Inferring recent migration rates from individual genotypes

We present a novel and straightforward method for estimating recent migration rates between discrete populations using multilocus genotype data. The approach builds upon a two-step sampling design, where individual genotypes are sampled before and after dispersal. We develop a model that estimates all pairwise backwards migration rates ( m_ij , the probability that an individual sampled in population i is a migrant from population j ) between a set of populations. The method is validated with simulated data and compared with the methods of BayesAss and Structure. First, we use data for an island model and then we consider more realistic data simulations for a metapopulation of the greater white-toothed shrew ( Crocidura russula ). We show that the precision and bias of estimates primarily depend upon the proportion of individuals sampled in each population. Weak sampling designs may particularly affect the quality of the coverage provided by 95% highest posterior density intervals. We further show that it is relatively insensitive to the number of loci sampled and the overall strength of genetic structure. The method can easily be extended and makes fewer assumptions about the underlying demographic and genetic processes than currently available methods. It allows backwards migration rates to be estimated across a wide range of realistic conditions.     

Population structure at two geographic scales in the burrowing crustacean Callichirus islagrande (Decapoda, Thalassinidea): historical and contemporary barriers to planktonic dispersal

There has been much recent interest in the extent to which marine planktonic larvae connect local populations demographically and genetically. Uncertainties about the true extent of larval dispersal have impeded our understanding of the ecology and evolution of marine species as well as our attempts to effectively manage marine populations. Because direct measurements of larval movements are difficult, genetic markers have often been used for indirect measurements of gene flow among marine populations. Here we examine data from allozymes, mitochondrial DNA sequences, and microsatellite length polymorphisms to assess the extent of gene flow among populations of the burrowing crustacean Callichirus islagrande. All three types of markers revealed a genetic break between populations separated by the Louisiana Chenier Plain. The extent of mitochondrial sequence divergence across this break indicates that the nominal species, C. islagrande, consists of at least two lineages that have been reproductively isolated for about a million years. Within the eastern lineage microsatellite allele frequencies were significantly heterogeneous among populations as little as 10 km apart. Maximum likelihood estimates of gene flow and effective population size based on a coalescent model for the microsatellite data indicated that local populations are nearly closed. A model-based clustering method identified four or five groups from the microsatellite data, although individuals sampled from each location generally consisted of mixtures of these groups. This suggests a mechanism that would lead to genetic differentiation of open populations: gene flow from different source populations that are themselves genetically distinct.     

A new Bayesian method to identify the environmental factors that influence recent migration

We present a new multilocus genotype method that makes inferences about recent immigration rates and identifies the environmental factors that are more likely to explain observed gene flow patterns. It also estimates population-specific inbreeding coefficients, allele frequencies, and local population F(ST)'s and performs individual assignments. We generate synthetic data sets to determine the region of the parameter space where our method is and is not able to provide accurate estimates. Our simulation study indicates that reliable results can be obtained when the global level of genetic differentiation (F(ST)) is >1%, the number of loci is only 10, and sample sizes are of the order of 50 individuals per population. We illustrate our method by applying it to Pakistani human data, considering altitude and geographic distance as explanatory factors. Our results suggest that altitude explains better the genetic data than geographic distance. Additionally, they show that southern low-altitude populations have higher migration rates than northern high-altitude ones.     

Controlling population evolution in the laboratory to evaluate methods of historical inference

Natural populations of known detailed past demographic history are extremely valuable to evaluate methods of historical inference, yet are extremely rare. As an alternative approach, we have generated multiple replicate microsatellite data sets from laboratory-cultured populations of a gonochoric free-living nematode, Caenorhabditis remanei, that were constrained to pre-defined demographic histories featuring different levels of migration among populations or bottleneck events of different magnitudes. These data sets were then used to evaluate the performances of two recently developed population genetics methods, BayesAss+, that estimates recent migration rates among populations, and Bottleneck, that detects the occurrence of recent bottlenecks. Migration rates inferred by BayesAss+ were generally over-estimates, although these were often included within the confidence interval. Analyses of data sets simulated in-silico, using a model mimicking the laboratory experiments, produced less biased estimates of the migration rates, and showed increased efficiency of the program when the number of loci and sampled genotypes per population was higher. In the replicates for which the pre-bottleneck laboratory-cultured populations did not significantly depart from a mutation/drift equilibrium, an important assumption of the program Bottleneck, only a portion of the bottleneck events were detected. This result was confirmed by in-silico simulations mirroring the laboratory bottleneck experiments. More generally, our study demonstrates the feasibility, and highlights some of the limits, of the approach that consists in generating molecular genetic data sets by controlling the evolution of laboratory-reared nematode populations, for the purpose of validating methods inferring population history.     

Homing behaviour facilitates subtle genetic differentiation among river populations of Alosa sapidissima: microsatellites and mtDNA

Significant but subtle differentiation was detected for both microsatellite DNA and mitochondrial DNA among four populations of American shad Alosa sapidissima . The data indicate that straying among rivers is sufficient to permit only marginal population differentiation in this species, but suggest that individual river populations should be managed as distinct stocks. Comparison of the Hudson and Columbia populations, the latter derived from the former over 100 years ago, revealed only a slight reduction in microsatellite DNA variation for the founded population but halving of mitochondrial DNA, consistent with the haploid maternal inheritance of the latter marker. The depleted and endangered James River (Virginia) population and two other Atlantic coast populations exhibited similar levels of microsatellite DNA variation, but mtDNA diversity in the James River was marginally lower than in other Atlantic populations, again consistent with the low effective population size of mtDNA.     

Rapid Assessment of Genetic Ancestry in Populations of Unknown Origin by Genome-Wide Genotyping of Pooled Samples

As we move forward from the current generation of genome-wide association (GWA) studies, additional cohorts of different ancestries will be studied to increase power, fine map association signals, and generalize association results to additional populations. Knowledge of genetic ancestry as well as population substructure will become increasingly important for GWA studies in populations of unknown ancestry. Here we propose genotyping pooled DNA samples using genome-wide SNP arrays as a viable option to efficiently and inexpensively estimate admixture proportion and identify ancestry informative markers (AIMs) in populations of unknown origin. We constructed DNA pools from African American, Native Hawaiian, Latina, and Jamaican samples and genotyped them using the Affymetrix 6.0 array. Aided by individual genotype data from the African American cohort, we established quality control filters to remove poorly performing SNPs and estimated allele frequencies for the remaining SNPs in each panel. We then applied a regression-based method to estimate the proportion of admixture in each cohort using the allele frequencies estimated from pooling and populations from the International HapMap Consortium as reference panels, and identified AIMs unique to each population. In this study, we demonstrated that genotyping pooled DNA samples yields estimates of admixture proportion that are both consistent with our knowledge of population history and similar to those obtained by genotyping known AIMs. Furthermore, through validation by individual genotyping, we demonstrated that pooling is quite effective for identifying SNPs with large allele frequency differences (i.e., AIMs) and that these AIMs are able to differentiate two closely related populations (HapMap JPT and CHB).     

Finding confidence limits on population growth rates

Recent concern with the survival of endangered species has renewed interest in estimating the growth rates of natural populations. Estimates of population growth rate are subject to uncertainties because of both sampling and experimental errors incurred when estimating rates of fecundity and survivorship. In recent years, a variety of methods have been proposed for placing confidence limits on estimated growth rates. The commonly used analytical approximation assumes that errors are relatively small. There are several computer-intensive methods, including methods based on jackknife and bootsrap procedures, that test the robustness of that approximation. In addition, several computer simulations of hypothetical populations have led to some generalizations about the performance of different methods. In general, it is possible to find confidence intervals for estimates of population growth rates but the appropriate method for doing so depends on the kind of data available and on the magnitude and correlation structure of the errors.     

Landscape scale genetic effects of habitat fragmentation on a high gene flow species: Speyeria idalia (Nymphalidae)

Detection of the genetic effects of recent habitat fragmentation in natural populations can be a difficult task, especially for high gene flow species. Previous analyses of mitochondrial DNA data from across the current range of Speyeria idalia indicated that the species exhibited high levels of gene flow among populations, with the exception of an isolated population in the eastern portion of its range. However, some populations are found on isolated habitat patches, which were recently separated from one another by large expanses of uninhabitable terrain, in the form of row crop agriculture. The goal of this study was to compare levels of genetic differentiation and diversity among populations found in relatively continuous habitat to populations in both recently and historically isolated habitat. Four microsatellite loci were used to genotype over 300 individuals from five populations in continuous habitat, five populations in recently fragmented habitat, and one historically isolated population. Results from the historically isolated population were concordant with previous analyses and suggest significant differentiation. Also, microsatellite data were consistent with the genetic effects of habitat fragmentation for the recently isolated populations, in the form of increased differentiation and decreased genetic diversity when compared to nonfragmented populations. These results suggest that given the appropriate control populations, microsatellite markers can be used to detect the effects of recent habitat fragmentation in natural populations, even at a large geographical scale in high gene flow species.     

Evaluation of methodology for detection of genetic bottlenecks: inferences from temporally replicated lake trout populations

Statistical methods have been proposed to detect recent bottlenecks on the basis of genetic characterizations of natural populations. In the absence of direct estimates of contemporary or historical population numbers, we tested the indirect M-ratio method based on microsatellite motif size frequency profiles using three historical and three contemporary Great Lakes populations of Salvelinus namaysuch for which severe reductions in population numbers are documented. Simulations employing plausible ranges of empirical population parameter values were used to explore bottleneck likelihood surfaces. We show that single values of the M-ratio are not sufficient to unambiguously infer a bottleneck without knowledge of mutation rates and effective population size (i.e., 4Ne mu or [symbol: see text]). Inferences of the degree of population bottleneck would be best supported if analyses were conducted across plausible ranges of [symbol: see text] and by qualitative comparisons among population samples.     

Microsatellite analysis of the phylogeography, Pleistocene history and secondary contact hypotheses for the killifish, Fundulus heteroclitus

The mummichog, Fundulus heteroclitus, exhibits extensive latitudinal clinal variation in a number of physiological and biochemical traits, coupled with phylogeographical patterns at mitochondrial and nuclear DNA loci that suggest a complicated history of spatially variable selection and secondary intergradation. This species continues to serve as a model for understanding local and regional adaptation to variable environments. Resolving the influences of historical processes on the distribution of genetic variation within and among extant populations of F. heteroclitus is crucial to a better understanding of how populations evolve in the context of contemporary environments. In this study, we analysed geographical patterns of genetic variation at eight microsatellite loci among 15 populations of F. heteroclitus distributed throughout the North American range of the species from Nova Scotia to Georgia. Genetic variation in Northern populations was lower than in Southern populations and was strongly correlated with latitude throughout the species range. The most common Northern alleles at all eight loci exhibited concordant latitudinal clinal patterns, and the existence of an abrupt transition zone in allele frequencies between Northern and Southern populations was similar to that observed for mitochondrial DNA and allozyme loci. A significant pattern of isolation by distance was observed both within and between northern and southern regions. This pattern was unexpected, particularly for northern populations, given the recent colonization history of post-Pleistocene habitats, and was inconsistent with either a recent northward population expansion or a geographically restricted northern Pleistocene refugium. The data provided no evidence for recent population bottlenecks, and estimates of historical effective population sizes suggest that post-Pleistocene populations have been large throughout the species distribution. These results suggest that F. heteroclitus was broadly distributed throughout most of its current range during the last glacial event and that the abrupt transition in allele frequencies that separate Northern and Southern populations may reflect regional disequilibrium conditions associated with the post-Pleistocene colonization history of habitats in that region.     

Native breeds demonstrate high contributions to the molecular variation in northern European sheep

Population contribution to genetic diversity can be estimated using neutral variation. However, population expansion or hybridization of diverged ancestries may weaken correlation between neutral and non-neutral variation. Microsatellite variation was studied at 25 loci in 20 native and 12 modern or imported northern European sheep breeds. Breed contributions to total gene diversity, allelic richness and mean allele-sharing distance between individuals were measured. Indications of changes in population size and admixtures of divergent ancestries were investigated and the extent of inbreeding was estimated. The northern European sheep demonstrated signs of reduction in effective population size. Many old, small populations made a substantial positive contribution to total molecular variation, but populations with several divergent major ancestries did not contribute substantially to molecular variation, with the exception of the Norwegian Rygja sheep. However, several diverged major ancestries may cause it to contribute less to non-neutral variation than expected from the microsatellite data. Breed uniqueness and within-breed variability generally had opposite effects on breed contributions to molecular diversity. The degree of inbreeding did not reflect the breed contribution to total gene diversity or allelic richness, but inbred populations increased the mean allele-sharing distance between individuals. Our study indicates breed conservation to be especially important in maintaining allelic variation in northern European sheep and supports the evolutionary importance of peripheral populations.     

Maximum-likelihood estimation of allelic dropout and false allele error rates from microsatellite genotypes in the absence of reference data

The importance of quantifying and accounting for stochastic genotyping errors when analyzing microsatellite data is increasingly being recognized. This awareness is motivating the development of data analysis methods that not only take errors into consideration but also recognize the difference between two distinct classes of error, allelic dropout and false alleles. Currently methods to estimate rates of allelic dropout and false alleles depend upon the availability of error-free reference genotypes or reliable pedigree data, which are often not available. We have developed a maximum-likelihood-based method for estimating these error rates from a single replication of a sample of genotypes. Simulations show it to be both accurate and robust to modest violations of its underlying assumptions. We have applied the method to estimating error rates in two microsatellite data sets. It is implemented in a computer program, Pedant, which estimates allelic dropout and false allele error rates with 95% confidence regions from microsatellite genotype data and performs power analysis. Pedant is freely available at http://www.stats.gla.ac.uk/ approximately paulj/pedant.html.     

Linked vs unlinked markers: multilocus microsatellite haplotype-sharing as a tool to estimate gene flow and introgression

We have explored the use of multilocus microsatellite haplotypes to study introgression from cultivated (Malus domestica) into wild apple (Malus sylvestris), and to study gene flow among remnant populations of M. sylvestris. A haplotype consisted of alleles at microsatellite loci along one chromosome. As destruction of haplotypes through recombination occurs much faster than loss of alleles due to genetic drift, the lifespan of a multilocus haplotype is much shorter than that of the underlying alleles. When different populations share the same haplotype, this may indicate recent gene flow between populations. Similarly, haplotypes shared between two species would be a strong signal for introgression. As the expected lifespan of a haplotype depends on the strength of the linkage, the length [in centiMorgans (cM)] of the haplotype shared contains information on the number of generations passed. This application of shared haplotypes is distinct from using haplotype-sharing to detect association between markers and a certain trait. We inferred haplotypes for four to eight microsatellite loci on Linkage Group 10 of apple from genotype data using the program phase, and then identified those haplotypes shared between populations and species. Compared with a Bayesian analysis of unlinked microsatellite loci using the program structure, haplotype-sharing detected a partially different set of putative hybrids. Cultivated haplotypes present in M. sylvestris were short (< 1.5 cM), indicating that introgression had taken place many generations ago, except for two Belgian plants that contained a haplotype of 47.1 cM, indicating recent introgression. In the estimation of gene flow, F(ST) based on unlinked loci indicated small (0.032-0.058) but statistically significant differentiation between some populations only. However, various M. sylvestris haplotypes were shared in nearly all pairwise comparisons of populations, and their length indicated recent gene flow. Hence, all Dutch populations should be considered as one conservation unit. The added value of using sharing of multilocus microsatellite haplotypes as a source of population genetic information is discussed.     

Genetic differentiation among North Atlantic killer whale populations

Population genetic structure of North Atlantic killer whale samples was resolved from differences in allele frequencies of 17 microsatellite loci, mtDNA control region haplotype frequencies and for a subset of samples, using complete mitogenome sequences. Three significantly differentiated populations were identified. Differentiation based on microsatellite allele frequencies was greater between the two allopatric populations than between the two pairs of partially sympatric populations. Spatial clustering of individuals within each of these populations overlaps with the distribution of particular prey resources: herring, mackerel and tuna, which each population has been seen predating. Phylogenetic analyses using complete mitogenomes suggested two populations could have resulted from single founding events and subsequent matrilineal expansion. The third population, which was sampled at lower latitudes and lower density, consisted of maternal lineages from three highly divergent clades. Pairwise population differentiation was greater for estimates based on mtDNA control region haplotype frequencies than for estimates based on microsatellite allele frequencies, and there were no mitogenome haplotypes shared among populations. This suggests low or no female migration and that gene flow was primarily male mediated when populations spatially and temporally overlap. These results demonstrate that genetic differentiation can arise through resource specialization in the absence of physical barriers to gene flow.     

Genetic relatedness in the antCamponotus herculeanus. A comparison of estimates from allozyme and DNA microsatellite markers

Summary Genetic structure ofCamponotus herculeanus populations was studied using both traditional allozyme markers and recently discovered DNA microsatellites. Relatedness among worker nest mates was high in one study population (0.70), but lower in another (0.48). The estimates lower than 0.75, together with the multilocus genotype patterns, indicate either multiple mating by queens, or multiple queens reproducing in the colonies. These two could not be distinguished with the current data, although multiple matings seem a more probable explanation for the relatedness estimates bearing social biology of the species in mind. Inbreeding coefficients suggested random mating in both populations. Both allozyme and DNA microsatellite markers gave the same result concerning genetic parameters estimated, but the higher variability of the microsatellites resulted in more precise estimates of both parameters.     

Estimation and adjustment of microsatellite null alleles in nonequilibrium populations

Nonamplified (null) alleles are a common feature of microsatellite genotyping and can bias estimates of allele and genotype frequencies, thereby hindering population genetic analyses. The frequency of microsatellite null alleles in diploid populations can be estimated for populations that are in Hardy–Weinberg equilibrium. However, many microsatellite data sets are from nonequilibrium populations, often with known inbreeding coefficients (F) or fixation indices (F_IS or F_ST). Here, we propose a novel null allele estimator that can be used to estimate the null allele frequency and adjust visible allele frequencies in populations for which independent estimates of F, F_IS or F_ST are available. The algorithm is currently available as an Excel macro that can be downloaded at no cost from http://www.microchecker.hull.ac.uk/ and will be incorporated into the software micro ‐checker .     

Evaluating the performance of a multilocus Bayesian method for the estimation of migration rates

Bayesian methods have become extremely popular in molecular ecology studies because they allow us to estimate demographic parameters of complex demographic scenarios using genetic data. Articles presenting new methods generally include sensitivity studies that evaluate their performance, but they tend to be limited and need to be followed by a more thorough evaluation. Here we evaluate the performance of a recent method, bayesass , which allows the estimation of recent migration rates among populations, as well as the inbreeding coefficient of each local population. We expand the simulation study of the original publication by considering multi-allelic markers and scenarios with varying number of populations. We also investigate the effect of varying migration rates and F _ST more thoroughly in order to identify the region of parameter space where the method is and is not able to provide accurate estimates of migration rate. Results indicate that if the demographic history of the species being studied fits the assumptions of the inference model, and if genetic differentiation is not too low ( F _ST ≥ 0.05), then the method can give fairly accurate estimates of migration rates even when they are fairly high (about 0.1). However, when the assumptions of the inference model are violated, accurate estimates are obtained only if migration rates are very low ( m  = 0.01) and genetic differentiation is high ( F _ST ≥ 0.10). Our results also show that using posterior assignment probabilities as an indication of how much confidence we can place on the assignments is problematical since the posterior probability of assignment can be very high even when the individual assignments are very inaccurate.     

Mixed mating in androdioecious Mercurialis annua inferred using progeny arrays and diploid-acting microsatellite loci in a hexaploid background

Background and Aims

The frequency at which males can be maintained with hermaphrodites in androdioecious populations is predicted to depend on the selfing rate, because self-fertilization by hermaphrodites reduces prospective siring opportunities for males. In particular, high selfing rates by hermaphrodites are expected to exclude males from a population. Here, the first estimates are provided of the mating system from two wild hexaploid populations of the androdioecious European wind-pollinated plant M. annua with contrasting male frequencies.

Methods

Four diploid microsatellite loci were used to genotype 19–20 progeny arrays from two populations of M. annua, one with males and one without. Mating-system parameters were estimated using the program MLTR.

Key Results

Both populations had similar, intermediate outcrossing rates (t_m = 0·64 and 0·52 for the population with and without males, respectively). The population without males showed a lower level of correlated paternity and biparental inbreeding and higher allelic richness and gene diversity than the population with males.

Conclusions

The results demonstrate the utility of new diploid microsatellite loci for mating system analysis in a hexaploid plant. It would appear that androdioecious M. annua has a mixed-mating system in the wild, an uncommon finding for wind-pollinated species. This study sets a foundation for future research to assess the relative importance of the sexual system, plant-density variation and stochastic processes for the regulation of male frequencies in M. annua over space and time.     

Migration patterns among global populations of the pathogenic fungus Mycosphaerella graminicola

DNA sequences from five nuclear loci and data from three microsatellites were collected from 360 isolates representing 14 globally distributed populations of the plant pathogenic fungus Mycosphaerella graminicola. Haplotype networks were constructed for the five sequence loci and population subdivision was assessed using Hudson's permutation test. Migration estimates were calculated using six regional populations for both the sequence and microsatellite loci. While subdivision was detected among the six regional populations, significant gene flow was indicated among some of the populations. The European and Israeli populations contributed the majority of historical immigrants to the New World. Migration estimates for microsatellite loci were used to infer more recent migration events among specific New World populations. We conclude that gene flow was an important factor in determining the demographic history of Mycosphaerella graminicola.     

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

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