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Neutral Markers (neutral + marker)

Distribution by Scientific Domains

Life Sciences	86%
3 Other Domains	14%

Selected Abstracts

Neutral markers mirror small-scale quantitative genetic differentiation in an avian island population

BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2009
ERIK POSTMA
We still know remarkably little about the extent to which neutral markers can provide a biologically relevant description of population structure. In the present study, we address this question, and quantify microsatellite differentiation among a small, structured island population of great tits (Parus major), and a large mainland population 150 km away. Although only a few kilometres apart, we found small but statistically significant levels of differentiation between the eastern and the western part of the island. On the other hand, there was no differentiation between the western part of the island and the mainland population, whereas the eastern part and the mainland did differ significantly. This initially counterintuitive result provides powerful support for the hypothesis that the large genetic difference in clutch size between both parts of the island found earlier is maintained by different levels of gene flow into both parts of the island, and illustrates the capacity of microsatellites to provide a meaningful description of population structure. Importantly, because the level of microsatellite differentiation is very low, we were unable to infer any population structure without grouping individuals a priori. Hence, these low levels of differentiation in neutral markers could easily remain undetected, or incorrectly be dismissed as biologically irrelevant. Thus, although microsatellites can provide a powerful tool to study genetic structure in wild populations, they should be used in conjunction with a range of other sources of information, rather than as a replacement. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 867,875. [source]

Comparative studies of quantitative trait and neutral marker divergence: a meta-analysis

JOURNAL OF EVOLUTIONARY BIOLOGY, Issue 1 2008
T. LEINONEN
Abstract Comparative studies of quantitative genetic and neutral marker differentiation have provided means for assessing the relative roles of natural selection and random genetic drift in explaining among-population divergence. This information can be useful for our fundamental understanding of population differentiation, as well as for identifying management units in conservation biology. Here, we provide comprehensive review and meta-analysis of the empirical studies that have compared quantitative genetic (QST) and neutral marker (FST) differentiation among natural populations. Our analyses confirm the conclusion from previous reviews , based on ca. 100% more data , that the QST values are on average higher than FST values [mean difference 0.12 (SD 0.27)] suggesting a predominant role for natural selection as a cause of differentiation in quantitative traits. However, although the influence of trait (life history, morphological and behavioural) and marker type (e.g. microsatellites and allozymes) on the variance of the difference between QST and FST is small, there is much heterogeneity in the data attributable to variation between specific studies and traits. The latter is understandable as there is no reason to expect that natural selection would be acting in similar fashion on all populations and traits (except for fitness itself). We also found evidence to suggest that QST and FST values across studies are positively correlated, but the significance of this finding remains unclear. We discuss these results in the context of utility of the QST,FST comparisons as a tool for inferring natural selection, as well as associated methodological and interpretational problems involved with individual and meta-analytic studies. [source]

Heterozygosity,fitness correlations and associative overdominance: new detection method and proof of principle in the Iberian wild boar

MOLECULAR ECOLOGY, Issue 13 2009
AURELIO F. MALO
Heterozygosity-fitness correlations (HFC) may result from a genome-wide process , inbreeding , or local effects within the genome. The majority of empirical studies reporting HFCs have attributed correlations to inbreeding depression. However, HFCs are unlikely to be caused by inbreeding depression because heterozygosity measured at a small number of neutral markers is unlikely to accurately capture a genome-wide pattern. Testing the strengths of localized effects caused by associative overdominance has proven challenging. In their current paper, Amos and Acevedo-Whitehouse present a novel test for local HFCs. Using stochastic simulations, they determine the conditions under which single-locus HFCs arise, before testing the strength of the correlation between the neutral marker and a linked gene under selection in their simulations. They used insights gained from simulation to statistically investigate the likely cause of correlations between heterozygosity and disease status using data on bovine tuberculosis infections in a wild boar population. They discover that a single microsatellite marker is an excellent predictor of tuberculosis progression in infected individuals. The results are relevant for wild boar management but, more generally, they demonstrate how single-locus HFCs could be used to identify coding loci under selection in free-living populations. [source]

Hierarchical comparative analysis of genetic and genitalic geographical structure: testing patterns of male and female genital evolution in the scarab beetle Phyllophaga hirticula (Coleoptera: Scarabaeidae)

BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2009
MAXI POLIHRONAKIS
It is generally accepted that genitalia are among the fastest evolving characters in insects and that selection on these structures may increase speciation rates in groups with polygamous mating systems. If selection is causing genitalic divergence between or among populations of a species, one prediction is that geographical structure of genitalic morphology would be in place before genetic structure of a rapidly evolving neutral marker. The current study tests this hypothesis in the geographically widespread scarab beetle Phyllophaga hirticula by evaluating whether standing variation in male and female genitalia is more or less geographically structured than a mitochondrial genetic marker. Geographical structure of mitochondrial (mt)DNA and male and female genitalic shape were analysed using analysis of variance, multivariate analysis of variance, Mantel tests, and tests of spatial autocorrelation. The results show that, although female genitalia are more geographically structured than mtDNA, male genitalia are not. This pattern suggests that selection on female genitalic variation may be causing divergence of these structures among populations. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 96, 135,149. [source]

Is natural selection a plausible explanation for the distribution of Idh- 1 alleles in the cricket Allonemobius socius?

ECOLOGICAL ENTOMOLOGY, Issue 1 2006
Diana L. Huestis
Abstract., 1.,Allozyme alleles in natural populations have been proposed as either neutral markers of genetic diversity or the product of natural selection on enzyme function, as amino acid substitutions that change electrophoretic mobility may also alter enzyme performance. To address these possibilities, researchers have used both correlative analyses and empirical studies. 2.,Here, geographically structured variation of the enzyme isocitrate dehydrogenase (Idh- 1) in the striped ground cricket Allonemobius socius Scudder (Orthoptera: Gryllidae) is examined. The distributions of Idh- 1 alleles appear to be related to environmental gradients, as allele frequencies showed significant relationships with mean annual temperature and precipitation. Specifically, the slowest mobility allele was more frequent at colder temperatures, while the converse occurred for the fastest mobility allele. 3.,An exploratory experiment was performed to examine fitness effects of possessing different Idh- 1 alleles at two temperatures to test the hypothesis that the geographic structure of this locus may reflect environmental adaptation. Results showed that a significant interaction between temperature and Idh- 1 genotype affected the number of eggs laid, with success of homozygous individuals matching environmental expectations. 4.,The above results show that (1) variation in the frequency of Idh- 1 alleles is significantly related to environmental gradients in the eastern U.S.A. and (2) alternative alleles of Idh- 1 appear to influence the egg-laying ability of individuals differently depending on environmental temperature. Together, these results suggest that natural selection is a plausible mechanism underlying the distribution of Idh- 1 alleles in this species, although more detailed studies are needed. [source]

HETEROZYGOTE EXCESS IN SMALL POPULATIONS AND THE HETEROZYGOTE-EXCESS EFFECTIVE POPULATION SIZE

EVOLUTION, Issue 9 2004
Franclois Balloux
Abstract It has been proposed that effective size could be estimated in small dioecious population by considering the heterozygote excess observed at neutral markers. When the number of breeders is small, allelic frequencies in males and females will slightly differ due to binomial sampling error. However, this excess of heterozygotes is not generated by dioecy but by the absence of individuals produced through selfing. Consequently, the approach can also be applied to self-incompatible monoecious species. Some inaccuracies in earlier equations expressing effective size as function of the heterozygote excess are also corrected in this paper. The approach is then extended to subdivided populations, where time of sampling becomes crucial. When adults are sampled, the effective size of the entire population can be estimated, whereas when juveniles are sampled, the average effective number of breeders per subpopulations can be estimated. The main limitation of the heterozygote excess method is that it will only perform satisfactorily for populations with a small number of reproducing individuals. While this situation is unlikely to happen frequently at the scale of the entire population, structured populations with small subpopulations are likely to be common. The estimation of the average number of breeders per subpopulations is thus expected to be applicable to many natural populations. The approach is straightforward to compute and independent of equilibrium assumptions. Applications to simulated data suggest the estimation of the number of breeders to be robust to mutation and migration rates, and to specificities of the mating system. [source]

Clonal erosion and genetic drift in cyclical parthenogens , the interplay between neutral and selective processes

JOURNAL OF EVOLUTIONARY BIOLOGY, Issue 5 2010
J. VANOVERBEKE
Abstract The occurrence of alternating phases of clonal and sexual reproduction may strongly impact the interplay between neutral and selective genetic variation in populations. Using a physiologically structured model of the life history of Daphnia, we investigated to what extent clonal erosion associated with selection during the clonal phase affects the genetic structure as observed by neutral markers. Incorporating conservative levels of quantitative genetic variation at 11 physiological and life history traits induces strong clonal erosion, reducing clonal diversity (CD) near the end of the simulations (1000 days) to a level between 1 and 5, even in habitats with high initial CD (108 clones). This strong clonal erosion caused by selection can result in reduced genetic diversity, significant excess of heterozygotes and significant genetic differentiation between populations as observed by neutral markers. Our results indicate that, especially in relatively small habitats, clonal selection may strongly impact the genetic structure and may contribute to the often observed high level of neutral genetic differentiation among natural populations of cyclical parthenogens. [source]

Evolutionary history shapes the association between developmental instability and population-level genetic variation in three-spined sticklebacks

JOURNAL OF EVOLUTIONARY BIOLOGY, Issue 8 2009
S. VAN DONGEN
Abstract Developmental instability (DI) is the sensitivity of a developing trait to random noise and can be measured by degrees of directionally random asymmetry [fluctuating asymmetry (FA)]. FA has been shown to increase with loss of genetic variation and inbreeding as measures of genetic stress, but associations vary among studies. Directional selection and evolutionary change of traits have been hypothesized to increase the average levels of FA of these traits and to increase the association strength between FA and population-level genetic variation. We test these two hypotheses in three-spined stickleback (Gasterosteus aculeatus L.) populations that recently colonized the freshwater habitat. Some traits, like lateral bone plates, length of the pelvic spine, frontal gill rakers and eye size, evolved in response to selection regimes during colonization. Other traits, like distal gill rakers and number of pelvic fin rays, did not show such phenotypic shifts. Contrary to a priori predictions, average FA did not systematically increase in traits that were under presumed directional selection, and the increases observed in a few traits were likely to be attributable to other factors. However, traits under directional selection did show a weak but significantly stronger negative association between FA and selectively neutral genetic variation at the population level compared with the traits that did not show an evolutionary change during colonization. These results support our second prediction, providing evidence that selection history can shape associations between DI and population-level genetic variation at neutral markers, which potentially reflect genetic stress. We argue that this might explain at least some of the observed heterogeneities in the patterns of asymmetry. [source]

Morphological and genetic divergence of intralacustrine stickleback morphs in Iceland: a case for selective differentiation?

JOURNAL OF EVOLUTIONARY BIOLOGY, Issue 2 2007
G. Á. ÓLAFSDÓTTIR
Abstract The evolutionary processes involved in population divergence and local adaptation are poorly understood. Theory predicts that divergence of adjacent populations is possible but depends on several factors including gene flow, divergent selection, population size and the number of genes involved in divergence and their distribution on the genome. We analyse variation in neutral markers, markers linked to putative quantitative trait loci and morphological traits in a recent (< 10 000 years) zone of primary divergence between stickleback morphs in Lake Thingvallavatn, Iceland. Environmental factors, especially predation, are clearly implicated in reducing gene flow between morphs. There is continuous morphological and genetic variation between habitats with a zone centre similar to secondary contact zones. Individual microsatellite loci are implicated as being linked to adaptive variation by direct tests as well as by differences in cline shape. Patterns of linkage disequilibria indicate that the morphs have diverged at several loci. This divergence shows parallels and differences with the well-studied limnetic,benthic stickleback morphs, both in phenotypic divergence and at the genomic level. [source]

Spatial and temporal scales of adaptive divergence in marine fishes and the implications for conservation

JOURNAL OF FISH BIOLOGY, Issue 2006
D. O. Conover
Knowledge of geographic and temporal scales of adaptive genetic variation is crucial to species conservation, yet understanding of these phenomena, particularly in marine systems, is scant. Until recently, the belief has been that because most marine species have highly dispersive or mobile life stages, local adaptation could occur only on broad geographic scales. This view is supported by comparatively low levels of genetic variation among populations as detected by neutral markers. Similarly, the time scale of adaptive divergence has also been assumed to be very long, requiring thousands of generations. Recent studies of a variety of species have challenged these beliefs. First, there is strong evidence of geographically structured local adaptation in physiological and morphological traits. Second, the proportion of quantitative trait variation at the among-population level (QST) is much higher than it is for neutral markers (FST) and these two metrics of genetic variation are poorly correlated. Third, evidence that selection is a potent evolutionary force capable of sustaining adaptive divergence on contemporary time scales is summarized. The differing spatial and temporal scales of adaptive v. neutral genetic divergence call for a new paradigm in thinking about the relationship between phenogeography (the geography of phenotypic variation) and phylogeography (the geography of lineages) in marine species. The idea that contemporary selective processes can cause fine-scale spatial and temporal divergence underscores the need for a new emphasis on Darwinian fishery science. [source]

Diversity and food quality properties of farmers' varieties of sorghum from Bénin

JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 7 2006
AP Polycarpe Kayodé
Abstract Farmers' varieties of sorghum from three communities in different regions of northern Bénin were analysed for their food quality and agro-morphological properties, and also for their genetic diversity using amplified fragment length polymorphism (AFLP). Farmers' varieties of sorghum differed greatly with respect to their morphology and agronomic and food traits. Most of the varieties had long (>200 cm) stems (87%), loose panicles (79%) and a red or pink colour (52%). Most were susceptible to drought (54%) and to attacks by striga (79%), insects (99%) and birds (77%). Farmers evaluated the quality of the seeds for preparing porridges as being high for 60% of the varieties and 26% of the varieties were regarded as suitable for making beverages. Late-maturing, large-seeded, red or pink varieties are preferred by farmers for porridges and beverages. Gene diversity among varieties within regions, as measured by neutral markers, was similar for the three regions (0.211,0.240). However, across regions the short (<150 cm) stem varieties showed relatively high genetic diversity compared with long or medium stem varieties (0.378 vs 0.184,0.216 for long,medium stem varieties). Genetic differentiation (Fst) among regions and among stem lengths of varieties was significant and ranged between 0.086 and 0.135. Grain colour, stem length and panicle shape varied significantly with the region/stem length and correlated with the genetic differentiation of regions. No relationship could be detected between the genetic differentiation of the varieties and their food quality as expressed by the farmers. Implications of the findings for crop conservation and breeding are discussed. Copyright © 2006 Society of Chemical Industry [source]

When can ecological speciation be detected with neutral loci?

MOLECULAR ECOLOGY, Issue 11 2010
XAVIER THIBERT-PLANTE
Abstract It is not yet clear under what conditions empirical studies can reliably detect progress toward ecological speciation through the analysis of allelic variation at neutral loci. We use a simulation approach to investigate the range of parameter space under which such detection is, and is not, likely. We specifically test for the conditions under which divergent natural selection can cause a ,generalized barrier to gene flow' that is present across the genome. Our individual-based numerical simulations focus on how population divergence at neutral loci varies in relation to recombination rate with a selected locus, divergent selection on that locus, migration rate and population size. We specifically test whether genetic differences at neutral markers are greater between populations in different environments than between populations in similar environments. We find that this expected signature of ecological speciation can be detected under part of the parameter space, most consistently when divergent selection is strong and migration is intermediate. By contrast, the expected signature of ecological speciation is not reliably detected when divergent selection is weak or migration is low or high. These findings provide insights into the strengths and weaknesses of using neutral markers to infer ecological speciation in natural systems. [source]

Local selection and population structure in a deep-sea fish, the roundnose grenadier (Coryphaenoides rupestris)

MOLECULAR ECOLOGY, Issue 2 2010
THOMAS A. WHITE
Abstract Local populations within a species can become isolated by stochastic or adaptive processes, though it is most commonly the former that we quantify. Using presumably neutral markers we can assess the time-dependent process of genetic drift, and thereby quantify patterns of differentiation in support of the effective management of diversity. However, adaptive differences can be overlooked in these studies, and these are the very characteristics that we hope to conserve by managing neutral diversity. In this study, we used 16 hypothetically neutral microsatellite markers to investigate the genetic structure of the roundnose grenadier in the North Atlantic. We found that one locus was a clear outlier under directional selection, with FST values much greater than at the remaining loci. Differentiation between populations at this locus was related to depth, suggesting directional selection, presumably acting on a linked locus. Considering only the loci identified as neutral, there remained significant population structure over the region of the North Atlantic studied. In addition to a weak pattern of isolation by distance, we identified a putative barrier to gene flow between sample sites either side of the Charlie-Gibbs Fracture Zone, which marks the location where the sub-polar front crosses the Mid-Atlantic Ridge. This may reflect a boundary across which larvae are differentially distributed in separate current systems to some extent, promoting differentiation by drift. Structure due to both drift and apparent selection should be considered in management policy. [source]

Heterozygosity,fitness correlations and associative overdominance: new detection method and proof of principle in the Iberian wild boar

Spatio-temporal variation in the strength and mode of selection acting on major histocompatibility complex diversity in water vole (Arvicola terrestris) metapopulations

MOLECULAR ECOLOGY, Issue 1 2009
MATTHEW K. OLIVER
Abstract Patterns of spatio-temporal genetic variation at a class II major histocompatibility complex (MHC) locus and multiple microsatellite loci were analysed within and between three water vole metapopulations in Scotland, UK. Comparisons of MHC and microsatellite spatial genetic differentiation, based on standardised tests between two demographically asynchronous zones within a metapopulation, suggested that spatial MHC variation was affected by balancing selection, directional selection and random genetic drift, but that the relative effects of these microevolutionary forces vary temporally. At the metapopulation level, between-year differentiation for MHC loci was significantly correlated with that of microsatellites, signifying that neutral factors such as migration and drift were primarily responsible for overall temporal genetic change at the metapopulation scale. Between metapopulations, patterns of genetic differentiation implied that, at large spatial scales, MHC variation was primarily affected by directional selection and drift. Levels of MHC heterozygosity in excess of Hardy,Weinberg expectations were consistent with overdominant balancing selection operating on MHC variation within metapopulations. However, this effect was not constant among all samples, indicating temporal variation in the strength of selection relative to other factors. The results highlight the benefit of contrasting variation at MHC with neutral markers to separate the effects of stochastic and deterministic microevolutionary forces, and add to a growing body of evidence showing that the mode and relative strength of selection acting on MHC diversity varies both spatially and temporally. [source]

Geographical variation of genetic and phenotypic traits in the Mexican sailfin mollies, Poecilia velifera and P. petenensis

MOLECULAR ECOLOGY, Issue 9 2008
S. J. HANKISON
Abstract Comparing the patterns of population divergence using both neutral genetic and phenotypic traits provides an opportunity to examine the relative importance of evolutionary mechanisms in shaping population differences. We used microsatellite markers to examine population genetic structure in the Mexican sailfin mollies Poecilia velifera and P. petenensis. We compared patterns of genetic structure and divergence to that in two types of phenotypic traits: morphological characters and mating behaviours. Populations within each species were genetically distinct, and conformed to a model of isolation by distance, with populations within different geographical regions being more genetically similar to one another than were populations from different regions. Bayesian clustering and barrier analyses provided additional support for population separation, especially between geographical regions. In contrast, none of the phenotypic traits showed any type of geographical pattern, and population divergence in these traits was uncorrelated with that found in neutral markers. There was also a weaker pattern of regional differences among geographical regions compared to neutral genetic divergence. These results suggest that while divergence in neutral traits is likely a product of population history and genetic drift, phenotypic divergence is governed by different mechanisms, such as natural and sexual selection, and arises at spatial scales independent from those of neutral markers. [source]

Major histocompatibility complex class II variation in the giant panda (Ailuropoda melanoleuca)

MOLECULAR ECOLOGY, Issue 9 2006
QIU-HONG WAN
Abstract Habitat destruction and human activity have greatly impacted the natural history of the giant panda (Ailuropoda melanoleuca). Although the genetic diversity of neutral markers has been examined in this endangered species, no previous work has examined adaptive molecular polymorphisms in the giant panda. Here, the major histocompatibility complex (MHC) class II DRB locus was investigated in the giant panda, using single-strand conformation polymorphism (SSCP) and sequence analysis. Comparisons of DNA samples extracted from faecal and blood samples from the same individual revealed that the two materials yielded similar quantities and qualities of DNA, as well as identical SSCP patterns and allelic sequences, demonstrating the reliability of DNA isolation from panda faeces. Analysis of faecal samples from 60 giant pandas revealed relatively low number of alleles: seven alleles. However, the alleles were quite divergent, varying from each other by a range of 7,47 nucleotide substitutions (4,25 amino acid substitutions). Construction of a neighbour-joining tree and comparisons among DRB alleles from other species revealed that both similar and highly divergent alleles survived in the bottlenecked panda populations. Despite species-specific primers used and excellent faecal DNA isolated, a lower level of heterozygosity than expected was still observed due to inbreeding. There were three types of evidence supporting the presence of balancing selection in the giant panda: (i) an obvious excess of nonsynonymous substitutions over synonymous at the antigen-binding positions; (ii) trans -species evolution of two alleles between the giant panda and other felids; and (iii) a more even distribution of alleles than expected from neutrality. [source]

Bayesian analyses of admixture in wild and domestic cats (Felis silvestris) using linked microsatellite loci

MOLECULAR ECOLOGY, Issue 1 2006
R. LECIS
Abstract Methods recently developed to infer population structure and admixture mostly use individual genotypes described by unlinked neutral markers. However, Hardy,Weinberg and linkage disequilibria among independent markers decline rapidly with admixture time, and the admixture signals could be lost in a few generations. In this study, we aimed to describe genetic admixture in 182 European wild and domestic cats (Felis silvestris), which hybridize sporadically in Italy and extensively in Hungary. Cats were genotyped at 27 microsatellites, including 21 linked loci mapping on five distinct feline linkage groups. Genotypes were analysed with structure 2.1, a Bayesian procedure designed to model admixture linkage disequilibrium, which promises to assess efficiently older admixture events using tightly linked markers. Results showed that domestic and wild cats sampled in Italy were split into two distinct clusters with average proportions of membership Q > 0.90, congruent with prior morphological identifications. In contrast, free-living cats sampled in Hungary were assigned partly to the domestic and the wild cat clusters, with Q < 0.50. Admixture analyses of individual genotypes identified, respectively, 5/61 (8%), and 16,20/65 (25,31%) hybrids among the Italian wildcats and Hungarian free-living cats. Similar results were obtained in the past using unlinked loci, although the new linked markers identified additional admixed wildcats in Italy. Linkage analyses confirm that hybridization is limited in Italian, but widespread in Hungarian wildcats, a population that is threatened by cross-breeding with free-ranging domestic cats. The total panel of 27 loci performed better than the linked loci alone in the identification of domestic and known hybrid cats, suggesting that a large number of linked plus unlinked markers can improve the results of admixture analyses. Inferred recombination events led to identify the population of origin of chromosomal segments, suggesting that admixture mapping experiments can be designed also in wild populations. [source]

Frontiers in identifying conservation units: from neutral markers to adaptive genetic variation

ANIMAL CONSERVATION, Issue 2 2009
B. Gebremedhin
No abstract is available for this article. [source]

Empirical tests for ecological exchangeability

ANIMAL CONSERVATION, Issue 3 2005
Russell B. Rader
The concept of ecological exchangeability, together with genetic exchangeability, is central to both the Cohesion Species Concept as well as to some definitions of Evolutionarily Significant Units. While there are well-established criteria for measuring genetic exchangeability, the concept of ecological exchangeability has generated considerable confusion. We describe a procedure that uses the complementary strengths, while recognising the limitations, of both molecular genetic data and ecological experiments to determine the ecological exchangeability of local populations within a species. This is the first synthesis of a combined approach (experiments and genetics) and the first explicit discussion of testing ecological exchangeability. Although it would be ideal to find functional genes that interact to influence quantitative traits resulting in ecological differences (e.g. growth, size, fecundity), we suggest that our current knowledge of functional markers is too limited for most species to use them to differentiate adaptively different local populations. Thus, we argue that ecological experiments using whole organisms combined with neutral markers that indicate evolutionary divergence, provide the strongest case for detecting adaptive differences among local populations. Both genetic divergence and ecological experiments provide the best information for infering ecological exchangeability. This procedure can be used to decide which local populations should be preserved to maintain intraspecific variation and to determine which populations would enhance captive-breeding programs, augment endangered local populations and could best be used to re-introduce native species into historically occupied areas. [source]

Ancestral Inference in Population Genetics Models with Selection (with Discussion)

AUSTRALIAN & NEW ZEALAND JOURNAL OF STATISTICS, Issue 4 2003
Matthew Stephens
Summary A new algorithm is presented for exact simulation from the conditional distribution of the genealogical history of a sample, given the composition of the sample, for population genetics models with general diploid selection. The method applies to the usual diffusion approximation of evolution at a single locus, in a randomly mating population of constant size, for mutation models in which the distribution of the type of a mutant does not depend on the type of the progenitor allele; this includes any model with only two alleles. The new method is applied to ancestral inference for the two-allele case, both with genic selection and heterozygote advantage and disadvantage, where one of the alleles is assumed to have resulted from a unique mutation event. The paper describes how the method could be used for inference when data are also available at neutral markers linked to the locus under selection. It also informally describes and constructs the non-neutral Fleming,Viot measure-valued diffusion. [source]

A land snail's view of a fragmented landscape

BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2009
HEIKE KAPPES
Habitat fragmentation may influence the genetic structure of populations, especially of species with low mobility. So far, these effects have been mainly studied by surveying neutral markers, and much less by looking at ecologically relevant characters. Therefore, we aimed to explore eventual patterns of covariation between population structuring in neutral markers and variation in shell morphometrics in the forest-associated snail Discus rotundatus in relation to habitat fragment characteristics. To this end, we screened shell morphometric variability and sequence variation in a fragment of the mitochondrial 16S rDNA gene in D. rotundatus from the fragmented landscape of the Lower Rhine Embayment, Germany. The 16S rDNA of D. rotundatus was highly variable, with a total of 118 haplotypes (384 individuals) forming four clades and one unresolved group. There was a geographic pattern in the distribution of the clades with the river Rhine apparently separating two groups. Yet, at the geographic scale considered, there was no obvious effect of fragmentation on shell morphometrics and 16S rDNA variation because GST often was as high within, as between forests. Instead, the age of the habitat and (re-)afforestation events appeared to affect shell shape and 16S rDNA in terms of the number of clades per site. The ecologically relevant characters thus supported the presumably neutral mitochondrial DNA markers by indicating that populations of not strictly stenecious species may be (relatively) stable in fragments. However, afforestation after large clearcuts and habitat gain after the amendment of deforestation are accompanied by several, seemingly persistent peculiarities, such as altered genetic composition and shell characters (e.g. aperture size). © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 839,850. [source]