and trnL-trnF) were used to analyze the phylogenetic relationships and assess genetic and phylogeographical structure of Urophysa. Isolation by distance (IBD) was performed to research the effects of geographical isolation. We detected high genetic diversity at the species level but low genetic diversity within populations. Striking genetic differentiation (AMOVA) among populations and a significant phylogeographical structure (NST > GST, p < 0.01) were detected among U. henryi populations, along with significant effects of isolation by distance (IBD). Molecular clock estimation using calibration strategy and cpDNA substitution rate indicated that the divergence of U. henryi occurred during late Miocene to early Quaternary, when the orogeny of Yungui Plateau was violent. U. rockii originated at the early Quaternary and further differentiated at early Pleistocene. Our results suggested that habitat fragmentation played an important role in the genetic diversity and population differentiation of U. rockii and U. henryi. Heterogenous geomorphological configuration and complicated environment resulted from rapid uplift of the Yungui Plateau were inferred as important incentives for the modern phylogeograhpical pattern and species divergence of Urophysa. The geographical isolation, limited gene flow, specialized morphologies and the Pleistocene climatic oscillation greatly contributed to the allopatric divergence of U. rockii. Significant genetic drift and inbreeding were detected in these two species, in situ measures should be implemented to protect them. PMID:29053749

Comparative Study of Drift Compensation Methods for Environmental Gas Sensors

NASA Astrophysics Data System (ADS)

Abidin, M. Z.; Asmat, Arnis; Hamidon, M. N.

2018-02-01

Most drift compensation attempts in environmental gas sensors are only emphasize on the “already-known” drift-causing parameter (i.e., ambient temperature, relative humidity) in compensating the sensor drift. Less consideration is taken to another parameter (i.e., baseline responses) that might have affected indirectly with the promotion of drift-causing parameter variable (in this context, is ambient temperature variable). In this study, the “indirect” drift-causing parameter (drifted baseline responses) has been taken into consideration in compensating the sensor drift caused by ambient temperature variable, by means of a proposed drift compensation method (named as RT-method). The effectiveness of this method in its efficacy of compensating drift was analysed and compared with the common method that used the “already-known” drift-causing parameter (named as T-method), using drift reduction percentage. From the results analysis, the RT-method has outperformed T- method in the drift reduction percentage, with its ability to reduce drift up to 64% rather than the T-method which only able to reduce up to 45% for TGS2600 sensor. It has proven that the inclusion of drifted baseline responses into drift compensation attempt would resulted to an improved drift compensation efficiency.

Population dynamics of HIV-1 inferred from gene sequences.

PubMed Central

Grassly, N C; Harvey, P H; Holmes, E C

1999-01-01

A method for the estimation of population dynamic history from sequence data is described and used to investigate the past population dynamics of HIV-1 subtypes A and B. Using both gag and env gene alignments the effective population size of each subtype is estimated and found to be surprisingly small. This may be a result of the selective sweep of mutations through the population, or may indicate an important role of genetic drift in the fixation of mutations. The implications of these results for the spread of drug-resistant mutations and transmission dynamics, and also the roles of selection and recombination in shaping HIV-1 genetic diversity, are discussed. A larger estimated effective population size for subtype A may be the result of differences in time of origin, transmission dynamics, and/or population structure. To investigate the importance of population structure a model of population subdivision was fitted to each subtype, although the improvement in likelihood was found to be nonsignificant. PMID:9927440

Integrating social science and behavioral genetics: testing the origin of socioeconomic disparities in depression using a genetically informed design.

PubMed

Mezuk, Briana; Myers, John M; Kendler, Kenneth S

2013-10-01

We tested 3 hypotheses-social causation, social drift, and common cause-regarding the origin of socioeconomic disparities in major depression and determined whether the relationship between socioeconomic status (SES) and major depression varied by genetic liability for major depression. Data were from a sample of female twins in the baseline Virginia Adult Twin Study of Psychiatric and Substance Use Disorders interviewed between 1987 and 1989 (n = 2153). We used logistic regression and structural equation twin models to evaluate these 3 hypotheses. Consistent with the social causation hypothesis, education (odds ratio [OR] = 0.78; 95% confidence interval [CI] = 0.66, 0.93; P < .01) and income (OR = 0.93; 95% CI = 0.89, 0.98; P < .01) were significantly related to past-year major depression. Upward social mobility was associated with lower risk of depression. There was no evidence that childhood SES was related to development of major depression (OR = 0.98; 95% CI = 0.89, 1.09; P > .1). Consistent with a common genetic cause, there was a negative correlation between the genetic components of major depression and education (r(2) = -0.22). Co-twin control analyses indicated a protective effect of education and income on major depression even after accounting for genetic liability. This study utilized a genetically informed design to address how social position relates to major depression. Results generally supported the social causation model.

Striking Phenotypic Variation yet Low Genetic Differentiation in Sympatric Lake Trout (Salvelinus namaycush)

PubMed Central

Coon, Andrew; Carson, Robert; Debes, Paul V.

2016-01-01

The study of population differentiation in the context of ecological speciation is commonly assessed using populations with obvious discreteness. Fewer studies have examined diversifying populations with occasional adaptive variation and minor reproductive isolation, so factors impeding or facilitating the progress of early stage differentiation are less understood. We detected non-random genetic structuring in lake trout (Salvelinus namaycush) inhabiting a large, pristine, postglacial lake (Mistassini Lake, Canada), with up to five discernible genetic clusters having distinctions in body shape, size, colouration and head shape. However, genetic differentiation was low (FST = 0.017) and genetic clustering was largely incongruent between several population- and individual-based clustering approaches. Genotype- and phenotype-environment associations with spatial habitat, depth and fish community structure (competitors and prey) were either inconsistent or weak. Striking morphological variation was often more continuous within than among defined genetic clusters. Low genetic differentiation was a consequence of relatively high contemporary gene flow despite large effective population sizes, not migration-drift disequilibrium. Our results suggest a highly plastic propensity for occupying multiple habitat niches in lake trout and a low cost of morphological plasticity, which may constrain the speed and extent of adaptive divergence. We discuss how factors relating to niche conservatism in this species may also influence how plasticity affects adaptive divergence, even where ample ecological opportunity apparently exists. PMID:27680019

Long-range dispersal moved Francisella tularensis into Western Europe from the East.

PubMed

Dwibedi, Chinmay; Birdsell, Dawn; Lärkeryd, Adrian; Myrtennäs, Kerstin; Öhrman, Caroline; Nilsson, Elin; Karlsson, Edvin; Hochhalter, Christian; Rivera, Andrew; Maltinsky, Sara; Bayer, Brittany; Keim, Paul; Scholz, Holger C; Tomaso, Herbert; Wittwer, Matthias; Beuret, Christian; Schuerch, Nadia; Pilo, Paola; Hernández Pérez, Marta; Rodriguez-Lazaro, David; Escudero, Raquel; Anda, Pedro; Forsman, Mats; Wagner, David M; Larsson, Pär; Johansson, Anders

2016-12-01

For many infections transmitting to humans from reservoirs in nature, disease dispersal patterns over space and time are largely unknown. Here, a reversed genomics approach helped us understand disease dispersal and yielded insight into evolution and biological properties of Francisella tularensis , the bacterium causing tularemia. We whole-genome sequenced 67 strains and characterized by single-nucleotide polymorphism assays 138 strains, collected from individuals infected 1947-2012 across Western Europe. We used the data for phylogenetic, population genetic and geographical network analyses. All strains ( n =205) belonged to a monophyletic population of recent ancestry not found outside Western Europe. Most strains ( n =195) throughout the study area were assigned to a star-like phylogenetic pattern indicating that colonization of Western Europe occurred via clonal expansion. In the East of the study area, strains were more diverse, consistent with a founder population spreading from east to west. The relationship of genetic and geographic distance within the F. tularensis population was complex and indicated multiple long-distance dispersal events. Mutation rate estimates based on year of isolation indicated null rates; in outbreak hotspots only, there was a rate of 0.4 mutations/genome/year. Patterns of nucleotide substitution showed marked AT mutational bias suggestive of genetic drift. These results demonstrate that tularemia has moved from east to west in Europe and that F. tularensis has a biology characterized by long-range geographical dispersal events and mostly slow, but variable, replication rates. The results indicate that mutation-driven evolution, a resting survival phase, genetic drift and long-distance geographical dispersal events have interacted to generate genetic diversity within this species.

Genetic markers and population history: Finland revisited.

PubMed

Palo, Jukka U; Ulmanen, Ismo; Lukka, Matti; Ellonen, Pekka; Sajantila, Antti

2009-10-01

The Finnish population in Northern Europe has been a target of extensive genetic studies during the last decades. The population is considered as a homogeneous isolate, well suited for gene mapping studies because of its reduced diversity and homogeneity. However, several studies have shown substantial differences between the eastern and western parts of the country, especially in the male-mediated Y chromosome. This divergence is evident in non-neutral genetic variation also and it is usually explained to stem from founder effects occurring in the settlement of eastern Finland as late as in the 16th century. Here, we have reassessed this population historical scenario using Y-chromosomal, mitochondrial and autosomal markers and geographical sampling covering entire Finland. The obtained results suggest substantial Scandinavian gene flow into south-western, but not into the eastern, Finland. Male-biased Scandinavian gene flow into the south-western parts of the country would plausibly explain the large inter-regional differences observed in the Y-chromosome, and the relative homogeneity in the mitochondrial and autosomal data. On the basis of these results, we suggest that the expression of 'Finnish Disease Heritage' illnesses, more common in the eastern/north-eastern Finland, stems from long-term drift, rather than from relatively recent founder effects.

Drift and geodesic effects on the ion sound eigenmode in tokamak plasmas

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

Elfimov, A. G., E-mail: elfimov@if.usp.br; Smolyakov, A. I., E-mail: andrei.smolyakov@usask.ca; Melnikov, A. V.

A kinetic treatment of geodesic acoustic modes (GAMs), taking into account ion parallel dynamics, drift and the second poloidal harmonic effects is presented. It is shown that first and second harmonics of the ion sound modes, which have respectively positive and negative radial dispersion, can be coupled due to the geodesic and drift effects. This coupling results in the drift geodesic ion sound eigenmode with a frequency below the standard GAM continuum frequency. Such eigenmode may be able to explain the split modes observed in some experiments.

Geographic population structure in an outcrossing plant invasion after centuries of cultivation and recent founding events

USDA-ARS?s Scientific Manuscript database

Population structure and genetic diversity of invasions are the result of evolutionary processes such as natural selection, drift, and founding events. Some invasions are also molded by additional human activities such as selection for cultivars and intentional introduction of desired phenotypes, wh...

"Hoffman v. Monsanto": Courts, Class Actions, and Perceptions of the Problem of GM Drift

ERIC Educational Resources Information Center

McLeod-Kilmurray, Heather

2007-01-01

"Hoffman v. Monsanto" raises questions about the civil litigation system. Are courts appropriate institutions, and are class actions the appropriate procedure, for resolving disputes about genetically modified organisms (GMOs)? After addressing the institutional question, this article focuses on procedure. Although class actions are…

Glyphosate drift promotes changes in fitness and transgene flow in canola (Brassica napus) and hybrids

EPA Science Inventory

1. With the advent of transgenic crops, genetically modified, herbicide resistant B. napus has become a model system for examining the risks of escape of transgenes from cultivation and for evaluating potential ecological consequences of novel genes in wild species. 2. We exam...

Anthropogenic fragmentation may not alter pre-existing patterns of genetic diversity and differentiation in perennial shrubs.

PubMed

Llorens, Tanya M; Ayre, David J; Whelan, Robert J

2018-04-01

Many plant species have pollination and seed dispersal systems and evolutionary histories that have produced strong genetic structuring. These genetic patterns may be consistent with expectations following recent anthropogenic fragmentation, making it difficult to detect fragmentation effects if no prefragmentation genetic data are available. We used microsatellite markers to investigate whether severe habitat fragmentation may have affected the structure and diversity of populations of the endangered Australian bird-pollinated shrub Grevillea caleyi R.Br., by comparing current patterns of genetic structure and diversity with those of the closely related G. longifolia R.Br. that has a similar life history but has not experienced anthropogenic fragmentation. Grevillea caleyi and G. longifolia showed similar and substantial population subdivision at all spatial levels (global F' ST  = 0.615 and 0.454; S p  = 0.039 and 0.066), marked isolation by distance and large heterozygous deficiencies. These characteristics suggest long-term effects of inbreeding in self-compatible species that have poor seed dispersal, limited connectivity via pollen flow and undergo population bottlenecks because of periodic fires. Highly structured allele size distributions, most notably in G. caleyi, imply historical processes of drift and mutation were important in isolated subpopulations. Genetic diversity did not vary with population size but was lower in more isolated populations for both species. Through this comparison, we reject the hypothesis that anthropogenic fragmentation has impacted substantially on the genetic composition or structure of G. caleyi populations. Our results suggest that highly self-compatible species with limited dispersal may be relatively resilient to the genetic changes predicted to follow habitat fragmentation. © 2018 John Wiley & Sons Ltd.

Diversity Outbred Mice at 21: Maintaining Allelic Variation in the Face of Selection.

PubMed

Chesler, Elissa J; Gatti, Daniel M; Morgan, Andrew P; Strobel, Marge; Trepanier, Laura; Oberbeck, Denesa; McWeeney, Shannon; Hitzemann, Robert; Ferris, Martin; McMullan, Rachel; Clayshultle, Amelia; Bell, Timothy A; Manuel de Villena, Fernando Pardo; Churchill, Gary A

2016-12-07

Multi-parent populations (MPPs) capture and maintain the genetic diversity from multiple inbred founder strains to provide a resource for high-resolution genetic mapping through the accumulation of recombination events over many generations. Breeding designs that maintain a large effective population size with randomized assignment of breeders at each generation can minimize the impact of selection, inbreeding, and genetic drift on allele frequencies. Small deviations from expected allele frequencies will have little effect on the power and precision of genetic analysis, but a major distortion could result in reduced power and loss of important functional alleles. We detected strong transmission ratio distortion in the Diversity Outbred (DO) mouse population on chromosome 2, caused by meiotic drive favoring transmission of the WSB/EiJ allele at the R2d2 locus. The distorted region harbors thousands of polymorphisms derived from the seven non-WSB founder strains and many of these would be lost if the sweep was allowed to continue. To ensure the utility of the DO population to study genetic variation on chromosome 2, we performed an artificial selection against WSB/EiJ alleles at the R2d2 locus. Here, we report that we have purged the WSB/EiJ allele from the drive locus while preserving WSB/EiJ alleles in the flanking regions. We observed minimal disruption to allele frequencies across the rest of the autosomal genome. However, there was a shift in haplotype frequencies of the mitochondrial genome and an increase in the rate of an unusual sex chromosome aneuploidy. The DO population has been restored to genome-wide utility for genetic analysis, but our experience underscores that vigilant monitoring of similar genetic resource populations is needed to ensure their long-term utility. Copyright © 2016 by the Genetics Society of America.

Genetic Diversity and Population Structure of Varronia curassavica: A Medicinal Polyploid Species in a Threatened Ecosystem.

PubMed

Hoeltgebaum, Marcia Patricia; Dos Reis, Maurício Sedrez

2017-06-01

Varronia curassavica is an important medicinal species associated with the restinga, one of the most threatened coastal ecosystems of the Atlantic Forest. These circumstances call for studies aimed at estimating effective population size and gene flow to improve conservation efforts. Hence, the present study aimed to characterize the genetic diversity, ploidy level, and population structure of this species in different areas of restinga using microsatellites. Varronia curassavica was characterized as an autotetraploid, with high genetic variability, low divergence, and no significant fixation indices, indicating the absence of, or reduced, inbreeding and genetic drift in the study area. About 44% of the alleles occurred at low frequency in adults of all populations and 41% in the progenies evaluated. Gene flow was high, consistent with outcrossing species with high dispersal capacity (Nm = 4.87). The results showed no tendency toward isolation by distance. The estimated effective size indicates that the populations studied have the potential to ensure conservation of the species in the long term. The genetic variability and population structure of V. curassavica, as determined in this study, could form the foundation for activities directed toward the sustainable use of this resource and its conservation. Even though the restinga ecosystem has suffered dramatic reductions in area, this study provides evidence that this species is resilient to anthropogenic threats to its genetic integrity, since it is a polyploid with self-incompatibility mechanisms that contribute to maintaining high genetic diversity in an panmictic meta-population along the coast of Santa Catarina. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Spatial Genetic Structure and Mitochondrial DNA Phylogeography of Argentinean Populations of the Grasshopper Dichroplus elongatus

PubMed Central

Rosetti, Natalia; Remis, Maria Isabel

2012-01-01

Many grasshopper species are considered of agronomical importance because they cause damage to pastures and crops. Comprehension of pest population dynamics requires a clear understanding of the genetic diversity and spatial structure of populations. In this study we report on patterns of genetic variation in the South American grasshopper Dichroplus elongatus which is an agricultural pest of crops and forage grasses of great economic significance in Argentina. We use Direct Amplification of Minisatellite Regions (DAMD) and partial sequences of the cytochrome oxydase 1 (COI) mitochondrial gene to investigate intraspecific structure, demographic history and gene flow patterns in twenty Argentinean populations of this species belonging to different geographic and biogeographic regions. DAMD data suggest that, although genetic drift and migration occur within and between populations, measurable relatedness among neighbouring populations declines with distance and dispersal over distances greater than 200 km is not typical, whereas effective gene flow may occur for populations separated by less than 100 km. Landscape analysis was useful to detect genetic discontinuities associated with environmental heterogeneity reflecting the changing agroecosystem. The COI results indicate the existence of strong genetic differentiation between two groups of populations located at both margins of the Paraná River which became separated during climate oscillations of the Middle Pleistocene, suggesting a significant restriction in effective dispersion mediated by females and large scale geographic differentiation. The number of migrants between populations estimated through mitochondrial and DAMD markers suggest that gene flow is low prompting a non-homogeneous spatial structure and justifying the variation through space. Moreover, the genetic analysis of both markers allows us to conclude that males appear to disperse more than females, reducing the chance of the genetic loss associated with recent anthropogenic fragmentation of the D. elongatus studied range. PMID:22859953

Directional selection can drive the evolution of modularity in complex traits

PubMed Central

Melo, Diogo; Marroig, Gabriel

2015-01-01

Modularity is a central concept in modern biology, providing a powerful framework for the study of living organisms on many organizational levels. Two central and related questions can be posed in regard to modularity: How does modularity appear in the first place, and what forces are responsible for keeping and/or changing modular patterns? We approached these questions using a quantitative genetics simulation framework, building on previous results obtained with bivariate systems and extending them to multivariate systems. We developed an individual-based model capable of simulating many traits controlled by many loci with variable pleiotropic relations between them, expressed in populations subject to mutation, recombination, drift, and selection. We used this model to study the problem of the emergence of modularity, and hereby show that drift and stabilizing selection are inefficient at creating modular variational structures. We also demonstrate that directional selection can have marked effects on the modular structure between traits, actively promoting a restructuring of genetic variation in the selected population and potentially facilitating the response to selection. Furthermore, we give examples of complex covariation created by simple regimes of combined directional and stabilizing selection and show that stabilizing selection is important in the maintenance of established covariation patterns. Our results are in full agreement with previous results for two-trait systems and further extend them to include scenarios of greater complexity. Finally, we discuss the evolutionary consequences of modular patterns being molded by directional selection. PMID:25548154

Directional selection can drive the evolution of modularity in complex traits.

PubMed

Melo, Diogo; Marroig, Gabriel

2015-01-13

Modularity is a central concept in modern biology, providing a powerful framework for the study of living organisms on many organizational levels. Two central and related questions can be posed in regard to modularity: How does modularity appear in the first place, and what forces are responsible for keeping and/or changing modular patterns? We approached these questions using a quantitative genetics simulation framework, building on previous results obtained with bivariate systems and extending them to multivariate systems. We developed an individual-based model capable of simulating many traits controlled by many loci with variable pleiotropic relations between them, expressed in populations subject to mutation, recombination, drift, and selection. We used this model to study the problem of the emergence of modularity, and hereby show that drift and stabilizing selection are inefficient at creating modular variational structures. We also demonstrate that directional selection can have marked effects on the modular structure between traits, actively promoting a restructuring of genetic variation in the selected population and potentially facilitating the response to selection. Furthermore, we give examples of complex covariation created by simple regimes of combined directional and stabilizing selection and show that stabilizing selection is important in the maintenance of established covariation patterns. Our results are in full agreement with previous results for two-trait systems and further extend them to include scenarios of greater complexity. Finally, we discuss the evolutionary consequences of modular patterns being molded by directional selection.

Geographic Distribution of Disease Mutations in the Ashkenazi Jewish Population Supports Genetic Drift over Selection

PubMed Central

Risch, Neil; Tang, Hua; Katzenstein, Howard; Ekstein, Josef

2003-01-01

The presence of four lysosomal storage diseases (LSDs) at increased frequency in the Ashkenazi Jewish population has suggested to many the operation of natural selection (carrier advantage) as the driving force. We compare LSDs and nonlysosomal storage diseases (NLSDs) in terms of the number of mutations, allele-frequency distributions, and estimated coalescence dates of mutations. We also provide new data on the European geographic distribution, in the Ashkenazi population, of seven LSD and seven NLSD mutations. No differences in any of the distributions were observed between LSDs and NLSDs. Furthermore, no regular pattern of geographic distribution was observed for LSD versus NLSD mutations—with some being more common in central Europe and others being more common in eastern Europe, within each group. The most striking disparate pattern was the geographic distribution of the two primary Tay-Sachs disease mutations, with the first being more common in central Europe (and likely older) and the second being exclusive to eastern Europe (primarily Lithuania and Russia) (and likely much younger). The latter demonstrates a pattern similar to two other recently arisen Lithuanian mutations, those for torsion dystonia and familial hypercholesterolemia. These observations provide compelling support for random genetic drift (chance founder effects, one ∼11 centuries ago that affected all Ashkenazim and another ∼5 centuries ago that affected Lithuanians), rather than selection, as the primary determinant of disease mutations in the Ashkenazi population. PMID:12612865

Drifting to oblivion? Rapid genetic differentiation in an endangered lizard following habitat fragmentation and drought

USGS Publications Warehouse

Vandergast, Amy; Wood, Dustin A.; Thompson, Andrew R.; Fisher, Mark; Barrows, Cameron W.; Grant, Tyler J.

2016-01-01

Aim The frequency and severity of habitat alterations and disturbance are predicted to increase in upcoming decades, and understanding how disturbance affects population integrity is paramount for adaptive management. Although rarely is population genetic sampling conducted at multiple time points, pre- and post-disturbance comparisons may provide one of the clearest methods to measure these impacts. We examined how genetic properties of the federally threatened Coachella Valley fringe-toed lizard (Uma inornata) responded to severe drought and habitat fragmentation across its range. Location Coachella Valley, California, USA. Methods We used 11 microsatellites to examine population genetic structure and diversity in 1996 and 2008, before and after a historic drought. We used Bayesian assignment methods and F-statistics to estimate genetic structure. We compared allelic richness across years to measure loss of genetic diversity and employed approximate Bayesian computing methods and heterozygote excess tests to explore the recent demographic history of populations. Finally, we compared effective population size across years and to abundance estimates to determine whether diversity remained low despite post-drought recovery. Results Genetic structure increased between sampling periods, likely as a result of population declines during the historic drought of the late 1990s–early 2000s, and habitat loss and fragmentation that precluded post-drought genetic rescue. Simulations supported recent demographic declines in 3 of 4 main preserves, and in one preserve, we detected significant loss of allelic richness. Effective population sizes were generally low across the range, with estimates ≤100 in most sites. Main conclusions Fragmentation and drought appear to have acted synergistically to induce genetic change over a short time frame. Progressive deterioration of connectivity, low Ne and measurable loss of genetic diversity suggest that conservation efforts have not maintained the genetic integrity of this species. Genetic sampling over time can help evaluate population trends to guide management.

Sex ratio rather than population size affects genetic diversity in Antennaria dioica.

PubMed

Rosche, C; Schrieber, K; Lachmuth, S; Durka, W; Hirsch, H; Wagner, V; Schleuning, M; Hensen, I

2018-03-09

Habitat fragmentation and small population size can lead to genetic erosion in threatened plant populations. Classical theory implies that dioecy can counteract genetic erosion as it decreases the magnitude of inbreeding and genetic drift due to obligate outcrossing. However, in small populations, sex ratios may be strongly male- or female-biased, leading to substantial reductions in effective population size. This may theoretically result in a unimodal relationship between sex ratios and genetic diversity; yet, empirical studies on this relationship are scarce. Using AFLP markers, we studied genetic diversity, structure and differentiation in 14 highly fragmented Antennaria dioica populations from the Central European lowlands. Our analyses focused on the relationship between sex ratio, population size and genetic diversity. Although most populations were small (mean: 35.5 patches), genetic diversity was moderately high. We found evidence for isolation-by-distance, but overall differentiation of the populations was rather weak. Females dominated 11 populations, which overall resulted in a slightly female-biased sex ratio (61.5%). There was no significant relationship between population size and genetic diversity. The proportion of females was not unimodally but positively linearly related to genetic diversity. The high genetic diversity and low genetic differentiation suggest that A. dioica has been widely distributed in the Central European lowlands in the past, while fragmentation occurred only in the last decades. Sex ratio has more immediate consequences on genetic diversity than population size. An increasing proportion of females can increase genetic diversity in dioecious plants, probably due to a higher amount of sexual reproduction. © 2018 German Society for Plant Sciences and The Royal Botanical Society of the Netherlands.

Self-shielding flex-circuit drift tube, drift tube assembly and method of making

DOEpatents

Jones, David Alexander

2016-04-26

The present disclosure is directed to an ion mobility drift tube fabricated using flex-circuit technology in which every other drift electrode is on a different layer of the flex-circuit and each drift electrode partially overlaps the adjacent electrodes on the other layer. This results in a self-shielding effect where the drift electrodes themselves shield the interior of the drift tube from unwanted electro-magnetic noise. In addition, this drift tube can be manufactured with an integral flex-heater for temperature control. This design will significantly improve the noise immunity, size, weight, and power requirements of hand-held ion mobility systems such as those used for explosive detection.

Random genetic drift, natural selection, and noise in human cranial evolution.

PubMed

Roseman, Charles C

2016-08-01

This study assesses the extent to which relationships among groups complicate comparative studies of adaptation in recent human cranial variation and the extent to which departures from neutral additive models of evolution hinder the reconstruction of population relationships among groups using cranial morphology. Using a maximum likelihood evolutionary model fitting approach and a mixed population genomic and cranial data set, I evaluate the relative fits of several widely used models of human cranial evolution. Moreover, I compare the goodness of fit of models of cranial evolution constrained by genomic variation to test hypotheses about population specific departures from neutrality. Models from population genomics are much better fits to cranial variation than are traditional models from comparative human biology. There is not enough evolutionary information in the cranium to reconstruct much of recent human evolution but the influence of population history on cranial variation is strong enough to cause comparative studies of adaptation serious difficulties. Deviations from a model of random genetic drift along a tree-like population history show the importance of environmental effects, gene flow, and/or natural selection on human cranial variation. Moreover, there is a strong signal of the effect of natural selection or an environmental factor on a group of humans from Siberia. The evolution of the human cranium is complex and no one evolutionary process has prevailed at the expense of all others. A holistic unification of phenome, genome, and environmental context, gives us a strong point of purchase on these problems, which is unavailable to any one traditional approach alone. Am J Phys Anthropol 160:582-592, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

The interaction of neutral evolutionary processes with climatically-driven adaptive changes in the 3D shape of the human os coxae.

PubMed

Betti, Lia; von Cramon-Taubadel, Noreen; Manica, Andrea; Lycett, Stephen J

2014-08-01

Differences in the breadth of the pelvis among modern human populations and among extinct hominin species have often been interpreted in the light of thermoregulatory adaptation, whereby a larger pelvic girdle would help preserve body temperature in cold environments while a narrower pelvis would help dissipate heat in tropical climates. There is, however, a theoretical problem in interpreting a pattern of variation as evidence of selection without first accounting for the effects of neutral evolutionary processes (i.e., mutation, genetic drift and migration). Here, we analyse 3D configurations of 27 landmarks on the os coxae of 1494 modern human individuals representing 30 male and 23 female populations from five continents and a range of climatic conditions. We test for the effects of climate on the size and shape of the pelvic bone, while explicitly accounting for population history (i.e., geographically-mediated gene flow and genetic drift). We find that neutral processes account for a substantial proportion of shape variance in the human os coxae in both sexes. Beyond the neutral pattern due to population history, temperature is a significant predictor of shape and size variation in the os coxae, at least in males. The effect of climate on the shape of the pelvic bone, however, is comparatively limited, explaining only a small percentage of shape variation in males and females. In accordance with previous hypotheses, the size of the os coxae tends to increase with decreasing temperature, although the significance of the association is reduced when population history is taken into account. In conclusion, the shape and size of the human os coxae reflect both neutral evolutionary processes and climatically-driven adaptive changes. Neutral processes have a substantial effect on pelvic variation, suggesting such factors will need to be taken into account in future studies of human and fossil hominin coxal variation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Macroinvertebrate short-term responses to flow variation and oxygen depletion: A mesocosm approach.

PubMed

Calapez, Ana R; Branco, Paulo; Santos, José M; Ferreira, Teresa; Hein, Thomas; Brito, António G; Feio, Maria João

2017-12-01

In Mediterranean rivers, water scarcity is a key stressor with direct and indirect effects on other stressors, such as water quality decline and inherent oxygen depletion associated with pollutants inputs. Yet, predicting the responses of macroinvertebrates to these stressors combination is quite challenging due to the reduced available information, especially if biotic and abiotic seasonal variations are taken under consideration. This study focused on the response of macroinvertebrates by drift to single and combined effects of water scarcity and dissolved oxygen (DO) depletion over two seasons (winter and spring). A factorial design of two flow velocity levels - regular and low (vL) - with three levels of oxygen depletion - normoxia, medium depletion (dM) and higher depletion (dH) - was carried out in a 5-artificial channels system, in short-term experiments. Results showed that both stressors individually and together had a significant effect on macroinvertebrate drift ratio for both seasons. Single stressor effects showed that macroinvertebrate drift decreased with flow velocity reduction and increased with DO depletion, in both winter and spring experiments. Despite single stressors opposing effects in drift ratio, combined stressors interaction (vL×dM and vL×dH) induced a positive synergistic drift effect for both seasons, but only in winter the drift ratio was different between the levels of DO depletion. Stressors interaction in winter seemed to intensify drift response when reached lower oxygen saturation. Also, drift patterns were different between seasons for all treatments, which may depend on individual's life stage and seasonal behaviour. Water scarcity seems to exacerbate the oxygen depletion conditions resulting into a greater drifting of invertebrates. The potential effects of oxygen depletion should be evaluated when addressing the impacts of water scarcity on river ecosystems, since flow reductions will likely contribute to a higher oxygen deficit, particularly in Mediterranean rivers. Copyright © 2017 Elsevier B.V. All rights reserved.

Estimation of a genetically viable population for multigenerational interstellar voyaging: Review and data for project Hyperion

NASA Astrophysics Data System (ADS)

Smith, Cameron M.

2014-04-01

Designing interstellar starships for human migration to exoplanets requires establishing the starship population, which factors into many variables including closed-ecosystem design, architecture, mass and propulsion. I review the central issues of population genetics (effects of mutation, migration, selection and drift) for human populations on such voyages, specifically referencing a roughly 5-generation (c. 150-year) voyage currently in the realm of thought among Icarus Interstellar's Project Hyperion research group. I present several formulae as well as concrete numbers that can be used to help determine populations that could survive such journeys in good health. I find that previously proposed such populations, on the order of a few hundred individuals, are significantly too low to consider based on current understanding of vertebrate (including human) genetics and population dynamics. Population genetics theory, calculations and computer modeling determine that a properly screened and age- and sex-structured total founding population (Nc) of anywhere from roughly 14,000 to 44,000 people would be sufficient to survive such journeys in good health. A safe and well-considered Nc figure is 40,000, an Interstellar Migrant Population (IMP) composed of an Effective Population [Ne] of 23,400 reproductive males and females, the rest being pre- or post-reproductive individuals. This number would maintain good health over five generations despite (a) increased inbreeding resulting from a relatively small human population, (b) depressed genetic diversity due to the founder effect, (c) demographic change through time and (d) expectation of at least one severe population catastrophe over the 5-generation voyage.

Evolutionary domestication in Drosophila subobscura.

PubMed

Simões, P; Rose, M R; Duarte, A; Gonçalves, R; Matos, M

2007-03-01

The domestication of plants and animals is historically one of the most important topics in evolutionary biology. The evolutionary genetic changes arising from human cultivation are complex because of the effects of such varied processes as continuing natural selection, artificial selection, deliberate inbreeding, genetic drift and hybridization of different lineages. Despite the interest of domestication as an evolutionary process, few studies of multicellular sexual species have approached this topic using well-replicated experiments. Here we present a comprehensive study in which replicated evolutionary trajectories from several Drosophila subobscura populations provide a detailed view of the evolutionary dynamics of domestication in an outbreeding animal species. Our results show a clear evolutionary response in fecundity traits, but no clear pattern for adult starvation resistance and juvenile traits such as development time and viability. These results supply new perspectives on the confounding of adaptation with other evolutionary mechanisms in the process of domestication.

Predicting connectivity of green turtles at Palmyra Atoll, central Pacific: a focus on mtDNA and dispersal modelling

PubMed Central

Naro-Maciel, Eugenia; Gaughran, Stephen J.; Putman, Nathan F.; Amato, George; Arengo, Felicity; Dutton, Peter H.; McFadden, Katherine W.; Vintinner, Erin C.; Sterling, Eleanor J.

2014-01-01

Population connectivity and spatial distribution are fundamentally related to ecology, evolution and behaviour. Here, we combined powerful genetic analysis with simulations of particle dispersal in a high-resolution ocean circulation model to investigate the distribution of green turtles foraging at the remote Palmyra Atoll National Wildlife Refuge, central Pacific. We analysed mitochondrial sequences from turtles (n = 349) collected there over 5 years (2008–2012). Genetic analysis assigned natal origins almost exclusively (approx. 97%) to the West Central and South Central Pacific combined Regional Management Units. Further, our modelling results indicated that turtles could potentially drift from rookeries to Palmyra Atoll via surface currents along a near-Equatorial swathe traversing the Pacific. Comparing findings from genetics and modelling highlighted the complex impacts of ocean currents and behaviour on natal origins. Although the Palmyra feeding ground was highly differentiated genetically from others in the Indo-Pacific, there was no significant differentiation among years, sexes or stage-classes at the Refuge. Understanding the distribution of this foraging population advances knowledge of green turtles and contributes to effective conservation planning for this threatened species. PMID:24451389

So long to genetic diversity, and thanks for all the fish.

PubMed

Allendorf, Fred W; Berry, Oliver; Ryman, Nils

2014-01-01

The world faces a global fishing crisis. Wild marine fisheries comprise nearly 15% of all animal protein in the human diet, but, according to the U.N. Food and Agriculture Organization, nearly 60% of all commercially important marine fish stocks are overexploited, recovering, or depleted (FAO 2012; Fig. 1). Some authors have suggested that the large population sizes of harvested marine fish make even collapsed populations resistant to the loss of genetic variation by genetic drift (e.g. Beverton 1990). In contrast, others have argued that the loss of alleles because of overfishing may actually be more dramatic in large populations than in small ones (Ryman et al. 1995). In this issue, Pinsky & Palumbi (2014) report that overfished populations have approximately 2% lower heterozygosity and 12% lower allelic richness than populations that are not overfished. They also performed simulations which suggest that their estimates likely underestimate the actual loss of rare alleles by a factor of three or four. This important paper shows that the harvesting of marine fish can have genetic effects that threaten the long-term sustainability of this valuable resource. © 2013 John Wiley & Sons Ltd.

Predicting connectivity of green turtles at Palmyra Atoll, central Pacific: a focus on mtDNA and dispersal modelling

USGS Publications Warehouse

Naro-Maciel, Eugenia; Gaughran, Stephen J.; Putman, Nathan F.; Amato, George; Arengo, Felicity; Dutton, Peter H.; McFadden, Katherine W.; Vintinner, Erin C.; Sterling, Eleanor J.

2014-01-01

Population connectivity and spatial distribution are fundamentally related to ecology, evolution and behaviour. Here, we combined powerful genetic analysis with simulations of particle dispersal in a high-resolution ocean circulation model to investigate the distribution of green turtles foraging at the remote Palmyra Atoll National Wildlife Refuge, central Pacific. We analysed mitochondrial sequences from turtles (n = 349) collected there over 5 years (2008–2012). Genetic analysis assigned natal origins almost exclusively (approx. 97%) to the West Central and South Central Pacific combined Regional Management Units. Further, our modelling results indicated that turtles could potentially drift from rookeries to Palmyra Atoll via surface currents along a near-Equatorial swathe traversing the Pacific. Comparing findings from genetics and modelling highlighted the complex impacts of ocean currents and behaviour on natal origins. Although the Palmyra feeding ground was highly differentiated genetically from others in the Indo-Pacific, there was no significant differentiation among years, sexes or stage-classes at the Refuge. Understanding the distribution of this foraging population advances knowledge of green turtles and contributes to effective conservation planning for this threatened species.

Evaluating the genetic impact of South and Southeast Asia on the peopling of Bangladesh.

PubMed

Sultana, Gazi Nurun Nahar; Sharif, Mohd Istiaq; Asaduzzaman, Md; Chaubey, Gyaneshwer

2015-11-01

Despite rapidly growing understandings and dependency on single nucleotide polymorphisms (SNPs), highly variable autosomal short tandem repeats (STRs) are still regarded as the most established method to differentiate individuals at forensic level. Here with large number of various ethnic groups we undertook this study to reveal the genetic structure of the most densely populated part of South Asia i.e. the Bangladesh. The purpose of this work was to estimate population parameters based on the allele frequencies obtained for 15 polymorphic autosomal STR loci investigated in caste and tribal populations from Bangladesh (n=706). We compared the results in a broader context by merging 24 different populations of Asia to pertain their affinity. Various statistical analyses suggested a clear cut demarcation of tribal and non-tribal in Bangladesh. Moreover, beside the phylogenetic structure of the studied populations, it is found that the mean heterozygosity value was highest among the populations of Bangladesh, likely because of gene flow from different directions. However, Tonchangya, Adi and Khumi showed sign of genetic isolation and reduced diversity, possibly as a result of genetic drift and/or strong founder effects working on small endogamous populations. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Effects of complex life cycles on genetic diversity: cyclical parthenogenesis.

PubMed

Rouger, R; Reichel, K; Malrieu, F; Masson, J P; Stoeckel, S

2016-11-01

Neutral patterns of population genetic diversity in species with complex life cycles are difficult to anticipate. Cyclical parthenogenesis (CP), in which organisms undergo several rounds of clonal reproduction followed by a sexual event, is one such life cycle. Many species, including crop pests (aphids), human parasites (trematodes) or models used in evolutionary science (Daphnia), are cyclical parthenogens. It is therefore crucial to understand the impact of such a life cycle on neutral genetic diversity. In this paper, we describe distributions of genetic diversity under conditions of CP with various clonal phase lengths. Using a Markov chain model of CP for a single locus and individual-based simulations for two loci, our analysis first demonstrates that strong departures from full sexuality are observed after only a few generations of clonality. The convergence towards predictions made under conditions of full clonality during the clonal phase depends on the balance between mutations and genetic drift. Second, the sexual event of CP usually resets the genetic diversity at a single locus towards predictions made under full sexuality. However, this single recombination event is insufficient to reshuffle gametic phases towards full-sexuality predictions. Finally, for similar levels of clonality, CP and acyclic partial clonality (wherein a fixed proportion of individuals are clonally produced within each generation) differentially affect the distribution of genetic diversity. Overall, this work provides solid predictions of neutral genetic diversity that may serve as a null model in detecting the action of common evolutionary or demographic processes in cyclical parthenogens (for example, selection or bottlenecks).

An Investigation of Accelerating Mechanisms in a Plasma Focus Relevant to Interrupting Switches.

DTIC Science & Technology

1983-07-01

drift region so as to reduce beam loss due to contact with the conductive walls of the drift tube . The beam guiding apparatus was shown *i to increase...secondary discharge had an adverse effect on the trans- mission of the electron beam through the drift tube . This effect, which was shown to be...the electron beam from entering the drift tube region. .A -4 Io For CiA&- TAR - ’ ’--, U Unclassified SECURITY CLASSIFICATION OF THIS PAGEfhe, 00i Ent

Toward a Greater Understanding of the Reduction of Drift Coefficients in the Presence of Turbulence

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

Engelbrecht, N. E.; Strauss, R. D.; Burger, R. A.

2017-06-01

Drift effects play a significant role in the transport of charged particles in the heliosphere. A turbulent magnetic field is also known to reduce the effects of particle drifts. The exact nature of this reduction, however, is not clear. This study aims to provide some insight into this reduction and proposes a relatively simple, tractable means of modeling it that provides results in reasonable agreement with numerical simulations of the drift coefficient in a turbulent magnetic field.

The infinitesimal model: Definition, derivation, and implications.

PubMed

Barton, N H; Etheridge, A M; Véber, A

2017-12-01

Our focus here is on the infinitesimal model. In this model, one or several quantitative traits are described as the sum of a genetic and a non-genetic component, the first being distributed within families as a normal random variable centred at the average of the parental genetic components, and with a variance independent of the parental traits. Thus, the variance that segregates within families is not perturbed by selection, and can be predicted from the variance components. This does not necessarily imply that the trait distribution across the whole population should be Gaussian, and indeed selection or population structure may have a substantial effect on the overall trait distribution. One of our main aims is to identify some general conditions on the allelic effects for the infinitesimal model to be accurate. We first review the long history of the infinitesimal model in quantitative genetics. Then we formulate the model at the phenotypic level in terms of individual trait values and relationships between individuals, but including different evolutionary processes: genetic drift, recombination, selection, mutation, population structure, …. We give a range of examples of its application to evolutionary questions related to stabilising selection, assortative mating, effective population size and response to selection, habitat preference and speciation. We provide a mathematical justification of the model as the limit as the number M of underlying loci tends to infinity of a model with Mendelian inheritance, mutation and environmental noise, when the genetic component of the trait is purely additive. We also show how the model generalises to include epistatic effects. We prove in particular that, within each family, the genetic components of the individual trait values in the current generation are indeed normally distributed with a variance independent of ancestral traits, up to an error of order 1∕M. Simulations suggest that in some cases the convergence may be as fast as 1∕M. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Population genomics of the killer whale indicates ecotype evolution in sympatry involving both selection and drift.

PubMed

Moura, Andre E; Kenny, John G; Chaudhuri, Roy; Hughes, Margaret A; J Welch, Andreanna; Reisinger, Ryan R; de Bruyn, P J Nico; Dahlheim, Marilyn E; Hall, Neil; Hoelzel, A Rus

2014-11-01

The evolution of diversity in the marine ecosystem is poorly understood, given the relatively high potential for connectivity, especially for highly mobile species such as whales and dolphins. The killer whale (Orcinus orca) has a worldwide distribution, and individual social groups travel over a wide geographic range. Even so, regional populations have been shown to be genetically differentiated, including among different foraging specialists (ecotypes) in sympatry. Given the strong matrifocal social structure of this species together with strong resource specializations, understanding the process of differentiation will require an understanding of the relative importance of both genetic drift and local adaptation. Here we provide a high-resolution analysis based on nuclear single-nucleotide polymorphic markers and inference about differentiation at both neutral loci and those potentially under selection. We find that all population comparisons, within or among foraging ecotypes, show significant differentiation, including populations in parapatry and sympatry. Loci putatively under selection show a different pattern of structure compared to neutral loci and are associated with gene ontology terms reflecting physiologically relevant functions (e.g. related to digestion). The pattern of differentiation for one ecotype in the North Pacific suggests local adaptation and shows some fixed differences among sympatric ecotypes. We suggest that differential habitat use and resource specializations have promoted sufficient isolation to allow differential evolution at neutral and functional loci, but that the process is recent and dependent on both selection and drift. © 2014 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.

Population genomics of the killer whale indicates ecotype evolution in sympatry involving both selection and drift

PubMed Central

Moura, Andre E; Kenny, John G; Chaudhuri, Roy; Hughes, Margaret A; J Welch, Andreanna; Reisinger, Ryan R; de Bruyn, P J Nico; Dahlheim, Marilyn E; Hall, Neil; Hoelzel, A Rus

2014-01-01

The evolution of diversity in the marine ecosystem is poorly understood, given the relatively high potential for connectivity, especially for highly mobile species such as whales and dolphins. The killer whale (Orcinus orca) has a worldwide distribution, and individual social groups travel over a wide geographic range. Even so, regional populations have been shown to be genetically differentiated, including among different foraging specialists (ecotypes) in sympatry. Given the strong matrifocal social structure of this species together with strong resource specializations, understanding the process of differentiation will require an understanding of the relative importance of both genetic drift and local adaptation. Here we provide a high-resolution analysis based on nuclear single-nucleotide polymorphic markers and inference about differentiation at both neutral loci and those potentially under selection. We find that all population comparisons, within or among foraging ecotypes, show significant differentiation, including populations in parapatry and sympatry. Loci putatively under selection show a different pattern of structure compared to neutral loci and are associated with gene ontology terms reflecting physiologically relevant functions (e.g. related to digestion). The pattern of differentiation for one ecotype in the North Pacific suggests local adaptation and shows some fixed differences among sympatric ecotypes. We suggest that differential habitat use and resource specializations have promoted sufficient isolation to allow differential evolution at neutral and functional loci, but that the process is recent and dependent on both selection and drift. PMID:25244680

Genetic effects of landscape, habitat preference and demography on three co-occurring turtle species.

PubMed

Reid, Brendan N; Mladenoff, David J; Peery, M Zachariah

2017-02-01

Expanding the scope of landscape genetics beyond the level of single species can help to reveal how species traits influence responses to environmental change. Multispecies studies are particularly valuable in highly threatened taxa, such as turtles, in which the impacts of anthropogenic change are strongly influenced by interspecific differences in life history strategies, habitat preferences and mobility. We sampled approximately 1500 individuals of three co-occurring turtle species across a gradient of habitat change (including varying loss of wetlands and agricultural conversion of upland habitats) in the Midwestern USA. We used genetic clustering and multiple regression methods to identify associations between genetic structure and permanent landscape features, past landscape composition and landscape change in each species. Two aquatic generalists (the painted turtle, Chrysemys picta, and the snapping turtle Chelydra serpentina) both exhibited population genetic structure consistent with isolation by distance, modulated by aquatic landscape features. Genetic divergence for the more terrestrial Blanding's turtle (Emydoidea blandingii), on the other hand, was not strongly associated with geographic distance or aquatic features, and Bayesian clustering analysis indicated that many Emydoidea populations were genetically isolated. Despite long generation times, all three species exhibited associations between genetic structure and postsettlement habitat change, indicating that long generation times may not be sufficient to delay genetic drift resulting from recent habitat fragmentation. The concordances in genetic structure observed between aquatic species, as well as isolation in the endangered, long-lived Emydoidea, reinforce the need to consider both landscape composition and demographic factors in assessing differential responses to habitat change in co-occurring species. © 2016 John Wiley & Sons Ltd.

An effective drift correction for dynamical downscaling of decadal global climate predictions

NASA Astrophysics Data System (ADS)

Paeth, Heiko; Li, Jingmin; Pollinger, Felix; Müller, Wolfgang A.; Pohlmann, Holger; Feldmann, Hendrik; Panitz, Hans-Jürgen

2018-04-01

Initialized decadal climate predictions with coupled climate models are often marked by substantial climate drifts that emanate from a mismatch between the climatology of the coupled model system and the data set used for initialization. While such drifts may be easily removed from the prediction system when analyzing individual variables, a major problem prevails for multivariate issues and, especially, when the output of the global prediction system shall be used for dynamical downscaling. In this study, we present a statistical approach to remove climate drifts in a multivariate context and demonstrate the effect of this drift correction on regional climate model simulations over the Euro-Atlantic sector. The statistical approach is based on an empirical orthogonal function (EOF) analysis adapted to a very large data matrix. The climate drift emerges as a dramatic cooling trend in North Atlantic sea surface temperatures (SSTs) and is captured by the leading EOF of the multivariate output from the global prediction system, accounting for 7.7% of total variability. The SST cooling pattern also imposes drifts in various atmospheric variables and levels. The removal of the first EOF effectuates the drift correction while retaining other components of intra-annual, inter-annual and decadal variability. In the regional climate model, the multivariate drift correction of the input data removes the cooling trends in most western European land regions and systematically reduces the discrepancy between the output of the regional climate model and observational data. In contrast, removing the drift only in the SST field from the global model has hardly any positive effect on the regional climate model.

A role for molecular genetics in biological conservation.

PubMed Central

O'Brien, S J

1994-01-01

The recognition of recent accelerated depletion of species as a consequence of human industrial development has spawned a wide interest in identifying threats to endangered species. In addition to ecological and demographic perils, it has become clear that small populations that narrowly survive demographic contraction may undergo close inbreeding, genetic drift, and loss of overall genomic variation due to allelic loss or reduction to homozygosity. I review here the consequences of such genetic depletion revealed by applying molecular population genetic analysis to four endangered mammals: African cheetah, lion, Florida panther, and humpback whale. The accumulated genetic results, combined with physiological, ecological, and ethological data, provide a multifaceted perspective of the process of species diminution. An emerging role of population genetics, phylogenetics, and phylogeography as indicators of a population's natural history and its future prognosis provides valuable data of use in the development of conservation management plans for endangered species. PMID:7912434

Ethnohistory, intertribal relationships, and genetic diversity among Amazonian Indians.

PubMed

Aguiar, G F

1991-12-01

The influence of recent ethnohistorical factors on the microevolution of South American Indians has not been adequately evaluated by population geneticists. This makes difficult a reasonable interpretation of the present genetic structure of these groups. In this article the genetic diversity of 18 tribes of the Amazon and neighboring areas belonging to 3 linguistic groups (Tupi, Carib, and Gê) is analyzed in light of documentary sources about historical events, such as demographic changes, geographic movements, intertribal relationships, and marriage practices, that have taken place since the end of the eighteenth century. The high depopulation rate suffered by the Tupi groups (61.4% on average) is a probable factor conditioning the large intergroup genetic distances in this linguistic stock, for depopulation is a phenomenon associated with random genetic drift caused by a bottleneck effect. On the other hand, the relatively high similarity of the Gê and the Carib shows an association with two main factors: (1) reduced spatial dispersion of the Gê in the recent past, providing adequate conditions for within-stock gene flow, and (2) strong tradition of intergroup contacts among the Carib, frequently followed by genetic admixture and even fusion of groups, as verified for the Wayana and the Aparaí. The patterns of biologic variation of some Tupi tribes (Waiãpi, Emerillon, Parakanã, and Assurini) are better explained by historical and regional contingencies than by linguistic classification.

Determinants of echolocation call frequency variation in the Formosan lesser horseshoe bat (Rhinolophus monoceros)

PubMed Central

Chen, Shiang-Fan; Jones, Gareth; Rossiter, Stephen J.

2009-01-01

The origin and maintenance of intraspecific variation in vocal signals is important for population divergence and speciation. Where vocalizations are transmitted by vertical cultural inheritance, similarity will reflect co-ancestry, and thus vocal divergence should reflect genetic structure. Horseshoe bats are characterized by echolocation calls dominated by a constant frequency component that is partly determined by maternal imprinting. Although previous studies showed that constant frequency calls are also influenced by some non-genetic factors, it is not known how frequency relates to genetic structure. To test this, we related constant frequency variation to genetic and non-genetic variables in the Formosan lesser horseshoe bat (Rhinolophus monoceros). Recordings of bats from across Taiwan revealed that females called at higher frequencies than males; however, we found no effect of environmental or morphological factors on call frequency. By comparison, variation showed clear population structure, with frequencies lower in the centre and east, and higher in the north and south. Within these regions, frequency divergence was directional and correlated with geographical distance, suggesting that call frequencies are subject to cultural drift. However, microsatellite clustering analysis showed that broad differences in constant frequency among populations corresponded to discontinuities in allele frequencies resulting from vicariant events. Our results provide evidence that the processes shaping genetic subdivision have concomitant consequences for divergence in echolocation call frequency. PMID:19692399

Investigating Holocene human population history in North Asia using ancient mitogenomes.

PubMed

Kılınç, Gülşah Merve; Kashuba, Natalija; Yaka, Reyhan; Sümer, Arev Pelin; Yüncü, Eren; Shergin, Dmitrij; Ivanov, Grigorij Leonidovich; Kichigin, Dmitrii; Pestereva, Kjunnej; Volkov, Denis; Mandryka, Pavel; Kharinskii, Artur; Tishkin, Alexey; Ineshin, Evgenij; Kovychev, Evgeniy; Stepanov, Aleksandr; Alekseev, Aanatolij; Fedoseeva, Svetlana Aleksandrovna; Somel, Mehmet; Jakobsson, Mattias; Krzewińska, Maja; Storå, Jan; Götherström, Anders

2018-06-12

Archaeogenomic studies have largely elucidated human population history in West Eurasia during the Stone Age. However, despite being a broad geographical region of significant cultural and linguistic diversity, little is known about the population history in North Asia. We present complete mitochondrial genome sequences together with stable isotope data for 41 serially sampled ancient individuals from North Asia, dated between c.13,790 BP and c.1,380 BP extending from the Palaeolithic to the Iron Age. Analyses of mitochondrial DNA sequences and haplogroup data of these individuals revealed the highest genetic affinity to present-day North Asian populations of the same geographical region suggesting a possible long-term maternal genetic continuity in the region. We observed a decrease in genetic diversity over time and a reduction of maternal effective population size (N e ) approximately seven thousand years before present. Coalescent simulations were consistent with genetic continuity between present day individuals and individuals dating to 7,000 BP, 4,800 BP or 3,000 BP. Meanwhile, genetic differences observed between 7,000 BP and 3,000 BP as well as between 4,800 BP and 3,000 BP were inconsistent with genetic drift alone, suggesting gene flow into the region from distant gene pools or structure within the population. These results indicate that despite some level of continuity between ancient groups and present-day populations, the region exhibits a complex demographic history during the Holocene.

Genetic structure of populations of whale sharks among ocean basins and evidence for their historic rise and recent decline.

PubMed

Vignaud, Thomas M; Maynard, Jeffrey A; Leblois, Raphael; Meekan, Mark G; Vázquez-Juárez, Ricardo; Ramírez-Macías, Dení; Pierce, Simon J; Rowat, David; Berumen, Michael L; Beeravolu, Champak; Baksay, Sandra; Planes, Serge

2014-05-01

This study presents genetic evidence that whale sharks, Rhincodon typus, are comprised of at least two populations that rarely mix and is the first to document a population expansion. Relatively high genetic structure is found when comparing sharks from the Gulf of Mexico with sharks from the Indo-Pacific. If mixing occurs between the Indian and Atlantic Oceans, it is not sufficient to counter genetic drift. This suggests whale sharks are not all part of a single global metapopulation. The significant population expansion we found was indicated by both microsatellite and mitochondrial DNA. The expansion may have happened during the Holocene, when tropical species could expand their range due to sea-level rise, eliminating dispersal barriers and increasing plankton productivity. However, the historic trend of population increase may have reversed recently. Declines in genetic diversity are found for 6 consecutive years at Ningaloo Reef in Australia. The declines in genetic diversity being seen now in Australia may be due to commercial-scale harvesting of whale sharks and collision with boats in past decades in other countries in the Indo-Pacific. The study findings have implications for models of population connectivity for whale sharks and advocate for continued focus on effective protection of the world's largest fish at multiple spatial scales. © 2014 John Wiley & Sons Ltd.

Body ownership and agency: task-dependent effects of the virtual hand illusion on proprioceptive drift.

PubMed

Shibuya, Satoshi; Unenaka, Satoshi; Ohki, Yukari

2017-01-01

Body ownership and agency are fundamental to self-consciousness. These bodily experiences have been intensively investigated using the rubber hand illusion, wherein participants perceive a fake hand as their own. After presentation of the illusion, the position of the participant's hand then shifts toward the location of the fake hand (proprioceptive drift). However, it remains controversial whether proprioceptive drift is able to provide an objective measurement of body ownership, and whether agency also affects drift. Using the virtual hand illusion (VHI), the current study examined the effects of body ownership and agency on proprioceptive drift, with three different visuo-motor tasks. Twenty healthy adults (29.6 ± 9.2 years old) completed VH manipulations using their right hand under a 2 × 2 factorial design (active vs. passive manipulation, and congruent vs. incongruent virtual hand). Prior to and after VH manipulation, three different tasks were performed to assess proprioceptive drift, in which participants were unable to see their real hands. The effects of the VHI on proprioceptive drift were task-dependent. When participants were required to judge the position of their right hand using a ruler, or by reaching toward a visual target, both body ownership and agency modulated proprioceptive drift. Comparatively, when participants aligned both hands, drift was influenced by ownership but not agency. These results suggest that body ownership and agency might differentially modulate various body representations in the brain.

Diversity Outbred Mice at 21: Maintaining Allelic Variation in the Face of Selection

PubMed Central

Chesler, Elissa J.; Gatti, Daniel M.; Morgan, Andrew P.; Strobel, Marge; Trepanier, Laura; Oberbeck, Denesa; McWeeney, Shannon; Hitzemann, Robert; Ferris, Martin; McMullan, Rachel; Clayshultle, Amelia; Bell, Timothy A.; de Villena, Fernando Pardo-Manuel; Churchill, Gary A.

2016-01-01

Multi-parent populations (MPPs) capture and maintain the genetic diversity from multiple inbred founder strains to provide a resource for high-resolution genetic mapping through the accumulation of recombination events over many generations. Breeding designs that maintain a large effective population size with randomized assignment of breeders at each generation can minimize the impact of selection, inbreeding, and genetic drift on allele frequencies. Small deviations from expected allele frequencies will have little effect on the power and precision of genetic analysis, but a major distortion could result in reduced power and loss of important functional alleles. We detected strong transmission ratio distortion in the Diversity Outbred (DO) mouse population on chromosome 2, caused by meiotic drive favoring transmission of the WSB/EiJ allele at the R2d2 locus. The distorted region harbors thousands of polymorphisms derived from the seven non-WSB founder strains and many of these would be lost if the sweep was allowed to continue. To ensure the utility of the DO population to study genetic variation on chromosome 2, we performed an artificial selection against WSB/EiJ alleles at the R2d2 locus. Here, we report that we have purged the WSB/EiJ allele from the drive locus while preserving WSB/EiJ alleles in the flanking regions. We observed minimal disruption to allele frequencies across the rest of the autosomal genome. However, there was a shift in haplotype frequencies of the mitochondrial genome and an increase in the rate of an unusual sex chromosome aneuploidy. The DO population has been restored to genome-wide utility for genetic analysis, but our experience underscores that vigilant monitoring of similar genetic resource populations is needed to ensure their long-term utility. PMID:27694113

Geographic Distributions of Idh-1 Alleles in a Cricket are Linked to Differential Enzyme Kinetic Performance Across Thermal Environments

USDA-ARS?s Scientific Manuscript database

Geographic clines within species are often interpreted as evidence of adaptation to varying environmental conditions. However, clines can also result from genetic drift, and these competing hypotheses must therefore be tested empirically. The striped ground cricket, Allonemobius socius, is widely-di...

Evidence for ecological speciation via a host shift in the holly leafminer, Phytomyza glabricola (Diptera: Agromyzidae)

USDA-ARS?s Scientific Manuscript database

Evolutionary radiations have been well documented in plants and insects, but we have yet to determine the relative impact of genetic drift and natural selection underlying these radiations. If radiations are adaptive, the diversity of species could be due to ecological speciation in these lineages. ...

Low genetic variation in the MHC class II DRB gene and MHC-linked microsatellites in endangered island populations of the leopard cat (Prionailurus bengalensis) in Japan.

PubMed

Saka, Toshinori; Nishita, Yoshinori; Masuda, Ryuichi

2018-02-01

Isolated populations of the leopard cat (Prionailurus bengalensis) on Tsushima and Iriomote islands in Japan are classified as subspecies P. b. euptilurus and P. b. iriomotensis, respectively. Because both populations have decreased to roughly 100, an understanding of their genetic diversity is essential for conservation. We genotyped MHC class II DRB exon 2 and MHC-linked microsatellite loci to evaluate the diversity of MHC genes in the Tsushima and Iriomote cat populations. We detected ten and four DRB alleles in these populations, respectively. A phylogenetic analysis showed DRB alleles from both populations to be closely related to those in other felid DRB lineages, indicating trans-species polymorphism. The MHC-linked microsatellites were more polymorphic in the Tsushima than in the Iriomote population. The MHC diversity of both leopard cat populations is much lower than in the domestic cat populations on these islands, probably due to inbreeding associated with founder effects, geographical isolation, or genetic drift. Our results predict low resistance of the two endangered populations to new pathogens introduced to the islands.

Eye regression in blind Astyanax cavefish may facilitate the evolution of an adaptive behavior and its sensory receptors.

PubMed

Borowsky, Richard

2013-07-11

The forces driving the evolutionary loss or simplification of traits such as vision and pigmentation in cave animals are still debated. Three alternative hypotheses are direct selection against the trait, genetic drift, and indirect selection due to antagonistic pleiotropy. Recent work establishes that Astyanax cavefish exhibit vibration attraction behavior (VAB), a presumed behavioral adaptation to finding food in the dark not exhibited by surface fish. Genetic analysis revealed two regions in the genome with quantitative trait loci (QTL) for both VAB and eye size. These observations were interpreted as genetic evidence that selection for VAB indirectly drove eye regression through antagonistic pleiotropy and, further, that this is a general mechanism to account for regressive evolution. These conclusions are unsupported by the data; the analysis fails to establish pleiotropy and ignores the numerous other QTL that map to, and potentially interact, in the same regions. It is likely that all three forces drive evolutionary change. We will be able to distinguish among them in individual cases only when we have identified the causative alleles and characterized their effects.

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

PubMed

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

2013-03-01

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

Frequent long-distance plant colonization in the changing Arctic.

PubMed

Alsos, Inger Greve; Eidesen, Pernille Bronken; Ehrich, Dorothee; Skrede, Inger; Westergaard, Kristine; Jacobsen, Gro Hilde; Landvik, Jon Y; Taberlet, Pierre; Brochmann, Christian

2007-06-15

The ability of species to track their ecological niche after climate change is a major source of uncertainty in predicting their future distribution. By analyzing DNA fingerprinting (amplified fragment-length polymorphism) of nine plant species, we show that long-distance colonization of a remote arctic archipelago, Svalbard, has occurred repeatedly and from several source regions. Propagules are likely carried by wind and drifting sea ice. The genetic effect of restricted colonization was strongly correlated with the temperature requirements of the species, indicating that establishment limits distribution more than dispersal. Thus, it may be appropriate to assume unlimited dispersal when predicting long-term range shifts in the Arctic.

Phylogeographic analysis reveals significant spatial genetic structure of Incarvillea sinensis as a product of mountain building.

PubMed

Chen, Shaotian; Xing, Yaowu; Su, Tao; Zhou, Zhekun; Dilcher, Emeritus David L; Soltis, Douglas E

2012-04-30

Incarvillea sinensis is widely distributed from Southwest China to Northeast China and in the Russian Far East. The distribution of this species was thought to be influenced by the uplift of the Qinghai-Tibet Plateau and Quaternary glaciation. To reveal the imprints of geological events on the spatial genetic structure of Incarvillea sinensis, we examined two cpDNA segments ( trnH- psbA and trnS- trnfM) in 705 individuals from 47 localities. A total of 16 haplotypes was identified, and significant genetic differentiation was revealed (GST =0.843, NST = 0.975, P < 0.05). The survey detected two highly divergent cpDNA lineages connected by a deep gap with allopatric distributions: the southern lineage with higher genetic diversity and differentiation in the eastern Qinghai-Tibet Plateau, and the northern lineage in the region outside the Qinghai-Tibet Plateau. The divergence between these two lineages was estimated at 4.4 MYA. A correlation between the genetic and the geographic distances indicates that genetic drift was more influential than gene flow in the northern clade with lower diversity and divergence. However, a scenario of regional equilibrium between gene flow and drift was shown for the southern clade. The feature of spatial distribution of the genetic diversity of the southern lineage possibly indicated that allopatric fragmentation was dominant in the collections from the eastern Qinghai-Tibet Plateau. The results revealed that the uplift of the Qinghai-Tibet Plateau likely resulted in the significant divergence between the lineage in the eastern Qinghai-Tibet Plateau and the other one outside this area. The diverse niches in the eastern Qinghai-Tibet Plateau created a wide spectrum of habitats to accumulate and accommodate new mutations. The features of genetic diversity of populations outside the eastern Qinghai-Tibet Plateau seemed to reveal the imprints of extinction during the Glacial and the interglacial and postglacial recolonization. Our study is a typical case of the significance of the uplift of the Qinghai-Tibet Plateau and the Quaternary Glacial in spatial genetic structure of eastern Asian plants, and sheds new light on the evolution of biodiversity in the Qinghai-Tibet Plateau at the intraspecies level.

Genomes of the Mouse Collaborative Cross.

PubMed

Srivastava, Anuj; Morgan, Andrew P; Najarian, Maya L; Sarsani, Vishal Kumar; Sigmon, J Sebastian; Shorter, John R; Kashfeen, Anwica; McMullan, Rachel C; Williams, Lucy H; Giusti-Rodríguez, Paola; Ferris, Martin T; Sullivan, Patrick; Hock, Pablo; Miller, Darla R; Bell, Timothy A; McMillan, Leonard; Churchill, Gary A; de Villena, Fernando Pardo-Manuel

2017-06-01

The Collaborative Cross (CC) is a multiparent panel of recombinant inbred (RI) mouse strains derived from eight founder laboratory strains. RI panels are popular because of their long-term genetic stability, which enhances reproducibility and integration of data collected across time and conditions. Characterization of their genomes can be a community effort, reducing the burden on individual users. Here we present the genomes of the CC strains using two complementary approaches as a resource to improve power and interpretation of genetic experiments. Our study also provides a cautionary tale regarding the limitations imposed by such basic biological processes as mutation and selection. A distinct advantage of inbred panels is that genotyping only needs to be performed on the panel, not on each individual mouse. The initial CC genome data were haplotype reconstructions based on dense genotyping of the most recent common ancestors (MRCAs) of each strain followed by imputation from the genome sequence of the corresponding founder inbred strain. The MRCA resource captured segregating regions in strains that were not fully inbred, but it had limited resolution in the transition regions between founder haplotypes, and there was uncertainty about founder assignment in regions of limited diversity. Here we report the whole genome sequence of 69 CC strains generated by paired-end short reads at 30× coverage of a single male per strain. Sequencing leads to a substantial improvement in the fine structure and completeness of the genomes of the CC. Both MRCAs and sequenced samples show a significant reduction in the genome-wide haplotype frequencies from two wild-derived strains, CAST/EiJ and PWK/PhJ. In addition, analysis of the evolution of the patterns of heterozygosity indicates that selection against three wild-derived founder strains played a significant role in shaping the genomes of the CC. The sequencing resource provides the first description of tens of thousands of new genetic variants introduced by mutation and drift in the CC genomes. We estimate that new SNP mutations are accumulating in each CC strain at a rate of 2.4 ± 0.4 per gigabase per generation. The fixation of new mutations by genetic drift has introduced thousands of new variants into the CC strains. The majority of these mutations are novel compared to currently sequenced laboratory stocks and wild mice, and some are predicted to alter gene function. Approximately one-third of the CC inbred strains have acquired large deletions (>10 kb) many of which overlap known coding genes and functional elements. The sequence of these mice is a critical resource to CC users, increases threefold the number of mouse inbred strain genomes available publicly, and provides insight into the effect of mutation and drift on common resources. Copyright © 2017 Srivastava et al.

Genomes of the Mouse Collaborative Cross

PubMed Central

Srivastava, Anuj; Morgan, Andrew P.; Najarian, Maya L.; Sarsani, Vishal Kumar; Sigmon, J. Sebastian; Shorter, John R.; Kashfeen, Anwica; McMullan, Rachel C.; Williams, Lucy H.; Giusti-Rodríguez, Paola; Ferris, Martin T.; Sullivan, Patrick; Hock, Pablo; Miller, Darla R.; Bell, Timothy A.; McMillan, Leonard; Churchill, Gary A.; de Villena, Fernando Pardo-Manuel

2017-01-01

The Collaborative Cross (CC) is a multiparent panel of recombinant inbred (RI) mouse strains derived from eight founder laboratory strains. RI panels are popular because of their long-term genetic stability, which enhances reproducibility and integration of data collected across time and conditions. Characterization of their genomes can be a community effort, reducing the burden on individual users. Here we present the genomes of the CC strains using two complementary approaches as a resource to improve power and interpretation of genetic experiments. Our study also provides a cautionary tale regarding the limitations imposed by such basic biological processes as mutation and selection. A distinct advantage of inbred panels is that genotyping only needs to be performed on the panel, not on each individual mouse. The initial CC genome data were haplotype reconstructions based on dense genotyping of the most recent common ancestors (MRCAs) of each strain followed by imputation from the genome sequence of the corresponding founder inbred strain. The MRCA resource captured segregating regions in strains that were not fully inbred, but it had limited resolution in the transition regions between founder haplotypes, and there was uncertainty about founder assignment in regions of limited diversity. Here we report the whole genome sequence of 69 CC strains generated by paired-end short reads at 30× coverage of a single male per strain. Sequencing leads to a substantial improvement in the fine structure and completeness of the genomes of the CC. Both MRCAs and sequenced samples show a significant reduction in the genome-wide haplotype frequencies from two wild-derived strains, CAST/EiJ and PWK/PhJ. In addition, analysis of the evolution of the patterns of heterozygosity indicates that selection against three wild-derived founder strains played a significant role in shaping the genomes of the CC. The sequencing resource provides the first description of tens of thousands of new genetic variants introduced by mutation and drift in the CC genomes. We estimate that new SNP mutations are accumulating in each CC strain at a rate of 2.4 ± 0.4 per gigabase per generation. The fixation of new mutations by genetic drift has introduced thousands of new variants into the CC strains. The majority of these mutations are novel compared to currently sequenced laboratory stocks and wild mice, and some are predicted to alter gene function. Approximately one-third of the CC inbred strains have acquired large deletions (>10 kb) many of which overlap known coding genes and functional elements. The sequence of these mice is a critical resource to CC users, increases threefold the number of mouse inbred strain genomes available publicly, and provides insight into the effect of mutation and drift on common resources. PMID:28592495

Long-range dispersal moved Francisella tularensis into Western Europe from the East

PubMed Central

Dwibedi, Chinmay; Birdsell, Dawn; Lärkeryd, Adrian; Myrtennäs, Kerstin; Öhrman, Caroline; Nilsson, Elin; Karlsson, Edvin; Hochhalter, Christian; Rivera, Andrew; Maltinsky, Sara; Bayer, Brittany; Keim, Paul; Scholz, Holger C.; Tomaso, Herbert; Wittwer, Matthias; Beuret, Christian; Schuerch, Nadia; Pilo, Paola; Hernández Pérez, Marta; Rodriguez-Lazaro, David; Escudero, Raquel; Anda, Pedro; Forsman, Mats; Wagner, David M.; Larsson, Pär

2016-01-01

For many infections transmitting to humans from reservoirs in nature, disease dispersal patterns over space and time are largely unknown. Here, a reversed genomics approach helped us understand disease dispersal and yielded insight into evolution and biological properties of Francisella tularensis, the bacterium causing tularemia. We whole-genome sequenced 67 strains and characterized by single-nucleotide polymorphism assays 138 strains, collected from individuals infected 1947-2012 across Western Europe. We used the data for phylogenetic, population genetic and geographical network analyses. All strains (n=205) belonged to a monophyletic population of recent ancestry not found outside Western Europe. Most strains (n=195) throughout the study area were assigned to a star-like phylogenetic pattern indicating that colonization of Western Europe occurred via clonal expansion. In the East of the study area, strains were more diverse, consistent with a founder population spreading from east to west. The relationship of genetic and geographic distance within the F. tularensis population was complex and indicated multiple long-distance dispersal events. Mutation rate estimates based on year of isolation indicated null rates; in outbreak hotspots only, there was a rate of 0.4 mutations/genome/year. Patterns of nucleotide substitution showed marked AT mutational bias suggestive of genetic drift. These results demonstrate that tularemia has moved from east to west in Europe and that F. tularensis has a biology characterized by long-range geographical dispersal events and mostly slow, but variable, replication rates. The results indicate that mutation-driven evolution, a resting survival phase, genetic drift and long-distance geographical dispersal events have interacted to generate genetic diversity within this species. PMID:28348839

A multi-perspective view of genetic variation in Cameroon.

PubMed

Coia, V; Brisighelli, F; Donati, F; Pascali, V; Boschi, I; Luiselli, D; Battaggia, C; Batini, C; Taglioli, L; Cruciani, F; Paoli, G; Capelli, C; Spedini, G; Destro-Bisol, G

2009-11-01

In this study, we report the genetic variation of autosomal and Y-chromosomal microsatellites in a large Cameroon population dataset (a total of 11 populations) and jointly analyze novel and previous genetic data (mitochondrial DNA and protein coding loci) taking geographic and cultural factors into consideration. The complex pattern of genetic variation of Cameroon can in part be described by contrasting two geographic areas (corresponding to the northern and southern part of the country), which differ substantially in environmental, biological, and cultural aspects. Northern Cameroon populations show a greater within- and among-group diversity, a finding that reflects the complex migratory patterns and the linguistic heterogeneity of this area. A striking reduction of Y-chromosomal genetic diversity was observed in some populations of the northern part of the country (Podokwo and Uldeme), a result that seems to be related to their demographic history rather than to sampling issues. By exploring patterns of genetic, geographic, and linguistic variation, we detect a preferential correlation between genetics and geography for mtDNA. This finding could reflect a female matrimonial mobility that is less constrained by linguistic factors than in males. Finally, we apply the island model to mitochondrial and Y-chromosomal data and obtain a female-to-male migration Nnu ratio that was more than double in the northern part of the country. The combined effect of the propensity to inter-populational admixture of females, favored by cultural contacts, and of genetic drift acting on Y-chromosomal diversity could account for the peculiar genetic pattern observed in northern Cameroon.

Comparative Analysis of the Pattern of Population Genetic Diversity in Three Indo-West Pacific Rhizophora Mangrove Species

PubMed Central

Yan, Yu-Bin; Duke, Norm C.; Sun, Mei

2016-01-01

Rhizophora species are the most widely distributed mangrove trees in the Indo-West Pacific (IWP) region. Comparative studies of these species with shared life history traits can help identify evolutionary factors that have played most important roles in determining genetic diversity within and between populations in ocean-current dispersed mangrove tree species. We sampled 935 individuals from 54 natural populations for genotyping with 13 microsatellite markers to investigate the level of genetic variation, population structure, and gene flow on a broad geographic scale in Rhizophora apiculata, Rhizophora mucronata, and Rhizophora stylosa across the IWP region. In contrast to the pattern expected of long-lived woody plants with predominant wind-pollination, water-dispersed seeds and wide geographic range, genetic variation within populations was generally low in all the three species, especially in those peripheral populations from geographic range limits. Although the large water-buoyant propagules of Rhizophora have capacity for long distance dispersal, such events might be rare in reality, as reflected by the low level of gene flow and high genetic differentiation between most of population pairs within each species. Phylogeographic separation of Australian and Pacific island populations from SE Asian lineages previously revealed with DNA sequence data was still detectable in R. apiculata based on genetic distances, but this pattern of disjunction was not always evident in R. mucronata and R. stylosa, suggesting that fast-evolving molecular markers could be more suitable for detecting contemporary genetic structure but not deep evolutionary divergence caused by historical vicariance. Given that mangrove species generally have small effective population sizes, we conclude that genetic drift coupled with limited gene flow have played a dominant role in producing the current pattern of population genetic diversity in the IWP Rhizophora species, overshadowing the effects of their life history traits. Recent population fragmentation and disturbances arising from human activities could further endanger genetic diversity in mangrove trees. PMID:27746790

Comparative Analysis of the Pattern of Population Genetic Diversity in Three Indo-West Pacific Rhizophora Mangrove Species.

PubMed

Yan, Yu-Bin; Duke, Norm C; Sun, Mei

2016-01-01

Rhizophora species are the most widely distributed mangrove trees in the Indo-West Pacific (IWP) region. Comparative studies of these species with shared life history traits can help identify evolutionary factors that have played most important roles in determining genetic diversity within and between populations in ocean-current dispersed mangrove tree species. We sampled 935 individuals from 54 natural populations for genotyping with 13 microsatellite markers to investigate the level of genetic variation, population structure, and gene flow on a broad geographic scale in Rhizophora apiculata, Rhizophora mucronata , and Rhizophora stylosa across the IWP region. In contrast to the pattern expected of long-lived woody plants with predominant wind-pollination, water-dispersed seeds and wide geographic range, genetic variation within populations was generally low in all the three species, especially in those peripheral populations from geographic range limits. Although the large water-buoyant propagules of Rhizophora have capacity for long distance dispersal, such events might be rare in reality, as reflected by the low level of gene flow and high genetic differentiation between most of population pairs within each species. Phylogeographic separation of Australian and Pacific island populations from SE Asian lineages previously revealed with DNA sequence data was still detectable in R. apiculata based on genetic distances, but this pattern of disjunction was not always evident in R. mucronata and R. stylosa , suggesting that fast-evolving molecular markers could be more suitable for detecting contemporary genetic structure but not deep evolutionary divergence caused by historical vicariance. Given that mangrove species generally have small effective population sizes, we conclude that genetic drift coupled with limited gene flow have played a dominant role in producing the current pattern of population genetic diversity in the IWP Rhizophora species, overshadowing the effects of their life history traits. Recent population fragmentation and disturbances arising from human activities could further endanger genetic diversity in mangrove trees.

Determining the drift potential of Venturi nozzles compared with standard nozzles across three insecticide spray solutions in a wind tunnel.

PubMed

Ferguson, J Connor; Chechetto, Rodolfo G; O'Donnell, Chris C; Dorr, Gary J; Moore, John H; Baker, Greg J; Powis, Kevin J; Hewitt, Andrew J

2016-08-01

Previous research has sought to adopt the use of drift-reducing technologies (DRTs) for use in field trials to control diamondback moth (DBM) Plutella xylostella (L.) (Lepidoptera: Plutellidae) in canola (Brassica napus L.). Previous studies observed no difference in canopy penetration from fine to coarse sprays, but the coverage was higher for fine sprays. DBM has a strong propensity to avoid sprayed plant material, putting further pressure on selecting technologies that maximise coverage, but often this is at the expense of a greater drift potential. This study aims to examine the addition of a DRT oil that is labelled for control of DBM as well and its effect on the drift potential of the spray solution. The objectives of the study are to quantify the droplet size spectrum and spray drift potential of each nozzle type to select technologies that reduce spray drift, to examine the effect of the insecticide tank mix at both (50 and 100 L ha(-1) ) application rates on droplet size and spray drift potential across tested nozzle type and to compare the droplet size results of each nozzle by tank mix against the drift potential of each nozzle. The nozzle type affected the drift potential the most, but the spray solution also affected drift potential. The fine spray quality (TCP) resulted in the greatest drift potential (7.2%), whereas the coarse spray quality (AIXR) resulted in the lowest (1.3%), across all spray solutions. The spray solutions mixed at the 100 L ha(-1) application volume rate resulted in a higher drift potential than the same products mixed at the 50 L ha(-1) mix rate. The addition of the paraffinic DRT oil was significant in reducing the drift potential of Bacillus thuringiensis var. kurstkai (Bt)-only treatments across all tested nozzle types. The reduction in drift potential from the fine spray quality to the coarse spray quality was up to 85%. The addition of a DRT oil is an effective way to reduce the spray solution drift potential across all nozzle types and tank mixes evaluated in this study. The greatest reduction in drift potential can be achieved by changing nozzle type, which can reduce the losses of the spray to the surrounding environment. Venturi nozzles greatly reduce the drift potential compared with standard nozzles by as much as 85% across all three insecticide spray solutions. Results suggest that a significant reduction in drift potential can be achieved by changing the nozzle type, and can be achieved without a loss in control of DBM. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

The Effects of Clock Drift on the Mars Exploration Rovers

NASA Technical Reports Server (NTRS)

Ali, Khaled S.; Vanelli, C. Anthony

2012-01-01

All clocks drift by some amount, and the mission clock on the Mars Exploration Rovers (MER) is no exception. The mission clock on both MER rovers drifted significantly since the rovers were launched, and it is still drifting on the Opportunity rover. The drift rate is temperature dependent. Clock drift causes problems for onboard behaviors and spacecraft operations, such as attitude estimation, driving, operation of the robotic arm, pointing for imaging, power analysis, and telecom analysis. The MER operations team has techniques to deal with some of these problems. There are a few techniques for reducing and eliminating the clock drift, but each has drawbacks. This paper presents an explanation of what is meant by clock drift on the rovers, its relationship to temperature, how we measure it, what problems it causes, how we deal with those problems, and techniques for reducing the drift.

Detection of mastitis in dairy cattle by use of mixture models for repeated somatic cell scores: a Bayesian approach via Gibbs sampling.

PubMed

Odegård, J; Jensen, J; Madsen, P; Gianola, D; Klemetsdal, G; Heringstad, B

2003-11-01

The distribution of somatic cell scores could be regarded as a mixture of at least two components depending on a cow's udder health status. A heteroscedastic two-component Bayesian normal mixture model with random effects was developed and implemented via Gibbs sampling. The model was evaluated using datasets consisting of simulated somatic cell score records. Somatic cell score was simulated as a mixture representing two alternative udder health statuses ("healthy" or "diseased"). Animals were assigned randomly to the two components according to the probability of group membership (Pm). Random effects (additive genetic and permanent environment), when included, had identical distributions across mixture components. Posterior probabilities of putative mastitis were estimated for all observations, and model adequacy was evaluated using measures of sensitivity, specificity, and posterior probability of misclassification. Fitting different residual variances in the two mixture components caused some bias in estimation of parameters. When the components were difficult to disentangle, so were their residual variances, causing bias in estimation of Pm and of location parameters of the two underlying distributions. When all variance components were identical across mixture components, the mixture model analyses returned parameter estimates essentially without bias and with a high degree of precision. Including random effects in the model increased the probability of correct classification substantially. No sizable differences in probability of correct classification were found between models in which a single cow effect (ignoring relationships) was fitted and models where this effect was split into genetic and permanent environmental components, utilizing relationship information. When genetic and permanent environmental effects were fitted, the between-replicate variance of estimates of posterior means was smaller because the model accounted for random genetic drift.

Evidence for a Common Origin of Blacksmiths and Cultivators in the Ethiopian Ari within the Last 4500 Years: Lessons for Clustering-Based Inference

PubMed Central

van Dorp, Lucy; Balding, David; Myers, Simon; Pagani, Luca; Tyler-Smith, Chris; Bekele, Endashaw; Tarekegn, Ayele; Thomas, Mark G.; Bradman, Neil; Hellenthal, Garrett

2015-01-01

The Ari peoples of Ethiopia are comprised of different occupational groups that can be distinguished genetically, with Ari Cultivators and the socially marginalised Ari Blacksmiths recently shown to have a similar level of genetic differentiation between them (F ST ≈ 0.023 − 0.04) as that observed among multiple ethnic groups sampled throughout Ethiopia. Anthropologists have proposed two competing theories to explain the origins of the Ari Blacksmiths as (i) remnants of a population that inhabited Ethiopia prior to the arrival of agriculturists (e.g. Cultivators), or (ii) relatively recently related to the Cultivators but presently marginalized in the community due to their trade. Two recent studies by different groups analysed genome-wide DNA from samples of Ari Blacksmiths and Cultivators and suggested that genetic patterns between the two groups were more consistent with model (i) and subsequent assimilation of the indigenous peoples into the expanding agriculturalist community. We analysed the same samples using approaches designed to attenuate signals of genetic differentiation that are attributable to allelic drift within a population. By doing so, we provide evidence that the genetic differences between Ari Blacksmiths and Cultivators can be entirely explained by bottleneck effects consistent with hypothesis (ii). This finding serves as both a cautionary tale about interpreting results from unsupervised clustering algorithms, and suggests that social constructions are contributing directly to genetic differentiation over a relatively short time period among previously genetically similar groups. PMID:26291793

MAINTENANCE OF ECOLOGICALLY SIGNIFICANT GENETIC VARIATION IN THE TIGER SWALLOWTAIL BUTTERFLY THROUGH DIFFERENTIAL SELECTION AND GENE FLOW.

PubMed

Bossart, J L; Scriber, J M

1995-12-01

Differential selection in a heterogeneous environment is thought to promote the maintenance of ecologically significant genetic variation. Variation is maintained when selection is counterbalanced by the homogenizing effects of gene flow and random mating. In this study, we examine the relative importance of differential selection and gene flow in maintaining genetic variation in Papilio glaucus. Differential selection on traits contributing to successful use of host plants (oviposition preference and larval performance) was assessed by comparing the responses of southern Ohio, north central Georgia, and southern Florida populations of P. glaucus to three hosts: Liriodendron tulipifera, Magnolia virginiana, and Prunus serotina. Gene flow among populations was estimated using allozyme frequencies from nine polymorphic loci. Significant genetic differentiation was observed among populations for both oviposition preference and larval performance. This differentiation was interpreted to be the result of selection acting on Florida P. glaucus for enhanced use of Magnolia, the prevalent host in Florida. In contrast, no evidence of population differentiation was revealed by allozyme frequencies. F ST -values were very small and Nm, an estimate of the relative strengths of gene flow and genetic drift, was large, indicating that genetic exchange among P. glaucus populations is relatively unrestricted. The contrasting patterns of spatial differentiation for host-use traits and lack of differentiation for electrophoretically detectable variation implies that differential selection among populations will be counterbalanced by gene flow, thereby maintaining genetic variation for host-use traits. © 1995 The Society for the Study of Evolution.

Genetic monitoring of horses in the Czech Republic: A large-scale study with a focus on the Czech autochthonous breeds.

PubMed

Putnová, L; Štohl, R; Vrtková, I

2018-02-01

We propose the first comprehensive in-depth study monitoring horses in the Czech Republic. We scanned 9,289 animals from 44 populations for 17 equine STRs. Other equids analysed involved Equus przewalskii and Equus asinus. The total of 228 different alleles were detected, with the mean number of 13.4 per locus. The highest allelic richness (AR) was found in the Welsh Part Bred (6.01), followed by the Camargue (5.93) and Czech Sport Pony (5.91), whereas the Friesian exhibited the lowest AR (3.06). Interpopulation differences explained approximately nine per cent of the total genetic diversity. Reynold's genetic distance ranged from 0.003 between the Czech Warmblood and the Slovak Warmblood to 0.404 between the Friesian and donkeys. Close genetic proximity between the Silesian Noriker and Noriker was revealed. The Moravian Warmblood was better differentiated and more distant from the Czech Warmblood than the Kinsky Horse and retained the original genes of the old Austro-Hungarian tribes. A high gene flow level and a lack of genetic structure were found in the seven studied populations. Despite the historical bottlenecks and previous inbreeding, the Czech-Moravian Belgian Horse, Hucul, Old Kladruber Horse and Silesian Noriker did not suffer a serious loss of genetic diversity due to genetic drift/low effective population size. A NeighborNet dendrogram revealed breeds not classified in their groups according to the nomenclature (the Friesian, Hafling and Merens). © 2018 Blackwell Verlag GmbH.

Contrasting Patterns of Genomic Diversity Reveal Accelerated Genetic Drift but Reduced Directional Selection on X-Chromosome in Wild and Domestic Sheep Species.

PubMed

Chen, Ze-Hui; Zhang, Min; Lv, Feng-Hua; Ren, Xue; Li, Wen-Rong; Liu, Ming-Jun; Nam, Kiwoong; Bruford, Michael W; Li, Meng-Hua

2018-04-01

Analyses of genomic diversity along the X chromosome and of its correlation with autosomal diversity can facilitate understanding of evolutionary forces in shaping sex-linked genomic architecture. Strong selective sweeps and accelerated genetic drift on the X-chromosome have been inferred in primates and other model species, but no such insight has yet been gained in domestic animals compared with their wild relatives. Here, we analyzed X-chromosome variability in a large ovine data set, including a BeadChip array for 943 ewes from the world's sheep populations and 110 whole genomes of wild and domestic sheep. Analyzing whole-genome sequences, we observed a substantially reduced X-to-autosome diversity ratio (∼0.6) compared with the value expected under a neutral model (0.75). In particular, one large X-linked segment (43.05-79.25 Mb) was found to show extremely low diversity, most likely due to a high density of coding genes, featuring highly conserved regions. In general, we observed higher nucleotide diversity on the autosomes, but a flat diversity gradient in X-linked segments, as a function of increasing distance from the nearest genes, leading to a decreased X: autosome (X/A) diversity ratio and contrasting to the positive correlation detected in primates and other model animals. Our evidence suggests that accelerated genetic drift but reduced directional selection on X chromosome, as well as sex-biased demographic events, explain low X-chromosome diversity in sheep species. The distinct patterns of X-linked and X/A diversity we observed between Middle Eastern and non-Middle Eastern sheep populations can be explained by multiple migrations, selection, and admixture during the domestic sheep's recent postdomestication demographic expansion, coupled with natural selection for adaptation to new environments. In addition, we identify important novel genes involved in abnormal behavioral phenotypes, metabolism, and immunity, under selection on the sheep X-chromosome.

Contrasting Patterns of Genomic Diversity Reveal Accelerated Genetic Drift but Reduced Directional Selection on X-Chromosome in Wild and Domestic Sheep Species

PubMed Central

Chen, Ze-Hui; Zhang, Min; Lv, Feng-Hua; Ren, Xue; Li, Wen-Rong; Liu, Ming-Jun; Nam, Kiwoong; Bruford, Michael W; Li, Meng-Hua

2018-01-01

Abstract Analyses of genomic diversity along the X chromosome and of its correlation with autosomal diversity can facilitate understanding of evolutionary forces in shaping sex-linked genomic architecture. Strong selective sweeps and accelerated genetic drift on the X-chromosome have been inferred in primates and other model species, but no such insight has yet been gained in domestic animals compared with their wild relatives. Here, we analyzed X-chromosome variability in a large ovine data set, including a BeadChip array for 943 ewes from the world’s sheep populations and 110 whole genomes of wild and domestic sheep. Analyzing whole-genome sequences, we observed a substantially reduced X-to-autosome diversity ratio (∼0.6) compared with the value expected under a neutral model (0.75). In particular, one large X-linked segment (43.05–79.25 Mb) was found to show extremely low diversity, most likely due to a high density of coding genes, featuring highly conserved regions. In general, we observed higher nucleotide diversity on the autosomes, but a flat diversity gradient in X-linked segments, as a function of increasing distance from the nearest genes, leading to a decreased X: autosome (X/A) diversity ratio and contrasting to the positive correlation detected in primates and other model animals. Our evidence suggests that accelerated genetic drift but reduced directional selection on X chromosome, as well as sex-biased demographic events, explain low X-chromosome diversity in sheep species. The distinct patterns of X-linked and X/A diversity we observed between Middle Eastern and non-Middle Eastern sheep populations can be explained by multiple migrations, selection, and admixture during the domestic sheep’s recent postdomestication demographic expansion, coupled with natural selection for adaptation to new environments. In addition, we identify important novel genes involved in abnormal behavioral phenotypes, metabolism, and immunity, under selection on the sheep X-chromosome. PMID:29790980

Associations between forest fragmentation patterns and geneticstructure in Pfrimer’s Parakeet (Pyrrhura pfrimeri), an endangered endemic to central Brazil’s dry forests

USGS Publications Warehouse

Haig, Susan M.; Miller, Leonard F.; Bianchi, Carlos; Mullins, Thomas D.

2012-01-01

When habitat becomes fragmented, populations of species may become increasingly isolated. In the absence of habitat corridors, genetic structure may develop and populations risk reductions in genetic diversity from increased genetic drift and inbreeding. Deforestation of the Cerrado biome of Brazil, particularly of the dry forests within the Parana˜ River Basin, has incrementally occurred since the 1970s and increased forest fragmentation within the region. We performed landscape genetic analyses of Pfrimer’s parakeet (Pyrrhura pfrimeri), a globally endangered endemic to the region, to determine if forest fragmentation patterns were associated with genetic structuring in this species. We used previously generated satellite imagery that identified the locations of Parana˜ River Basin forest fragments in 1977, 1993/94, and 2008. Behavioral data quantifying the affinity of Pfrimer’s parakeet for forest habitat was used to parameterize empirically derived landscape conductance surfaces. Though genetic structure was observed among Pfrimer’s parakeet populations, no association between genetic and geographic distance was detected. Likewise, least cost path lengths, circuit theorybased resistance distances, and a new measure of least cost path length complexity could not be conclusively associated with genetic structure patterns. Instead, a new quantity that encapsulated connection redundancy from the 1977 forest fragmentation data provided the clearest associations with pairwise genetic differentiation patterns (Jost’s D: r = 0.72, P = 0.006; FST: r = 0.741, P = 0.001). Our analyses suggest a 35-year or more lag between deforestation and its effect on genetic structure. Because 66 % of the Parana˜ River Basin has been deforested since 1977, we expect that genetic structure will increase substantially among Pfrimer’s Parakeet populations in the future, especially if fragmentation continues at its current pace.

Analysis of drift correction in different simulated weighing schemes

NASA Astrophysics Data System (ADS)

Beatrici, A.; Rebelo, A.; Quintão, D.; Cacais, F. L.; Loayza, V. M.

2015-10-01

In the calibration of high accuracy mass standards some weighing schemes are used to reduce or eliminate the zero drift effects in mass comparators. There are different sources for the drift and different methods for its treatment. By using numerical methods, drift functions were simulated and a random term was included in each function. The comparison between the results obtained from ABABAB and ABBA weighing series was carried out. The results show a better efficacy of ABABAB method for drift with smooth variation and small randomness.

Landscape-scale evaluation of genetic structure among barrier-isolated populations of coastal cutthroat trout, Oncorhynchus clarkii clarkii

USGS Publications Warehouse

Guy, T.J.; Gresswell, R.E.; Banks, M.A.

2008-01-01

Relationships among landscape structure, stochastic disturbance, and genetic diversity were assessed by examining interactions between watershed-scale environmental factors and genetic diversity of coastal cutthroat trout (Oncorhynchus clarkii clarkii) in 27 barrier-isolated watersheds from western Oregon, USA. Headwater populations of coastal cutthroat trout were genetically differentiated (mean FST = 0.33) using data from seven microsatellite loci (2232 individuals), but intrapopulation microsatellite genetic diversity (mean number of alleles per locus = 5, mean He = 0.60) was only moderate. Genetic diversity of coastal cutthroat trout was greater (P = 0.02) in the Coast Range ecoregion (mean alleles = 47) than in the Cascades ecoregion (mean alleles = 30), and differences coincided with indices of regional within-watershed complexity and connectivity. Furthermore, regional patterns of diversity evident from isolation-by-distance plots suggested that retention of within-population genetic diversity in the Coast Range ecoregion is higher than that in the Cascades, where genetic drift is the dominant factor influencing genetic patterns. Thus, it appears that physical landscape features have influenced genetic patterns in these populations isolated from short-term immigration. ?? 2008 NRC.

Spray particle drift mitigation using field corn (Zea mays L.) as a drift barrier.

PubMed

Vieira, Bruno C; Butts, Thomas R; Rodrigues, Andre O; Golus, Jeffrey A; Schroeder, Kasey; Kruger, Greg R

2018-04-24

Herbicide particle drift reduces application efficacy and can cause severe impacts on nearby vegetation depending on the herbicide mode-of-action, exposure level, and tolerance to the herbicide. A particle drift mitigation effort placing windbreaks or barriers on the field boundaries to reduce off-target movement of spray particles has been utilized in the past. The objective of this research was to evaluate the effectiveness of field corn (Zea mays L.) at different heights as a particle drift barrier. Applications with a non-air inclusion flat fan nozzle (ER11004) resulted in greater particle drift when compared to an air inclusion nozzle (TTI11004). Eight rows of corn were used as barriers (0.91, 1.22, and 1.98 m height) which reduced the particle drift for both nozzles, especially at shorter downwind distances. Applications with the ER11004 nozzle without corn barriers had 1% of the applied rate (D 99 ) predicted to deposit at 14.8 m downwind, whereas this distance was reduced (up to 7-fold) when applications were performed with corn barriers. The combination of corn drift barriers and nozzle selection (TTI11004) provided satisfactory particle drift reduction when the D 99 estimates were compared to applications with the ER11004 nozzle without corn barriers (up to 10-fold difference). The corn drift barriers were effective in reducing particle drift from applications with the ER11004 and the TTI11004 nozzles (Fine and Ultra Coarse spray classifications, respectively). The corn drift barrier had appropriate porosity and width as the airborne spray was captured within its canopy instead of deflecting up and over it. This article is protected by copyright. All rights reserved.

Effects of plasma flows on particle diffusion in stochastic magnetic fields

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

Vlad, M.; Spineanu, F.; Misguich, J.H.

1996-07-01

The study of collisional test particle diffusion in stochastic magnetic fields is extended to include the effects of the macroscopic flows of the plasma (drifts). We show that a substantial amplification of the diffusion coefficient can be obtained. This effect is produced by the combined action of the parallel collisional velocity and of the average drifts. The perpendicular collisional velocity influences the effective diffusion only in the limit of small average drifts. {copyright} {ital 1996 The American Physical Society.}

Propeller wash effects on spray drift

Treesearch

Steven J. Thompson; Alvin R. Womac; Joseph Mulrooney; Sidney Deck

2005-01-01

for aerial spray application, there is some question if off-target drift (both near and far) is influenced by which boom is spraying and the direction of propeller wash rotation. This information may be useful when switching off one boom close to a field boundary. The effect of alternate boom switching and propeller wash direction on aerial spray drift from a turbine-...

Estimates of effective population size and inbreeding in South African indigenous chicken populations: implications for the conservation of unique genetic resources.

PubMed

Mtileni, Bohani; Dzama, Kennedy; Nephawe, Khathutshelo; Rhode, Clint

2016-06-01

Conservation of locally adapted indigenous livestock breeds has become an important objective in sustainable animal breeding, as these breeds represent a unique genetic resource. Therefore, the Agricultural Research Council of South Africa initiated a conservation programme for four South African indigenous chicken breeds. The evaluation and monitoring of the genetic constitution of these conservation flocks is important for proper management of the conservation programme. Using molecular genetic analyses, the effective population sizes and relatedness of these conservation flocks were compared to village (field) chicken populations from which they were derived. Genetic diversity within and between these populations are further discussed within the context of population size. The conservation flocks for the respective breeds had relatively small effective population sizes (point estimate range 38.6-78.6) in comparison to the field populations (point estimate range 118.9-580.0). Furthermore, evidence supports a transient heterozygous excess, generally associated with the occurrence of a recent population bottleneck. Genetic diversity, as measured by the number of alleles, heterozygosity and information index, was also significantly reduced in the conservation flocks. The average relatedness amongst the conservation flocks was high, whilst it remained low for the field populations. There was also significant evidence for population differentiation between field and conservation populations. F st estimates for conservation flocks were moderate to high with a maximum reached between VD_C and VD_F (0.285). However, F st estimates for field population were excessively low between the NN_C and EC_F (0.007) and between EC_F and OV_F (0.009). The significant population differentiation of the conservation flocks from their geographically correlated field populations of origin is further supported by the analysis of molecular variance (AMOVA), with 10.51 % of genetic diversity ascribed to population differences within groups (F SC = 0.106). The results suggest that significant genetic erosion has occurred within the conservation flocks due to inbreeding, pronounced effects of random drift and selection. It might be necessary to introduce new breeding individuals from the respective field populations in order to increase the effective population sizes of the conservation flocks and counter the effects of genetic erosion.

On the Nocturnal Downward and Westward Equatorial Ionospheric Plasma Drifts During the 17 March 2015 Geomagnetic Storm

NASA Astrophysics Data System (ADS)

Bagiya, Mala S.; Vichare, Geeta; Sinha, A. K.; Sripathi, S.

2018-02-01

During quiet period, the nocturnal equatorial ionospheric plasma drifts eastward in the zonal direction and downward in the vertical direction. This quiet time drift pattern could be understood through dynamo processes in the nighttime equatorial ionosphere. The present case study reports the nocturnal simultaneous occurrence of the vertically downward and zonally westward plasma drifts over the Indian latitudes during the geomagnetic storm of 17 March 2015. After 17:00 UT ( 22:10 local time), the vertical plasma drift became downward and coincided with the westward zonal drift, a rarely observed feature of low latitude plasma drifts. The vertical drift turned upward after 18:00 UT, while the zonal drift became eastward. We mainly emphasize here the distinct bipolar type variations of vertical and zonal plasma drifts observed around 18:00 UT. We explain the vertical plasma drift in terms of the competing effects between the storm time prompt penetration and disturbance dynamo electric fields. Whereas, the westward drift is attributed to the storm time local electrodynamical changes mainly through the disturbance dynamo field in addition to the vertical Pedersen current arising from the spatial (longitudinal) gradient of the field aligned Pedersen conductivity.

Validation testing of drift reduction technology testing protocol

EPA Science Inventory

A number of pesticide application technologies offer the potential to reduce spray drift from pesticide applications. However, limited information exists on the effectiveness of these technologies in reducing spray drift. Working with a stakeholder technical panel under EPA's Env...

Optical drift effects in general relativity

NASA Astrophysics Data System (ADS)

Korzyński, Mikołaj; Kopiński, Jarosław

2018-03-01

We consider the question of determining the optical drift effects in general relativity, i.e. the rate of change of the apparent position, redshift, Jacobi matrix, angular distance and luminosity distance of a distant object as registered by an observer in an arbitrary spacetime. We present a fully relativistic and covariant approach, in which the problem is reduced to a hierarchy of ODE's solved along the line of sight. The 4-velocities and 4-accelerations of the observer and the emitter and the geometry of the spacetime along the line of sight constitute the input data. We build on the standard relativistic geometric optics formalism and extend it to include the time derivatives of the observables. In the process we obtain two general, non-perturbative relations: the first one between the gravitational lensing, represented by the Jacobi matrix, and the apparent position drift, also called the cosmic parallax, and the second one between the apparent position drift and the redshift drift. The applications of the results include the theoretical study of the drift effects of cosmological origin (so-called real-time cosmology) in numerical or exact Universe models.

Genetic markers and population history: Finland revisited

PubMed Central

Palo, Jukka U; Ulmanen, Ismo; Lukka, Matti; Ellonen, Pekka; Sajantila, Antti

2009-01-01

The Finnish population in Northern Europe has been a target of extensive genetic studies during the last decades. The population is considered as a homogeneous isolate, well suited for gene mapping studies because of its reduced diversity and homogeneity. However, several studies have shown substantial differences between the eastern and western parts of the country, especially in the male-mediated Y chromosome. This divergence is evident in non-neutral genetic variation also and it is usually explained to stem from founder effects occurring in the settlement of eastern Finland as late as in the 16th century. Here, we have reassessed this population historical scenario using Y-chromosomal, mitochondrial and autosomal markers and geographical sampling covering entire Finland. The obtained results suggest substantial Scandinavian gene flow into south-western, but not into the eastern, Finland. Male-biased Scandinavian gene flow into the south-western parts of the country would plausibly explain the large inter-regional differences observed in the Y-chromosome, and the relative homogeneity in the mitochondrial and autosomal data. On the basis of these results, we suggest that the expression of ‘Finnish Disease Heritage' illnesses, more common in the eastern/north-eastern Finland, stems from long-term drift, rather than from relatively recent founder effects. PMID:19367325

Development and Application of Genomic Resources in an Endangered Palaeoendemic Tree, Parrotia subaequalis (Hamamelidaceae) From Eastern China

PubMed Central

Zhang, Yun-Yan; Shi, En; Yang, Zhao-Ping; Geng, Qi-Fang; Qiu, Ying-Xiong; Wang, Zhong-Sheng

2018-01-01

Parrotia subaequalis is an endangered palaeoendemic tree from disjunct montane sites in eastern China. Due to the lack of effective genomic resources, the genetic diversity and population structure of this endangered species are not clearly understood. In this study, we conducted paired-end shotgun sequencing (2 × 125 bp) of genomic DNA for two individuals of P. subaequalis on the Illumina HiSeq platform. Based on the resulting sequences, we have successfully assembled the complete chloroplast genome of P. subaequalis, as well as identified the polymorphic chloroplast microsatellites (cpSSRs), nuclear microsatellites (nSSRs) and mutational hotspots of chloroplast. Ten polymorphic cpSSR loci and 12 polymorphic nSSR loci were used to genotype 96 individuals of P. subaequalis from six populations to estimate genetic diversity and population structure. Our results revealed that P. subaequalis exhibited abundant genetic diversity (e.g., cpSSRs: Hcp = 0.862; nSSRs: HT = 0.559) and high genetic differentiation (e.g., cpSSRs: RST = 0.652; nSSRs: RST = 0.331), and characterized by a low pollen-to-seed migration ratio (r ≈ 1.78). These genetic patterns are attributable to its long evolutionary histories and low levels of contemporary inter-population gene flow by pollen and seed. In addition, lack of isolation-by-distance pattern and strong population genetic structuring in both marker systems, suggests that long-term isolation and/or habitat fragmentation as well as genetic drift may have also contributed to the geographic differentiation of P. subaequalis. Therefore, long-term habitat protection is the most important methods to prevent further loss of genetic variation and a decrease in effective population size. Furthermore, both cpSSRs and nSSRs revealed that P. subaequalis populations consisted of three genetic clusters, which should be considered as separated conservation units. PMID:29545814

Genetic diversity and population structure of Prunus mira (Koehne) from the Tibet plateau in China and recommended conservation strategies

PubMed Central

Bao, Wenquan; Li, Tiezhu; Liu, Huimin; Jiang, Zhongmao; Zhu, Xuchun; Du, Hongyan; Bai, Yu-e

2017-01-01

Prunus mira Koehne, an important economic fruit crop with high breeding and medicinal values, and an ancestral species of many cultivated peach species, has recently been declared an endangered species. However, basic information about genetic diversity, population structure, and morphological variation is still limited for this species. In this study, we sampled 420 P. mira individuals from 21 wild populations in the Tibet plateau to conduct a comprehensive analysis of genetic and morphological characteristics. The results of molecular analyses based on simple sequence repeat (SSR) markers indicated moderate genetic diversity and inbreeding (A = 3.8, Ae = 2.5, He = 0.52, Ho = 0.44, I = 0.95, FIS = 0.17) within P. mira populations. STRUCTURE, GENELAND, and phylogenetic analyses assigned the 21 populations to three genetic clusters that were moderately correlated with geographic altitudes, and this may have resulted from significantly different climatic and environmental factors at different altitudinal ranges. Significant isolation-by-distance was detected across the entire distribution of P. mira populations, but geographic altitude might have more significant effects on genetic structure than geographic distance in partial small-scale areas. Furthermore, clear genetic structure, high genetic differentiation, and restricted gene flow were detected between pairwise populations from different geographic groups, indicating that geographic barriers and genetic drift have significant effects on P. mira populations. Analyses of molecular variance based on the SSR markers indicated high variation (83.7% and 81.7%), whereas morphological analyses revealed low variation (1.30%–36.17%) within the populations. Large and heavy fruits were better adapted than light fruits and nutlets to poor climate and environmental conditions at high altitudes. Based on the results of molecular and morphological analyses, we classified the area into three conservation units and proposed several conservation strategies for wild P. mira populations in the Tibet plateau. PMID:29186199

Genetic diversity and population structure of Prunus mira (Koehne) from the Tibet plateau in China and recommended conservation strategies.

PubMed

Bao, Wenquan; Wuyun, Tana; Li, Tiezhu; Liu, Huimin; Jiang, Zhongmao; Zhu, Xuchun; Du, Hongyan; Bai, Yu-E

2017-01-01

Prunus mira Koehne, an important economic fruit crop with high breeding and medicinal values, and an ancestral species of many cultivated peach species, has recently been declared an endangered species. However, basic information about genetic diversity, population structure, and morphological variation is still limited for this species. In this study, we sampled 420 P. mira individuals from 21 wild populations in the Tibet plateau to conduct a comprehensive analysis of genetic and morphological characteristics. The results of molecular analyses based on simple sequence repeat (SSR) markers indicated moderate genetic diversity and inbreeding (A = 3.8, Ae = 2.5, He = 0.52, Ho = 0.44, I = 0.95, FIS = 0.17) within P. mira populations. STRUCTURE, GENELAND, and phylogenetic analyses assigned the 21 populations to three genetic clusters that were moderately correlated with geographic altitudes, and this may have resulted from significantly different climatic and environmental factors at different altitudinal ranges. Significant isolation-by-distance was detected across the entire distribution of P. mira populations, but geographic altitude might have more significant effects on genetic structure than geographic distance in partial small-scale areas. Furthermore, clear genetic structure, high genetic differentiation, and restricted gene flow were detected between pairwise populations from different geographic groups, indicating that geographic barriers and genetic drift have significant effects on P. mira populations. Analyses of molecular variance based on the SSR markers indicated high variation (83.7% and 81.7%), whereas morphological analyses revealed low variation (1.30%-36.17%) within the populations. Large and heavy fruits were better adapted than light fruits and nutlets to poor climate and environmental conditions at high altitudes. Based on the results of molecular and morphological analyses, we classified the area into three conservation units and proposed several conservation strategies for wild P. mira populations in the Tibet plateau.

Land, language, and loci: mtDNA in Native Americans and the genetic history of Peru.

PubMed

Lewis, Cecil M; Tito, Raúl Y; Lizárraga, Beatriz; Stone, Anne C

2005-07-01

Despite a long history of complex societies and despite extensive present-day linguistic and ethnic diversity, relatively few populations in Peru have been sampled for population genetic investigations. In order to address questions about the relationships between South American populations and about the extent of correlation between genetic distance, language, and geography in the region, mitochondrial DNA (mtDNA) hypervariable region I sequences and mtDNA haplogroup markers were examined in 33 individuals from the state of Ancash, Peru. These sequences were compared to those from 19 American Indian populations using diversity estimates, AMOVA tests, mismatch distributions, a multidimensional scaling plot, and regressions. The results show correlations between genetics, linguistics, and geographical affinities, with stronger correlations between genetics and language. Additionally, the results suggest a pattern of differential gene flow and drift in western vs. eastern South America, supporting previous mtDNA and Y chromosome investigations. (c) 2004 Wiley-Liss, Inc

Constraints on the Genetic and Antigenic Variability of Measles Virus.

PubMed

Beaty, Shannon M; Lee, Benhur

2016-04-21

Antigenic drift and genetic variation are significantly constrained in measles virus (MeV). Genetic stability of MeV is exceptionally high, both in the lab and in the field, and few regions of the genome allow for rapid genetic change. The regions of the genome that are more tolerant of mutations (i.e., the untranslated regions and certain domains within the N, C, V, P, and M proteins) indicate genetic plasticity or structural flexibility in the encoded proteins. Our analysis reveals that strong constraints in the envelope proteins (F and H) allow for a single serotype despite known antigenic differences among its 24 genotypes. This review describes some of the many variables that limit the evolutionary rate of MeV. The high genomic stability of MeV appears to be a shared property of the Paramyxovirinae, suggesting a common mechanism that biologically restricts the rate of mutation.

Constraints on the Genetic and Antigenic Variability of Measles Virus

PubMed Central

Beaty, Shannon M.; Lee, Benhur

2016-01-01

Antigenic drift and genetic variation are significantly constrained in measles virus (MeV). Genetic stability of MeV is exceptionally high, both in the lab and in the field, and few regions of the genome allow for rapid genetic change. The regions of the genome that are more tolerant of mutations (i.e., the untranslated regions and certain domains within the N, C, V, P, and M proteins) indicate genetic plasticity or structural flexibility in the encoded proteins. Our analysis reveals that strong constraints in the envelope proteins (F and H) allow for a single serotype despite known antigenic differences among its 24 genotypes. This review describes some of the many variables that limit the evolutionary rate of MeV. The high genomic stability of MeV appears to be a shared property of the Paramyxovirinae, suggesting a common mechanism that biologically restricts the rate of mutation. PMID:27110809

Effective population sizes of a major vector of human diseases, Aedes aegypti.

PubMed

Saarman, Norah P; Gloria-Soria, Andrea; Anderson, Eric C; Evans, Benjamin R; Pless, Evlyn; Cosme, Luciano V; Gonzalez-Acosta, Cassandra; Kamgang, Basile; Wesson, Dawn M; Powell, Jeffrey R

2017-12-01

The effective population size ( N e ) is a fundamental parameter in population genetics that determines the relative strength of selection and random genetic drift, the effect of migration, levels of inbreeding, and linkage disequilibrium. In many cases where it has been estimated in animals, N e is on the order of 10%-20% of the census size. In this study, we use 12 microsatellite markers and 14,888 single nucleotide polymorphisms (SNPs) to empirically estimate N e in Aedes aegypti , the major vector of yellow fever, dengue, chikungunya, and Zika viruses. We used the method of temporal sampling to estimate N e on a global dataset made up of 46 samples of Ae. aegypti that included multiple time points from 17 widely distributed geographic localities. Our N e estimates for Ae. aegypti fell within a broad range (~25-3,000) and averaged between 400 and 600 across all localities and time points sampled. Adult census size (N c ) estimates for this species range between one and five thousand, so the N e / N c ratio is about the same as for most animals. These N e values are lower than estimates available for other insects and have important implications for the design of genetic control strategies to reduce the impact of this species of mosquito on human health.

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 expected from complex environments with many obstacles. PMID:26696601

Drift induced by repeated hydropeaking waves in controlled conditions

NASA Astrophysics Data System (ADS)

Maiolini, Bruno; Bruno, M. Cristina; Biffi, Sofia; Cashman, Matthew J.

2014-05-01

Repeated hydropeaking events characterize most alpine rivers downstream of power plants fed by high elevation reservoirs. The effects of hydropeaking on the benthic communities are well known, and usually each hydropeaking wave causes an increase in tractive force and changes in temperature and water quality. Simulations of hydropeaking in artificial system can help to disentangle the direct effects of the modified flow regime from impacts associated with other associated physio-chemical changes, and with the effects of river regulation and land-use changes that often accompany water resource development. In September 2013 we conducted a set of controlled simulations in five steel flumes fed by an Alpine stream (Fersina stream, Adige River catchment, Trentino, Italy), where benthic invertebrates can freely colonize the flumes. One flume was used as control with no change in flow, in the other four flumes we simulated an hydropeaking wave lasting six hours, and repeated for five consecutive days. Flow was increased by twice baseflow in two flumes, and three times in the other two. We collected benthic samples before the beginning (morning of day 1) and after the end (afternoon of day 5) of the set of simulations to evaluate changes in the benthic communities due to induced drift migration. During each simulation, we collected drifting organisms at short time intervals to assess the responses to: 1) the initial discharge increase, 2) the persistence of high flows for several hours; 3) the decrease of discharge to the baseflow; 4) the change in drift with each successive day. Preliminary results indicate typical strong increases of catastrophic drift on the onset of each simulated hydropeaking, drift responses proportional to the absolute discharge increase, a decrease in the drift responses over successive days. Different taxa responded with different patterns: taxa which resist tractive force increased in drift only during the periods of baseflow that follow the habitat stress (behavioral drift) (e.g., Simuliidae, behavioral drift); other taxa which can not resist the increase in tractive force, drifted from the beginning of the simulation (e.g., Chironomidae, catastrophic drift).

Effects of complex life cycles on genetic diversity: cyclical parthenogenesis

PubMed Central

Rouger, R; Reichel, K; Malrieu, F; Masson, J P; Stoeckel, S

2016-01-01

Neutral patterns of population genetic diversity in species with complex life cycles are difficult to anticipate. Cyclical parthenogenesis (CP), in which organisms undergo several rounds of clonal reproduction followed by a sexual event, is one such life cycle. Many species, including crop pests (aphids), human parasites (trematodes) or models used in evolutionary science (Daphnia), are cyclical parthenogens. It is therefore crucial to understand the impact of such a life cycle on neutral genetic diversity. In this paper, we describe distributions of genetic diversity under conditions of CP with various clonal phase lengths. Using a Markov chain model of CP for a single locus and individual-based simulations for two loci, our analysis first demonstrates that strong departures from full sexuality are observed after only a few generations of clonality. The convergence towards predictions made under conditions of full clonality during the clonal phase depends on the balance between mutations and genetic drift. Second, the sexual event of CP usually resets the genetic diversity at a single locus towards predictions made under full sexuality. However, this single recombination event is insufficient to reshuffle gametic phases towards full-sexuality predictions. Finally, for similar levels of clonality, CP and acyclic partial clonality (wherein a fixed proportion of individuals are clonally produced within each generation) differentially affect the distribution of genetic diversity. Overall, this work provides solid predictions of neutral genetic diversity that may serve as a null model in detecting the action of common evolutionary or demographic processes in cyclical parthenogens (for example, selection or bottlenecks). PMID:27436524

The genetic structure of Nautilus pompilius populations surrounding Australia and the Philippines.

PubMed

Williams, Rachel C; Jackson, Benjamin C; Duvaux, Ludovic; Dawson, Deborah A; Burke, Terry; Sinclair, William

2015-07-01

Understanding the distribution of genetic diversity in exploited species is fundamental to successful conservation. Genetic structure and the degree of gene flow among populations must be assessed to design appropriate strategies to prevent the loss of distinct populations. The cephalopod Nautilus pompilius is fished unsustainably in the Philippines for the ornamental shell trade and has limited legislative protection, despite the species' recent dramatic decline in the region. Here, we use 14 microsatellite markers to evaluate the population structure of N. pompilius around Australia and the Philippines. Despite their relative geographical proximity, Great Barrier Reef individuals are genetically isolated from Osprey Reef and Shark Reef in the Coral Sea (FST  = 0.312, 0.229, respectively). Conversely, despite the larger geographical distances between the Philippines and west Australian reefs, samples display a small degree of genetic structure (FST  = 0.015). Demographic scenarios modelled using approximate Bayesian computation analysis indicate that this limited divergence is not due to contemporary gene flow between the Philippines and west Australia. Instead, present-day genetic similarity can be explained by very limited genetic drift that has occurred due to large average effective population sizes that persisted at both locations following their separation. The lack of connectivity among populations suggests that immigrants from west Australia would not facilitate natural recolonization if Philippine populations were fished to extinction. These data help to rectify the paucity of information on the species' biology currently inhibiting their conservation classification. Understanding population structure can allow us to facilitate sustainable harvesting, thereby preserving the diversity of genetically distinct stocks. © 2015 John Wiley & Sons Ltd.

Evolution of sociality in spiders leads to depleted genomic diversity at both population and species levels.

PubMed

Settepani, V; Schou, M F; Greve, M; Grinsted, L; Bechsgaard, J; Bilde, T

2017-08-01

Across several animal taxa, the evolution of sociality involves a suite of characteristics, a "social syndrome," that includes cooperative breeding, reproductive skew, primary female-biased sex ratio, and the transition from outcrossing to inbreeding mating system, factors that are expected to reduce effective population size (Ne). This social syndrome may be favoured by short-term benefits but come with long-term costs, because the reduction in Ne amplifies loss of genetic diversity by genetic drift, ultimately restricting the potential of populations to respond to environmental change. To investigate the consequences of this social life form on genetic diversity, we used a comparative RAD-sequencing approach to estimate genomewide diversity in spider species that differ in level of sociality, reproductive skew and mating system. We analysed multiple populations of three independent sister-species pairs of social inbreeding and subsocial outcrossing Stegodyphus spiders, and a subsocial outgroup. Heterozygosity and within-population diversity were sixfold to 10-fold lower in social compared to subsocial species, and demographic modelling revealed a tenfold reduction in Ne of social populations. Species-wide genetic diversity depends on population divergence and the viability of genetic lineages. Population genomic patterns were consistent with high lineage turnover, which homogenizes the genetic structure that builds up between inbreeding populations, ultimately depleting genetic diversity at the species level. Indeed, species-wide genetic diversity of social species was 5-8 times lower than that of subsocial species. The repeated evolution of species with this social syndrome is associated with severe loss of genomewide diversity, likely to limit their evolutionary potential. © 2017 John Wiley & Sons Ltd.

Marshes as "Mountain Tops": Genetic Analyses of the Critically Endangered São Paulo Marsh Antwren (Aves: Thamnophilidae).

PubMed

de Camargo, Crisley; Gibbs, H Lisle; Costa, Mariellen C; Del-Rio, Glaucia; Silveira, Luís F; Wasko, Adriane P; Francisco, Mercival R

2015-01-01

Small populations of endangered species can be impacted by genetic processes such as drift and inbreeding that reduce population viability. As such, conservation genetic analyses that assess population levels of genetic variation and levels of gene flow can provide important information for managing threatened species. The São Paulo Marsh Antwren (Formicivora paludicola) is a recently-described and critically endangered bird from São Paulo State (Brazil) whose total estimated population is around 250-300 individuals, distributed in only 15 isolated marshes around São Paulo metropolitan region. We used microsatellite DNA markers to estimate the population genetic characteristics of the three largest remaining populations of this species all within 60 km of each other. We detected a high and significant genetic structure between all populations (overall FST = 0.103) which is comparable to the highest levels of differentiation ever documented for birds, (e.g., endangered birds found in isolated populations on the tops of African mountains), but also evidence for first-generation immigrants, likely from small local unsampled populations. Effective population sizes were small (between 28.8-99.9 individuals) yet there are high levels of genetic variability within populations and no evidence for inbreeding. Conservation implications of this work are that the high levels of genetic structure suggests that translocations between populations need to be carefully considered in light of possible local adaptation and that remaining populations of these birds should be managed as conservation units that contain both main populations studied here but also small outlying populations which may be a source of immigrants.

A need to define characteristics to be used in the taxonomy of the expanding pestivirus genus

USDA-ARS?s Scientific Manuscript database

The relatively high rate of genetic drift observed with pestiviruses results not only in the emergence of new species but also in heterogeneity within recognized species. The grouping of pestiviruses into species was first based on host and to a lesser extent clinical presentation, then later by an...

Development and Preliminary Evaluation of the Measure of Understanding of Macroevolution: Introducing the MUM

ERIC Educational Resources Information Center

Nadelson, Louis S.; Southerland, Sherry A.

2010-01-01

The challenges in teaching and learning of biological evolution continue to be documented (NAS, 2008). Developers of science standards continue their work to increase emphasis on evolution. Although gains have been made, many K-12 science curricula focus on microevolution (i.e., natural selection, genetic drift), and a more limited effort is in…

Influenza A virus in pigs – protection, provocation and predisposition

USDA-ARS?s Scientific Manuscript database

Endemic strains of influenza A virus (IAV) in North America pigs consist of the subtypes H1N1, H1N2, and H3N2. These circulating strains contain the triple reassortant internal gene (TRIG) cassette resulting from incorporation of genes from swine, avian, and human IAV's. Genetic drift and reassortme...

ENCOURAGING THE USE OF DRIFT REDUCTION TECHNOLOGIES IN THE UNITED STATES

EPA Science Inventory

A number of pesticide application technologies offer the potential to reduce spray drift from pesticide applications. However, limited information exists on their effectiveness in reducing spray drift. The United States Environmental Protection Agency (EPA) is taking initiatives ...

Diamagnetic drift effects on the low-n magnetohydrodynamic modes at the high mode pedestal with plasma rotation

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

Zheng, L. J.; Kotschenreuther, M. T.; Valanju, P.

2014-06-15

The diamagnetic drift effects on the low-n magnetohydrodynamic instabilities at the high-mode (H-mode) pedestal are investigated in this paper with the inclusion of bootstrap current for equilibrium and rotation effects for stability, where n is the toroidal mode number. The AEGIS (Adaptive EiGenfunction Independent Solutions) code [L. J. Zheng and M. T. Kotschenreuther, J. Comp. Phys. 211 (2006)] is extended to include the diamagnetic drift effects. This can be viewed as the lowest order approximation of the finite Larmor radius effects in consideration of the pressure gradient steepness at the pedestal. The H-mode discharges at Jointed European Torus is reconstructedmore » numerically using the VMEC code [P. Hirshman and J. C. Whitson, Phys. Fluids 26, 3553 (1983)], with bootstrap current taken into account. Generally speaking, the diamagnetic drift effects are stabilizing. Our results show that the effectiveness of diamagnetic stabilization depends sensitively on the safe factor value (q{sub s}) at the safety-factor reversal or plateau region. The diamagnetic stabilization are weaker, when q{sub s} is larger than an integer; while stronger, when q{sub s} is smaller or less larger than an integer. We also find that the diamagnetic drift effects also depend sensitively on the rotation direction. The diamagnetic stabilization in the co-rotation case is stronger than in the counter rotation case with respect to the ion diamagnetic drift direction.« less

Genetic structure and seed-mediated dispersal rates of an endangered shrub in a fragmented landscape: a case study for Juniperus communis in northwestern Europe

PubMed Central

2011-01-01

Background Population extinction risk in a fragmented landscape is related to the differential ability of the species to spread its genes across the landscape. The impact of landscape fragmentation on plant population dynamics will therefore vary across different spatial scales. We quantified successful seed-mediated dispersal of the dioecious shrub Juniperus communis in a fragmented landscape across northwestern Europe by using amplified fragment length polymorphism (AFLP) markers. Furthermore we investigated the genetic diversity and structure on two spatial scales: across northwestern Europe and across Flanders (northern Belgium). We also studied whether seed viability and populations size were correlated with genetic diversity. Results Unexpectedly, estimated seed-mediated dispersal rates were quite high and ranged between 3% and 14%. No population differentiation and no spatial genetic structure were detected on the local, Flemish scale. A significant low to moderate genetic differentiation between populations was detected at the regional, northwest European scale (PhiPT = 0.10). In general, geographically nearby populations were also genetically related. High levels of within-population genetic diversity were detected but no correlation was found between any genetic diversity parameter and population size or seed viability. Conclusions In northwestern Europe, landscape fragmentation has lead to a weak isolation-by-distance pattern but not to genetic impoverishment of common juniper. Substantial rates of successful migration by seed-mediated gene flow indicate a high dispersal ability which could enable Juniperus communis to naturally colonize suitable habitats. However, it is not clear whether the observed levels of migration will suffice to counterbalance the effects of genetic drift in small populations on the long run. PMID:21859457

Genetic structure and seed-mediated dispersal rates of an endangered shrub in a fragmented landscape: a case study for Juniperus communis in northwestern Europe.

PubMed

Vanden-Broeck, An; Gruwez, Robert; Cox, Karen; Adriaenssens, Sandy; Michalczyk, Inga M; Verheyen, Kris

2011-08-22

Population extinction risk in a fragmented landscape is related to the differential ability of the species to spread its genes across the landscape. The impact of landscape fragmentation on plant population dynamics will therefore vary across different spatial scales. We quantified successful seed-mediated dispersal of the dioecious shrub Juniperus communis in a fragmented landscape across northwestern Europe by using amplified fragment length polymorphism (AFLP) markers. Furthermore we investigated the genetic diversity and structure on two spatial scales: across northwestern Europe and across Flanders (northern Belgium). We also studied whether seed viability and populations size were correlated with genetic diversity. Unexpectedly, estimated seed-mediated dispersal rates were quite high and ranged between 3% and 14%. No population differentiation and no spatial genetic structure were detected on the local, Flemish scale. A significant low to moderate genetic differentiation between populations was detected at the regional, northwest European scale (PhiPT = 0.10). In general, geographically nearby populations were also genetically related. High levels of within-population genetic diversity were detected but no correlation was found between any genetic diversity parameter and population size or seed viability. In northwestern Europe, landscape fragmentation has lead to a weak isolation-by-distance pattern but not to genetic impoverishment of common juniper. Substantial rates of successful migration by seed-mediated gene flow indicate a high dispersal ability which could enable Juniperus communis to naturally colonize suitable habitats. However, it is not clear whether the observed levels of migration will suffice to counterbalance the effects of genetic drift in small populations on the long run.

Effects of Item Parameter Drift on Vertical Scaling with the Nonequivalent Groups with Anchor Test (NEAT) Design

ERIC Educational Resources Information Center

Ye, Meng; Xin, Tao

2014-01-01

The authors explored the effects of drifting common items on vertical scaling within the higher order framework of item parameter drift (IPD). The results showed that if IPD occurred between a pair of test levels, the scaling performance started to deviate from the ideal state, as indicated by bias of scaling. When there were two items drifting…

Changes in human skull morphology across the agricultural transition are consistent with softer diets in preindustrial farming groups.

PubMed

Katz, David C; Grote, Mark N; Weaver, Timothy D

2017-08-22

Agricultural foods and technologies are thought to have eased the mechanical demands of diet-how often or how hard one had to chew-in human populations worldwide. Some evidence suggests correspondingly worldwide changes in skull shape and form across the agricultural transition, although these changes have proved difficult to characterize at a global scale. Here, adapting a quantitative genetics mixed model for complex phenotypes, we quantify the influence of diet on global human skull shape and form. We detect modest directional differences between foragers and farmers. The effects are consistent with softer diets in preindustrial farming groups and are most pronounced and reliably directional when the farming class is limited to dairying populations. Diet effect magnitudes are relatively small, affirming the primary role of neutral evolutionary processes-genetic drift, mutation, and gene flow structured by population history and migrations-in shaping diversity in the human skull. The results also bring an additional perspective to the paradox of why Homo sapiens , particularly agriculturalists, appear to be relatively well suited to efficient (high-leverage) chewing.

Genetic variation in bacterial kidney disease (BKD) susceptibility in Lake Michigan Chinook Salmon and its progenitor population from the Puget Sound.

PubMed

Purcell, Maureen K; Hard, Jeffrey J; Neely, Kathleen G; Park, Linda K; Winton, James R; Elliott, Diane G

2014-03-01

Mass mortality events in wild fish due to infectious diseases are troubling, especially given the potential for long-term, population-level consequences. Evolutionary theory predicts that populations with sufficient genetic variation will adapt in response to pathogen pressure. Chinook Salmon Oncorhynchus tshawytscha were introduced into Lake Michigan in the late 1960s from a Washington State hatchery population. In the late 1980s, collapse of the forage base and nutritional stress in Lake Michigan were thought to contribute to die-offs of Chinook Salmon due to bacterial kidney disease (BKD). Previously, we demonstrated that Lake Michigan Chinook Salmon from a Wisconsin hatchery have greater survival following BKD challenge relative to their progenitor population. Here, we evaluated whether the phenotypic divergence of these populations in BKD susceptibility was due to selection rather than genetic drift. Comparison of the overall magnitude of quantitative trait to neutral marker divergence between the populations suggested selection had occurred but a direct test of quantitative trait divergence was not significant, preventing the rejection of the null hypothesis of differentiation through genetic drift. Estimates of phenotypic variation (VP ), additive genetic variation (VA ) and narrow-sense heritability (h (2)) were consistently higher in the Wisconsin relative to the Washington population. If selection had acted on the Wisconsin population there was no evidence of a concomitant loss of genetic variation in BKD susceptibility. The Renibacterium salmoninarum exposures were conducted at both 14°C and 9°C; the warmer temperature accelerated time to death in both populations and there was no evidence of phenotypic plasticity or a genotype-by-environment (G × E) interaction. High h (2) estimates for BKD susceptibility in the Wisconsin population, combined with a lack of phenotypic plasticity, predicts that future adaptive gains in BKD resistance are still possible and that these adaptive gains would be stable under the temperature range evaluated here.

Genetic variation in bacterial kidney disease (BKD) susceptibility in Lake Michigan Chinook Salmon and its progenitor population from the Puget Sound

USGS Publications Warehouse

Purcell, Maureen K.; Hard, Jeffrey J.; Neely, Kathleen G.; Park, Linda K.; Winton, James R.; Elliott, Diane G.

2014-01-01

Mass mortality events in wild fish due to infectious diseases are troubling, especially given the potential for long-term, population-level consequences. Evolutionary theory predicts that populations with sufficient genetic variation will adapt in response to pathogen pressure. Chinook Salmon Oncorhynchus tshawytscha were introduced into Lake Michigan in the late 1960s from a Washington State hatchery population. In the late 1980s, collapse of the forage base and nutritional stress in Lake Michigan were thought to contribute to die-offs of Chinook Salmon due to bacterial kidney disease (BKD). Previously, we demonstrated that Lake Michigan Chinook Salmon from a Wisconsin hatchery have greater survival following BKD challenge relative to their progenitor population. Here, we evaluated whether the phenotypic divergence of these populations in BKD susceptibility was due to selection rather than genetic drift. Comparison of the overall magnitude of quantitative trait to neutral marker divergence between the populations suggested selection had occurred but a direct test of quantitative trait divergence was not significant, preventing the rejection of the null hypothesis of differentiation through genetic drift. Estimates of phenotypic variation (VP), additive genetic variation (VA) and narrow-sense heritability (h2) were consistently higher in the Wisconsin relative to the Washington population. If selection had acted on the Wisconsin population there was no evidence of a concomitant loss of genetic variation in BKD susceptibility. The Renibacterium salmoninarum exposures were conducted at both 14°C and 9°C; the warmer temperature accelerated time to death in both populations and there was no evidence of phenotypic plasticity or a genotype-by-environment (G × E) interaction. High h2 estimates for BKD susceptibility in the Wisconsin population, combined with a lack of phenotypic plasticity, predicts that future adaptive gains in BKD resistance are still possible and that these adaptive gains would be stable under the temperature range evaluated here.

Drift studies--comparison of field and wind tunnel experiments.

PubMed

Stadler, R; Regenauer, W

2005-01-01

Drift at pesticide application leads to a pollution of non-target crops, non-target species and surface water. Spray drift is influenced by many factors like environmental conditions, vegetation, technical conditions, and physical properties of the tank mixes and influenced by Chemicals. Field experiments to characterise spray drift effects with the risk of permanent changing weather conditions can be supported by wind tunnel experiments. Wind tunnel experiments do not lead to the same soil deposition curves like field experiments, but the ratio of drift reduction potential is comparable.

From Wolves to Dogs, and Back: Genetic Composition of the Czechoslovakian Wolfdog.

PubMed

Smetanová, Milena; Černá Bolfíková, Barbora; Randi, Ettore; Caniglia, Romolo; Fabbri, Elena; Galaverni, Marco; Kutal, Miroslav; Hulva, Pavel

2015-01-01

The Czechoslovakian Wolfdog is a unique dog breed that originated from hybridization between German Shepherds and wild Carpathian wolves in the 1950s as a military experiment. This breed was used for guarding the Czechoslovakian borders during the cold war and is currently kept by civilian breeders all round the world. The aim of our study was to characterize, for the first time, the genetic composition of this breed in relation to its known source populations. We sequenced the hypervariable part of the mtDNA control region and genotyped the Amelogenin gene, four sex-linked microsatellites and 39 autosomal microsatellites in 79 Czechoslovakian Wolfdogs, 20 German Shepherds and 28 Carpathian wolves. We performed a range of population genetic analyses based on both empirical and simulated data. Only two mtDNA and two Y-linked haplotypes were found in Czechoslovakian Wolfdogs. Both mtDNA haplotypes were of domestic origin, while only one of the Y-haplotypes was shared with German Shepherds and the other was unique to Czechoslovakian Wolfdogs. The observed inbreeding coefficient was low despite the small effective population size of the breed, possibly due to heterozygote advantages determined by introgression of wolf alleles. Moreover, Czechoslovakian Wolfdog genotypes were distinct from both parental populations, indicating the role of founder effect, drift and/or genetic hitchhiking. The results revealed the peculiar genetic composition of the Czechoslovakian Wolfdog, showing a limited introgression of wolf alleles within a higher proportion of the dog genome, consistent with the reiterated backcrossing used in the pedigree. Artificial selection aiming to keep wolf-like phenotypes but dog-like behavior resulted in a distinctive genetic composition of Czechoslovakian Wolfdogs, which provides a unique example to study the interactions between dog and wolf genomes.

A Population Genetic Signal of Polygenic Adaptation

PubMed Central

Berg, Jeremy J.; Coop, Graham

2014-01-01

Adaptation in response to selection on polygenic phenotypes may occur via subtle allele frequencies shifts at many loci. Current population genomic techniques are not well posed to identify such signals. In the past decade, detailed knowledge about the specific loci underlying polygenic traits has begun to emerge from genome-wide association studies (GWAS). Here we combine this knowledge from GWAS with robust population genetic modeling to identify traits that may have been influenced by local adaptation. We exploit the fact that GWAS provide an estimate of the additive effect size of many loci to estimate the mean additive genetic value for a given phenotype across many populations as simple weighted sums of allele frequencies. We use a general model of neutral genetic value drift for an arbitrary number of populations with an arbitrary relatedness structure. Based on this model, we develop methods for detecting unusually strong correlations between genetic values and specific environmental variables, as well as a generalization of comparisons to test for over-dispersion of genetic values among populations. Finally we lay out a framework to identify the individual populations or groups of populations that contribute to the signal of overdispersion. These tests have considerably greater power than their single locus equivalents due to the fact that they look for positive covariance between like effect alleles, and also significantly outperform methods that do not account for population structure. We apply our tests to the Human Genome Diversity Panel (HGDP) dataset using GWAS data for height, skin pigmentation, type 2 diabetes, body mass index, and two inflammatory bowel disease datasets. This analysis uncovers a number of putative signals of local adaptation, and we discuss the biological interpretation and caveats of these results. PMID:25102153

Population structure and genetic diversity of the amphiatlantic haploid peatmoss Sphagnum affine (Sphagnopsida).

PubMed

Thingsgaard, K

2001-10-01

Nineteen populations of Sphagnum affine were included in a study of genetic diversity and structure in fragmented and less fragmented landscapes, and differentiation at intercontinental and three regional levels. Isozyme electrophoresis of eight enzyme systems revealed 12 variable loci, which could be used for haplotype identification. A hierachical analysis of variance (AMOVA) revealed no significant intercontinental differentiation, and very limited differentiation among European regions. A trend of decreasing diversity with increasing latitude was apparent. Gametic phase disequilibria was high, suggesting nonrandom mating and regionally high incidences of inbreeding. The partitioning of genetic variation within and among populations in each region varied among regions, the northernmost populations having 86% of the total variation among populations, the southernmost in Scandinavia having 25% of the variation among populations, whereas the American populations displayed 89% of the variation within populations. Fifteen alleles at eight loci occurred in the U.S.A. which were not encountered in Europe, whereas only three European alleles at one locus in three populations were not encountered in U.S.A. The differences in diversity between North America and Europe may result from loss of genetic diversity caused by founder effects during postglacial recolonization of northern Europe. In Europe, the main mountain ranges extend E-W, posing severe barriers to northwards migration of lowland species, compared to the N-S trend of mountain ranges in North America. The decline in genetic diversity and increase in population differentiation and gametic phase disequilibria towards the north in Scandinavia may be caused by a series of founder effects during postglacial migration. These may have corresponded to minor climatic oscillations that influenced the migration front/leading edge in the suboceanic lowlands of Norway. According to this model random genetic drift will be an increasingly important structuring factor with latitude.

Spatial patterns of AFLP diversity in Bulbophyllum occultum (Orchidaceae) indicate long-term refugial isolation in Madagascar and long-distance colonization effects in La Réunion.

PubMed

Jaros, U; Fischer, G A; Pailler, T; Comes, H P

2016-05-01

Bulbophyllum occultum, an epiphytic orchid mainly distributed in the rainforests of (north)eastern Madagascar and La Réunion, represents an interesting model case for testing the effects of anthropogenic vs historical (e.g., climate induced) habitat isolation and long-distance colonization on the genetic structure of plant species with disjunct distributions in the Madagascan region. To this aim, we surveyed amplified fragment length polymorphisms (AFLPs) across 13 populations in Madagascar and nine in La Réunion (206 individuals in total). We found overall high levels of population subdivision (Φ(PT)=0.387) and low within-population diversity (H(E), range: 0.026-0.124), indicating non-equilibrium conditions in a mainly selfing species. There was no impact of recent deforestation (Madagascar) or habitat disturbance (La Réunion) detectable on AFLP diversity. K-means clustering and BARRIER analyses identified multiple gene pools and several genetic breaks, both within and among islands. Inter-island levels of population genetic diversity and subdivision were similar, whereby inter-individual divergence in flower colour explained a significant part of gene pool divergence in La Réunion. Our results suggest that (i) B. occultum persisted across multiple isolated ('refugial') regions along the eastern rainforest corridor of Madagascar over recent climatic cycles and (ii) populations in La Réunion arose from either single or few independent introductions from Madagascar. High selfing rates and sufficient time for genetic drift likely promoted unexpectedly high population genetic and phenotypic (flower colour) differentiation in La Réunion. Overall, this study highlights a strong imprint of history on the genetic structure of a low-gene-dispersing epiphytic orchid from the Madagascan region.

Interspecific hybridization contributes to high genetic diversity and apparent effective population size in an endemic population of mottled ducks (Anas fulvigula maculosa)

USGS Publications Warehouse

Peters, Jeffrey L.; Sonsthagen, Sarah A.; Lavretsky, Philip; Rezsutek, Michael; Johnson, William P.; McCracken, Kevin G.

2014-01-01

Under drift-mutation equilibrium, genetic diversity is expected to be correlated with effective population size (Ne). Changes in population size and gene flow are two important processes that can cause populations to deviate from this expected relationship. In this study, we used DNA sequences from six independent loci to examine the influence of these processes on standing genetic diversity in endemic mottled ducks (Anas fulvigula) and geographically widespread mallards (A. platyrhynchos), two species known to hybridize. Mottled ducks have an estimated census size that is about two orders-of-magnitude smaller than that of mallards, yet these two species have similar levels of genetic diversity, especially at nuclear DNA. Coalescent analyses suggest that a population expansion in the mallard at least partly explains this discrepancy, but the mottled duck harbors higher genetic diversity and apparent N e than expected for its census size even after accounting for a population decline. Incorporating gene flow into the model, however, reduced the estimated Ne of mottled ducks to 33 % of the equilibrium Ne and yielded an estimated Ne consistent with census size. We also examined the utility of these loci to distinguish among mallards, mottled ducks, and their hybrids. Most putatively pure individuals were correctly assigned to species, but the power for detecting hybrids was low. Although hybridization with mallards potentially poses a conservation threat to mottled ducks by creating a risk of extinction by hybridization, introgression of mallard alleles has helped maintain high genetic diversity in mottled ducks and might be important for the adaptability and survival of this species.

Genetic structure of red-handed howler monkey populations in the fragmented landscape of Eastern Brazilian Amazonia

PubMed Central

2010-01-01

We genotyped 15 microsatellite loci in order to evaluate the effects of habitat fragmentation, caused by flooding of the Tucuruí reservoir, on the genetic structure of Alouatta belzebul in eastern Amazonia. The analysis included two populations sampled in 1984, representing both margins of the Tocantins river, and three populations sampled 18 years later. Minimal differences in the diversity levels between present-day (Ho = 0.62-0.69 and AR = 6.07-7.21) and pre-flooding (Ho = 0.60-0.62 and A R = 6.27-6.77) populations indicated there was no significant loss of genetic variability, possibly because of successful management strategies applied during the flooding. The changes observed were limited to shifts in the composition of alleles, which presumably reflect the admixture of subpopulations during flooding. Given this, there were significant differences in the Rst values (p = 0.05) in all but one between-site comparison. Both present-day and original populations showed a deficit of heterozygotes, which suggests that this may be typical of the species, at least at a local level, perhaps because of specific ecological characteristics. The relatively large number of private alleles recorded in all populations may be a consequence of the Wahlund effect resulting from population admixture or a process of expansion rather than the loss of rare alleles through genetic drift. Additionally, the levels of genetic variability observed in this study were higher than those reported for other species of Neotropical primates, suggesting good fitness levels in these A. belzebul populations. Regular genetic monitoring of remnant populations, especially on islands, should nevertheless be an integral component of long-term management strategies. PMID:21637590

Mechanisms of population differentiation in marbled murrelets: historical versus contemporary processes

USGS Publications Warehouse

Congdon, B.C.; Piatt, John F.; Martin, Kathy; Friesen, Vicki L.

2000-01-01

Mechanisms of population differentiation in highly vagile species such as seabirds are poorly understood. Previous studies of marbled murrelets (Brachyramphus marmoratus; Charadriiformes: Alcidae) found significant population genetic structure, but could not determine whether this structure is due to historical vicariance (e.g., due to Pleistocene glaciers), isolation by distance, drift or selection in peripheral populations, or nesting habitat selection. To discriminate among these possibilities, we analyzed sequence variation in nine nuclear introns from 120 marbled murrelets sampled from British Columbia to the western Aleutian Islands. Mismatch distributions indicated that murrelets underwent at least one population expansion during the Pleistocene and probably are not in genetic equilibrium. Maximum-likelihood analysis of allele frequencies suggested that murrelets from 'mainland' sites (from the Alaskan Peninsula east) are genetically different from those in the Aleutians and that these two lineages diverged prior to the last glaciation. Analyses of molecular variance, as well as estimates of gene flow derived using coalescent theory, indicate that population genetic structure is best explained by peripheral isolation of murrelets in the Aleutian Islands, rather than by selection associated with different nesting habitats. No isolation-by-distance effects could be detected. Our results are consistent with a rapid expansion of murrelets from a single refugium during the early-mid Pleistocene, subsequent isolation and divergence in two or more refugia during the final Pleistocene glacial advance, and secondary contact following retreat of the ice sheets. Population genetic structure now appears to be maintained by distance effects combined with small populations and a highly fragmented habitat in the Aleutian Islands.

Optimization of curved drift tubes for ultraviolet-ion mobility spectrometry

NASA Astrophysics Data System (ADS)

Ni, Kai; Ou, Guangli; Zhang, Xiaoguo; Yu, Zhou; Yu, Quan; Qian, Xiang; Wang, Xiaohao

2015-08-01

Ion mobility spectrometry (IMS) is a key trace detection technique for toxic pollutants and explosives in the atmosphere. Ultraviolet radiation photoionization source is widely used as an ionization source for IMS due to its advantages of high selectivity and non-radioactivity. However, UV-IMS bring problems that UV rays will be launched into the drift tube which will cause secondary ionization and lead to the photoelectric effect of the Faraday disk. So air is often used as working gas to reduce the effective distance of UV rays, but it will limit the application areas of UV-IMS. In this paper, we propose a new structure of curved drift tube, which can avoid abnormally incident UV rays. Furthermore, using curved drift tube may increase the length of drift tube and then improve the resolution of UV-IMS according to previous research. We studied the homogeneity of electric field in the curved drift tube, which determined the performance of UV-IMS. Numerical simulation of electric field in curved drift tube was conducted by SIMION in our study. In addition, modeling method and homogeneity standard for electric field were also presented. The influences of key parameters include radius of gyration, gap between electrode as well as inner diameter of curved drift tube, on the homogeneity of electric field were researched and some useful laws were summarized. Finally, an optimized curved drift tube is designed to achieve homogenous drift electric field. There is more than 98.75% of the region inside the curved drift tube where the fluctuation of the electric field strength along the radial direction is less than 0.2% of that along the axial direction.

Effective size of a wild salmonid population is greatly reduced by hatchery supplementation

PubMed Central

Christie, M R; Marine, M L; French, R A; Waples, R S; Blouin, M S

2012-01-01

Many declining and commercially important populations are supplemented with captive-born individuals that are intentionally released into the wild. These supplementation programs often create large numbers of offspring from relatively few breeding adults, which can have substantial population-level effects. We examined the genetic effects of supplementation on a wild population of steelhead (Oncorhynchus mykiss) from the Hood River, Oregon, by matching 12 run-years of hatchery steelhead back to their broodstock parents. We show that the effective number of breeders producing the hatchery fish (broodstock parents; Nb) was quite small (harmonic mean Nb=25 fish per brood-year vs 373 for wild fish), and was exacerbated by a high variance in broodstock reproductive success among individuals within years. The low Nb caused hatchery fish to have decreased allelic richness, increased average relatedness, more loci in linkage disequilibrium and substantial levels of genetic drift in comparison with their wild-born counterparts. We also documented a substantial Ryman–Laikre effect whereby the additional hatchery fish doubled the total number of adult fish on the spawning grounds each year, but cut the effective population size of the total population (wild and hatchery fish combined) by nearly two-thirds. We further demonstrate that the Ryman–Laikre effect is most severe in this population when (1) >10% of fish allowed onto spawning grounds are from hatcheries and (2) the hatchery fish have high reproductive success in the wild. These results emphasize the trade-offs that arise when supplementation programs attempt to balance disparate goals (increasing production while maintaining genetic diversity and fitness). PMID:22805657

Determinants of male floating behaviour and floater reproduction in a threatened population of the hihi (Notiomystis cincta)

PubMed Central

Brekke, Patricia; Ewen, John G; Clucas, Gemma; Santure, Anna W

2015-01-01

Floating males are usually thought of as nonbreeders. However, some floating individuals are able to reproduce through extra-pair copulations. Floater reproductive success can impact breeders’ sex ratio, reproductive variance, multiple paternity and inbreeding, particularly in small populations. Changes in reproductive variance alter the rate of genetic drift and loss of genetic diversity. Therefore, genetic management of threatened species requires an understanding of floater reproduction and determinants of floating behaviour to effectively conserve species. Here, we used a pedigreed, free-living population of the endangered New Zealand hihi (Notiomystis cincta) to assess variance in male reproductive success and test the genetic (inbreeding and heritability) and conditional (age and size) factors that influence floater behaviour and reproduction. Floater reproduction is common in this species. However, floater individuals have lower reproductive success and variance in reproductive success than territorial males (total and extra-pair fledglings), so their relative impact on the population's reproductive performance is low. Whether an individual becomes a floater, and if so then how successful they are, is determined mainly by individual age (young and old) and to lesser extents male size (small) and inbreeding level (inbred). Floating males have a small, but important role in population reproduction and persistence of threatened populations. PMID:26366197

Looking Beyond the Genes: The Interplay Between Signaling Pathways and Mechanics in the Shaping and Diversification of Epithelial Tissues.

PubMed

Urdy, S; Goudemand, N; Pantalacci, S

2016-01-01

The core of Evo-Devo lies in the intuition that the way tissues grow during embryonic development, the way they sustain their structure and function throughout lifetime, and the way they evolve are closely linked. Epithelial tissues are ubiquitous in metazoans, covering the gut and internal branched organs, as well as the skin and its derivatives (ie, teeth). Here, we discuss in vitro, in vivo, and in silico studies on epithelial tissues to illustrate the conserved, dynamical, and complex aspects of their development. We then explore the implications of the dynamical and nonlinear nature of development on the evolution of their size and shape at the phenotypic and genetic levels. In rare cases, when the interplay between signaling and mechanics is well understood at the cell level, it is becoming clear that the structure of development leads to covariation of characters, an integration which in turn provides some predictable structure to evolutionary changes. We suggest that such nonlinear systems are prone to genetic drift, cryptic genetic variation, and context-dependent mutational effects. We argue that experimental and theoretical studies at the cell level are critical to our understanding of the phenotypic and genetic evolution of epithelial tissues, including carcinomas. © 2016 Elsevier Inc. All rights reserved.

Colonizing genetic populations as units of regulated change

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

Harding, J.

1973-01-01

The interrelationships among natural selection, inbreeding, and genetic drift are reviewed with emphasis on colonization. Genetic variation at four loci in Lupinus succulentus exists in samples taken from California. A mathematical model was developed, and estimators were derived for gene frequency, heterozygote frequency, rate of cross-fertilization, and a coefficient of inbreeding. These parameters were estimated for 29 populations. The results indicate that (1) variation is nearly always present for the S/s locus affecting seed pigmentation, but generally absent for the three loci affecting flower pigmentation; (2) variation is not reduced in populations from recently colonized sites; (3) self-fertilization ranges frommore » nearly 0 to nearly 100%, with mean near 0.50; and, (4) inbreeding coefficients vary from 0 to 0.80, with mean near 0.40. The results do not suggest that man's disturbance of the environment has had any deleterious effect on the genetic structure of Lupinus succulentus populations. On the contrary, this species has been an opportunistic colonizer of these new habitats. However, Lupinus succulentus was chosen for study because it has been a successsful colonizer. These conclusions, if general at all, therefore, apply to successful colonizing species and not to those that cannot adapt to environmental disturbances and are now threatened with extinction.« less

Loss of genetic diversity in Culex quinquefasciatus targeted by a lymphatic filariasis vector control program in Recife, Brazil.

PubMed

Cartaxo, Marina F S; Ayres, Constância F J; Weetman, David

2011-09-01

Recife is one of the largest cities in north-eastern Brazil and is endemic for lymphatic filariasis transmitted by Culex quinquefasciatus. Since 2003 a control program has targeted mosquito larvae by elimination of breeding sites and bimonthly application of Bacillus sphaericus. To assess the impact of this program on the local vector population we monitored the genetic diversity and differentiation of Cx. quinquefasciatus using microsatellites and a B. sphaericus-resistance associated mutation (cqm1(REC)) over a 3-year period. We detected a significant but gradual decline in allelic diversity, which, coupled with subtle temporal genetic structure, suggests a major impact of the control program on the vector population. Selection on cqm1(REC) does not appear to be involved with loss of neutral diversity from the population, with no temporal trend in resistant allele frequency and no correlation with microsatellite differentiation. The evidence for short-term genetic drift we detected suggests a low ratio of effective population size: census population size for Cx. quinquefasciatus, perhaps coupled with strong geographically-restricted population structure. Spatial definition of populations will be an important step for success of an expanded vector control program. Copyright © 2011 Royal Society of Tropical Medicine and Hygiene. Published by Elsevier Ltd. All rights reserved.

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

PubMed Central

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

2009-01-01

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

Trends in genome-wide and region-specific genetic diversity in the Dutch-Flemish Holstein-Friesian breeding program from 1986 to 2015.

PubMed

Doekes, Harmen P; Veerkamp, Roel F; Bijma, Piter; Hiemstra, Sipke J; Windig, Jack J

2018-04-11

In recent decades, Holstein-Friesian (HF) selection schemes have undergone profound changes, including the introduction of optimal contribution selection (OCS; around 2000), a major shift in breeding goal composition (around 2000) and the implementation of genomic selection (GS; around 2010). These changes are expected to have influenced genetic diversity trends. Our aim was to evaluate genome-wide and region-specific diversity in HF artificial insemination (AI) bulls in the Dutch-Flemish breeding program from 1986 to 2015. Pedigree and genotype data (~ 75.5 k) of 6280 AI-bulls were used to estimate rates of genome-wide inbreeding and kinship and corresponding effective population sizes. Region-specific inbreeding trends were evaluated using regions of homozygosity (ROH). Changes in observed allele frequencies were compared to those expected under pure drift to identify putative regions under selection. We also investigated the direction of changes in allele frequency over time. Effective population size estimates for the 1986-2015 period ranged from 69 to 102. Two major breakpoints were observed in genome-wide inbreeding and kinship trends. Around 2000, inbreeding and kinship levels temporarily dropped. From 2010 onwards, they steeply increased, with pedigree-based, ROH-based and marker-based inbreeding rates as high as 1.8, 2.1 and 2.8% per generation, respectively. Accumulation of inbreeding varied substantially across the genome. A considerable fraction of markers showed changes in allele frequency that were greater than expected under pure drift. Putative selected regions harboured many quantitative trait loci (QTL) associated to a wide range of traits. In consecutive 5-year periods, allele frequencies changed more often in the same direction than in opposite directions, except when comparing the 1996-2000 and 2001-2005 periods. Genome-wide and region-specific diversity trends reflect major changes in the Dutch-Flemish HF breeding program. Introduction of OCS and the shift in breeding goal were followed by a drop in inbreeding and kinship and a shift in the direction of changes in allele frequency. After introduction of GS, rates of inbreeding and kinship increased substantially while allele frequencies continued to change in the same direction as before GS. These results provide insight in the effect of breeding practices on genomic diversity and emphasize the need for efficient management of genetic diversity in GS schemes.

Particle drift model for Z-pinch-driven magneto-Rayleigh-Taylor instability

NASA Astrophysics Data System (ADS)

Dan, Jia Kun; Xu, Qiang; Wang, Kun Lun; Ren, Xiao Dong; Huang, Xian Bin

2016-09-01

A theoretical model of Z-pinch driven magneto-Rayleigh-Taylor instability is proposed based on the particle drift point of view, which can explain the helical instability structure observed in premagnetized imploding liner experiments. It is demonstrated that all possible drift motions, including polarization drift, gradient drift, and curvature drift, which can lead to charge separations, each will attribute to an effective gravity acceleration. Theoretical predictions given by this model are dramatically different from those given by previous theories which have been readily recovered in the theory presented here as a limiting case. The theory shows qualitative agreement with available experimental data of the pitch angle and provides certain predictions to be verified.

Geographic pattern of genetic variation in the European globeflower Trollius europaeus L. (Ranunculaceae) inferred from amplified fragment length polymorphism markers.

PubMed

Despres, Laurence; Loriot, Sandrine; Gaudeul, Myriam

2002-11-01

The distribution of genetic variation and the phylogenetic relationships between 18 populations of the arctic-alpine plant Trollius europaeus were analysed in three main regions (Alps, Pyrenees and Fennoscandia) by using dominant AFLP markers. Analysis of molecular variance revealed that most of the genetic variability was found within populations (64%), although variation among regions (17%) and among populations within regions (19%) was highly significant (P < 0.001). Accordingly, the global fixation index FST averaged over loci was high (0.39). The among-population differentiation indicates restricted gene flow, congruent with limited dispersal of specific globeflower's pollinating flies (Chiastocheta spp.). Within-population diversity levels were significantly higher in the Alps (mean Nei's expected heterozygosity HE = 0.229) than in the Pyrenees (HE= 0.197) or in Fennoscandia (HE = 0.158). This finding is congruent with the species-richness of the associated flies, which is maximum in the Alps. We discuss the processes involved in shaping observed patterns of genetic diversity within and among T. europaeus populations. Genetic drift is the major factor acting on the small Pyrenean populations at the southern edge of T. europaeus distribution, while large Fennoscandian populations result probably from a founder effect followed by demographic expansion. The Alpine populations represent moderately fragmented relics of large southern ancestral populations. The patterns of genetic variability observed in the host plant support the hypothesis of sympatric speciation in associated flies, rather than recurrent allopatric speciations.

Genetic heritage of the Old Order Mennonites of southeastern Pennsylvania.

PubMed

Puffenberger, E G

2003-08-15

The Old Order Mennonites of southeastern Pennsylvania are a religious isolate with origins in 16th-century Switzerland. The Swiss Mennonites immigrated to Pennsylvania over a 50-year period in the early 18th century. The history of this population in the United States provides insight into the increased incidence of several genetic diseases, most notably maple syrup urine disease (MSUD), Hirschsprung disease (HSCR), and congenital nephrotic syndrome. A comparison between the Old Order Mennonites and the Old Order Amish demonstrates the unique genetic heritage of each group despite a common religious and geographic history. Unexpectedly, several diseases in both groups demonstrate allelic and/or locus heterogeneity. The population genetics of the 1312T --> A BCKDHA gene mutation, which causes classical MSUD, are presented in detail. The incidence of MSUD in the Old Order Mennonites is estimated to be 1/358 births, yielding a corrected carrier frequency of 7.96% and a mutation allele frequency of 4.15%. Analysis of the population demonstrates that repeated cycles of sampling effects, population bottlenecks, and subsequent genetic drift were important in shaping the current allele frequencies. A linkage disequilibrium analysis of 1312T --> A mutation haplotypes is provided and discussed in the context of the known genealogical history of the population. Finally, data from microsatellite marker genotyping within the Old Order Mennonite population are provided that show a significant but modest decrease in genetic diversity and elevated levels of background linkage disequilibrium. Copyright 2003 Wiley-Liss, Inc.

Continuous and discontinuous phase transitions in the evolution of a polygenic trait under stabilizing selective pressure

NASA Astrophysics Data System (ADS)

Fierro, Annalisa; Cocozza, Sergio; Monticelli, Antonella; Scala, Giovanni; Miele, Gennaro

2017-06-01

The presence of phenomena analogous to phase transition in Statistical Mechanics has been suggested in the evolution of a polygenic trait under stabilizing selection, mutation and genetic drift. By using numerical simulations of a model system, we analyze the evolution of a population of N diploid hermaphrodites in random mating regime. The population evolves under the effect of drift, selective pressure in form of viability on an additive polygenic trait, and mutation. The analysis allows to determine a phase diagram in the plane of mutation rate and strength of selection. The involved pattern of phase transitions is characterized by a line of critical points for weak selective pressure (smaller than a threshold), whereas discontinuous phase transitions, characterized by metastable hysteresis, are observed for strong selective pressure. A finite-size scaling analysis suggests the analogy between our system and the mean-field Ising model for selective pressure approaching the threshold from weaker values. In this framework, the mutation rate, which allows the system to explore the accessible microscopic states, is the parameter controlling the transition from large heterozygosity ( disordered phase) to small heterozygosity ( ordered one).

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

PubMed

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

2017-01-01

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

Actor-network theory: a tool to support ethical analysis of commercial genetic testing.

PubMed

Williams-Jones, Bryn; Graham, Janice E

2003-12-01

Social, ethical and policy analysis of the issues arising from gene patenting and commercial genetic testing is enhanced by the application of science and technology studies, and Actor-Network Theory (ANT) in particular. We suggest the potential for transferring ANT's flexible nature to an applied heuristic methodology for gathering empirical information and for analysing the complex networks involved in the development of genetic technologies. Three concepts are explored in this paper--actor-networks, translation, and drift--and applied to the case of Myriad Genetics and their commercial BRACAnalysis genetic susceptibility test for hereditary breast cancer. Treating this test as an active participant in socio-technical networks clarifies the extent to which it interacts with, shapes and is shaped by people, other technologies, and institutions. Such an understanding enables more sophisticated and nuanced technology assessment, academic analysis, as well as public debate about the social, ethical and policy implications of the commercialization of new genetic technologies.

Maize Germplasm Conservation in Southern California's Urban Gardens: Introduced Diversity Beyond ex situ and in situ Management.

PubMed

Heraty, Joanne M; Ellstrand, Norman C

Contemporary germplasm conservation studies largely focus on ex situ and in situ management of diversity within centers of genetic diversity. Transnational migrants who transport and introduce landraces to new locations may catalyze a third type of conservation that combines both approaches. Resulting populations may support reduced diversity as a result of evolutionary forces such as genetic drift, selection, and gene flow, yet they may also be more diverse as a result of multiple introductions, selective breeding and cross pollination among multiple introduced varietals. In this study, we measured the amount and structure of maize molecular genetic diversity in samples collected from home gardens and community gardens maintained by immigrant farmers in Southern California. We used the same markers to measure the genetic diversity and structure of commercially available maize varieties and compared our data to previously reported genetic diversity statistics of Mesoamerican landraces. Our results reveal that transnational dispersal creates an opportunity for the maintenance of maize genetic diversity beyond its recognized centers of diversity.

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

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

PubMed

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

2012-09-01

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.

Genetic diversity in Oryza glumaepatula wild rice populations in Costa Rica and possible gene flow from O. sativa.

PubMed

Fuchs, Eric J; Meneses Martínez, Allan; Calvo, Amanda; Muñoz, Melania; Arrieta-Espinoza, Griselda

2016-01-01

Wild crop relatives are an important source of genetic diversity for crop improvement. Diversity estimates are generally lacking for many wild crop relatives. The objective of the present study was to analyze how genetic diversity is distributed within and among populations of the wild rice species Oryza glumaepatula in Costa Rica. We also evaluated the likelihood of gene flow between wild and commercial rice species because the latter is commonly sympatric with wild rice populations. Introgression may change wild species by incorporating alleles from domesticated species, increasing the risk of losing original variation. Specimens from all known O. glumaepatula populations in Costa Rica were analyzed with 444 AFLP markers to characterize genetic diversity and structure. We also compared genetic diversity estimates between O. glumaepatula specimens and O. sativa commercial rice. Our results showed that O. glumaepatula populations in Costa Rica have moderately high levels of genetic diversity, comparable to those found in South American populations. Despite the restricted distribution of this species in Costa Rica, populations are fairly large, reducing the effects of drift on genetic diversity. We found a dismissible but significant structure (θ = 0.02 ± 0.001) among populations. A Bayesian structure analysis suggested that some individuals share a significant proportion of their genomes with O. sativa. These results suggest that gene flow from cultivated O. sativa populations may have occurred in the recent past. These results expose an important biohazard: recurrent hybridization may reduce the genetic diversity of this wild rice species. Introgression may transfer commercial traits into O. glumaepatula, which in turn could alter genetic diversity and increase the likelihood of local extinction. These results have important implications for in situ conservation strategies of the only wild populations of O. glumaepatula in Costa Rica.

Genetic diversity in Oryza glumaepatula wild rice populations in Costa Rica and possible gene flow from O. sativa

PubMed Central

Meneses Martínez, Allan; Calvo, Amanda; Muñoz, Melania

2016-01-01

Wild crop relatives are an important source of genetic diversity for crop improvement. Diversity estimates are generally lacking for many wild crop relatives. The objective of the present study was to analyze how genetic diversity is distributed within and among populations of the wild rice species Oryza glumaepatula in Costa Rica. We also evaluated the likelihood of gene flow between wild and commercial rice species because the latter is commonly sympatric with wild rice populations. Introgression may change wild species by incorporating alleles from domesticated species, increasing the risk of losing original variation. Specimens from all known O. glumaepatula populations in Costa Rica were analyzed with 444 AFLP markers to characterize genetic diversity and structure. We also compared genetic diversity estimates between O. glumaepatula specimens and O. sativa commercial rice. Our results showed that O. glumaepatula populations in Costa Rica have moderately high levels of genetic diversity, comparable to those found in South American populations. Despite the restricted distribution of this species in Costa Rica, populations are fairly large, reducing the effects of drift on genetic diversity. We found a dismissible but significant structure (θ = 0.02 ± 0.001) among populations. A Bayesian structure analysis suggested that some individuals share a significant proportion of their genomes with O. sativa. These results suggest that gene flow from cultivated O. sativa populations may have occurred in the recent past. These results expose an important biohazard: recurrent hybridization may reduce the genetic diversity of this wild rice species. Introgression may transfer commercial traits into O. glumaepatula, which in turn could alter genetic diversity and increase the likelihood of local extinction. These results have important implications for in situ conservation strategies of the only wild populations of O. glumaepatula in Costa Rica. PMID:27077002

Inferring Fitness Effects from Time-Resolved Sequence Data with a Delay-Deterministic Model

PubMed Central

Nené, Nuno R.; Dunham, Alistair S.; Illingworth, Christopher J. R.

2018-01-01

A common challenge arising from the observation of an evolutionary system over time is to infer the magnitude of selection acting upon a specific genetic variant, or variants, within the population. The inference of selection may be confounded by the effects of genetic drift in a system, leading to the development of inference procedures to account for these effects. However, recent work has suggested that deterministic models of evolution may be effective in capturing the effects of selection even under complex models of demography, suggesting the more general application of deterministic approaches to inference. Responding to this literature, we here note a case in which a deterministic model of evolution may give highly misleading inferences, resulting from the nondeterministic properties of mutation in a finite population. We propose an alternative approach that acts to correct for this error, and which we denote the delay-deterministic model. Applying our model to a simple evolutionary system, we demonstrate its performance in quantifying the extent of selection acting within that system. We further consider the application of our model to sequence data from an evolutionary experiment. We outline scenarios in which our model may produce improved results for the inference of selection, noting that such situations can be easily identified via the use of a regular deterministic model. PMID:29500183

Ambiguity in measuring matrix diffusion with single-well injection/recovery tracer tests

USGS Publications Warehouse

Lessoff, S.C.; Konikow, Leonard F.

1997-01-01

Single-well injection/recovery tracer tests are considered for use in characterizing and quantifying matrix diffusion in dual-porosity aquifers. Numerical modeling indicates that neither regional drift in homogeneous aquifers, nor heterogeneity in aquifers having no regional drift, nor hydrodynamic dispersion significantly affects these tests. However, when drift is coupled simultaneously with heterogeneity, they can have significant confounding effects on tracer return. This synergistic effect of drift and heterogeneity may help explain irreversible flow and inconsistent results sometimes encountered in previous single-well injection/recovery tracer tests. Numerical results indicate that in a hypothetical single-well injection/recovery tracer test designed to demonstrate and measure dual-porosity characteristics in a fractured dolomite, the simultaneous effects of drift and heterogeneity sometimes yields responses similar to those anticipated in a homogeneous dual-porosity formation. In these cases, tracer recovery could provide a false indication of the occurrence of matrix diffusion. Shortening the shut-in period between injection and recovery periods may make the test less sensitive to drift. Using multiple tracers having different diffusion characteristics, multiple tests having different pumping schedules, and testing the formation at more than one location would decrease the ambiguity in the interpretation of test data.

Drift effects on the tokamak power scrape-off width

NASA Astrophysics Data System (ADS)

Meier, E. T.; Goldston, R. J.; Kaveeva, E. G.; Mordijck, S.; Rozhansky, V. A.; Senichenkov, I. Yu.; Voskoboynikov, S. P.

2015-11-01

Recent experimental analysis suggests that the scrape-off layer (SOL) heat flux width (λq) for ITER will be near 1 mm, sharply narrowing the planned operating window. In this work, motivated by the heuristic drift (HD) model, which predicts the observed inverse plasma current scaling, SOLPS-ITER is used to explore drift effects on λq. Modeling focuses on an H-mode DIII-D discharge. In initial results, target recycling is set to 90%, resulting in sheath-limited SOL conditions. SOL particle diffusivity (DSOL) is varied from 0.1 to 1 m2/s. When drifts are included, λq is insensitive to DSOL, consistent with the HD model, with λq near 3 mm; in no-drift cases, λq varies from 2 to 5 mm. Drift effects depress near-separatrix potential, generating a channel of strong electron heat convection that is insensitive to DSOL. Sensitivities to thermal diffusivities, plasma current, toroidal magnetic field, and device size are also assessed. These initial results will be discussed in detail, and progress toward modeling experimentally relevant high-recycling conditions will be reported. Supported by U.S. DOE Contract DE-SC0010434.

Decreased Serologic Response in Vaccinated Military Recruits during 2011 Correspond to Genetic Drift in Concurrent Circulating Pandemic A/H1N1 Viruses

DTIC Science & Technology

2012-04-13

that gave 75% cytopathic effect (CPE) were utilized in the MN assays. The proportions of LAIV and TIV vaccinees for the range of post- vaccination ...titers were plotted for the vaccine strain H3N2 and 2009 pH1N1 viruses and the circulating 2011 pH1N1 virus (Figure 1). Overall, titers in TIV vaccinees ...seroresponse against H3N2 than the 2009 and 2011 pH1N1 viruses. Post- vaccine seroprotection among LAIV vaccinees for 2009 pH1N1, H3N2, and 2011 pH1N1

DEVELOPMENT OF A TEST PLAN TO VERIFY PESTICIDE DRIFT REDUCTION TECHNOLOGIES

EPA Science Inventory

Considerable research has taken place in recent years to determine the sources, pathways, and exposure to the environment from airborne pesticide spray which can often drift off target at the time of spray application. Verification of the effectiveness of pesticide spray drift r...

Interception of spray drift by border structures. Part 1: wind tunnel experiments.

PubMed

De Schampheleire, M; Nuyttens, D; Dekeyser, D; Verboven, P; Cornelis, W; Gabriels, D; Spanoghe, P

2008-01-01

This research investigated the drift-intercepting potential of structures surrounding the field borders, like artificial screens and crops, which are not yet a part of the drift mitigation measures for field crop sprayers in Belgium. Drift-interception experiments were performed in the wind tunnel of the International Centre for Eremology (Ghent University, Belgium) with various interception structures: Artificial screens with heights of 0.5, 0.75 and 1 m and screen open areas of 16, 36 and 63%; a row of plastic Christmas trees with heights of 0.5 and 0.75 m; and a potato canopy. The interception structure was positioned at 1 m from the field border. From the results it was found that type of border structure has a pronounced effect on the drift interception, while the height of the border structure had no significant effect.

Effects of Drift-Shell Splitting by Chorus Waves on Radiation Belt Electrons

NASA Astrophysics Data System (ADS)

Chan, A. A.; Zheng, L.; O'Brien, T. P., III; Tu, W.; Cunningham, G.; Elkington, S. R.; Albert, J.

2015-12-01

Drift shell splitting in the radiation belts breaks all three adiabatic invariants of charged particle motion via pitch angle scattering, and produces new diffusion terms that fully populate the diffusion tensor in the Fokker-Planck equation. Based on the stochastic differential equation method, the Radbelt Electron Model (REM) simulation code allows us to solve such a fully three-dimensional Fokker-Planck equation, and to elucidate the sources and transport mechanisms behind the phase space density variations. REM has been used to perform simulations with an empirical initial phase space density followed by a seed electron injection, with a Tsyganenko 1989 magnetic field model, and with chorus wave and ULF wave diffusion models. Our simulation results show that adding drift shell splitting changes the phase space location of the source to smaller L shells, which typically reduces local electron energization (compared to neglecting drift-shell splitting effects). Simulation results with and without drift-shell splitting effects are compared with Van Allen Probe measurements.

Dike/Drift Interactions

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

E. Gaffiney

2004-11-23

This report presents and documents the model components and analyses that represent potential processes associated with propagation of a magma-filled crack (dike) migrating upward toward the surface, intersection of the dike with repository drifts, flow of magma in the drifts, and post-magma emplacement effects on repository performance. The processes that describe upward migration of a dike and magma flow down the drift are referred to as the dike intrusion submodel. The post-magma emplacement processes are referred to as the post-intrusion submodel. Collectively, these submodels are referred to as a conceptual model for dike/drift interaction. The model components and analyses ofmore » the dike/drift interaction conceptual model provide the technical basis for assessing the potential impacts of an igneous intrusion on repository performance, including those features, events, and processes (FEPs) related to dike/drift interaction (Section 6.1).« less

A baseline drift detrending technique for fast scan cyclic voltammetry.

PubMed

DeWaele, Mark; Oh, Yoonbae; Park, Cheonho; Kang, Yu Min; Shin, Hojin; Blaha, Charles D; Bennet, Kevin E; Kim, In Young; Lee, Kendall H; Jang, Dong Pyo

2017-11-06

Fast scan cyclic voltammetry (FSCV) has been commonly used to measure extracellular neurotransmitter concentrations in the brain. Due to the unstable nature of the background currents inherent in FSCV measurements, analysis of FSCV data is limited to very short amounts of time using traditional background subtraction. In this paper, we propose the use of a zero-phase high pass filter (HPF) as the means to remove the background drift. Instead of the traditional method of low pass filtering across voltammograms to increase the signal to noise ratio, a HPF with a low cutoff frequency was applied to the temporal dataset at each voltage point to remove the background drift. As a result, the HPF utilizing cutoff frequencies between 0.001 Hz and 0.01 Hz could be effectively used to a set of FSCV data for removing the drifting patterns while preserving the temporal kinetics of the phasic dopamine response recorded in vivo. In addition, compared to a drift removal method using principal component analysis, this was found to be significantly more effective in reducing the drift (unpaired t-test p < 0.0001, t = 10.88) when applied to data collected from Tris buffer over 24 hours although a drift removal method using principal component analysis also showed the effective background drift reduction. The HPF was also applied to 5 hours of FSCV in vivo data. Electrically evoked dopamine peaks, observed in the nucleus accumbens, were clearly visible even without background subtraction. This technique provides a new, simple, and yet robust, approach to analyse FSCV data with an unstable background.

Integrating Social Science and Behavioral Genetics: Testing the Origin of Socioeconomic Disparities in Depression Using a Genetically Informed Design

PubMed Central

Myers, John M.; Kendler, Kenneth S.

2013-01-01

Objectives. We tested 3 hypotheses—social causation, social drift, and common cause—regarding the origin of socioeconomic disparities in major depression and determined whether the relationship between socioeconomic status (SES) and major depression varied by genetic liability for major depression. Methods. Data were from a sample of female twins in the baseline Virginia Adult Twin Study of Psychiatric and Substance Use Disorders interviewed between 1987 and 1989 (n = 2153). We used logistic regression and structural equation twin models to evaluate these 3 hypotheses. Results. Consistent with the social causation hypothesis, education (odds ratio [OR] = 0.78; 95% confidence interval [CI] = 0.66, 0.93; P < .01) and income (OR = 0.93; 95% CI = 0.89, 0.98; P < .01) were significantly related to past-year major depression. Upward social mobility was associated with lower risk of depression. There was no evidence that childhood SES was related to development of major depression (OR = 0.98; 95% CI = 0.89, 1.09; P > .1). Consistent with a common genetic cause, there was a negative correlation between the genetic components of major depression and education (r2 =  –0.22). Co-twin control analyses indicated a protective effect of education and income on major depression even after accounting for genetic liability. Conclusions. This study utilized a genetically informed design to address how social position relates to major depression. Results generally supported the social causation model. PMID:23927513

Marine dispersal determines the genetic population structure of migratory stream fauna of Puerto Rico: evidence for island-scale population recovery processes

Treesearch

Benjamin D. Cook; Sofie Bernays; Catherine M. Pringle; Jane M. Hughes

2009-01-01

Various components of island stream faunas, including caridean shrimps, fish, and gastropods, undertake obligate amphidromous migration, whereby larvae are released in upstream freshwater reaches, drift downstream to estuaries or marine waters, then migrate upstream as postlarvae to freshwater adult habitats. Longitudinal migration from estuaries to headwaters is well...

Investigating the case of human nose shape and climate adaptation

PubMed Central

Zaidi, Arslan A.; Claes, Peter; McEcoy, Brian; Shriver, Mark D.

2017-01-01

The evolutionary reasons for variation in nose shape across human populations have been subject to continuing debate. An import function of the nose and nasal cavity is to condition inspired air before it reaches the lower respiratory tract. For this reason, it is thought the observed differences in nose shape among populations are not simply the result of genetic drift, but may be adaptations to climate. To address the question of whether local adaptation to climate is responsible for nose shape divergence across populations, we use Qst–Fst comparisons to show that nares width and alar base width are more differentiated across populations than expected under genetic drift alone. To test whether this differentiation is due to climate adaptation, we compared the spatial distribution of these variables with the global distribution of temperature, absolute humidity, and relative humidity. We find that width of the nares is correlated with temperature and absolute humidity, but not with relative humidity. We conclude that some aspects of nose shape may indeed have been driven by local adaptation to climate. However, we think that this is a simplified explanation of a very complex evolutionary history, which possibly also involved other non-neutral forces such as sexual selection. PMID:28301464

Investigating the case of human nose shape and climate adaptation.

PubMed

Zaidi, Arslan A; Mattern, Brooke C; Claes, Peter; McEvoy, Brian; Hughes, Cris; Shriver, Mark D

2017-03-01

The evolutionary reasons for variation in nose shape across human populations have been subject to continuing debate. An import function of the nose and nasal cavity is to condition inspired air before it reaches the lower respiratory tract. For this reason, it is thought the observed differences in nose shape among populations are not simply the result of genetic drift, but may be adaptations to climate. To address the question of whether local adaptation to climate is responsible for nose shape divergence across populations, we use Qst-Fst comparisons to show that nares width and alar base width are more differentiated across populations than expected under genetic drift alone. To test whether this differentiation is due to climate adaptation, we compared the spatial distribution of these variables with the global distribution of temperature, absolute humidity, and relative humidity. We find that width of the nares is correlated with temperature and absolute humidity, but not with relative humidity. We conclude that some aspects of nose shape may indeed have been driven by local adaptation to climate. However, we think that this is a simplified explanation of a very complex evolutionary history, which possibly also involved other non-neutral forces such as sexual selection.

Drift as a mechanism for cultural change: an example from baby names.

PubMed Central

Hahn, Matthew W; Bentley, R Alexander

2003-01-01

In the social sciences, there is currently no consensus on the mechanism by which cultural elements come and go in human society. For elements that are value-neutral, an appropriate null model may be one of random copying between individuals in the population. We show that the frequency distributions of baby names used in the United States in each decade of the twentieth century, for both males and females, obey a power law that is maintained over 100 years even though the population is growing, names are being introduced and lost every decade and large changes in the frequencies of specific names are common. We show that these distributions are satisfactorily explained by a simple process in which individuals randomly copy names from each other, a process that is analogous to the infinite-allele model of population genetics with random genetic drift. By its simplicity, this model provides a powerful null hypothesis for cultural change. It further explains why a few elements inevitably become highly popular, even if they have no intrinsic superiority over alternatives. Random copying could potentially explain power law distributions in other cultural realms, including the links on the World Wide Web. PMID:12952655

Evolution of Inbreeding Avoidance and Inbreeding Preference through Mate Choice among Interacting Relatives.

PubMed

Duthie, A Bradley; Reid, Jane M

2016-12-01

While extensive population genetic theory predicts conditions favoring evolution of self-fertilization versus outcrossing, there is no analogous theory that predicts conditions favoring evolution of inbreeding avoidance or inbreeding preference enacted through mate choice given obligate biparental reproduction. Multiple interacting processes complicate the dynamics of alleles underlying such inbreeding strategies, including sexual conflict, distributions of kinship, genetic drift, purging of mutation load, direct costs, and restricted kin discrimination. We incorporated these processes into an individual-based model to predict conditions where selection should increase or decrease frequencies of alleles causing inbreeding avoidance or inbreeding preference when females or males controlled mating. Selection for inbreeding avoidance occurred given strong inbreeding depression when either sex chose mates, while selection for inbreeding preference occurred given very weak inbreeding depression when females chose but never occurred when males chose. Selection for both strategies was constrained by direct costs and restricted kin discrimination. Purging was negligible, but allele frequencies were strongly affected by drift in small populations, while selection for inbreeding avoidance was weak in larger populations because inbreeding risk decreased. Therefore, while selection sometimes favored alleles underlying inbreeding avoidance or preference, evolution of such strategies may be much more restricted and stochastic than is commonly presumed.

The US Navy Coupled Ocean-Wave Prediction System

DTIC Science & Technology

2014-09-01

Stokes drift to be the dominant wave effect and that it increased surface drift speeds by 35% and veered the current in the direction of the wind...ocean model has been modified to incorporate the effect of the Stokes drift current, wave radiation stresses due to horizontal gradients of the momentum...for fourth-order differences for horizontal baroclinic pressure gradients and for interpolation of Coriolis terms. There is an option to use the

Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns.

PubMed

Enge, Martin; Arda, H Efsun; Mignardi, Marco; Beausang, John; Bottino, Rita; Kim, Seung K; Quake, Stephen R

2017-10-05

As organisms age, cells accumulate genetic and epigenetic errors that eventually lead to impaired organ function or catastrophic transformation such as cancer. Because aging reflects a stochastic process of increasing disorder, cells in an organ will be individually affected in different ways, thus rendering bulk analyses of postmitotic adult cells difficult to interpret. Here, we directly measure the effects of aging in human tissue by performing single-cell transcriptome analysis of 2,544 human pancreas cells from eight donors spanning six decades of life. We find that islet endocrine cells from older donors display increased levels of transcriptional noise and potential fate drift. By determining the mutational history of individual cells, we uncover a novel mutational signature in healthy aging endocrine cells. Our results demonstrate the feasibility of using single-cell RNA sequencing (RNA-seq) data from primary cells to derive insights into genetic and transcriptional processes that operate on aging human tissue. Copyright © 2017 Elsevier Inc. All rights reserved.

Novel tetra-nucleotide microsatellite DNA markers for assessing the evolutionary genetics and demographics of Northern Snakehead (Channa argus) invading North America

USGS Publications Warehouse

King, Timothy L.; Johnson, Robin L.

2011-01-01

We document the isolation and characterization of 19 tetra-nucleotide microsatellite DNA markers in northern snakehead (Channa argus) fish that recently colonized Meadow Lake, New York City, New York. These markers displayed moderate levels of allelic diversity (averaging 6.8 alleles/locus) and heterozygosity (averaging 74.2%). Demographic analyses suggested that the Meadow Lake collection has not achieved mutation-drift equilibrium. These results were consistent with instances of deviations from Hardy–Weinberg equilibrium and the presence of some linkage disequilibrium. A comparison of individual pair-wise distances suggested the presence of multiple differentiated groups of related individuals. Results of all analyses are consistent with a pattern of multiple, recent introductions. The microsatellite markers developed for C. argus yielded sufficient genetic diversity to potentially: (1) delineate kinship; (2) elucidate fine-scale population structure; (3) define management (eradication) units; (4) estimate dispersal rates; (5) estimate population sizes; and (6) provide unique demographic perspectives of control or eradication effectiveness.

Reducing pesticide drift by considering propeller rotation effects from aerial application and near buffer zones

USDA-ARS?s Scientific Manuscript database

Off-target drift of chemical from agricultural spraying can damage sensitive crops, destroy beneficial insects, and intrude on human and domestic animal habitats, threatening environmental quality. Reduction of drift from aerial application can be facilitated at the edge of a field by offsetting spr...

Radar studies of midlatitude ionospheric plasma drifts

NASA Astrophysics Data System (ADS)

Scherliess, L.; Fejer, B. G.; Holt, J.; Goncharenko, L.; Amory-Mazaudier, C.; Buonsanto, M. J.

2001-02-01

We use incoherent scatter radar measurements from Millstone Hill and Saint Santin to study the midlatitude F region electrodynamic plasma drifts during geomagnetically quiet and active periods. We present initially a local time, season, and solar flux dependent analytical model of the quiet time zonal and meridional E×B drifts over these stations. We discuss, for the first time, the Saint Santin drift patterns during solar maximum. We have used these quiet time models to extract the geomagnetic perturbation drifts which were modeled as a function of the time history of the auroral electrojet indices. Our results illustrate the evolution of the disturbance drifts driven by the combined effects of prompt penetration and longer lasting perturbation electric fields. The meridional electrodynamic disturbance drifts have largest amplitudes in the midnight-noon sector. The zonal drifts are predominantly westward, with largest amplitudes in the dusk-midnight sector and, following a decrease in the high-latitude convection, they decay more slowly than the meridional drifts. The prompt penetration and steady state zonal disturbance drifts derived from radar measurements are in good agreement with results obtained from both the ion drift meter data on board the Dynamics Explorer 2 (DE 2) satellite and from the Rice Convection Model.

Theoretical study of the effect of pump wavelength drift on mode instability in a high-power fiber amplifier

NASA Astrophysics Data System (ADS)

Liu, Yakun; Tao, Rumao; Su, Rongtao; Wang, Xiaolin; Ma, Pengfei; Zhang, Hanwei; Zhou, Pu; Si, Lei

2018-04-01

This paper presents an investigation of the effect of pump wavelength drift on the threshold of mode instability (MI) in high-power ytterbium-doped fiber lasers. By using a semi-analytical model, we study the effects of pump wavelength drift with a central pump wavelength around 976 nm and 915 nm, respectively. The influences of the pump absorption coefficient and total pump absorption are considered simultaneously. The results indicate that the effect of pump wavelength drift around 976 nm is stronger than that around 915 nm. For more efficient suppression of MI by shifting the pump wavelength, efficient absorption of pump power is required. The MI thresholds for fibers with different total pump absorptions and cladding diameters are compared. When the total pump absorption is increased, the gain saturation is enhanced, which results in the MI being mitigated more effectively and being more sensitive to pump wavelength drift. The MI threshold in gain fibers with larger inner cladding diameter is higher but more dependent upon pump wavelength. The results of this work can help in optimizing the pump wavelength and fiber parameters and suppressing MI in high-power fiber lasers.

Investigation of drift gas selectivity in high resolution ion mobility spectrometry with mass spectrometry detection.

PubMed

Matz, Laura M; Hill, Herbert H; Beegle, Luther W; Kanik, Isik

2002-04-01

Recent studies in electrospray ionization (ESI)/ion mobility spectrometry (IMS) have focussed on employing different drift gases to alter separation efficiency for some molecules. This study investigates four structurally similar classes of molecules (cocaine and metabolites, amphetamines, benzodiazepines, and small peptides) to determine the effect of structure on relative mobility changes in four drift gases (helium, nitrogen, argon, carbon dioxide). Collision cross sections were plotted against drift gas polarizability and a linear relationship was found for the nineteen compounds evaluated in the study. Based on the reduced mobility database, all nineteen compounds could be separated in one of the four drift gases, however, the drift gas that provided optimal separation was specific for the two compounds.

Genetic parameters and signatures of selection in two divergent laying hen lines selected for feather pecking behaviour.

PubMed

Grams, Vanessa; Wellmann, Robin; Preuß, Siegfried; Grashorn, Michael A; Kjaer, Jörgen B; Bessei, Werner; Bennewitz, Jörn

2015-09-30

Feather pecking (FP) in laying hens is a well-known and multi-factorial behaviour with a genetic background. In a selection experiment, two lines were developed for 11 generations for high (HFP) and low (LFP) feather pecking, respectively. Starting with the second generation of selection, there was a constant difference in mean number of FP bouts between both lines. We used the data from this experiment to perform a quantitative genetic analysis and to map selection signatures. Pedigree and phenotypic data were available for the last six generations of both lines. Univariate quantitative genetic analyses were conducted using mixed linear and generalized mixed linear models assuming a Poisson distribution. Selection signatures were mapped using 33,228 single nucleotide polymorphisms (SNPs) genotyped on 41 HFP and 34 LFP individuals of generation 11. For each SNP, we estimated Wright's fixation index (FST). We tested the null hypothesis that FST is driven purely by genetic drift against the alternative hypothesis that it is driven by genetic drift and selection. The mixed linear model failed to analyze the LFP data because of the large number of 0s in the observation vector. The Poisson model fitted the data well and revealed a small but continuous genetic trend in both lines. Most of the 17 genome-wide significant SNPs were located on chromosomes 3 and 4. Thirteen clusters with at least two significant SNPs within an interval of 3 Mb maximum were identified. Two clusters were mapped on chromosomes 3, 4, 8 and 19. Of the 17 genome-wide significant SNPs, 12 were located within the identified clusters. This indicates a non-random distribution of significant SNPs and points to the presence of selection sweeps. Data on FP should be analysed using generalised linear mixed models assuming a Poisson distribution, especially if the number of FP bouts is small and the distribution is heavily peaked at 0. The FST-based approach was suitable to map selection signatures that need to be confirmed by linkage or association mapping.

Modeling and Compensation of Random Drift of MEMS Gyroscopes Based on Least Squares Support Vector Machine Optimized by Chaotic Particle Swarm Optimization.

PubMed

Xing, Haifeng; Hou, Bo; Lin, Zhihui; Guo, Meifeng

2017-10-13

MEMS (Micro Electro Mechanical System) gyroscopes have been widely applied to various fields, but MEMS gyroscope random drift has nonlinear and non-stationary characteristics. It has attracted much attention to model and compensate the random drift because it can improve the precision of inertial devices. This paper has proposed to use wavelet filtering to reduce noise in the original data of MEMS gyroscopes, then reconstruct the random drift data with PSR (phase space reconstruction), and establish the model for the reconstructed data by LSSVM (least squares support vector machine), of which the parameters were optimized using CPSO (chaotic particle swarm optimization). Comparing the effect of modeling the MEMS gyroscope random drift with BP-ANN (back propagation artificial neural network) and the proposed method, the results showed that the latter had a better prediction accuracy. Using the compensation of three groups of MEMS gyroscope random drift data, the standard deviation of three groups of experimental data dropped from 0.00354°/s, 0.00412°/s, and 0.00328°/s to 0.00065°/s, 0.00072°/s and 0.00061°/s, respectively, which demonstrated that the proposed method can reduce the influence of MEMS gyroscope random drift and verified the effectiveness of this method for modeling MEMS gyroscope random drift.

Long term assessment of blood pressure transducer drift in rhesus monkeys chronically instrumented with telemetry implants.

PubMed

Regan, Hillary K; Lynch, Joseph J; Regan, Christopher P

2009-01-01

The accurate assessment of blood pressure is often a key component of preclinical cardiovascular disease/efficacy models and of screening models used to determine the effects of test agents on cardiovascular physiology. Of the many methods utilized in large animals, telemetry is becoming more widely used throughout preclinical testing, and non-human primates are playing an ever increasing role as a large animal model to evaluate the cardiovascular effect of novel test agents. Therefore, we sought to characterize pressure transducer drift of a telemetry implant in primates over an extended duration. We instrumented ten rhesus monkeys with a Konigsberg T27F implant and a chronic indwelling arterial catheter and cross calibrated the diastolic pressure recorded by the implant to the diastolic pressure that was simultaneously recorded through the arterial catheter using a calibrated external transducer/amplifier system. While all implanted pressure transducers experienced drift to some degree, magnitude of drift varied across animals (range of average drift 0.7-20.5 mmHg/month). Specifically, we found that all implants could be calibrated within the voltage range of the instrument up to 6 months after implantation despite the drift observed. Between 6 and 12 months, 3 of the 10 implants studied drifted outside the defined voltage range and were unusable, two more drifted off scale within 2 years, while the remainder remained within the operating voltage range. Given that pressure transducer drift was not consistent across implants or time, these data suggest careful assessment and quantitative correction for in vivo drift of telemetry blood pressure transducers implanted for extended duration should be considered.

Causes of the longitudinal differences in the equatorial vertical E × B drift during the 2013 SSW period as simulated by the TIME-GCM

NASA Astrophysics Data System (ADS)

Maute, A.; Hagan, M. E.; Yudin, V.; Liu, H.-L.; Yizengaw, E.

2015-06-01

During stratospheric sudden warming (SSW) periods large changes in the low-latitude vertical drift have been observed at Jicamarca as well as in other longitudinal sectors. In general, a strengthening of the daytime maximum vertical drift with a shift from prenoon to the afternoon is observed. During the January 2013 stratospheric warming significant longitudinal differences in the equatorial vertical drift were observed. At Jicamarca the previously reported SSW behavior prevails; however, no shift of the daytime maximum drift was exhibited in the African sector. Using the National Center for Atmospheric Research thermosphere-ionosphere-mesosphere electrodynamics general circulation model (TIME-GCM) the possible causes for the longitudinal difference are examined. The timing of the strong SSW effect in the vertical drift (15-20 January) coincides with moderate geomagnetic activity. The simulation indicates that approximately half of the daytime vertical drift increase in the American sector may be related to the moderate geophysical conditions (Kp = 4) with the effect being negligible in the African sector. The simulation suggests that the wind dynamo accounts for approximately 50% of the daytime vertical drift in the American sector and almost 100% in the African sector. The simulation agrees with previous findings that the migrating solar tides and the semidiurnal westward propagating tide with zonal wave number 1 (SW1) mainly contribute to the daytime wind dynamo and vertical drift. Numerical experiments suggest that the neutral wind and the geomagnetic main field contribute to the presence (absence) of a local time shift in the daytime maximum drift in the American (African) sector.

Structural Genomics: Correlation Blocks, Population Structure, and Genome Architecture

PubMed Central

Hu, Xin-Sheng; Yeh, Francis C.; Wang, Zhiquan

2011-01-01

An integration of the pattern of genome-wide inter-site associations with evolutionary forces is important for gaining insights into the genomic evolution in natural or artificial populations. Here, we assess the inter-site correlation blocks and their distributions along chromosomes. A correlation block is broadly termed as the DNA segment within which strong correlations exist between genetic diversities at any two sites. We bring together the population genetic structure and the genomic diversity structure that have been independently built on different scales and synthesize the existing theories and methods for characterizing genomic structure at the population level. We discuss how population structure could shape correlation blocks and their patterns within and between populations. Effects of evolutionary forces (selection, migration, genetic drift, and mutation) on the pattern of genome-wide correlation blocks are discussed. In eukaryote organisms, we briefly discuss the associations between the pattern of correlation blocks and genome assembly features in eukaryote organisms, including the impacts of multigene family, the perturbation of transposable elements, and the repetitive nongenic sequences and GC-rich isochores. Our reviews suggest that the observable pattern of correlation blocks can refine our understanding of the ecological and evolutionary processes underlying the genomic evolution at the population level. PMID:21886455

Progressive retinal atrophy in the Border Collie: a new XLPRA.

PubMed

Vilboux, Thierry; Chaudieu, Gilles; Jeannin, Patricia; Delattre, Delphine; Hedan, Benoit; Bourgain, Catherine; Queney, Guillaume; Galibert, Francis; Thomas, Anne; André, Catherine

2008-03-03

Several forms of progressive retinal atrophy (PRA) segregate in more than 100 breeds of dog with each PRA segregating in one or a few breeds. This breed specificity may be accounted for by founder effects and genetic drift, which have reduced the genetic heterogeneity of each breed, thereby facilitating the identification of causal mutations. We report here a new form of PRA segregating in the Border Collie breed. The clinical signs, including the loss of night vision and a progressive loss of day vision, resulting in complete blindness, occur at the age of three to four years and may be detected earlier through systematic ocular fundus examination and electroretinography (ERG). Ophthalmic examinations performed on 487 dogs showed that affected dogs present a classical form of PRA. Of those, 274 have been sampled for DNA extraction and 87 could be connected through a large pedigree. Segregation analysis suggested an X-linked mode of transmission; therefore both XLPRA1 and XLPRA2 mutations were excluded through the genetic tests. Having excluded these mutations, we suggest that this PRA segregating in Border Collie is a new XLPRA (XLPRA3) and propose it as a potential model for the homologous human disease, X-Linked Retinitis Pigmentosa.

Variable continental distribution of polymorphisms in the coding regions of DNA-repair genes.

PubMed

Mathonnet, Géraldine; Labuda, Damian; Meloche, Caroline; Wambach, Tina; Krajinovic, Maja; Sinnett, Daniel

2003-01-01

DNA-repair pathways are critical for maintaining the integrity of the genetic material by protecting against mutations due to exposure-induced damages or replication errors. Polymorphisms in the corresponding genes may be relevant in genetic epidemiology by modifying individual cancer susceptibility or therapeutic response. We report data on the population distribution of potentially functional variants in XRCC1, APEX1, ERCC2, ERCC4, hMLH1, and hMSH3 genes among groups representing individuals of European, Middle Eastern, African, Southeast Asian and North American descent. The data indicate little interpopulation differentiation in some of these polymorphisms and typical FST values ranging from 10 to 17% at others. Low FST was observed in APEX1 and hMSH3 exon 23 in spite of their relatively high minor allele frequencies, which could suggest the effect of balancing selection. In XRCC1, hMSH3 exon 21 and hMLH1 Africa clusters either with Middle East and Europe or with Southeast Asia, which could be related to the demographic history of human populations, whereby human migrations and genetic drift rather than selection would account for the observed differences.

Inferring modes of colonization for pest species using heterozygosity comparisons and a shared-allele test.

PubMed

Sved, J A; Yu, H; Dominiak, B; Gilchrist, A S

2003-02-01

Long-range dispersal of a species may involve either a single long-distance movement from a core population or spreading via unobserved intermediate populations. Where the new populations originate as small propagules, genetic drift may be extreme and gene frequency or assignment methods may not prove useful in determining the relation between the core population and outbreak samples. We describe computationally simple resampling methods for use in this situation to distinguish between the different modes of dispersal. First, estimates of heterozygosity can be used to test for direct sampling from the core population and to estimate the effective size of intermediate populations. Second, a test of sharing of alleles, particularly rare alleles, can show whether outbreaks are related to each other rather than arriving as independent samples from the core population. The shared-allele statistic also serves as a genetic distance measure that is appropriate for small samples. These methods were applied to data on a fruit fly pest species, Bactrocera tryoni, which is quarantined from some horticultural areas in Australia. We concluded that the outbreaks in the quarantine zone came from a heterogeneous set of genetically differentiated populations, possibly ones that overwinter in the vicinity of the quarantine zone.

Footprints of Directional Selection in Wild Atlantic Salmon Populations: Evidence for Parasite-Driven Evolution?

PubMed Central

Zueva, Ksenia J.; Lumme, Jaakko; Veselov, Alexey E.; Kent, Matthew P.; Lien, Sigbjørn; Primmer, Craig R.

2014-01-01

Mechanisms of host-parasite co-adaptation have long been of interest in evolutionary biology; however, determining the genetic basis of parasite resistance has been challenging. Current advances in genome technologies provide new opportunities for obtaining a genome-scale view of the action of parasite-driven natural selection in wild populations and thus facilitate the search for specific genomic regions underlying inter-population differences in pathogen response. European populations of Atlantic salmon (Salmo salar L.) exhibit natural variance in susceptibility levels to the ectoparasite Gyrodactylus salaris Malmberg 1957, ranging from resistance to extreme susceptibility, and are therefore a good model for studying the evolution of virulence and resistance. However, distinguishing the molecular signatures of genetic drift and environment-associated selection in small populations such as land-locked Atlantic salmon populations presents a challenge, specifically in the search for pathogen-driven selection. We used a novel genome-scan analysis approach that enabled us to i) identify signals of selection in salmon populations affected by varying levels of genetic drift and ii) separate potentially selected loci into the categories of pathogen (G. salaris)-driven selection and selection acting upon other environmental characteristics. A total of 4631 single nucleotide polymorphisms (SNPs) were screened in Atlantic salmon from 12 different northern European populations. We identified three genomic regions potentially affected by parasite-driven selection, as well as three regions presumably affected by salinity-driven directional selection. Functional annotation of candidate SNPs is consistent with the role of the detected genomic regions in immune defence and, implicitly, in osmoregulation. These results provide new insights into the genetic basis of pathogen susceptibility in Atlantic salmon and will enable future searches for the specific genes involved. PMID:24670947

Footprints of directional selection in wild Atlantic salmon populations: evidence for parasite-driven evolution?

PubMed

Zueva, Ksenia J; Lumme, Jaakko; Veselov, Alexey E; Kent, Matthew P; Lien, Sigbjørn; Primmer, Craig R

2014-01-01

Mechanisms of host-parasite co-adaptation have long been of interest in evolutionary biology; however, determining the genetic basis of parasite resistance has been challenging. Current advances in genome technologies provide new opportunities for obtaining a genome-scale view of the action of parasite-driven natural selection in wild populations and thus facilitate the search for specific genomic regions underlying inter-population differences in pathogen response. European populations of Atlantic salmon (Salmo salar L.) exhibit natural variance in susceptibility levels to the ectoparasite Gyrodactylus salaris Malmberg 1957, ranging from resistance to extreme susceptibility, and are therefore a good model for studying the evolution of virulence and resistance. However, distinguishing the molecular signatures of genetic drift and environment-associated selection in small populations such as land-locked Atlantic salmon populations presents a challenge, specifically in the search for pathogen-driven selection. We used a novel genome-scan analysis approach that enabled us to i) identify signals of selection in salmon populations affected by varying levels of genetic drift and ii) separate potentially selected loci into the categories of pathogen (G. salaris)-driven selection and selection acting upon other environmental characteristics. A total of 4631 single nucleotide polymorphisms (SNPs) were screened in Atlantic salmon from 12 different northern European populations. We identified three genomic regions potentially affected by parasite-driven selection, as well as three regions presumably affected by salinity-driven directional selection. Functional annotation of candidate SNPs is consistent with the role of the detected genomic regions in immune defence and, implicitly, in osmoregulation. These results provide new insights into the genetic basis of pathogen susceptibility in Atlantic salmon and will enable future searches for the specific genes involved.

A selective sweep in a Varroa destructor resistant honeybee (Apis mellifera) population.

PubMed

Lattorff, H Michael G; Buchholz, Josephine; Fries, Ingemar; Moritz, Robin F A

2015-04-01

The mite Varroa destructor is one of the most dangerous parasites of the Western honeybee (Apis mellifera) causing enormous colony losses worldwide. Various chemical treatments for the control of the Varroa mite are currently in use, which, however, lead to residues in bee products and often to resistance in mites. This facilitated the exploration of alternative treatment methods and breeding for mite resistant honeybees has been in focus for breeders in many parts of the world with variable results. Another approach has been applied to a honeybee population on Gotland (Sweden) that was exposed to natural selection and survived Varroa-infestation for more than 10years without treatment. Eventually this population became resistant to the parasite by suppressing the reproduction of the mite. A previous QTL mapping study had identified a region on chromosome 7 with major loci contributing to the mite resistance. Here, a microsatellite scan of the significant candidate QTL regions was used to investigate potential footprints of selection in the original population by comparing the study population on Gotland before (2000) and after selection (2007). Genetic drift had caused an extreme loss of genetic diversity in the 2007 population for all genetic markers tested. In addition to this overall reduction of heterozygosity, two loci on chromosome 7 showed an even stronger and significant reduction in diversity than expected from genetic drift alone. Within the selective sweep eleven genes are annotated, one of them being a putative candidate to interfere with reduced mite reproduction. A glucose-methanol-choline oxidoreductase (GMCOX18) might be involved in changing volatiles emitted by bee larvae that might be essential to trigger oogenesis in Varroa. Copyright © 2015 Elsevier B.V. All rights reserved.

Temperature modulation of the visible and near infrared absorption and scattering coefficients of human skin.

PubMed

Khalil, Omar S; Yeh, Shu-Jen; Lowery, Michael G; Wu, Xiaomao; Hanna, Charles F; Kantor, Stanislaw; Jeng, Tzyy-Wen; Kanger, Johannes S; Bolt, Rene A; de Mul, Frits F

2003-04-01

We determine temperature effect on the absorption and reduced scattering coefficients (mu(a) and mu(s)(')) of human forearm skin. Optical and thermal simulation data suggest that mu( a) and mu(s)(') are determined within a temperature-controlled depth of approximately 2 mm. Cutaneous mu(s)(') change linearly with temperature. Change in mu(a) was complex and irreversible above body normal temperatures. Light penetration depth (delta) in skin increased on cooling, with considerable person-to-person variations. We attribute the effect of temperature on mu(s)(') to change in refractive index mismatch, and its effect on mu(a) to perfusion changes. The reversible temperature effect on mu (s)(' ) was maintained during more than 90 min. contact between skin and the measuring probe, where temperature was modulated between 38 and 22 degrees C for multiple cycles While temperature modulated mu(s)(' ) instantaneously and reversibly, mu(a) exhibited slower response time and consistent drift. There was a statistically significant upward drift in mu(a) and a mostly downward drift in mu( s)(') over the contact period. The drift in temperature-induced fractional change in mu(s)(') was less statistically significant than the drift in mu(s)('). Deltamu( s)(') values determined under temperature modulation conditions may have less nonspecific drift than mu(s)(') which may have significance for noninvasive determination of analytes in human tissue.

Temperature effects on drift of suspended single-domain particles induced by the Magnus force

NASA Astrophysics Data System (ADS)

Denisov, S. I.; Lyutyy, T. V.; Reva, V. V.; Yermolenko, A. S.

2018-03-01

We study the temperature dependence of the drift velocity of single-domain ferromagnetic particles induced by the Magnus force in a dilute suspension. A set of stochastic equations describing the translational and rotational dynamics of particles is derived, and the particle drift velocity that depends on components of the average particle magnetization is introduced. The Fokker-Planck equation for the probability density of magnetization orientations is solved analytically in the limit of strong thermal fluctuations for both the planar rotor and general models. Using these solutions, we calculate the drift velocity and show that the out-of-plane fluctuations of magnetization, which are not accounted for in the planar rotor model, play an important role. In the general case of arbitrary fluctuations, we investigate the temperature dependence of the drift velocity by numerically simulating a set of effective stochastic differential equations for the magnetization dynamics.

Genetic studies among seven endogamous populations of the Koshi Zone, Bihar (India).

PubMed

Pandey, B N; Das, P K; Husain, S; Anwer, Md Rauf; Jha, A K

2003-09-01

The distribution of AB0 and Rhesus blood groups, PTC taste sensitivity and colour blindness was studied among seven endogamous populations (Tharu, Mushar, Santal, Dhobi, Julaha, Kulhaiya and Karan Kayastha) in the Koshi Zone of Bihar (India). The phenotype and allele frequencies of the four gene loci (AB0, RH, PTC and colour blindness) show considerable differences between these populations. The measurement of genetic distances revealed, that the lowest genetic distance is seen between Dhobi and Julaha, the highest between Mushar and Tharu. From the genetic distance analysis there is some evidence for a close genetic relationship among the population groups belonging to the same region, irrespective of their caste, religion, linguistic or any other affinities. It may be concluded that all these populations have arisen through a common ancestor and changed gene frequencies among them is due to evolutionary forces like mutation, selection, migration, temporal variation and genetic drift. However, these populations retain their separate entities by practising endogamy. Gene diversity analysis reveals that these populations are at an early stage of genetic differentiation.

Genetic variation and population structure of the mixed-mating cactus, Melocactus curvispinus (Cactaceae).

PubMed

Nassar, J M; Hamrick, J L; Fleming, T H

2001-07-01

Genetic diversity was measured in the mixed-mating cactus, Melocactus curvispinus, in Venezuela. Allozyme diversity was surveyed in 19 putative loci over 18 populations. Compared to other plant taxa, this cactus is rich in polymorphic loci (Ps=89.5%), with high numbers of alleles per polymorphic locus (APs=3.82), but moderate levels of heterozygosity (Hes=0.145). Substantial levels of inbreeding were detected across loci and populations at macrogeographic (FIS=0.348) and regional levels (FIS=0.194-0.402). Moderate levels of genetic differentiation among populations were detected at macrogeographical (FST=0.193) and regional (FST=0.084-0.187) scales, suggesting that gene flow is relatively restricted, but increases within regions without topographic barriers. The population genetic structure observed for this cactus was attributed to, at least, three factors: short-distance pollination and seed dispersal, the mixed-mating condition of the species, and genetic drift. High genetic identities between populations (I=0.942) supported the conspecific nature of all populations surveyed. The levels and patterns of genetic structure observed for M. curvispinus were consistent with its mating system and gene dispersal mechanisms.

Visualizing the geography of genetic variants.

PubMed

Marcus, Joseph H; Novembre, John

2017-02-15

One of the key characteristics of any genetic variant is its geographic distribution. The geographic distribution can shed light on where an allele first arose, what populations it has spread to, and in turn on how migration, genetic drift, and natural selection have acted. The geographic distribution of a genetic variant can also be of great utility for medical/clinical geneticists and collectively many genetic variants can reveal population structure. Here we develop an interactive visualization tool for rapidly displaying the geographic distribution of genetic variants. Through a REST API and dynamic front-end, the Geography of Genetic Variants (GGV) browser ( http://popgen.uchicago.edu/ggv/ ) provides maps of allele frequencies in populations distributed across the globe. GGV is implemented as a website ( http://popgen.uchicago.edu/ggv/ ) which employs an API to access frequency data ( http://popgen.uchicago.edu/freq_api/ ). Python and javascript source code for the website and the API are available at: http://github.com/NovembreLab/ggv/ and http://github.com/NovembreLab/ggv-api/ . jnovembre@uchicago.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Molecular genetic status of Aleutian Canada Geese from Buldir and the Semidi Islands, Alaska

USGS Publications Warehouse

Pierson, Barbara J.; Pearce, John M.; Talbot, Sandra L.; Shields, Gerald F.; Scribner, Kim T.

2000-01-01

We conducted genetic analyses of Aleutian Canada Geese (Branta canadensis leucopareia) from Buldir Island in the western Aleutians and the Semidi Islands in the eastern portion of their breeding range. We compared data from seven microsatellite DNA loci and 143 base pairs of the control region of mitochondrial DNA from the two populations of Aleutian Canada Geese and another small-bodied subspecies, the Cackling Canada Goose (B. c. minima) which nests in western Alaska. The widely separated island-nesting Aleutian geese were genetically more closely related to each other than to mainland-nesting small-bodied geese. The populations of Aleutian geese were genetically differentiated from one another in terms of mitochondrial DNA haplotype and microsatellite allele frequencies, suggesting limited contemporary gene flow and/or major shifts in gene frequency through genetic drift. The degree of population genetic differentiation suggests that Aleutian Canada Goose populations could be considered separate management units. There was some evidence of population bottlenecks, although we found no significant genetic evidence of non-random mating or inbreeding.

Sensor Drift Compensation Algorithm based on PDF Distance Minimization

NASA Astrophysics Data System (ADS)

Kim, Namyong; Byun, Hyung-Gi; Persaud, Krishna C.; Huh, Jeung-Soo

2009-05-01

In this paper, a new unsupervised classification algorithm is introduced for the compensation of sensor drift effects of the odor sensing system using a conducting polymer sensor array. The proposed method continues updating adaptive Radial Basis Function Network (RBFN) weights in the testing phase based on minimizing Euclidian Distance between two Probability Density Functions (PDFs) of a set of training phase output data and another set of testing phase output data. The output in the testing phase using the fixed weights of the RBFN are significantly dispersed and shifted from each target value due mostly to sensor drift effect. In the experimental results, the output data by the proposed methods are observed to be concentrated closer again to their own target values significantly. This indicates that the proposed method can be effectively applied to improved odor sensing system equipped with the capability of sensor drift effect compensation

Radiation effects on hole drift mobility in polysilanes

NASA Astrophysics Data System (ADS)

Seki, Shu; Shibata, Hiromi; Yoshida, Yoichi; Ishigure, Kenkichi; Tagawa, Seiichi

1997-03-01

The radiation effects on hole drift mobility in polysilane derivatives were studied in the present paper. The values of hole drift mobility (about 10 -4 cm 2/V·s) obtained by the DC Time-of-Flight (TOF) measurement were improved by ion beam irradiation for poly(methylphenylsilane) (PMPS) and poly(di-n-hexylsilane) (PDHS). The irradiated PMPS showed five times higher values of hole drift mobility than the non irradiated one. Their low photo-induced carrier yield, one of the highest barrier to use polysilanes as photoconductors, was also improved by the irradiation. The mechanism of the mobility improvement will be discussed in relation to the model of changes in the silicon skeleton structure induced by the radiation.

Colonizing the world in spite of reduced MHC variation

USGS Publications Warehouse

Gangoso, L.; Alcaide, M.; Grande, J.M.; Muñoz, J.; Talbot, Sandra L.; Sonsthagen, Sarah A.; Sage, Kevin; Figuerola, J.

2012-01-01

Reduced immune gene diversity is thought to negatively affect the capacity of organisms to adapt to pathogen challenges, which represent a major force in natural selection. Genes of the Major Histocompatibility Complex (MHC) are the most widely invoked adaptive loci in conservation biology, and have become the most popular genetic markers to investigate pathogen-host interactions in vertebrates. Although MHC genes are the most polymorphic genes described in the vertebrate genome, the extent to which MHC diversity determines the long-term persistence of populations is, unclear and often debated, as recent studies have documented the occurrence of natural populations thriving even after a depletion of MHC diversity caused by genetic drift. Here, we show that some phylogenetically related species belonging to the Falco genus (Aves: Falconidae) present a dramatically low MHC variability that has not precluded, nevertheless, the successful colonization of almost all existing regions and habitats worldwide. We found evidence for two remarkably different patterns of MHC variation within the genus. While kestrels show a high MHC variation according to the general theory, falcons exhibit an ancestrally low intra- and inter-specific MHC allelic diversity. We provide compelling evidence that this pattern is not caused by the degeneration of functional genes into pseudogenes, the inadvertent analyses of paralogous MHC genes, or the devastating action of genetic drift. Instead, our results strongly support the idea of an evolutionary transition driven and maintained by natural selection from primarily highly variable towards low polymorphic, but functional and expressed, MHC genes with species-specific pathogen-recognition capabilities.

Rapid expansion of the invasive oyster Crassostrea gigas at its northern distribution limit in Europe: Naturally dispersed or introduced?

PubMed Central

Anglès d’Auriac, Marc B.; Norling, Pia; Lapègue, Sylvie; Staalstrøm, André; Hjermann, Dag Ø.; Thaulow, Jens

2017-01-01

The Pacific oyster, Crassostrea gigas, was introduced to Europe for aquaculture purposes, and has had a rapid and unforeseen northward expansion in northern Europe. The recent dramatic increase in number of C. gigas populations along the species’ northern distribution limit has questioned the efficiency of Skagerrak as a dispersal barrier for transport and survival of larvae. We investigated the genetic connectivity and possible spreading patterns between Pacific oyster populations on the southern Norwegian coast (4 localities) and Swedish and Danish populations by means of DNA microsatellite analysis of adult oysters, and by simulating larvae drift. In the simulations we used a 3D oceanographic model to explore the influence of recent climate change (1990–2010) on development, survival, and successful spreading of Danish and Swedish Pacific oyster larvae to Norwegian coastal waters. The simulations indicated adequate temperature conditions for development, survival, and settlement of larvae across the Skagerrak in warm years since 2000. However, microsatellite genotyping revealed genetic differences between the Norwegian populations, and between the Norwegian populations and the Swedish and Danish populations, the latter two populations being more similar. This patchwork pattern of genetic dissimilarity among the Norwegian populations points towards multiple local introduction routes rather than the commonly assumed unidirectional entry of larvae drifted from Denmark and Sweden. Alternative origins of introduction and implications for management, such as forecasting and possible mitigation actions, are discussed. PMID:28486520

Genetic differentiation and trade among populations of peach palm ( Bactris gasipaes Kunth) in the Peruvian Amazon-implications for genetic resource management.

PubMed

Adin, A; Weber, J C; Sotelo Montes, C; Vidaurre, H; Vosman, B; Smulders, M J M

2004-05-01

Peach palm ( Bactris gasipaes Kunth) is cultivated for fruit and 'heart of palm', and is an important component of agroforestry systems in the Peruvian Amazon. In this study, AFLP was used to compare genetic diversity among domesticated populations along the Paranapura and Cuiparillo rivers, which are managed by indigenous and colonist farming communities, respectively. Gene diversity was 0.2629 for the populations in indigenous communities and 0.2534 in colonist communities. Genetic differentiation among populations ( G(st)) was 0.0377-0.0416 ( P<0.01) among populations along both rivers. There was no relation between genetic differentiation and the geographical location of populations along the rivers. Since natural seed dispersal by birds and rodents is thought to occur only across relatively short distances (100-200 m), it is likely that exchange of material by farmers and commercial traders is responsible for most of the 'long-distance' (over more than 20 km) gene flow among populations along the two rivers studied. This exchange of material may be important to counteract the effects of selection as well as genetic drift in small groups of trees in farmers' fields, much as in a metapopulation, and may account for the weak genetic differentiation between the two rivers ( G(st)=0.0249, P<0.01). A comparison with samples from other landraces in Peru and Brazil showed the existence of an isolation-by-distance structure up to 3,000 km, consistent with gene flow on a regional scale, likely mediated by trade in the Amazon Basin. Results are discussed with regard to practical implications for the management of genetic resources with farming communities.

Marshes as “Mountain Tops”: Genetic Analyses of the Critically Endangered São Paulo Marsh Antwren (Aves: Thamnophilidae)

PubMed Central

de Camargo, Crisley; Gibbs, H. Lisle; Costa, Mariellen C.; Del-Rio, Glaucia; Silveira, Luís F.

2015-01-01

Small populations of endangered species can be impacted by genetic processes such as drift and inbreeding that reduce population viability. As such, conservation genetic analyses that assess population levels of genetic variation and levels of gene flow can provide important information for managing threatened species. The São Paulo Marsh Antwren (Formicivora paludicola) is a recently-described and critically endangered bird from São Paulo State (Brazil) whose total estimated population is around 250–300 individuals, distributed in only 15 isolated marshes around São Paulo metropolitan region. We used microsatellite DNA markers to estimate the population genetic characteristics of the three largest remaining populations of this species all within 60 km of each other. We detected a high and significant genetic structure between all populations (overall F ST = 0.103) which is comparable to the highest levels of differentiation ever documented for birds, (e.g., endangered birds found in isolated populations on the tops of African mountains), but also evidence for first-generation immigrants, likely from small local unsampled populations. Effective population sizes were small (between 28.8–99.9 individuals) yet there are high levels of genetic variability within populations and no evidence for inbreeding. Conservation implications of this work are that the high levels of genetic structure suggests that translocations between populations need to be carefully considered in light of possible local adaptation and that remaining populations of these birds should be managed as conservation units that contain both main populations studied here but also small outlying populations which may be a source of immigrants. PMID:26447791

Northern Slavs from Serbia do not show a founder effect at autosomal and Y-chromosomal STRs and retain their paternal genetic heritage.

PubMed

Rębała, Krzysztof; Veselinović, Igor; Siváková, Daniela; Patskun, Erika; Kravchenko, Sergey; Szczerkowska, Zofia

2014-01-01

Studies on Y-chromosomal markers revealed significant genetic differentiation between Southern and Northern (Western and Eastern) Slavic populations. The northern Serbian region of Vojvodina is inhabited by Southern Slavic Serbian majority and, inter alia, Western Slavic (Slovak) and Eastern Slavic (Ruthenian) minorities. In the study, 15 autosomal STR markers were analysed in unrelated Slovaks, Ruthenians and Serbs from northern Serbia and western Slovakia. Additionally, Slovak males from Serbia were genotyped for 17 Y-chromosomal STR loci. The results were compared to data available for other Slavic populations. Genetic distances for autosomal markers revealed homogeneity between Serbs from northern Serbia and Slovaks from western Slovakia and distinctiveness of Serbian Slovaks and Ruthenians. Y-STR variation showed a clear genetic departure of the Slovaks and Ruthenians inhabiting Vojvodina from their Serbian neighbours and genetic similarity to the Northern Slavic populations of Slovakia and Ukraine. Admixture estimates revealed negligible Serbian paternal ancestry in both Northern Slavic minorities of Vojvodina, providing evidence for their genetic isolation from the Serbian majority population. No reduction of genetic diversity at autosomal and Y-chromosomal markers was found, excluding genetic drift as a reason for differences observed at autosomal STRs. Analysis of molecular variance detected significant population stratification of autosomal and Y-chromosomal microsatellites in the three Slavic populations of northern Serbia, indicating necessity for separate databases used for estimations of frequencies of autosomal and Y-chromosomal STR profiles in forensic casework. Our results demonstrate that regarding Y-STR haplotypes, Serbian Slovaks and Ruthenians fit in the Eastern European metapopulation defined in the Y chromosome haplotype reference database. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Effect of magnetic shear on dissipative drift instabilities

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

Guzdar, P.N.; Chen, L.; Kaw, P.K.

1978-03-01

In this letter we report the results of a linear radial eigenmode analysis of dissipative drift waves in a plasma with magnetic shear and spatially varying density gradient. The results of the analysis are shown to be consistent with a recent experiment on the study of dissipative drift instabilities in a toroidal stellarator.

Plasma Drift Rates During and Preceding Equatorial Spread F Inferred by the HF Doppler Technique

NASA Astrophysics Data System (ADS)

Miller, E. S.; Hilton, A. J.; Chartier, A.

2017-12-01

The quiet time afternoon and evening equatorial and low-latitude ionosphere is characterized by increasing vertical drift and sharpening plasma density gradient in the lower F region. This combination of effects leads to the plasma instability cascade known imprecisely as "equatorial spread F." In this work, we utilize a simple transequatorial HF Doppler observation to infer the vertical and horizontal plasma drifts preceding and during spread-F conditions. The data exhibit three behavior regimes indicative of three different processes: The first is a slow vertical drift that may be due to either increasing vertical plasma drifts or recombination of the bottomside. The second is an explosive spread Doppler signature (indicating relative velocities of 600 m/s or more) that is associated with the initiation of the spread-F depletions. Finally, the third is a structure that represents a changing HF propagation channel as radio rays propagate through the regions of depleted-but still unstable-plasma. Observations of the March 2016 Pacific total solar eclipse will also be included as a test case for the effects of vertical drifts versus recombination.

Genetic diversity and geographic differentiation in the threatened species Dysosma pleiantha in China as revealed by ISSR analysis.

PubMed

Zong, Min; Liu, Hai-Long; Qiu, Ying-Xiong; Yang, Shu-Zhen; Zhao, Ming-Shui; Fu, Cheng-Xin

2008-04-01

Dysosma pleiantha, an important threatened medicinal plant species, is restricted in distribution to southeastern China. The species is capable of reproducing both sexually and asexually. In this study, inter-simple sequence repeat marker data were obtained and analyzed with respect to genetic variation and genetic structure. The extent of clonality, together with the clonal and sexual reproductive strategies, varied among sites, and the populations under harsh ecological conditions tended to have large clones with relatively low clonal diversity caused by vegetative reproduction. The ramets sharing the same genotype show a clumped distribution. Across all populations surveyed, average within-population diversity was remarkably low (e.g., 0.111 for Nei's gene diversity), with populations from the nature reserves maintaining relatively high amounts of genetic diversity. Among all populations, high genetic differentiation (AMOVA: Phi(ST) = 0.500; Nei's genetic diversity: G (ST) = 0.465, Bayesian analysis: Phi(B) = 0.436) was detected, together with an isolation-by-distance pattern. Low seedling recruitment due to inbreeding, restricted gene flow, and genetic drift are proposed as determinant factors responsible for the low genetic diversity and high genetic differentiation observed.

The effects of the pre-reversal ExB drift, the EIA asymmetry, and magnetic activity on the equatorial spread F during solar maximum

NASA Astrophysics Data System (ADS)

Lee, C.-C.; Liu, J.-Y.; Reinisch, B. W.; Chen, W.-S.; Chu, F.-D.

2005-03-01

We use a digisonde at Jicamarca and a chain of GPS receivers on the west side of South America to investigate the effects of the pre-reversal enhancement (PRE) in ExB drift, the asymmetry (Ia) of equatorial ionization anomaly (EIA), and the magnetic activity (Kp) on the generation of equatorial spread F (ESF). Results show that the ESF appears frequently in summer (November, December, January, and February) and equinoctial (March, April, September, and October) months, but rarely in winter (May, June, July, and August) months. The seasonal variation in the ESF is associated with those in the PRE ExB drift and Ia. The larger ExB drift (>20m/s) and smaller |Ia| (<0.3) in summer and equinoctial months provide a preferable condition to development the ESF. Conversely, the smaller ExB drift and larger |Ia| are responsible for the lower ESF occurrence in winter months. Regarding the effects of magnetic activity, the ESF occurrence decreases with increasing Kp in the equinoctial and winter months, but not in the summer months. Furthermore, the larger and smaller ExB drifts are presented under the quiet (Kp<3) and disturbed (Kp≥3) conditions, respectively. These results indicate that the suppression in ESF and the decrease in ExB drifts are mainly caused by the decrease in the eastward electric field.

Learning From Short Text Streams With Topic Drifts.

PubMed

Li, Peipei; He, Lu; Wang, Haiyan; Hu, Xuegang; Zhang, Yuhong; Li, Lei; Wu, Xindong

2017-09-18

Short text streams such as search snippets and micro blogs have been popular on the Web with the emergence of social media. Unlike traditional normal text streams, these data present the characteristics of short length, weak signal, high volume, high velocity, topic drift, etc. Short text stream classification is hence a very challenging and significant task. However, this challenge has received little attention from the research community. Therefore, a new feature extension approach is proposed for short text stream classification with the help of a large-scale semantic network obtained from a Web corpus. It is built on an incremental ensemble classification model for efficiency. First, more semantic contexts based on the senses of terms in short texts are introduced to make up of the data sparsity using the open semantic network, in which all terms are disambiguated by their semantics to reduce the noise impact. Second, a concept cluster-based topic drifting detection method is proposed to effectively track hidden topic drifts. Finally, extensive studies demonstrate that as compared to several well-known concept drifting detection methods in data stream, our approach can detect topic drifts effectively, and it enables handling short text streams effectively while maintaining the efficiency as compared to several state-of-the-art short text classification approaches.

Life history and past demography maintain genetic structure, outcrossing rate, contemporary pollen gene flow of an understory herb in a highly fragmented rainforest

PubMed Central

Suárez-Montes, Pilar; Chávez-Pesqueira, Mariana

2016-01-01

Introduction Theory predicts that habitat fragmentation, by reducing population size and increasing isolation among remnant populations, can alter their genetic diversity and structure. A cascade of effects is expected: genetic drift and inbreeding after a population bottleneck, changes in biotic interactions that may affect, as in the case of plants, pollen dynamics, mating system, reproductive success. The detection of the effects of contemporary habitat fragmentation on the genetic structure of populations are conditioned by the magnitude of change, given the few number of generations since the onset of fragmentation, especially for long-lived organisms. However, the present-day genetic structure of populations may bear the signature of past demography events. Here, we examine the effects of rainforest fragmentation on the genetic diversity, population structure, mating system (outcrossing rate), indirect gene flow and contemporary pollen dynamics in the understory herb Aphelandra aurantiaca. Also, we assessed its present-day genetic structure under different past demographic scenarios. Methods Twelve populations of A. aurantiaca were sampled in large (4), medium (3), and small (5) forest fragments in the lowland tropical rainforest at Los Tuxtlas region. Variation at 11 microsatellite loci was assessed in 28–30 reproductive plants per population. In two medium- and two large-size fragments we estimated the density of reproductive plants, and the mating system by analyzing the progeny of different mother plants per population. Results Despite prevailing habitat fragmentation, populations of A. aurantiaca possess high genetic variation (He = 0.61), weak genetic structure (Rst = 0.037), and slight inbreeding in small fragments. Effective population sizes (Ne) were large, but slightly lower in small fragments. Migrants derive mostly from large and medium size fragments. Gene dispersal is highly restricted but long distance gene dispersal events were detected. Aphelandra aurantiaca shows a mixed mating system (tm = 0.81) and the outcrossing rate have not been affected by habitat fragmentation. A strong pollen pool structure was detected due to few effective pollen donors (Nep) and low distance pollen movement, pointing that most plants received pollen from close neighbors. Past demographic fluctuations may have affected the present population genetic structure as Bayesian coalescent analysis revealed the signature of past population expansion, possibly during warmer conditions after the last glacial maximum. Discussion Habitat fragmentation has not increased genetic differentiation or reduced genetic diversity of A. aurantiaca despite dozens of generations since the onset of fragmentation in the region of Los Tuxtlas. Instead, past population expansion is compatible with the lack of observed genetic structure. The predicted negative effects of rainforest fragmentation on genetic diversity and population structure of A. aurantiaca seem to have been buffered owing to its large effective populations and long-distance dispersal events. In particular, its mixed-mating system, mostly of outcrossing, suggests high efficiency of pollinators promoting connectivity and reducing inbreeding. However, some results point that the effects of fragmentation are underway, as two small fragments showed higher membership probabilities to their population of origin, suggesting genetic isolation. Our findings underscore the importance of fragment size to maintain genetic connectivity across the landscape. PMID:28028460

Population genetics of the cytoplasm and the units of selection on mitochondrial DNA in Drosophila melanogaster

PubMed Central

2011-01-01

Biological variation exists across a nested set of hierarchical levels from nucleotides within genes to populations within species to lineages within the tree of life. How selection acts across this hierarchy is a long-standing question in evolutionary biology. Recent studies have suggested that genome size is influenced largely by the balance of selection, mutation and drift in lineages with different population sizes. Here we use population cage and maternal transmission experiments to identify the relative strength of selection at an individual and cytoplasmic level. No significant trends were observed in the frequency of large (L) and small (S) mtDNAs across 14 generations in population cages. In all replicate cages, new length variants were observed in heteroplasmic states indicating that spontaneous length mutations occurred in these experimental populations. Heteroplasmic flies carrying L genomes were more frequent than those carrying S genomes suggesting an asymmetric mutation dynamic from larger to smaller mtDNAs. Mother-offspring transmission of heteroplasmy showed that the L mtDNA increased in frequency within flies both between and within generations despite sampling drift of the same intensity as occurred in population cages. These results suggest that selection for mtDNA size is stronger at the cytoplasmic than at the organismal level. The fixation of novel mtDNAs within and between species requires a transient intracellular heteroplasmic stage. The balance of population genetic forces at the cytoplasmic and individual levels governs the units of selection on mtDNA, and has implications for evolutionary inference as well as for the effects of mtDNA mutations on fitness, disease and aging. PMID:21538136

Equatorial Ionospheric Disturbance Field-Aligned Plasma Drifts Observed by C/NOFS

NASA Astrophysics Data System (ADS)

Zhang, Ruilong; Liu, Libo; Balan, N.; Le, Huijun; Chen, Yiding; Zhao, Biqiang

2018-05-01

Using C/NOFS satellite observations, this paper studies the disturbance field-aligned plasma drifts in the equatorial topside ionosphere during eight geomagnetic storms in 2011-2015. During all six storms occurred in the solstices, the disturbance field-aligned plasma drift is from winter to summer hemisphere especially in the morning-midnight local time sector and the disturbance is stronger in June solstice. The two storms occurred at equinoxes have very little effect on the field-aligned plasma drift. Using the plasma temperature data from DMSP satellites and Global Positioning System-total electron content, it is suggested that the plasma density gradient seems likely to cause the disturbance winter-to-summer plasma drift while the role of plasma temperature gradient is opposite to the observed plasma drift.

Drift of suspended ferromagnetic particles due to the Magnus effect

NASA Astrophysics Data System (ADS)

Denisov, S. I.; Pedchenko, B. O.

2017-01-01

A minimal system of equations is introduced and applied to study the drift motion of ferromagnetic particles suspended in a viscous fluid and subjected to a time-periodic driving force and a nonuniformly rotating magnetic field. It is demonstrated that the synchronized translational and rotational oscillations of these particles are accompanied by their drift in a preferred direction, which occurs under the action of the Magnus force. We calculate both analytically and numerically the drift velocity of particles characterized by single-domain cores and nonmagnetic shells and show that there are two types of drift, unidirectional and bidirectional, which can be realized in suspensions composed of particles with different core-shell ratios. The possibility of using the phenomenon of bidirectional drift for the separation of core-shell particles in suspensions is also discussed.

Primary and secondary pesticide drift profiles from a peach orchard.

PubMed

Zivan, Ohad; Bohbot-Raviv, Yardena; Dubowski, Yael

2017-06-01

Atmospheric drift is considered a major loss path of pesticide from target areas, but there is still a large gap of knowledge regarding this complex phenomenon. Pesticide drift may occur during application (Primary drift) and after it (Secondary drift). The present study focuses on primary and secondary drift from ground applications in peach orchard (tree height of 3 m), under Mediterranean climate. Detailed and prolonged vertical drift profiles at close proximity to orchard are presented, together with detailed measurements of key meteorological parameters. The effect of volatility on drift was also studied by simultaneously applying two pesticides that differ in their volatility. Drifting airborne pesticides were detected both during and after applications at sampling distances of 7 and 20 m away from orchard edge. Concentrations ranged between hundreds ng m -3 to a few μg m -3 and showed clear decrease with time and with upwind conditions. Almost no decline in concentrations with height was observed up to thrice canopy height (i.e., 10 m). These homogeneous profiles indicate strong mixing near orchard and are in line with the unstable atmospheric conditions that prevailed during measurements. While air concentrations during pesticide application were higher than after it, overall pesticide load drifted from the orchard during primary and secondary drift are comparable. To the best of our knowledge this is the first work to show such large vertical dispersion and long duration of secondary drift following ground application in orchards. The obtained information indicates that secondary drift should not be neglected in exposure and environmental impact estimations. Copyright © 2017 Elsevier Ltd. All rights reserved.

Noise-induced drift in two-dimensional anisotropic systems

NASA Astrophysics Data System (ADS)

Farago, Oded

2017-10-01

We study the isothermal Brownian dynamics of a particle in a system with spatially varying diffusivity. Due to the heterogeneity of the system, the particle's mean displacement does not vanish even if it does not experience any physical force. This phenomenon has been termed "noise-induced drift," and has been extensively studied for one-dimensional systems. Here, we examine the noise-induced drift in a two-dimensional anisotropic system, characterized by a symmetric diffusion tensor with unequal diagonal elements. A general expression for the mean displacement vector is derived and presented as a sum of two vectors, depicting two distinct drifting effects. The first vector describes the tendency of the particle to drift toward the high diffusivity side in each orthogonal principal diffusion direction. This is a generalization of the well-known expression for the noise-induced drift in one-dimensional systems. The second vector represents a novel drifting effect, not found in one-dimensional systems, originating from the spatial rotation in the directions of the principal axes. The validity of the derived expressions is verified by using Langevin dynamics simulations. As a specific example, we consider the relative diffusion of two transmembrane proteins, and demonstrate that the average distance between them increases at a surprisingly fast rate of several tens of micrometers per second.

Effects of Visual Feedback and Memory on Unintentional Drifts in Performance During Finger Pressing Tasks

PubMed Central

Solnik, Stanislaw; Qiao, Mu; Latash, Mark L.

2017-01-01

This study tested two hypotheses on the nature of unintentional force drifts elicited by removing visual feedback during accurate force production tasks. The role of working memory (memory hypothesis) was explored in tasks with continuous force production, intermittent force production, and rest intervals over the same time interval. The assumption of unintentional drifts in referent coordinate for the fingertips was tested using manipulations of visual feedback: Young healthy subjects performed accurate steady-state force production tasks by pressing with the two index fingers on individual force sensors with visual feedback on the total force, sharing ratio, both, or none. Predictions based on the memory hypothesis have been falsified. In particular, we observed consistent force drifts to lower force values during continuous force production trials only. No force drift or drifts to higher forces were observed during intermittent force production trials and following rest intervals. The hypotheses based on the idea of drifts in referent finger coordinates have been confirmed. In particular, we observed superposition of two drift processes: A drift of total force to lower magnitudes and a drift of the sharing ratio to 50:50. When visual feedback on total force only was provided, the two finger forces showed drifts in opposite directions. We interpret the findings as evidence for the control of motor actions with changes in referent coordinates for participating effectors. Unintentional drifts in performance are viewed as natural relaxation processes in the involved systems; their typical time reflects stability in the direction of the drift. The magnitude of the drift was higher in the right (dominant) hand, which is consistent with the dynamic dominance hypothesis. PMID:28168396

Genetic variability and effective population size when local extinction and recolonization of subpopulations are frequent

PubMed Central

Maruyama, Takeo; Kimura, Motoo

1980-01-01

If a population (species) consists of n haploid lines (subpopulations) which reproduce asexually and each of which is subject to random extinction and subsequent replacement, it is shown that, at equilibrium in which mutational production of new alleles and their random extinction balance each other, the genetic diversity (1 minus the sum of squares of allelic frequencies) is given by 2Nev/(1 + 2Nev), where [Formula: see text] in which Ñ is the harmonic mean of the population size per line, n is the number of lines (assumed to be large), λ is the rate of line extinction, and v is the mutation rate (assuming the infinite neutral allele model). In a diploid population (species) consisting of n colonies, if migration takes place between colonies at the rate m (the island model) in addition to extinction and recolonization of colonies, it is shown that effective population size is [Formula: see text] If the rate of colony extinction (λ) is much larger than the migration rate of individuals, the effective population size is greatly reduced compared with the case in which no colony extinctions occur (in which case Ne = nÑ). The stepping-stone type of recolonization scheme is also considered. Bearing of these results on the interpretation of the level of genetic variability at the enzyme level observed in natural populations is discussed from the standpoint of the neutral mutation-random drift hypothesis. PMID:16592920

Using different drift gases to change separation factors (alpha) in ion mobility spectrometry

PubMed

Asbury; Hill

2000-02-01

The use of different drift gases to alter separation factors (alpha) in ion mobility spectrometry has been demonstrated. The mobility of a series of low molecular weight compounds and three small peptides was determined in four different drift gases. The drift gases chosen were helium, argon, nitrogen, and carbon dioxide. These drift gases provide a range of polarizabilities and molecular weights. In all instances, the compounds showed the greatest mobility in helium and the lowest mobility in carbon dioxide; however the percentage change of mobility for each compound was different, effectively changing the alpha value. The alpha value changes were primarily due to differences in drift gas polarizability but were also influenced by the mass of the drift gas. In addition, gas-phase ion radii were calculated in each of the different drift gases. These radii were then plotted against drift gas polarizability producing linear plots with r2 values greater than 0.99. The intercept of these plots provides the gas-phase radius of an ion in a nonpolarizing environment, whereas the slope is indicative of the magnitude of the ion's mobility change related to polarizability. It therefore, should be possible to separate any two compounds that have different slopes with the appropriate drift gas.

Studies of dynamo field structure and related effects: DE satellite project guest investigator program

NASA Technical Reports Server (NTRS)

Coley, W. R.

1986-01-01

The establishment of the latitudinal and longitudinal structure of the low latitude dynamo electric (DE) field was initiated using data primarily from the Unified Abstract (UA) files of the Atmosphere Explorer E (AE-E) satellite. Mass plots of the vertical ion drift values were made for 1977, 1978, and 1979. The average diurnal variation of V sub v within 20 degrees of the dip equator is remarkably similar to that obtained at Jicamarca in the same years. The average meridional ion drift velocity vectors, obtained as a function of latitude by combining the average vertical and horizontal (nearly north-south) ion drift values from the AE-E, showed the expected variations with local time and season based on the well known equatorial fountain effect theory. The average diurnal variation of the vertical drift was found for four different ranges of dip latitude for a northern solstice season. The effect of the transequatorial neutral winds was as evident in this plotting format as in the meridional or fountain effect format. Finally, the average vertical drift velocity V sub v, not the east-west electric field E sub ew, was found to be approximately independent of longitude, as expected from the dynamo theory.

Demographic History of Indigenous Populations in Mesoamerica Based on mtDNA Sequence Data

PubMed Central

González-Martín, Antonio; Gorostiza, Amaya; Regalado-Liu, Lucía; Arroyo-Peña, Sergio; Tirado, Sergio; Nuño-Arana, Ismael; Rubi-Castellanos, Rodrigo; Sandoval, Karla; Coble, Michael D.; Rangel-Villalobos, Héctor

2015-01-01

The genetic characterization of Native American groups provides insights into their history and demographic events. We sequenced the mitochondrial D-loop region (control region) of 520 samples from eight Mexican indigenous groups. In addition to an analysis of the genetic diversity, structure and genetic relationship between 28 Native American populations, we applied Bayesian skyline methodology for a deeper insight into the history of Mesoamerica. AMOVA tests applying cultural, linguistic and geographic criteria were performed. MDS plots showed a central cluster of Oaxaca and Maya populations, whereas those from the North and West were located on the periphery. Demographic reconstruction indicates higher values of the effective number of breeding females (Nef) in Central Mesoamerica during the Preclassic period, whereas this pattern moves toward the Classic period for groups in the North and West. Conversely, Nef minimum values are distributed either in the Lithic period (i.e. founder effects) or in recent periods (i.e. population declines). The Mesomerican regions showed differences in population fluctuation as indicated by the maximum Inter-Generational Rate (IGRmax): i) Center-South from the lithic period until the Preclassic; ii) West from the beginning of the Preclassic period until early Classic; iii) North characterized by a wide range of temporal variation from the Lithic to the Preclassic. Our findings are consistent with the genetic variations observed between central, South and Southeast Mesoamerica and the North-West region that are related to differences in genetic drift, structure, and temporal survival strategies (agriculture versus hunter-gathering, respectively). Interestingly, although the European contact had a major negative demographic impact, we detect a previous decline in Mesoamerica that had begun a few hundred years before. PMID:26292226

Paternal phylogeographic structure of the brown bear (Ursus arctos) in northeastern Asia and the effect of male-mediated gene flow to insular populations.

PubMed

Hirata, Daisuke; Mano, Tsutomu; Abramov, Alexei V; Baryshnikov, Gennady F; Kosintsev, Pavel A; Murata, Koichi; Masuda, Ryuichi

2017-01-01

Sex-biased dispersal is widespread among mammals, including the brown bear ( Ursus arctos ). Previous phylogeographic studies of the brown bear based on maternally inherited mitochondrial DNA have shown intraspecific genetic structuring around the northern hemisphere. The brown bears on Hokkaido Island, northern Japan, comprise three distinct maternal lineages that presumably immigrated to the island from the continent in three different periods. Here, we investigate the paternal genetic structure across northeastern Asia and assess the connectivity among and within intraspecific populations in terms of male-mediated gene flow. We analyzed paternally inherited Y-chromosomal DNA sequence data and Y-linked microsatellite data of 124 brown bears from Hokkaido, the southern Kuril Islands (Kunashiri and Etorofu), Sakhalin, and continental Eurasia (Kamchatka Peninsula, Ural Mountains, European Russia, and Tibet). The Hokkaido brown bear population is paternally differentiated from, and lacked recent genetic connectivity with, the continental Eurasian and North American populations. We detected weak spatial genetic structuring of the paternal lineages on Hokkaido, which may have arisen through male-mediated gene flow among natal populations. In addition, our results suggest that the different dispersal patterns between male and female brown bears, combined with the founder effect and subsequent genetic drift, contributed to the makeup of the Etorofu Island population, in which the maternal and paternal lineages show different origins. Brown bears on Hokkaido and the adjacent southern Kuril Islands experienced different maternal and paternal evolutionary histories. Our results indicate that sex-biased dispersal has played a significant role in the evolutionary history of the brown bear in continental populations and in peripheral insular populations, such as on Hokkaido, the southern Kuril Islands, and Sakhalin.

Genealogical analyses of rabies virus strains from Brazil based on N gene alleles.

PubMed Central

Heinemann, M. B.; Fernandes-Matioli, F. M. C.; Cortez, A.; Soares, R. M.; Sakamoto, S. M.; Bernardi, F.; Ito, F. H.; Madeira, A. M. B. N.; Richtzenhain, L. J.

2002-01-01

Thirty rabies virus isolates from cows and vampire bats from different regions of São Paulo State, Southeastern Brazil and three rabies vaccines were studied genetically. The analysis was based on direct sequencing of PCR-amplified products of 600 nucleotides coding for the amino terminus of nucleoprotein gene. The sequences were checked to verify their genealogical and evolutionary relationships and possible implication for health programmes. Statistical data indicated that there were no significant genetic differences between samples isolated from distinct hosts, from different geographical regions and between samples collected in the last two decades. According to the HKA test, the variability observed in the sequences is probably due to genetic drift. Since changes in genetic material may produce modifications in the protein responsible for immunogenicity of virus, which may eventually cause vaccine failure in herds, we suggest that continuous efforts in monitoring genetic diversity in rabies virus field strains, in relation to vaccine strains, must be conducted. PMID:12113496

Admixture, Population Structure, and F-Statistics.

PubMed

Peter, Benjamin M

2016-04-01

Many questions about human genetic history can be addressed by examining the patterns of shared genetic variation between sets of populations. A useful methodological framework for this purpose isF-statistics that measure shared genetic drift between sets of two, three, and four populations and can be used to test simple and complex hypotheses about admixture between populations. This article provides context from phylogenetic and population genetic theory. I review how F-statistics can be interpreted as branch lengths or paths and derive new interpretations, using coalescent theory. I further show that the admixture tests can be interpreted as testing general properties of phylogenies, allowing extension of some ideas applications to arbitrary phylogenetic trees. The new results are used to investigate the behavior of the statistics under different models of population structure and show how population substructure complicates inference. The results lead to simplified estimators in many cases, and I recommend to replace F3 with the average number of pairwise differences for estimating population divergence. Copyright © 2016 by the Genetics Society of America.

Deleterious effects of net clogging on the quantification of stream drift

USGS Publications Warehouse

Muehlbauer, Jeffrey D.; Kennedy, Theodore A.; Copp, Adam J.; Sabol, Thomas

2017-01-01

Drift studies are central to stream and river ecological research. However, a fundamental aspect of quantifying drift — how net clogging affects the accuracy of results — has been widely ignored. Utilizing approaches from plankton and suspended sediment studies in oceanography and hydrology, we examined the rate and dynamics of net clogging across a range of conditions. We found that nets clog nonlinearly over time and that suspended solid concentrations and net mesh size exerted a strong effect on clogging rates. Critically, net clogging introduced unpredictable biases in resultant data due to the inaccuracies in water volume estimates introduced by progressive clogging. This renders the widespread approach to linearly “correct” for clogging inadequate. Using a meta-analysis of 77 drift studies spanning 25 years, we demonstrate that the detrimental effects of net clogging are routinely unappreciated, even though the results of most of these studies were likely affected by clogging. We close by describing an approach for avoiding net clogging, which will increase the accuracy and reproducibility of results in future freshwater, lotic drift studies.

Long-Term Stability of the SGA-WZ Strapdown Airborne Gravimeter

PubMed Central

Cai, Shaokun; Zhang, Kaidong; Wu, Meiping; Huang, Yangming

2012-01-01

Accelerometers are one of the most important sensors in a strapdown airborne gravimeter. The accelerometer's drift determines the long-term accuracy of the strapdown inertial navigation system (SINS), which is the primary and most critical component of the strapdown airborne gravimeter. A long-term stability test lasting 104 days was conducted to determine the characteristics of the strapdown airborne gravimeter's long-term drift. This stability test was based on the first set of strapdown airborne gravimeters built in China, the SGA-WZ. The test results reveal a quadratic drift in the strapdown airborne gravimeter data. A drift model was developed using the static data in the two end sections, and then this model was used to correct the test data. After compensating for the drift, the drift effect improved from 70 mGal to 3.46 mGal with a standard deviation of 0.63 mGal. The quadratic curve better reflects the drift's real characteristics. In comparison with other methodologies, modelling the drift as a quadratic curve was shown to be more appropriate. Furthermore, this method allows the drift to be adjusted throughout the course of the entire campaign. PMID:23112647

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

PubMed Central

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

2017-01-01

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

Microsatellite marker isolation and development for the giant Pacific Octopus (Enteroctopus dofleini)

USGS Publications Warehouse

Toussaint, Rebecca K.; Sage, G. Kevin; Talbot, Sandra L.; Scheel, David

2012-01-01

We isolated and developed 18 novel microsatellite markers for the giant Pacific octopus (Enteroctopus dofleini) and examined them for 31 individuals from Prince William Sound (PWS), Alaska. These loci displayed moderate levels of allelic diversity (averaging 11 alleles per locus) and heterozygosity (averaging 65%). Seven loci deviated from Hardy–Weinberg Equilibrium (HWE) due to heterozygote deficiency for the PWS population, although deviations were not observed for all these loci in other populations, suggesting the PWS population is not in mutation-drift equilibrium. These novel microsatellite loci yielded sufficient genetic diversity for potential use in population genetics, individual identification, and parentage studies.

Variable-energy drift-tube linear accelerator

DOEpatents

Swenson, Donald A.; Boyd, Jr., Thomas J.; Potter, James M.; Stovall, James E.

1984-01-01

A linear accelerator system includes a plurality of post-coupled drift-tubes wherein each post coupler is bistably positionable to either of two positions which result in different field distributions. With binary control over a plurality of post couplers, a significant accumlative effect in the resulting field distribution is achieved yielding a variable-energy drift-tube linear accelerator.

Variable-energy drift-tube linear accelerator

DOEpatents

Swenson, D.A.; Boyd, T.J. Jr.; Potter, J.M.; Stovall, J.E.

A linear accelerator system includes a plurality of post-coupled drift-tubes wherein each post coupler is bistably positionable to either of two positions which result in different field distributions. With binary control over a plurality of post couplers, a significant accumlative effect in the resulting field distribution is achieved yielding a variable-energy drift-tube linear accelerator.

Landscape effects on extremely fragmented populations of a rare solitary bee, Colletes floralis.

PubMed

Davis, Emily S; Murray, Tomás E; Fitzpatrick, Una; Brown, Mark J F; Paxton, Robert J

2010-11-01

Globally, there is concern over the decline of bees, an ecologically important group of pollinating insects. Genetic studies provide insights into population structure that are crucial for conservation management but that would be impossible to obtain by conventional ecological methods. Yet conservation genetic studies of bees have primarily focussed on social species rather than the more species-rich solitary bees. Here, we investigate the population structure of Colletes floralis, a rare and threatened solitary mining bee, in Ireland and Scotland using nine microsatellite loci. Genetic diversity was surprisingly as high in Scottish (Hebridean island) populations at the extreme northwestern edge of the species range as in mainland Irish populations further south. Extremely high genetic differentiation among populations was detected; multilocus F(ST) was up to 0.53, and and D(est) were even higher (maximum: 0.85 and 1.00, respectively). A pattern of isolation by distance was evident for sites separated by land. Water appears to act as a substantial barrier to gene flow yet sites separated by sea did not exhibit isolation by distance. C. floralis populations are extremely isolated and probably not in regional migration-drift equilibrium. GIS-based landscape genetic analysis reveals urban areas as a potential and substantial barrier to gene flow. Our results highlight the need for urgent site-specific management action to halt the decline of this and potentially other rare solitary bees. © 2010 Blackwell Publishing Ltd.

Mitochondrial DNA heritage of Cres Islanders--example of Croatian genetic outliers.

PubMed

Jeran, Nina; Havas Augustin, Dubravka; Grahovac, Blaienka; Kapović, Miljenko; Metspalu, Ene; Villems, Richard; Rudan, Pavao

2009-12-01

Diversity of mitochondrial DNA (mtDNA) lineages of the Island of Cres was determined by high-resolution phylogenetic analysis on a sample of 119 adult unrelated individuals from eight settlements. The composition of mtDNA pool of this Island population is in contrast with other Croatian and European populations. The analysis revealed the highest frequency of haplogroup U (29.4%) with the predominance of one single lineage of subhaplogroup U2e (20.2%). Haplogroup H is the second most prevalent one with only 27.7%. Other very interesting features of contemporary Island population are extremely low frequency of haplogroup J (only 0.84%), and much higher frequency of haplogroup W (12.6%) comparing to other Croatian and European populations. Especially interesting finding is a strikingly higher frequency of haplogroup N1a (9.24%) presented with African/south Asian branch almost absent in Europeans, while its European sister-branch, proved to be highly prevalent among Neolithic farmers, is present in contemporary Europeans with only 0.2%. Haplotype analysis revealed that only five mtDNA lineages account for almost 50% of maternal genetic heritage of this island and they present supposed founder lineages. All presented findings confirm that genetic drift, especially founder effect, has played significant role in shaping genetic composition of the isolated population of the Island of Cres. Due to presented data contemporary population of Cres Island can be considered as genetic "outlier" among Croatian populations.

When new human-modified habitats favour the expansion of an amphibian pioneer species: Evolutionary history of the natterjack toad (Bufo calamita) in a coal basin.

PubMed

Faucher, Leslie; Hénocq, Laura; Vanappelghem, Cédric; Rondel, Stéphanie; Quevillart, Robin; Gallina, Sophie; Godé, Cécile; Jaquiéry, Julie; Arnaud, Jean-François

2017-09-01

Human activities affect microevolutionary dynamics by inducing environmental changes. In particular, land cover conversion and loss of native habitats decrease genetic diversity and jeopardize the adaptive ability of populations. Nonetheless, new anthropogenic habitats can also promote the successful establishment of emblematic pioneer species. We investigated this issue by examining the population genetic features and evolutionary history of the natterjack toad (Bufo [Epidalea] calamita) in northern France, where populations can be found in native coastal habitats and coalfield habitats shaped by European industrial history, along with an additional set of European populations located outside this focal area. We predicted contrasting patterns of genetic structure, with newly settled coalfield populations departing from migration-drift equilibrium. As expected, coalfield populations showed a mosaic of genetically divergent populations with short-range patterns of gene flow, and native coastal populations indicated an equilibrium state with an isolation-by-distance pattern suggestive of postglacial range expansion. However, coalfield populations exhibited (i) high levels of genetic diversity, (ii) no evidence of local inbreeding or reduced effective population size and (iii) multiple maternal mitochondrial lineages, a genetic footprint depicting independent colonization events. Furthermore, approximate Bayesian computations suggested several evolutionary trajectories from ancient isolation in glacial refugia during the Pleistocene, with biogeographical signatures of recent expansion probably confounded by human-mediated mixing of different lineages. From an evolutionary and conservation perspective, this study highlights the ecological value of industrial areas, provided that ongoing regional gene flow is ensured within the existing lineage boundaries. © 2017 John Wiley & Sons Ltd.

Variation in migratory behavior influences regional genetic diversity and structure among American kestrel populations (Falco sparverius) in North America

USGS Publications Warehouse

Miller, Mark P.; Mullins, Thomas D.; Parrish, John G.; Walters, Jeffrey R.; Haig, Susan M.

2012-01-01

Birds employ numerous strategies to cope with seasonal fluctuations in high-quality habitat availability. Long distance migration is a common tactic; however, partial migration is especially common among broadly distributed species. Under partial migration systems, a portion of a species migrates, whereas the remainder inhabits breeding grounds year round. In this study, we identified effects of migratory behavior variation on genetic structure and diversity of American Kestrels (Falco sparverius), a widespread partial migrant in North America. American Kestrels generally migrate; however, a resident group inhabits the southeastern United States year round. The southeastern group is designated as a separate subspecies (F. s. paulus) from the migratory group (F. s. sparverius). Using mitochondrial DNA and microsatellites from 183 and 211 individuals, respectively, we illustrate that genetic structure is stronger among nonmigratory populations, with differentiation measures ranging from 0.060 to 0.189 depending on genetic marker and analysis approach. In contrast, measures from western North American populations ranged from 0 to 0.032. These findings suggest that seasonal migratory behavior is also associated with natal and breeding dispersal tendencies. We likewise detected significantly lower genetic diversity within nonmigratory populations, reflecting the greater influence of genetic drift in small populations. We identified the signal of population expansion among nonmigratory populations, consistent with the recent establishment of higher latitude breeding locations following Pleistocene glacial retreat. Differentiation of F. s. paulus and F. s. sparverius reflected subtle differences in allele frequencies. Because migratory behavior can evolve quickly, our analyses suggest recent origins of migratory American Kestrel populations in North America.

Molecular insights into the historic demography of bowhead whales: understanding the evolutionary basis of contemporary management practices

PubMed Central

Phillips, C D; Hoffman, J I; George, J C; Suydam, R S; Huebinger, R M; Patton, J C; Bickham, J W

2013-01-01

Patterns of genetic variation observed within species reflect evolutionary histories that include signatures of past demography. Understanding the demographic component of species' history is fundamental to informed management because changes in effective population size affect response to environmental change and evolvability, the strength of genetic drift, and maintenance of genetic variability. Species experiencing anthropogenic population reductions provide valuable case studies for understanding the genetic response to demographic change because historic changes in the census size are often well documented. A classic example is the bowhead whale, Balaena mysticetus, which experienced dramatic population depletion due to commercial whaling in the late 19th and early 20th centuries. Consequently, we analyzed a large multi-marker dataset of bowhead whales using a variety of analytical methods, including extended Bayesian skyline analysis and approximate Bayesian computation, to characterize genetic signatures of both ancient and contemporary demographic histories. No genetic signature of recent population depletion was recovered through any analysis incorporating realistic mutation assumptions, probably due to the combined influences of long generation time, short bottleneck duration, and the magnitude of population depletion. In contrast, a robust signal of population expansion was detected around 70,000 years ago, followed by a population decline around 15,000 years ago. The timing of these events coincides to a historic glacial period and the onset of warming at the end of the last glacial maximum, respectively. By implication, climate driven long-term variation in Arctic Ocean productivity, rather than recent anthropogenic disturbance, appears to have been the primary driver of historic bowhead whale demography. PMID:23403722