Shifting distributions and speciation: species divergence during rapid climate change

Questions about how shifting distributions contribute to species diversification remain virtually without answer, even though rapid climate change during the Pleistocene clearly impacted genetic variation within many species. One factor that has prevented this question from being adequately addressed is the lack of precision associated with estimates of species divergence made from a single genetic locus and without incorporating processes that are biologically important as populations diverge. Analysis of DNA sequences from multiple variable loci in a coalescent framework that (i) corrects for gene divergence pre-dating speciation, and (ii) derives divergence-time estimates without making a priori assumptions about the processes underlying patterns of incomplete lineage sorting between species (i.e. allows for the possibility of gene flow during speciation), is critical to overcoming the inherent logistical and analytical difficulties of inferring the timing and mode of speciation during the dynamic Pleistocene. Estimates of species divergence that ignore these processes, use single locus data, or do both can dramatically overestimate species divergence. For example, using a coalescent approach with data from six loci, the divergence between two species of montane Melanoplus grasshoppers is estimated at between 200,000 and 300,000 years before present, far more recently than divergence estimates made using single-locus data or without the incorporation of population-level processes. Melanoplus grasshoppers radiated in the sky islands of the Rocky Mountains, and the analysis of divergence between these species suggests that the isolation of populations in multiple glacial refugia was an important factor in promoting speciation. Furthermore, the low estimates of gene flow between the species indicate that reproductive isolation must have evolved rapidly for the incipient species boundaries to be maintained through the subsequent glacial periods and shifts in species distributions.     

Concordance of genetic divergence among sockeye salmon populations at allozyme, nuclear DNA, and mitochondrial DNA markers

Abstract.— We examined genetic variation at 21 polymorphic allozyme loci, 15 nuclear DNA loci, and mitochondrial DNA in four spawning populations of sockeye salmon ( Oncorhynchus nerka ) from Cook Inlet, Alaska, to test for differences in the patterns of divergence among different types of markers. We were specifically interested in testing the suggestion that natural selection at allozyme loci compromises the effectiveness of these markers for describing the amount and patterns of gene flow among populations. We found concordance among markers in the amount of genetic variation within and among populations, with the striking exception of one allozyme locus ( sAH ), which exhibited more than three times the amount of among-population differentiation as other loci. A consideration of reports of discordance between allozymes and other loci indicates that these differences usually result from one or two exceptional loci. We conclude that it is important to examine many loci when estimating genetic differentiation to infer historical amounts of gene flow and patterns of genetic exchange among populations. It is less important whether those loci are allozymes or nuclear DNA markers.     

Genetic Population Structure and Gene Flow in the Atlantic Cod Gadus Morhua: A Comparison of Allozyme and Nuclear RFLP Loci

High levels of gene flow have been implicated in producing uniform patterns of allozyme variation among populations of many marine fish species. We have examined whether gene flow is responsible for the limited population structure in the Atlantic cod, Gadus morhua L., by comparing the previously published patterns of variation at 10 allozyme loci to 17 nuclear restriction fragment length polymorphism (RFLP) loci scored by 11 anonymous cDNA clones. Unlike the allozyme loci, highly significant differences were observed among all populations at the DNA markers in a pattern consistent with an isolation-by-distance model of population structure. The magnitude of allele frequency variation at the nuclear RFLP loci significantly exceeded that observed at the protein loci (χ(2) = 24.6, d.f. = 5, P < 0.001). Estimates of gene flow from the private alleles method were similar for the allozymes and nuclear RFLPs. From the infinite island model, however, estimates of gene flow from the DNA markers were fivefold lower than indicated by the proteins. The discrepancy between gene flow estimates, combined with the observation of a large excess of rare RFLP alleles, suggests that the Atlantic cod has undergone a recent expansion in population size and that populations are significantly displaced from equilibrium. Because gene flow is a process that affects all loci equally, the heterogeneity observed among populations at the DNA level eliminates gene flow as the explanation for the homogeneous allozyme patterns. Our results suggest that a recent origin of cod populations has acted to constrain the extent of population differentiation observed at weakly polymorphic loci and implicate a role for selection in affecting the distribution of protein variation among natural populations in this species.     

LONG-DISTANCE GENE FLOW IN THE SEDENTARY BUTTERFLY,EUPHILOTES ENOPTES (LEPIDOPTERA: LYCAENIDAE)

The relationship between gene flow and geographic proximity has been assessed for many insect species, but dispersal distances are poorly known for most of these. Thus, we are able to assess the concordance between vagility and gene flow for only a few species. In this study, I documented variation at six allozyme loci among Washington and Oregon populations of the sedentary, patchily distributed, lycaenid butterfly, Euphilotes enoptes (Boisduval) to assess whether the relationship between gene flow and geographic distance is consistent with the dispersal biology of this species. Both a phenogram based on genetic distances between populations and a regression analysis of gene flow estimates on geographic distances showed a pattern consistent with genetic isolation by distance. Many estimates of gene flow among pairs of populations separated by more than 100 km exceeded the equivalent of 10 individuals exchanged per generation, a value much greater than would be predicted from the limited dispersal ability of this species. However, based on the allozyme data, genetic neighborhood size was estimated to be approximately 39 individuals, a value that is consistent with poor vagility. The results of this study speak to the power of stepping-stone gene flow among populations and are compared to the results of other studies that have examined the relationship between dispersal and gene flow in sedentary insects.     

Reconstructing recent divergence: evaluating nonequilibrium population structure in New Zealand chinook salmon

Newly established or perturbed populations are often the focus of conservation concerns but they pose special challenges for population genetics because drift?migration equilibrium is unlikely. To advance our understanding of the evolution of such populations, we investigated structure and gene flow among populations of chinook salmon that formed via natural straying following introduction to New Zealand in the early 1900s. We examined 11 microsatellite loci from samples collected in several sites and years to address two questions: (i) what population differentiation has arisen in the ≈ 30 generations since salmon were introduced to New Zealand, relative to temporal variation within populations; and (ii) what are the approximate effective population sizes and amounts of gene flow in these populations? These questions are routinely addressed in studies of indigenous populations, but less often in the case of new populations and rarely with consideration of equilibrium assumptions. We show that despite the recent introduction, continued gene flow and high temporal variability among samples, detectable population structure has arisen among the New Zealand populations, consistent with their colonization pattern and isolation by geographical distance. Furthermore, we use simple individual‐based simulations and estimates of effective population sizes to estimate the effective gene flow among drainages under likely nonequilibrium conditions. Similar methodology may be broadly applicable to other studies of population structure and phenotypic evolution under similar nonequilibrium, high gene flow conditions.     

The effect of natural selection on estimates of genetic divergence among populations of the Atlantic salmon

The effect of natural selection on the _mMEP-2 * locus on measures of genetic divergence among Atlantic salmon populations was investigated by examining the pattern of change in the level of genetic differentiation (F_ST) averaged over loci when data on the _mMEP-2 * locus were either included or excluded. The level of F_ST among populations at various geographic scales was estimated from allele frequencies at up to four loci (_s AAT-4 *, IDDH-1 *, IDHP-3 *, and _mMEP-2 *). At smaller geographic scales (within river systems or limited geographic regions) levels of variance in _mMEP-2 * allele frequencies were reduced relative to mean levels. At larger geographic scales (across continents or the species range) variation in _mMEP-2 * allele frequencies was greater than mean levels. These results suggest an a priori hypothesis for the effect of selection on the _mMEP-2 * locus which may be applied in future studies on variation in protein coding or other (e.g. mini- and microsatellite) loci in the Atlantic salmon. It is recommended that estimates of gene flow among populations of the Atlantic salmon based on mean F _ST estimates which include data on the _mMEP-2 * locus should be viewed with caution.     

Estimating divergence time with the use of microsatellite genetic distances: impacts of population growth and gene flow

Genetic distances play an important role in estimating divergence time of bifurcated populations. However, they can be greatly affected by demographic processes, such as migration and population dynamics, which complicate their interpretation. For example, the widely used distance for microsatellite loci, (deltamu)2, assumes constant population size, no gene flow, and mutation-drift equilibrium. It is shown here that (deltamu)2 strongly underestimates divergence time if populations are growing and/or connected by gene flow. In recent publications, the average estimate of divergence time between African and non-African populations obtained by using (deltamu)2 is about 34,000 years, although archaeological data show a much earlier presence of modern humans out of Africa. I introduce a different estimator of population separation time based on microsatellite statistics, T(D), that does not assume mutation-drift equilibrium, is independent of population dynamics in the absence of gene flow, and is robust to weak migration flow for growing populations. However, it requires a knowledge of the variance in the number of repeats at the beginning of population separation, V(0). One way to overcome this problem is to find minimal and maximal bounds for the variance and thus obtain the earliest and latest bounds for divergence time (this is not a confidence interval, and it simply reflects an uncertainty about the value of V(0) in an ancestral population). Another way to avoid the uncertainty is to choose from among present populations a reference whose variation is presumably close to what it might have been in an ancestral population. A different approach for using T(D) is to estimate the time difference between adjacent nodes on a phylogenetic population tree. Using data on variation at autosomal short tandem repeat loci with di-, tri-, and tetranucleotide repeats in worldwide populations, T(D) gives an estimate of 57,000 years for the separation of the out-of-Africa branch of modern humans from Africans based on the value of V(0) in the Southern American Indian populations; the earliest bound for this event has been estimated to be about 135,000 years. The data also suggest that the Asian and European populations diverged from each other about 20,000 years, after the occurrence of the out-of-Africa branch.     

Estimating a geographically explicit model of population divergence

Patterns of genetic variation can provide valuable insights for deciphering the relative roles of different evolutionary processes in species differentiation. However, population-genetic models for studying divergence in geographically structured species are generally lacking. Since these are the biogeographic settings where genetic drift is expected to predominate, not only are population-genetic tests of hypotheses in geographically structured species constrained, but generalizations about the evolutionary processes that promote species divergence may also be potentially biased. Here we estimate a population-divergence model in montane grasshoppers from the sky islands of the Rocky Mountains. Because this region was directly impacted by Pleistocene glaciation, both the displacement into glacial refugia and recolonization of montane habitats may contribute to differentiation. Building on the tradition of using information from the genealogical relationships of alleles to infer the geography of divergence, here the additional consideration of the process of gene-lineage sorting is used to obtain a quantitative estimate of population relationships and historical associations (i.e., a population tree) from the gene trees of five anonymous nuclear loci and one mitochondrial locus in the broadly distributed species Melanoplus oregonensis. Three different approaches are used to estimate a model of population divergence; this comparison allows us to evaluate specific methodological assumptions that influence the estimated history of divergence. A model of population divergence was identified that significantly fits the data better compared to the other approaches, based on per-site likelihood scores of the multiple loci, and that provides clues about how divergence proceeded in M. oregonensis during the dynamic Pleistocene. Unlike the approaches that either considered only the most recent coalescence (i.e., information from a single individual per population) or did not consider the pattern of coalescence in the gene genealogies, the population-divergence model that best fits the data was estimated by considering the pattern of gene lineage coalescence across multiple individuals, as well as loci. These results indicate that sampling of multiple individuals per population is critical to obtaining an accurate estimate of the history of divergence so that the signal of common ancestry can be separated from the confounding influence of gene flow-even though estimates suggest that gene flow is not a predominant factor structuring patterns of genetic variation across these sky island populations. They also suggest that the gene genealogies contain information about population relationships, despite the lack of complete sorting of gene lineages. What emerges from the analyses is a model of population divergence that incorporates both contemporary distributions and historical associations, and shows a latitudinal and regional structuring of populations reminiscent of population displacements into multiple glacial refugia. Because the population-divergence model itself is built upon the specific events shaping the history of M. oregonensis, it provides a framework for estimating additional population-genetic parameters relevant to understanding the processes governing differentiation in geographically structured species and avoids the problems of relying on overly simplified and inaccurate divergence models. The utility of these approaches, as well as the caveats and future improvements, for estimating population relationships and historical associations relevant to genetic analyses of geographically structured species are discussed.     

Gene flow across species boundaries in sympatric, sexually deceptive Ophrys (Orchidaceae) species

Abstract Orchids of the genus Ophrys (Orchidaceae) are pollinated by male bees and wasps through sexual deception. The Ophrys sphegodes group encompasses several closely related species that differ slightly in floral morphology and are pollinated by different solitary bee species. Populations representing different species of the O. sphegodes group often flower simultaneously in sympatry. To test whether gene flow across the species boundaries occurs in these sympatric populations, or whether they are reproductively isolated, we examined the distribution of genetic variation within and among populations and species of this group. We collected at each of five different localities in southern France and Italy two sympatric, co-flowering Ophrys populations, representing six Ophrys species in total. The six microsatellite loci surveyed were highly variable. Genetic differentiation among geographically distant populations of the same species was lower than differentiation among sympatric populations of different species. However, the strength of genetic differentiation among species was among the lowest reported for orchids. Genotype assignment tests and marker-based estimates of gene flow revealed that gene flow across species boundaries occurred and may account for the low observed differentiation among species. These results suggest that sexual deceit pollination in Ophrys may be less specific than thought, or that rare mistakes occur.     

Vicariance divergence and gene flow among islet populations of an endemic lizard

Allopatry and allopatric speciation can arise through two different mechanisms: vicariance or colonization through dispersal. Distinguishing between these different allopatric mechanisms is difficult and one of the major challenges in biogeographical research. Here, we address whether allopatric isolation in an endemic island lizard is the result of vicariance or dispersal. We estimated the amount and direction of gene flow during the divergence of isolated islet populations and subspecies of the endemic Skyros wall lizard Podarcis gaigeae, a phenotypically variable species that inhabits a major island and small islets in the Greek archipelago. We applied isolation-with-migration models to estimate population divergence times, population sizes and gene flow between islet-mainland population pairs. Divergence times were significantly correlated with independently estimated geological divergence times. This correlation strongly supports a vicariance scenario where islet populations have sequentially become isolated from the major island. We did not find evidence for significant gene flow within P. g. gaigeae. However, gene-flow estimates from the islet to the mainland populations were positively affected by islet area and negatively by distance between the islet and mainland. We also found evidence for gene flow from one subspecies (P. g. weigandi) into another (P. g. gaigeae), but not in the other direction. Ongoing gene flow between the subspecies suggests that even in this geographically allopatric scenario with the sea posing a strong barrier to dispersal, divergence with some gene flow is still feasible.     

Influence of gene flow on divergence dating – implications for the speciation history of Takydromus grass lizards

Dating the time of divergence and understanding speciation processes are central to the study of the evolutionary history of organisms but are notoriously difficult. The difficulty is largely rooted in variations in the ancestral population size or in the genealogy variation across loci. To depict the speciation processes and divergence histories of three monophyletic Takydromus species endemic to Taiwan, we sequenced 20 nuclear loci and combined with one mitochondrial locus published in GenBank. They were analysed by a multispecies coalescent approach within a Bayesian framework. Divergence dating based on the gene tree approach showed high variation among loci, and the divergence was estimated at an earlier date than when derived by the species‐tree approach. To test whether variations in the ancestral population size accounted for the majority of this variation, we conducted computer inferences using isolation‐with‐migration (IM) and approximate Bayesian computation (ABC) frameworks. The results revealed that gene flow during the early stage of speciation was strongly favoured over the isolation model, and the initiation of the speciation process was far earlier than the dates estimated by gene‐ and species‐based divergence dating. Due to their limited dispersal ability, it is suggested that geographical isolation may have played a major role in the divergence of these Takydromus species. Nevertheless, this study reveals a more complex situation and demonstrates that gene flow during the speciation process cannot be overlooked and may have a great impact on divergence dating. By using multilocus data and incorporating Bayesian coalescence approaches, we provide a more biologically realistic framework for delineating the divergence history of Takydromus.     

Differential patterns of male and female mtDNA exchange across the Atlantic Ocean in the blue mussel, Mytilus edulis

Comparisons among loci with differing modes of inheritance can reveal unexpected aspects of population history. We employ a multilocus approach to ask whether two types of independently assorting mitochondrial DNAs (maternally and paternally inherited: F- and M-mtDNA) and a nuclear locus (ITS) yield concordant estimates of gene flow and population divergence. The blue mussel, Mytilus edulis, is distributed on both North American and European coastlines and these populations are separated by the waters of the Atlantic Ocean. Gene flow across the Atlantic Ocean differs among loci, with F-mtDNA and ITS showing an imprint of some genetic interchange and M-mtDNA showing no evidence for gene flow. Gene flow of F-mtDNA and ITS causes trans-Atlantic population divergence times to be greatly underestimated for these loci, although a single trans-Atlantic population divergence time (1.2 MYA) can be accommodated by considering all three loci in combination in a coalescent framework. The apparent lack of gene flow for M-mtDNA is not readily explained by different dispersal capacities of male and female mussels. A genetic barrier to M-mtDNA exchange between North American and European mussel populations is likely to explain the observed pattern, perhaps associated with the double uniparental system of mitochondrial DNA inheritance.     

Re-examination of a proposed case of stasipatric speciation: phylogeography of the Australian morabine grasshoppers (Vandiemenella viatica species group)

Karyotypic differences have been used for delimiting populations or species, although whether these mutations provide strong barriers to gene flow between populations and promote speciation remains contentious. In this study, we assessed whether 11 chromosomal races of Australian morabine grasshoppers ( Vandiemenella viatica species group) represent genetically distinct populations by analyses of cytological and allozyme (35 loci) data and DNA sequences of the elongation factor-1 alpha ( EF -1α), anonymous Mvia11 , and mitochondrial cytochrome c oxidase subunit I ( COI ) loci. While the Vandiemenella chromosomal taxa generally represent genetically distinct units, a substantial portion of the total genetic variation in our samples was not explained by the chromosomal variation. Mantel tests indicated that Vandiemenella populations were spatially structured and have maintained gene flow at a local scale within each of the taxa. The group was subdivided into 13 genetic clusters; four chromosomal taxa comprised single exclusive clusters, while others comprised more than one cluster or clusters shared with other taxa. Boundaries of these cryptic population subdivisions correspond with several biogeographical barriers, such as straits, gulfs, the Murray River, and an ancient mega-lake, Lake Bungunnia. The viatica species group was previously proposed to have diversified without major geographical separation based on the stasipatric speciation model; however, the present study suggests the involvement of allopatric fragmentation. Given extensive nonmonophyly of chromosomal taxa and incomplete barriers to gene flow among taxa, all Vandiemenella chromosomal taxa and genetically distinct populations within chromosomal taxa, except Vandiemenella pichirichi , should be regarded as populations of one species: Vandiemenella viatica .     

Inferring the evolutionary history of divergence despite gene flow in a lizard species,Scincella lateralis (Scincidae), composed of cryptic lineages

Although recent radiations are fruitful for studying the process of speciation, they are difficult to characterize and require the use of multiple loci and analytical methods that account for processes such as gene flow and genetic drift. Using multilocus sequence data, we combine hierarchical cluster analysis, coalescent species tree inference, and isolation‐with‐migration analysis to investigate evolutionary relationships among cryptic lineages of North American ground skinks. We also estimate the extent that gene flow has accompanied or followed diversification, and also attempt to account for and minimize the influence of gene flow when reconstructing relationships. The data best support seven largely parapatric populations that are broadly concordant with mitochondrial (mt)DNA phylogeography throughout most of the species range, although they fail to fully represent extensive mtDNA divergence along the Gulf Coast. Relationships within and among three broad geographical groups are well supported, despite evidence of gene flow among them. Rejection of an allopatric divergence model partially depends on the inclusion of samples from near parapatric boundaries in the analyses, suggesting that allopatric divergence followed by recent migration may best explain migration rate estimates. Accounting for geographical variation in patterns of gene flow can improve estimates of migration–divergence parameters and minimize the influence of contemporary gene flow on phylogenetic inference. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Precision and accuracy of divergence time estimates from STR and SNPSTR variation

Inference of intraspecific population divergence patterns typically requires genetic data for molecular markers with relatively high mutation rates. Microsatellites, or short tandem repeat (STR) polymorphisms, have proven informative in many such investigations. These markers are characterized, however, by high levels of homoplasy and varying mutational properties, often leading to inaccurate inference of population divergence. A SNPSTR is a genetic system that consists of an STR polymorphism closely linked (typically < 500 bp) to one or more single-nucleotide polymorphisms (SNPs). SNPSTR systems are characterized by lower levels of homoplasy than are STR loci. Divergence time estimates based on STR variation (on the derived SNP allele background) should, therefore, be more accurate and precise. We use coalescent-based simulations in the context of several models of demographic history to compare divergence time estimates based on SNPSTR haplotype frequencies and STR allele frequencies. We demonstrate that estimates of divergence time based on STR variation on the background of a derived SNP allele are more accurate (3% to 7% bias for SNPSTR versus 11% to 20% bias for STR) and more precise than STR-based estimates, conditional on a recent SNP mutation. These results hold even for models involving complex demographic scenarios with gene flow, population expansion, and population bottlenecks. Varying the timing of the mutation event generating the SNP revealed that estimates of divergence time are sensitive to SNP age, with more recent SNPs giving more accurate and precise estimates of divergence time. However, varying both mutational properties of STR loci and SNP age demonstrated that multiple independent SNPSTR systems provide less biased estimates of divergence time. Furthermore, the combination of estimates based separately on STR and SNPSTR variation provides insight into the age of the derived SNP alleles. In light of our simulations, we interpret estimates from data for human populations.     

Genomic divergence between Spanish Littorina saxatilis ecotypes unravels limited admixture and extensive parallelism associated with population history

The rough periwinkle, Littorina saxatilis, is a model system for studying parallel ecological speciation in microparapatry. Phenotypically parallel wave‐adapted and crab‐adapted ecotypes that hybridize within the middle shore are replicated along the northwestern coast of Spain and have likely arisen from two separate glacial refugia. We tested whether greater geographic separation corresponding to reduced opportunity for contemporary or historical gene flow between parallel ecotypes resulted in less parallel genomic divergence. We sequenced double‐digested restriction‐associated DNA (ddRAD) libraries from individual snails from upper, mid, and low intertidal levels of three separate sites colonized from two separate refugia. Outlier analysis of 4256 SNP markers identified 34.4% sharing of divergent loci between two geographically close sites; however, these sites each shared only 9.9%–15.1% of their divergent loci with a third more‐distant site. STRUCTURE analysis revealed that genotypes from only three of 166 phenotypically intermediate mid‐shore individuals appeared to result from recent hybridization, suggesting that hybrids cannot be reliably identified using shell traits. Hierarchical AMOVA indicated that the primary source of genomic differentiation was geographic separation, but also revealed greater similarity of the same ecotype across the two geographically close sites than previously estimated with dominant markers. These results from a model system for ecological speciation suggest that genomic parallelism is affected by the opportunity for historical or contemporary gene flow between populations.     

COLOR-PATTERN VARIATION IN LAKE ERIE WATER SNAKES: THE ROLE OF GENE FLOW

In an effort to clarify the evolutionary processes influencing color-pattern variation in Lake Erie island water snake (Nerodia sipedon) populations, rates of gene flow among island and mainland populations were estimated from patterns of allozymic variation detected using electrophoresis. Rates of gene flow were high with Nm, the number of migrants per generation, averaging 25.5 among island sites, 9.2 between the Ontario mainland and the islands, and 3.6 between the Ohio mainland and the islands. Based on estimates of current population size from mark-recapture work and of past population size extrapolated from the extent of shoreline habitat, values of m between island and mainland populations ranged from 0.0008–0.01. Synthesis of estimates of the rate of gene flow with information on inheritance of color pattern, the strength of natural selection, and population history supports the hypothesis that color-pattern variation in island populations results from a balance between gene flow and natural selection. However, depending on the mode of inheritance of color pattern, stochastic processes such as drift may have been important in the initial stages of differentiation between island and mainland populations.     

Assessing natural introgression in 2 biomedical model species, the rhesus macaque (Macaca mulatta) and the long-tailed macaque (Macaca fascicularis)

Rhesus macaque (Macaca mulatta) and long-tailed macaque (Macaca fascicularis) are the 2 most commonly used primate model species in biomedical sciences. Although morphological studies have revealed a weak hybridization at the interspecific contact zone, in the north of Indochina, a molecular study has suggested an ancient introgression from rhesus to long-tailed macaque into the Indo-Chinese peninsula. However, the gene flow between these 2 taxa has never been quantified using genetic data and theoretical models. In this study, we have examined genetic variation within and between the parapatric Chinese rhesus macaque and Indo-Chinese long-tailed macaque populations, using 13 autosomal, 5 sex-linked microsatellite loci and mitochondrial DNA sequence data. From these data, we assessed genetic structure and estimated gene flow using a Bayesian clustering approach and the "Isolation with Migration" model. Our results reveal a weak interspecific genetic differentiation at both autosomal and sex-linked loci, suggesting large population sizes and/or gene flow between populations. According to the Bayesian clustering, Chinese rhesus macaque is a highly homogeneous gene pool that contributes strongly to the current Indo-Chinese long-tailed macaque genetic makeup, whether or not current admixture is assumed. Coalescent simulations, which integrated the characteristics of the loci, pointed out 1) a higher effective population size in rhesus macaque, 2) no mitochondrial gene flow, and 3) unilateral and male-mediated nuclear gene flow of approximately 10 migrants per generation from rhesus to long-tailed macaque. These patterns of genetic structure and gene flow suggest extensive ancient introgression from Chinese rhesus macaque into the Indo-Chinese long-tailed macaque population.     

Diversity and divergence patterns in regulatory genes suggest differential gene flow in recently derived species of the Hawaiian silversword alliance adaptive radiation (Asteraceae)

The impact of gene flow and population size fluctuations in shaping genetic variation during adaptive radiation, at both the genome-wide and gene-specific levels, is very poorly understood. To examine how historical population size and gene flow patterns within and between loci have influenced lineage divergence in the Hawaiian silversword alliance, we have investigated the nucleotide sequence diversity and divergence patterns of four floral regulatory genes (ASAP1-A, ASAP1-B, ASAP3-A, ASAP3-B) and a structural gene (ASCAB9). Levels and patterns of molecular divergence across these five nuclear loci were estimated between two recently derived species (Dubautia ciliolata and Dubautia arborea) which are presumed to be sibling species. This multilocus analysis of genetic variation, haplotype divergence and historical demography indicates that population expansion and differential gene flow occurred subsequent to the divergence of these two lineages. Moreover, contrasting patterns of allele- sharing for regulatory loci vs. a structural locus between these two sibling species indicate alternative histories of genetic variation and partitioning among loci where alleles of the floral regulatory loci are shared primarily from D. arborea to D. ciliolata and alleles of the structural locus are shared in both directions. Taken together, these results suggest that adaptively radiating species can exhibit contrasting allele migration rates among loci such that allele movement at specific loci may supersede genetic divergence caused by drift and that lineage divergence during adaptive radiation can be associated with population expansion.     

Geographically multifarious phenotypic divergence during speciation

Speciation is an important evolutionary process that occurs when barriers to gene flow evolve between previously panmictic populations. Although individual barriers to gene flow have been studied extensively, we know relatively little regarding the number of barriers that isolate species or whether these barriers are polymorphic within species. Herein, we use a series of field and lab experiments to quantify phenotypic divergence and identify possible barriers to gene flow between the butterfly species Lycaeides idas and Lycaeides melissa. We found evidence that L. idas and L. melissa have diverged along multiple phenotypic axes. Specifically, we identified major phenotypic differences in female oviposition preference and diapause initiation, and more moderate divergence in mate preference. Multiple phenotypic differences might operate as barriers to gene flow, as shown by correlations between genetic distance and phenotypic divergence and patterns of phenotypic variation in admixed Lycaeides populations. Although some of these traits differed primarily between species (e.g., diapause initiation), several traits also varied among conspecific populations (e.g., male mate preference and oviposition preference).