Evidence Of Recent Gene Flow Research Articles

Genetic structure of the European white elm (Ulmus laevis Pall., Ulmaceae) in Switzerland

Key messagePopulations of the European white elm (Ulmus laevis Pall.) in Switzerland can be considered natural. They show no evidence of genetic differentiation from other European populations. In the past, the U. laevis populations were probably more widespread and continuous in Switzerland with a larger gene flow.ContextIn Switzerland, at the margin of its distribution range, U. laevis is rare and considered endangered. Whether the species is native to Switzerland has been disputed, and it is often surmised to be solely cultivated, without any natural population in the country.AimsThe structure of genetic diversity among Swiss populations of U. laevis and comparison to European populations are expected to shed light on the origin of local populations and support their management.MethodsWe analyzed 19 populations (194 individuals) in Switzerland and 15 populations (158 individuals) from other European countries, using a set of five microsatellite loci.Results(1) 90% of the genetic variation in European and Swiss populations occurs within populations. (2) We did not detect isolation by distance at the regional or continental scale. (3) Clustering analysis did not reveal any spatial pattern in the level of admixture of individuals within Swiss or other European populations.ConclusionModerate levels of genetic diversity and evidence for recent gene flow between populations indicate that habitat deterioration, loss, and fragmentation are the main threats to the persistence of U. laevis populations in Switzerland.

Recent parallel speciation in Antirrhinum involved complex haplotypes and multiple adaptive characters.

A role of ecological adaptation in speciation can be obscured by stochastic processes and differences that species accumulate after genetic isolation. One way to identify adaptive characters and their underlying genes is to study cases of speciation involving parallel adaptations. Recently resolved phylogenies reveal that alpine morphology has evolved in parallel in the genus Antirrhinum (snapdragons): first in an early split of an alpine from a lowland lineage and, more recently, from within the lowland lineage to produce closely related sympatric species with contrasting alpine and lowland forms. Here, we find that two of these later diverged sympatric species are differentiated by only around 2% of nuclear loci. Though showing evidence of recent gene flow, the species remain distinct for a suite of morphological characters typical of earlier-diverged alpine or lowland lineages and their morphologies correlate with features of the local landscape, as expected of ecological adaptations. Morphological differences between the two species involve multiple, unlinked genes so that parental character combinations are readily broken up by recombination in hybrids. We detect little evidence for post-pollination barriers to gene flow or recombination, suggesting that genetic isolation related to ecological adaptation is important in maintaining character combinations and might have contributed to parallel speciation. We also find evidence that genes involved in the earlier alpine-lowland split were reused in parallel evolution of alpine species, consistent with introgressive hybridisation, and speculate that many non-ecological barriers to gene flow might have been purged during the process.

Population genetic structure of the endemic fish Gambusia marshi from the Cuatro Ciénegas basin and its outflow in Coahuila, Mexico

The valley of Cuatro Ciénegas in Coahuila, Mexico, has the highest degree of local endemism of any habitat in North America. Despite the arid desert climate, the basin harbours an extensive system of permanent streams, wetlands, and spring-fed pools, and is divided into two sub-basins by the central Sierra de San Marcos y Pinos. Microsatellite loci were surveyed to infer the genetic diversity and population structure of Gambusia marshi, a poeciliid fish endemic to the Cuatro Ciénegas basin and the Río Salado de Nadadores in north-east Mexico. Bayesian clustering analysis revealed four genetic populations within G. marshi and a major east–west division corresponding to the Sierra de San Marcos y Pinos. Most sample sites exhibited high levels of genetic differentiation, although there is evidence for recent gene flow between some of these locations. The population of G. marshi in Poza Anteojo is extremely divergent, and appears to represent a remnant of a different historical system. The G. marshi in Poza Anteojo should be considered an independent management unit. Documenting the number and distribution of distinct populations of G. marshi provides additional justification for protecting the Cuatro Ciénegas basin from additional water withdrawals and further homogenization via the construction of additional canals. By analysing the population structure of a widespread species within a region containing many range-restricted and endemic species, these results shed new light on historical connections among aquatic ecosystems and raise awareness of the possibility that units of conservation concern may exist in other, more range-restricted taxa in the Cuatro Ciénegas basin and encourage the assessment of their conservation status. The results also have implications for species in arid regions in other parts of the world that may also harbour as yet unrecognized isolated populations worthy of conservation.

Evidence for the Pleistocene Arc Hypothesis from genome-wide SNPs in a Neotropical dry forest specialist, the Rufous-fronted Thornbird (Furnariidae: Phacellodomus rufifrons).

South American dry forests have a complex and poorly understood biogeographic history. Based on the fragmented distribution of many Neotropical dry forest species, it has been suggested that this biome was more widely distributed and contiguous under drier climate conditions in the Pleistocene. To test this scenario, known as the Pleistocene Arc Hypothesis, we studied the phylogeography of the Rufous-fronted Thornbird (Phacellodomus rufifrons), a widespread dry forest bird with a disjunct distribution closely matching that of the biome itself. We sequenced mtDNA and used ddRADseq to sample 7,167 genome-wide single-nucleotide polymorphisms from 74 P.rufifrons individuals across its range. We found low genetic differentiation over two prominent geographic breaks - particularly across a 1,000km gap between populations in Bolivia and Northern Peru. Using demographic analyses of the joint site frequency spectrum, we found evidence of recent divergence without subsequent gene flow across those breaks. By contrast, parapatric morphologically distinct populations in northeastern Brazil show high genetic divergence with evidence of recent gene flow. These results, in combination with our paleoclimate species distribution modelling, support the idea that currently disjunct patches of dry forest were more connected in the recent past, probably during the Middle and Late Pleistocene. This notion fits the major predictions of the Pleistocene Arc Hypothesis and illustrates the importance of comprehensive genomic and geographic sampling for examining biogeographic and evolutionary questions in complex ecosystems like Neotropical dry forests.

Genotypic similarities among the parthenogenetic Darevskia rock lizards with different hybrid origins

BackgroundThe majority of parthenogenetic vertebrates derive from hybridization between sexually reproducing species, but the exact number of hybridization events ancestral to currently extant clonal lineages is difficult to determine. Usually, we do not know whether the parental species are able to contribute their genes to the parthenogenetic vertebrate lineages after the initial hybridization. In this paper, we address the hypothesis, whether some genotypes of seven phenotypically distinct parthenogenetic rock lizards (genus Darevskia) could have resulted from back-crosses of parthenogens with their presumed parental species. We also tried to identify, as precise as possible, the ancestral populations of all seven parthenogens.ResultsWe analysed partial mtDNA sequences and microsatellite genotypes of all seven parthenogens and their presumed ansectral species, sampled across the entire geographic range of parthenogenesis in this group. Our results confirm the previous designation of the parental species, but further specify the maternal populations that are likely ancestral to different parthenogenetic lineages. Contrary to the expectation of independent hybrid origins of the unisexual taxa, we found that genotypes at multiple loci were shared frequently between different parthenogenetic species. The highest proportions of shared genotypes were detected between (i) D. sapphirina and D. bendimahiensis and (ii) D. dahli and D. armeniaca, and less often between other parthenogens. In case (ii), genotypes at the remaining loci were notably distinct.ConclusionsWe suggest that both observations (i-ii) can be explained by two parthenogenetic forms tracing their origin to a single initial hybridization event. In case (ii), however, occasional gene exchange between the unisexual and the parental bisexual species could have taken place after the onset of parthenogenetic reproduction. Indeed, backcrossed polyploid hybrids are relatively frequent in Darevskia, although no direct evidence of recent gene flow has been previously documented. Our results further suggest that parthenogens are losing heterozygosity as a result of allelic conversion, hence their fitness is expected to decline over time as genetic diversity declines. Backcrosses with the parental species could be a rescue mechanism which might prevent this decline, and therefore increase the persistance of unisexual forms.

The role of island physiography in maintaining genetic diversity in the endemic Tyrrhenian wall lizard (Podarcis tiliguerta)

AbstractSea level oscillations occurred during the Pleistocene have strongly affected islands’ physiography by changing area, elevation, and even the number of islands rising above the sea level. Such changes had direct consequences on island genetic diversity by promoting genetic admixture during glacial marine regressions while fragmentation or even extinctions occurred because of marine transgressions. Here we investigated the effect of islands’ physiographic changes on the mitochondrial diversity of 84 individuals of the Tyrrhenian wall lizard (Podarcis tiliguerta) from different islands and island groups surrounding Corsica and Sardinia. The La Maddalena Archipelago that is the more complex of the studied island groups, showed the highest genetic diversity, while we detected decreasing genetic diversity in island groups with lower number of islands and elevation. The genetic imprint we found seems to have been shaped by eustatic changes occurred in the Mediterranean basin during Mid‐Pleistocene times. Indeed, a relevant component of ancient lineages was found on those island groups among which elevation of at least one island allowed populations to survive during the Mid‐Pleistocene marine transgressions. In contrast, we found evidence of recent gene flow between populations inhabiting islands or island groups characterized by low elevation. Our results suggest that many features such as number of islands and their elevation, may provide predictive information to identify those islands or “archipelagos” that deserve special attention in terms of conservation priority.

Genetic Structure of the Ryukyu Wild Boar Population on Tokunoshima Island (Japan) Based on Modern and Ancient DNA Analyses: Evidence of Recent Gene Flow from Pigs to Wild Boars

We investigated the genetic structure among populations of the Ryukyu wild boar (Sus scrofa riukiuanus) on Tokunoshima Island by analyzing DNA from modern and archaeological samples. Four and two mtDNA haplotypes were found in the modern and archaeological samples, respectively. One haplotype was shared between the modern and archaeological samples. Of the seven haplotypes, four were only found on Tokunoshima. These haplotypes were genetically close to each other and classified as those from the Ryukyu wild boars. This genetic similarity between modern and archaeological samples suggests that these four haplotypes originated from Tokunoshima. The chronology of the archaeological samples suggests that the genetic structure of the wild boar population on Tokunoshima has been maintained for over 1000 years. The representative glucosephosphate isomerase-processed pseudogene (GPIP) allele for the modern population on Tokunoshima was GPIP*3a and was found in a Ryukyu wild boar in a previous study. We detected three modern individuals that were genetically distinct from the Ryukyu wild boars based on mtDNA and GPIP analyses. They all had a different combination of the mtDNA haplotype and GPIP allele from each other. Our results indicate that gene flow events from pigs to wild boars have occurred on Tokunoshima.

Does Channel Island Acmispon (Fabaceae) form cohesive evolutionary groups?

The California Channel Islands are unique relative to other island chains due to their close proximity to the California mainland and the fact that individual islands, or groups of islands, vary in their distance to the mainland and other islands. This orientation raises questions about whether island taxa with widespread distributions form cohesive evolutionary units, or if they are actually composed of several distinct evolutionary entities, either derived from independent mainland-to-island colonization events or divergence due to prolonged allopatric isolation. The 4 northern islands are clustered in a line (6–8 km separation among islands), while the 4 southern islands are widely spaced (34–45 km separation among islands), which should impact the amount of gene flow and genetic connectivity among islands. We used nuclear microsatellite markers to examine the genetic structure and cohesion of 2 island shrubs, Acmispon dendroideus and A. argophyllus, which are widely distributed across the California Channel Islands. Both focal species contain varieties with multi-island distributions, with A. dendroideus exhibiting a greater distribution on the northern islands and A. argophyllus exhibiting a greater distribution on the southern islands. Substantial genetic divergence was observed for 2 single-island endemic varieties, A. dendroideus var. traskiae and A. agrophyllus var. niveus, confirming that allopatric isolation can lead to genetic divergence. The widespread Acmispon dendroideus var. dendroideus and single-island endemic A. dendroideus var. veatchii formed a cohesive evolutionary group that spans all 4 northern islands and 1 southern island, Santa Catalina, indicating that the northern and southern islands have been genetically linked in the past but do not display evidence of contemporary gene flow. In contrast, widespread A. argophyllus var. argenteus was composed of moderately distinct genetic groups on each of the 4 southern islands, with no evidence of recent gene flow among islands. These results demonstrate that isolation among islands has led to significant divergence among the southern islands, but that the commonly recognized split between northern and southern islands does not impact all taxa equally.

The Mating System of the Wild-to-Domesticated Complex of Gossypium hirsutum L. Is Mixed.

The domestication syndrome of many plants includes changes in their mating systems. The evolution of the latter is shaped by ecological and genetic factors that are particular to an area. Thus, the reproductive biology of wild relatives must be studied in their natural distribution to understand the mating system of a crop species as a whole. Gossypium hirsutum (upland cotton) includes both domesticated varieties and wild populations of the same species. Most studies on mating systems describe cultivated cotton as self-pollinated, while studies on pollen dispersal report outcrossing; however, the mating system of upland cotton has not been described as mixed and little is known about its wild relatives. In this study we selected two wild metapopulations for comparison with domesticated plants and one metapopulation with evidence of recent gene flow between wild relatives and the crop to evaluate the mating system of cotton’s wild-to-domesticated complex. Using classic reproductive biology methods, our data demonstrate that upland cotton presents a mixed mating system throughout the complex. Given cotton’s capacity for outcrossing, differences caused by the domestication process in cultivated individuals can have consequences for its wild relatives. This characterization of the diversity of the wild relatives in their natural distribution, as well as their interactions with the crop, will be useful to design and implement adequate strategies for conservation and biosecurity.

Insights into Platypus Population Structure and History from Whole-Genome Sequencing.

The platypus is an egg-laying mammal which, alongside the echidna, occupies a unique place in the mammalian phylogenetic tree. Despite widespread interest in its unusual biology, little is known about its population structure or recent evolutionary history. To provide new insights into the dispersal and demographic history of this iconic species, we sequenced the genomes of 57 platypuses from across the whole species range in eastern mainland Australia and Tasmania. Using a highly improved reference genome, we called over 6.7 M SNPs, providing an informative genetic data set for population analyses. Our results show very strong population structure in the platypus, with our sampling locations corresponding to discrete groupings between which there is no evidence for recent gene flow. Genome-wide data allowed us to establish that 28 of the 57 sampled individuals had at least a third-degree relative among other samples from the same river, often taken at different times. Taking advantage of a sampled family quartet, we estimated the de novo mutation rate in the platypus at 7.0 × 10−9/bp/generation (95% CI 4.1 × 10−9–1.2 × 10−8/bp/generation). We estimated effective population sizes of ancestral populations and haplotype sharing between current groupings, and found evidence for bottlenecks and long-term population decline in multiple regions, and early divergence between populations in different regions. This study demonstrates the power of whole-genome sequencing for studying natural populations of an evolutionarily important species.

Domestication Genomics of the Open-Pollinated Scarlet Runner Bean (Phaseolus coccineus L.).

The runner bean is a legume species from Mesoamerica closely related to common bean (Phaseolus vulgaris). It is a perennial species, but it is usually cultivated in small-scale agriculture as an annual crop for its dry seeds and edible immature pods. Unlike the common bean, P. coccineus has received little attention from a genetic standpoint. In this work we aim to (1) provide information about the domestication history and domestication events of P. coccineus; (2) examine the distribution and level of genetic diversity in wild and cultivated Mexican populations of this species; and, (3) identify candidate loci to natural and artificial selection. For this, we generated genotyping by sequencing data (42,548 SNPs) from 242 individuals of P. coccineus and the domesticated forms of the closely related species P. vulgaris (20) and P. dumosus (35). Eight genetic clusters were detected, of which half corresponds to wild populations and the rest to domesticated plants. The cultivated populations conform a monophyletic clade, suggesting that only one domestication event occurred in Mexico, and that it took place around populations of the Trans-Mexican Volcanic Belt. No difference between wild and domesticated levels of genetic diversity was detected and effective population sizes are relatively high, supporting a weak genetic bottleneck during domestication. Most populations presented an excess of heterozygotes, probably due to inbreeding depression. One population of P. coccineus subsp. striatus had the greatest excess and seems to be genetically isolated despite being geographically close to other wild populations. Contrasting with previous studies, we did not find evidence of recent gene flow between wild and cultivated populations. Based on outlier detection methods, we identified 24 domestication-related SNPs, 13 related to cultivar diversification and eight under natural selection. Few of these SNPs fell within annotated loci, but the annotated domestication-related SNPs are highly expressed in flowers and pods. Our results contribute to the understanding of the domestication history of P. coccineus, and highlight how the genetic signatures of domestication can be substantially different between closely related species.

Genomewide variation provides insight into evolutionary relationships in a monkeyflower species complex (Mimulus sect. Diplacus).

Evolutionary radiations provide excellent opportunities to study the origins of biodiversity, but rapid divergence and ongoing gene flow make inferring evolutionary relationships among taxa difficult. Consequently, combining morphological and genomic analyses will be necessary to clarify the evolutionary history of radiations. We used an integrative approach to shed light on relationships within a diverse radiation of monkeyflowers (Mimulus section Diplacus) with a controversial taxonomic history. We used genomewide single nucleotide polymorphism data and a combination of phylogenetic and population genomic analyses to infer the evolutionary relationships within the group. Tests for hybridization were performed to reveal sources of shared variation, and multivariate analyses of floral trait data were conducted to examine the correspondence between phenotypic and phylogenetic data. We identified four primary clades with evidence for some shared variation among them. We also detected evidence for recent gene flow between closely related subclades and populations. Strong discordance between floral trait and molecular data provides evidence for divergent and convergent phenotypic evolution. Mimulus section Diplacus has all the hallmarks of a rapid radiation, including diverse taxa that are at different stages of divergence, extensive shared variation among taxa, and complex patterns of phenotypic evolution. Our findings will direct future evolutionary research and have important taxonomic implications that highlight the need for a new revision of section Diplacus.

The Near East as a cradle of biodiversity: A phylogeography of banded newts (genus Ommatotriton) reveals extensive inter- and intraspecific genetic differentiation

The banded newt (genus Ommatotriton) is widely distributed in the Near East (Anatolia, Caucasus and the Levant) – an understudied region from the perspective of phylogeography. The genus is polytypic, but the number of species included and the phylogenetic relationships between them are not settled. We sequenced two mitochondrial and two nuclear DNA markers throughout the range of Ommatotriton. For mtDNA we constructed phylogenetic trees, estimated divergence times using fossil calibration, and investigated changes in effective population size with Bayesian skyline plots and mismatch analyses. For nuDNA we constructed phylogenetic trees and haplotype networks. Species trees were constructed for all markers and nuDNA only. Species distribution models were projected on current and Last Glacial Maximum climate layers. We confirm the presence of three Ommatotriton species: O. nesterovi, O. ophryticus and O. vittatus. These species are genetically distinct and their most recent common ancestor was dated at ∼25Ma (Oligocene). No evidence of recent gene flow between species was found. The species show deep intraspecific genetic divergence, represented by geographically structured clades, with crown nodes of species dated ∼8–13Ma (Miocene to Early Quaternary); evidence of long-term in situ evolution and survival in multiple glacial refugia. While a species tree based on nuDNA suggested a sister species relationship between O. vittatus and O. ophryticus, when mtDNA was included, phylogenetic relationships were unresolved, and we refrain from accepting a particular phylogenetic hypothesis at this stage. While species distribution models suggest reduced and fragmented ranges during the Last Glacial Maximum, we found no evidence for strong population bottlenecks. We discuss our results in the light of other phylogeographic studies from the Near East. Our study underlines the important role of the Near East in generating and sustaining biodiversity.

Global phylogenetic relationships, population structure and gene flow estimation of Trialeurodes vaporariorum (Greenhouse whitefly).

Trialeurodes vaporariorum (Westwood, 1856) (Greenhouse whitefly) is an agricultural pest of global importance. It is associated with damage to plants during feeding and subsequent virus transmission. Yet, global phylogenetic relationships, population structure, and estimation of the rates of gene flow within this whitefly species remain largely unexplored. In this study, we obtained and filtered 227 GenBank records of mitochondrial cytochrome c oxidase I (mtCOI) sequences of T. vaporariorum, across various global locations to obtain a final set of 217 GenBank records. We further amplified and sequenced a ~750 bp fragment of mtCOI from an additional 31 samples collected from Kenya in 2014. Based on a total of 248 mtCOI sequences, we identified 16 haplotypes, with extensive overlap across all countries. Population structure analysis did not suggest population differentiation. Phylogenetic analysis indicated the 2014 Kenyan collection of samples clustered with a single sequence from the Netherlands to form a well-supported clade (denoted clade 1a) nested within the total set of sequences (denoted clade 1). Pairwise distances between sequences show greater sequence divergence between clades than within clades. In addition, analysis using migrate-n gave evidence for recent gene flow between the two groups. Overall, we find that T. vaporariorum forms a single large group, with evidence of further diversification consisting primarily of Kenyan sequences and one sequence from the Netherlands forming a well-supported clade.

The genetic architecture of local adaptation and reproductive isolation in sympatry within the Mimulus guttatus species complex.

The genetic architecture of local adaptation has been of central interest to evolutionary biologists since the modern synthesis. In addition to classic theory on the effect size of adaptive mutations by Fisher, Kimura and Orr, recent theory addresses the genetic architecture of local adaptation in the face of ongoing gene flow. This theory predicts that with substantial gene flow between populations local adaptation should proceed primarily through mutations of large effect or tightly linked clusters of smaller effect loci. In this study, we investigate the genetic architecture of divergence in flowering time, mating system-related traits, and leaf shape between Mimulus laciniatus and a sympatric population of its close relative M.guttatus. These three traits are probably involved in M.laciniatus' adaptation to a dry, exposed granite outcrop environment. Flowering time and mating system differences are also reproductive isolating barriers making them 'magic traits'. Phenotypic hybrids in this population provide evidence of recent gene flow. Using next-generation sequencing, we generate dense SNP markers across the genome and map quantitative trait loci (QTLs) involved in flowering time, flower size and leaf shape. We find that interspecific divergence in all three traits is due to few QTL of large effect including a highly pleiotropic QTL on chromosome 8. This QTL region contains the pleiotropic candidate gene TCP4 and is involved in ecologically important phenotypes in other Mimulus species. Our results are consistent with theory, indicating that local adaptation and reproductive isolation with gene flow should be due to few loci with large and pleiotropic effects.

Congruent patterns of connectivity can inform management for broadcast spawning corals on the Great Barrier Reef.

Connectivity underpins the persistence and recovery of marine ecosystems. The Great Barrier Reef (GBR) is the world's largest coral reef ecosystem and managed by an extensive network of no-take zones; however, information about connectivity was not available to optimize the network's configuration. We use multivariate analyses, Bayesian clustering algorithms and assignment tests of the largest population genetic data set for any organism on the GBR to date (Acropora tenuis, >2500 colonies; >50 reefs, genotyped for ten microsatellite loci) to demonstrate highly congruent patterns of connectivity between this common broadcast spawning reef-building coral and its congener Acropora millepora (~950 colonies; 20 reefs, genotyped for 12 microsatellite loci). For both species, there is a genetic divide at around 19°S latitude, most probably reflecting allopatric differentiation during the Pleistocene. GBR reefs north of 19°S are essentially panmictic whereas southern reefs are genetically distinct with higher levels of genetic diversity and population structure, most notably genetic subdivision between inshore and offshore reefs south of 19°S. These broadly congruent patterns of higher genetic diversities found on southern GBR reefs most likely represent the accumulation of alleles via the southward flowing East Australia Current. In addition, signatures of genetic admixture between the Coral Sea and outer-shelf reefs in the northern, central and southern GBR provide evidence of recent gene flow. Our connectivity results are consistent with predictions from recently published larval dispersal models for broadcast spawning corals on the GBR, thereby providing robust connectivity information about the dominant reef-building genus Acropora for coral reef managers.

Deep Roots for Aboriginal Australian Y Chromosomes

SummaryAustralia was one of the earliest regions outside Africa to be colonized by fully modern humans, with archaeological evidence for human presence by 47,000 years ago (47 kya) widely accepted [1, 2]. However, the extent of subsequent human entry before the European colonial age is less clear. The dingo reached Australia about 4 kya, indirectly implying human contact, which some have linked to changes in language and stone tool technology to suggest substantial cultural changes at the same time [3]. Genetic data of two kinds have been proposed to support gene flow from the Indian subcontinent to Australia at this time, as well: first, signs of South Asian admixture in Aboriginal Australian genomes have been reported on the basis of genome-wide SNP data [4]; and second, a Y chromosome lineage designated haplogroup C∗, present in both India and Australia, was estimated to have a most recent common ancestor around 5 kya and to have entered Australia from India [5]. Here, we sequence 13 Aboriginal Australian Y chromosomes to re-investigate their divergence times from Y chromosomes in other continents, including a comparison of Aboriginal Australian and South Asian haplogroup C chromosomes. We find divergence times dating back to ∼50 kya, thus excluding the Y chromosome as providing evidence for recent gene flow from India into Australia.

Investigating the genetic variation and structure of a native unionid mussel in the Laurentian Great Lakes following an invasion of dreissenid mussels

Despite massive population declines in the open waters of Lake St. Clair due to invasive dreissenid mussels, the St. Clair River Delta has persisted as a refuge habitat for native unionid mussels. This study was conducted to determine how Dreissena-induced population declines might have impacted the genetic population structure of native unionid species. Nine variable microsatellite markers were used to assess the genetic population structure of the Fatmucket mussel (Lampsilis siliquoidea) across 18 sites (n = 341 individuals) within the delta and four of its tributaries. Results indicate that Fatmuckets within the various bays of the St. Clair Delta and tributaries show limited genetic differentiation by geographic distance but still represent a single population with evidence of recent gene flow, little differentiation among sampling sites, relatively high allelic richness at all sites, and little evidence supporting a recent genetic bottleneck. The Fatmucket is the most common species found in the delta and poor genetic health and connectivity of this species might have indicated a dire situation for less common and imperiled species found in the same habitats. Because this did not appear to be the case, little can be assumed about other mussel species.

Genetic analysis of hybridization between domesticated endangered pig breeds and wild boar

Black Slavonian (DBS) pig and Turopolje pig (DTP) are endangered autochthonous Croatian pig breeds that are still reared in a traditional way under semi-wild conditions in an area populated with growing wild boar populations. This raises the possibility of hybridization between domestic pigs and wild boars, a possibility often debated but rarely analyzed genetically. We analyzed potential hybridization between populations of domestic pigs (DBS, N=28; DTP, N=46) and wild boars (WBS) in eastern and western Slavonia (N=20 each) using 14 microsatellite markers and a Bayesian clustering algorithm (STRUCTURE). The STRUCTURE analysis classified all animals into corresponding WBS, DBS and DTP clusters. However, the DTP cluster contained four DTP animals with WBS membership coefficients (q) ranging from 0.25 to 0.35. These results provide genetic evidence of recent gene flow from WBS into DTP. We recommend monitoring the purity of DTP individuals to preserve the genetic integrity of this critically endangered breed. More generally, our findings provide an example of multiple hybridization events in the history of pig domestication.

An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences.

Once thought rare in animal taxa, hybridization has been increasingly recognized as an important and common force in animal evolution. In the past decade, a number of studies have suggested that hybridization has driven speciation in some animal groups. We investigate the signature of hybridization in the genome of a putative hybrid species, Xiphophorus clemenciae, through whole genome sequencing of this species and its hypothesized progenitors. Based on analysis of this data, we find that X. clemenciae is unlikely to have been derived from admixture between its proposed parental species. However, we find significant evidence for recent gene flow between Xiphophorus species. Although we detect genetic exchange in two pairs of species analyzed, the proportion of genomic regions that can be attributed to hybrid origin is small, suggesting that strong behavioral premating isolation prevents frequent hybridization in Xiphophorus. The direction of gene flow between species is potentially consistent with a role for sexual selection in mediating hybridization.