Allopatric Isolation Research Articles

Genetic and morphological support for possible sympatric origin of fish from subterranean habitats

Two blind Iran cave barbs, Garra typhlops and Garra lorestanensis, exist in sympatry in a single subterranean habitat, raising the hypothesis that they may represent a case of sympatric speciation following a colonization event. Their different mental disc forms have prompted some authors to propose the alternative hypothesis of two separate colonization events. In this study, we analysed a genome-wide panel of 11,257 SNPs genotyped by means of genotyping-by-sequencing combined with mitochondrial cytochrome c oxidase sub-unit I sequence data, field observations and morphological traits to test these two hypotheses. Field data suggest some degree of ecological divergence despite some possible niche overlap such that hybridization is possible. According to both nuclear and mtDNA data, the cave barb species are monophyletic with close phylogenetic relationships with Garra gymnothorax from the Karun-Dez and Karkheh river basins. The historical demography analysis revealed that a model of Isolation-with-Migration (IM) best fitted the data, therefore better supporting a scenario of sympatric origin than that of allopatric isolation followed by secondary contact. Overall, our results offer stronger support to the hypothesis that speciation in the subterranean habitat could have occurred in sympatry following a colonization event from the Karun-Dez-Karkheh basins in the Zagros Mountains of Iran.

The absence of reproductive isolation between non-sister and deeply diverged mitochondrial lineages of the black-throated tit (Aegithalos concinnus) revealed by a multilocus genetic analysis in a contact zone

BackgroundA deep divergence of mitochondrial DNA is common in species delimitated by morphological traits. Several hypotheses can explain such variations, such as cryptic species, introgression, allopatric divergence and ancestral lineage. The black-throated tit harbors several deeply divergent mitochondrial lineages. Two lineages with 5% divergence, but having a high level of gene flow, have been detected in its subspecies, A. C. concinnus and A. c. talifuenses. In this study, we conducted a genetic analysis at a contact zone of these two lineages to identify whether these lineages either reflect a high level of intraspecific variation in mitochondrial loci or represent incipient speciation. Mitochondrial ND2 and 11 microsatellite loci were used to conduct phylogenetic and population structure analyses.ResultsND2 haplotypes actually diverged into two groups within subspecies A. c. talifuenses; however, they formed a non-sister relationship when including all available GenBank ND2 sequences. Analyses of microsatellite data indicated no existing population structure and showed a pattern of isolation by distance. Individuals sampled at the contact zone were almost identified as F2 hybrids.ConclusionsIsolation for 2.4 Ma, as suggested by a previous study, appeared to be insufficient to develop robust reproductive barriers. Reproductive barriers were weak, or even absent between the divergent lineages, highlighting that incipient speciation was unlikely to be the case. Considering the results from previous studies, the divergent lineages may be better explained by secondary contact after allopatric isolation because of Pleistocene climate changes, but other hypotheses cannot be definitively ruled out because of the lack of representative samples from the other distribution region and its relatives. Considering that divergence in morphology was hardly observed and the particular split in genetics, the two subspecies might be better merged. The current findings also highlight the likely contribution of male-biased dispersal to male-biased gene flow among mitochondrial lineages; more efforts are needed to illustrate the evolutionary history of the black-throated tit.

Cryptic biodiversity and phylogeographic patterns of Seychellois Ligia isopods.

Ligia isopods are conspicuous inhabitants of rocky intertidal habitats exhibiting several biological traits that severely limit their dispersal potential. Their presence in patchy habitats and low vagility may lead to long term isolation, allopatric isolation and possible cryptic speciation. Indeed, various species of Ligia have been suggested to represent instead cryptic species complexes. Past studies; however, have largely focused in Eastern Pacific and Atlantic species of Ligia, leaving in doubt whether cryptic diversity occurs in other highly biodiverse areas. The Seychelles consists of 115 islands of different ages and geological origins spread across the western Indian Ocean. They are well known for their rich biodiversity with recent reports of cryptic species in terrestrial Seychellois organisms. Despite these studies, it is unclear whether coastal invertebrates from the Seychelles harbor any cryptic diversity. In this study, we examined patterns of genetic diversity and isolation within Ligia isopods across the Seychelles archipelago by characterizing individuals from locations across both inner and outer islands of the Seychelles using mitochondrial and nuclear markers. We report the presence of highly divergent lineages of independent origin. At Aldabra Atoll, we uncovered a lineage closely related to the Ligia vitiensis cryptic species complex. Within the inner islands of Cousine, Silhouette, and Mahé we detected the presence of two moderately divergent and geographically disjunct lineages most closely related to Ligia dentipes. Our findings suggest that the Seychelles may harbor at least three novel species of Ligia in need of description and that these species may have originated independently.

Deep-Sea Phylogeographic Structure Shaped by Paleoenvironmental Changes and Ongoing Ocean Currents Around the Sea of Japan in a Crangonid Shrimp, Argis lar.

The deep-sea crangonid shrimp, Argis lar, is a highly abundant species from the northern Pacific Ocean. We investigated its phylogeographic and demographic structure across the species' extensive range, using mitochondrial DNA sequence variation to evaluate the impact of deep-sea paleoenvironmental dynamics in the Sea of Japan on population histories. The haplotype network detected three distinct lineages with allopatric isolation, which roughly corresponded to the Sea of Japan (Lineage A), the northwestern Pacific off the Japanese Archipelago (Lineage B), and the Bering Sea/Gulf of Alaska (Lineage C). Lineage A showed relatively low haplotype and nucleotide diversity, a significantly negative value of Tajima's D, and a star-shaped network, suggesting that anoxic bottom-water in the Sea of Japan over the last glacial period may have brought about a reduction in the Sea of Japan population. Furthermore, unexpectedly, the distributions of Lineage A and B were closely related to the pathways of the two ocean currents, especially along the Sanriku Coast. This result indicated that A. lar could disperse across shallow straits through the ocean current, despite their deep-sea adult habitat. Bayesian inference of divergence time revealed that A. lar separated into three lineages approximately 1 million years before present (BP) in the Pleistocene, and then had been influenced by deep-sea paleoenvironmental change in the Sea of Japan during the last glacial period, followed by a more recent larval dispersal with the ocean current since ca. 6 kilo years BP.

Cryptic diversity and speciation in endemic Cytherissa (Ostracoda, Crustacea) from Lake Baikal

Lake Baikal (Siberia) is the most ancient and deepest of all ancient lakes on Earth. It holds a (mostly endemic) diversity of thousands of animal species, including a speciose radiation of ostracods of the genus Cytherissa. Applying molecular tools to this crustacean group reveals that several morphological species are actually species clusters. Based on combined 16S and 28S DNA sequence data from thirteen classic Cytherissa species and one subspecies sensu Mazepova (1990), we recognize 26 different genetic Cytherissa species, 18 with morphological variation and eight truly cryptic species. These results suggest that the actual specific diversity of Cytherissa in Lake Baikal might easily be double of what is presently known. Baikalian endemic species most likely live in the cradle in which they originated and this opens perspectives to infer modes of speciation. Our current distribution data of Cytherissa species provide first indications for both geographic (lakes basins and shores) and ecological (sediment type, water depth) separation. Our present data thus provide the first steps towards future, rigorous testing of focussed hypotheses on the causality of speciation through either allopatric isolation or parapatric ecological clines.

Dispersal assembly of rain forest tree communities across the Amazon basin

We investigate patterns of historical assembly of tree communities across Amazonia using a newly developed phylogeny for the species-rich neotropical tree genus Inga We compare our results with those for three other ecologically important, diverse, and abundant Amazonian tree lineages, Swartzia, Protieae, and Guatteria Our analyses using phylogenetic diversity metrics demonstrate a clear lack of geographic phylogenetic structure, and show that local communities of Inga and regional communities of all four lineages are assembled by dispersal across Amazonia. The importance of dispersal in the biogeography of Inga and other tree genera in Amazonian and Guianan rain forests suggests that speciation is not driven by vicariance, and that allopatric isolation following dispersal may be involved in the speciation process. A clear implication of these results is that over evolutionary timescales, the metacommunity for any local or regional tree community in the Amazon is the entire Amazon basin.

Isolation with asymmetric gene flow during the nonsynchronous divergence of dry forest birds.

Dry forest bird communities in South America are often fragmented by intervening mountains and rainforests, generating high local endemism. The historical assembly of dry forest communities likely results from dynamic processes linked to numerous population histories among codistributed species. Nevertheless, species may diversify in the same way through time if landscape and environmental features, or species ecologies, similarly structure populations. Here we tested whether six co-distributed taxon pairs that occur in the dry forests of the Tumbes and Marañón Valley of northwestern South America show concordant patterns and modes of diversification. We employed a genome reduction technique, double-digest restriction site-associated DNA sequencing, and obtained 4407-7186 genomewide SNPs. We estimated demographic history in each taxon pair and inferred that all pairs had the same best-fit demographic model: isolation with asymmetric gene flow from the Tumbes into the Marañón Valley, suggesting a common diversification mode. Overall, we also observed congruence in effective population size (Ne ) patterns where ancestral Ne were 2.9-11.0× larger than present-day Marañón Valley populations and 0.3-2.0× larger than Tumbesian populations. Present-day Marañón Valley Ne was smaller than Tumbes. In contrast, we found simultaneous population isolation due to a single event to be unlikely as taxon pairs diverged over an extended period of time (0.1-2.9Ma) with multiple nonoverlapping divergence periods. Our results show that even when populations of codistributed species asynchronously diverge, the mode of their differentiation can remain conserved over millions of years. Divergence by allopatric isolation due to barrier formation does not explain the mode of differentiation between these two bird assemblages; rather, migration of individuals occurred before and after geographic isolation.

A combination of long term fragmentation and glacial persistence drove the evolutionary history of the Italian wall lizard Podarcis siculus

BackgroundThe current distribution of genetic diversity is the result of a vast array of microevolutionary processes, including short-term demographic and ecological mechanisms and long-term allopatric isolation in response to Quaternary climatic fluctuations. We investigated past processes that drove the population differentiation and spatial genetic distribution of the Italian wall lizard Podarcis siculus by means of sequences of mitochondrial cytb (n = 277 from 115 localities) and nuclear mc1r and β-fibint7genes (n = 262 and n = 91, respectively) from all its distribution range. The pattern emerging from the genetic data was compared with current and past (last glacial maximum) species distribution modeling (SDM).ResultsWe identified seven deeply divergent parapatric clades which presumably remained isolated in different refugia scattered mainly throughout the Tyrrhenian coast. Conversely, the Adriatic coast showed only two haplogroups with low genetic variability. These results appear to agree with the SDM prediction at the last glacial maximum (LGM) indicating a narrow area of habitat suitability along the Tyrrhenian coast and much lower suitability along the Adriatic one. However, the considerable land exposure of the Adriatic coastline favored a glacial colonization of the Balkan Peninsula.ConclusionsOur population-level historical demography showed a common trend consistent with glacial expansions and regional persistence during the last glacial maximum. This complex genetic signature appears to be inconsistent with the expectation of the expansion-contraction model and post-LGM (re)colonizations from southern refugia. Hence it is one of an increasing number of cases in which these assumptions are not met, indicating that long-term fragmentation and pre-LGM events such as glacial persistence were more prominent in shaping genetic variation in this temperate species.

Parallel genetic divergence among coastal-marine ecotype pairs of European anchovy explained by differential introgression after secondary contact.

Ecophenotypic differentiation among replicate ecotype pairs within a species complex is often attributed to independent outcomes of parallel divergence driven by adaptation to similar environmental contrasts. However, the extent to which parallel phenotypic and genetic divergence patterns have emerged independently is increasingly questioned by population genomic studies. Here, we document the extent of genetic differentiation within and among two geographic replicates of the coastal and marine ecotypes of the European anchovy (Engraulis encrasicolus) gathered from Atlantic and Mediterranean locations. Using a genome-wide data set of RAD-derived SNPs, we show that habitat type (marine vs. coastal) is the most important component of genetic differentiation among populations of anchovy. By analysing the joint allele frequency spectrum of each coastal-marine ecotype pair, we show that genomic divergence patterns between ecotypes can be explained by a postglacial secondary contact following a long period of allopatric isolation (c. 300kyrs). We found strong support for a model including heterogeneous migration among loci, suggesting that secondary gene flow has eroded past differentiation at different rates across the genome. Markers experiencing reduced introgression exhibited strongly correlated differentiation levels among Atlantic and Mediterranean regions. These results support that partial reproductive isolation and parallel genetic differentiation among replicate pairs of anchovy ecotypes are largely due to a common divergence history prior to secondary contact. They moreover provide comprehensive insights into the origin of a surprisingly strong fine-scale genetic structuring in a high gene flow marine fish, which should improve stock management and conservation actions.

Phylogeography of Indo‐Pacific reef fishes: sister wrasses Coris gaimard and C. cuvieri in the Red Sea, Indian Ocean and Pacific Ocean

AbstractAimThe aim of this study was to resolve the evolutionary history, biogeographical barriers and population histories for sister species of wrasses, the African Coris (Coris cuvieri) in the Indian Ocean and Red Sea, and the Yellowtail Coris (Coris gaimard) in the Pacific Ocean. Glacial sea level fluctuations during the Pleistocene have shaped the evolutionary trajectories of Indo‐Pacific marine fauna, primarily by creating barriers between the Red Sea, Indian Ocean and Pacific Ocean. Here, we evaluate the influence of these episodic glacial barriers on sister species C. cuvieri and C. gaimard.LocationRed Sea, Indian Ocean, Pacific Ocean.MethodsSequences from mitochondrial DNA cytochrome oxidase c subunit I (COI), and nuclear introns gonadotropin‐releasing hormone (GnRH) and ribosomal S7 protein were analysed in 426 individuals from across the range of both species. Median‐joining networks, analysis of molecular variance and Bayesian estimates of the time since most recent common ancestor were used to resolve recent population history and connectivity.ResultsCytochrome oxidase c subunit I haplotypes showed a divergence of 0.97% between species, and nuclear alleles were shared between species. No population structure was detected between the Indian Ocean and Red Sea. The strongest signal of population structure was in C. gaimard between the Hawaiian biogeographical province and other Pacific locations (COI ϕST = 0.040–0.173, P < 0.006; S7 ϕST = 0.046, P < 0.001; GnRH ϕST = 0.022, P < 0.005). Time to most recent common ancestor is c. 2.12 Ma for C. cuvieri and 1.76 Ma for C. gaimard.Main conclusionsWe demonstrate an Indian‐Pacific divergence of < 2 Myr and high contemporary gene flow between the Red Sea and Indian Ocean, mediated in part by the long pelagic larval stage. The discovery of hybrids at Christmas Island indicates that Indian and Pacific lineages have come into secondary contact after allopatric isolation. Subspecies status may be appropriate for these two wrasses.

Long-term persisting hybrid swarm and geographic difference in hybridization pattern: genetic consequences of secondary contact between two Vincetoxicum species (Apocynaceae–Asclepiadoideae)

BackgroundDuring glacial periods, glacial advances caused temperate plant extirpation or retreat into localized warmer areas, and subsequent postglacial glacial retreats resulted in range expansions, which facilitated secondary contact of previously allopatric isolated lineages. The evolutionary outcomes of secondary contact, including hybrid zones, dynamic hybrid swarm, and resultant hybrid speciation, depends on the strengths of reproductive barriers that have arisen through epistatic and pleiotropic effects during allopatric isolation. The aim of this study was to demonstrate refugia isolation and subsequent secondary contact between two perennial Asclepioid species and to assess the genetic consequences of the secondary contact. We modeled the range shift of two ecologically distinct Vincetoxicum species using the species distribution model (SDM) and assessed the genetic consequences of secondary contact by combining morphological and genetic approaches. We performed morphometric analysis (592 individuals) and examined 10 nuclear microsatellites (671 individuals) in V. atratum, V. japonicum, and putative hybrid populations.ResultsMultivariate analysis, model-based Bayesian analysis, and non-model-based discriminant analysis of principal components confirmed the hybridization between V. atratum and V. japonicum. High pollen fertility and a lack of linkage disequilibrium suggested that the hybrid populations may be self-sustaining and have persisted since V. atratum and V. japonicum came into contact during the post-glacial period. Moreover, our findings show that the pattern of hybridization between V. atratum and V. japonicum is unidirectional and differs among populations. Geographically-isolated hybrid populations exist as genetically distinct hybrid swarms that consist of V. atratum-like genotypes, V. japonicum-like genotypes, or admixed genotypes. In addition, Bayesian-based clustering analysis and coalescent-based estimates of long-term gene flow showed patterns of introgressive hybridization in three morphologically ‘pure’ V. japonicum populations.ConclusionIn this study, we demonstrated that climatic oscillations during the Quaternary period likely led to species range shift and subsequently secondary contact. Hybrid populations may be self-sustaining and have persisted since V. atratum and V. japonicum came into contact during the post-glacial period. Pattern of hybridization between V. atratum and V. japonicum is unidirectional and differs among populations. We concluded that these differences in the genetic consequences of secondary contact are caused by historical colonization processes and/or natural selection.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0587-2) contains supplementary material, which is available to authorized users.

Genomic sequencing reveals historical, demographic and selective factors associated with the diversification of the fire-associated fungus Neurospora discreta.

Delineating microbial populations, discovering ecologically relevant phenotypes and identifying migrants, hybrids or admixed individuals have long proved notoriously difficult, thereby limiting our understanding of the evolutionary forces at play during the diversification of microbial species. However, recent advances in sequencing and computational methods have enabled an unbiased approach whereby incipient species and the genetic correlates of speciation can be identified by examining patterns of genomic variation within and between lineages. We present here a population genomic study of a phylogenetic species in the Neurospora discreta species complex, based on the resequencing of full genomes (~37 Mb) for 52 fungal isolates from nine sites in three continents. Population structure analyses revealed two distinct lineages in South-East Asia, and three lineages in North America/Europe with a broad longitudinal and latitudinal range and limited admixture between lineages. Genome scans for selective sweeps and comparisons of the genomic landscapes of diversity and recombination provided no support for a role of selection at linked sites on genomic heterogeneity in levels of divergence between lineages. However, demographic inference indicated that the observed genomic heterogeneity in divergence was generated by varying rates of gene flow between lineages following a period of isolation. Many putative cases of exchange of genetic material between phylogenetically divergent fungal lineages have been discovered, and our work highlights the quantitative importance of genetic exchanges between more closely related taxa to the evolution of fungal genomes. Our study also supports the role of allopatric isolation as a driver of diversification in saprobic microbes.

Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation.

One of the most celebrated examples of sympatric speciation in nature are monophyletic radiations of cichlid fishes endemic to Cameroon crater lakes. However, phylogenetic inference of monophyly may not detect complex colonization histories involving some allopatric isolation, such as double invasions obscured by genome-wide gene flow. Population genomic approaches are better suited to test hypotheses of sympatric speciation in these cases. Here, we use comprehensive sampling from all four sympatric crater lake cichlid radiations in Cameroon and outgroups across Africa combined with next-generation sequencing to genotype tens of thousands of SNPs. We find considerable evidence of gene flow between all four radiations and neighboring riverine populations after initial colonization. In a few cases, some sympatric species are more closely related to outgroups than others, consistent with secondary gene flow facilitating their speciation. Our results do not rule out sympatric speciation in Cameroon cichlids, but rather reveal a complex history of speciation with gene flow, including allopatric and sympatric phases, resulting in both reproductively isolated species and incipient species complexes. The best remaining non-cichlid examples of sympatric speciation all involve assortative mating within microhabitats. We speculate that this feature may be necessary to complete the process of sympatric speciation in nature.

Can we continue to neglect genomic variation in introgression rates when inferring the history of speciation? A case study in a Mytilus hybrid zone.

The use of molecular data to reconstruct the history of divergence and gene flow between populations of closely related taxa represents a challenging problem. It has been proposed that the long-standing debate about the geography of speciation can be resolved by comparing the likelihoods of a model of isolation with migration and a model of secondary contact. However, data are commonly only fit to a model of isolation with migration and rarely tested against the secondary contact alternative. Furthermore, most demographic inference methods have neglected variation in introgression rates and assume that the gene flow parameter (Nm) is similar among loci. Here, we show that neglecting this source of variation can give misleading results. We analysed DNA sequences sampled from populations of the marine mussels, Mytilus edulis and M.galloprovincialis, across a well-studied mosaic hybrid zone in Europe and evaluated various scenarios of speciation, with or without variation in introgression rates, using an Approximate Bayesian Computation (ABC) approach. Models with heterogeneous gene flow across loci always outperformed models assuming equal migration rates irrespective of the history of gene flow being considered. By incorporating this heterogeneity, the best-supported scenario was a long period of allopatric isolation during the first three-quarters of the time since divergence followed by secondary contact and introgression during the last quarter. By contrast, constraining migration to be homogeneous failed to discriminate among any of the different models of gene flow tested. Our simulations thus provide statistical support for the secondary contact scenario in the European Mytilus hybrid zone that the standard coalescent approach failed to confirm. Our results demonstrate that genomic variation in introgression rates can have profound impacts on the biological conclusions drawn from inference methods and needs to be incorporated in future studies.

Hopping out of Mindanao: Miocene‐Pliocene geological processes and cross‐island dispersal as major drivers of diversity for Philippine treehoppers

AbstractAimWe investigated the biogeographical history of an endemic Philippine treehopper, Pyrgonota bifoliata (Membracidae), to test the effect of Neogene geological events and Pleistocene climate change in generating speciation within the Philippines.LocationThe Philippine archipelago.MethodsPhylogenies were reconstructed based on the mitochondrial cytochrome c oxidase I subunit (cox1) and nuclear wingless (wg) genes using maximum parsimony, maximum likelihood and Bayesian criteria. Divergence times were estimated in beast based on a range of mutation rates. Ancestral ranges were reconstructed using rasp (Reconstruct Ancestral State in Phylogenies) and Bayesian stochastic search variable selection (BSSVS). Species boundaries were tested using the Bayesian general mixed Yule coalescent (bGMYC) and Bayesian phylogenetic and phylogeography (BPP) methods.ResultsPyrgonota bifoliata showed one of the lowest levels of between‐Pleistocene island genetic variation among all the taxa examined. Most Pleistocene aggregate island complex (PAIC) lineages and extant P. bifoliata originated before the onset of the first extensive Pleistocene glacial cycle. Ancestral P. bifoliata originated in the late Miocene from Mindanao, followed by a sequential northwards colonization of the Visayan Islands and Luzon in the Pliocene–early Pleistocene, which coincided with the spatial reorganization of the Philippines. The statistically delimited nine provisional species of what we now view as the P. bifoliata species complex correspond to current island boundaries and specialized host plants.Main conclusionsThe temporally calibrated phylogeny of P. bifoliata represents the first invertebrate study to support the hypothesis that Miocene–Pliocene geological events and consequent cross‐island dispersal were pivotal promoters of species diversity in the Philippines. We hypothesize that ecological adaptation to specialized host plants, together with either local selection or genetic drift through within‐island allopatric isolation, present a plausible in situ speciation mechanism for the origin of these herbivorous insects.

Pleistocene speciation with and without gene flow in Euphaea damselflies of subtropical and tropical East Asian islands

Climatic oscillations during the Pleistocene period could have had a profound impact on the origin of tropical species by the alternation of allopatric isolation and interpopulation gene flow cycles. However, whether tropical speciation involves strictly allopatric isolation, or proceeds in the face of homogenizing gene flow, is relatively unclear. Here, we investigated geographical modes of speciation in four closely related Euphaea damselfly species endemic to the subtropical and tropical East Asian islands using coalescent analyses of a multilocus data set. The reconstructed phylogenies demonstrated distinct species status for each of the four species and the existence of two sister species pairs, Euphaea formosa/E. yayeyamana and E. decorata/E. ornata. The species divergence time of the sibling Euphaea damselflies dates back to within the last one Mya of the Middle to Lower Pleistocene. The speciation between the populous E. formosa of Taiwan and the less numerous E. yayeyamana of the Yaeyama islands occurred despite significant bidirectional, asymmetric gene flow, which is strongly inconsistent with a strictly allopatric model. In contrast, speciation of the approximately equal-sized populations of E. decorata of the southeast Asian mainland and E. ornata of Hainan is inferred to have involved allopatric divergence without gene flow. Our findings suggest that differential selection of natural or sexual environments is a prominent driver of species divergence in subtropical E. formosa and E. yayeyamana; whereas for tropical E. decorata and E. ornata at lower latitudes, allopatric isolation may well be a pivotal promoter of species formation.

Intercontinental divergence in the Populus‐associated ectomycorrhizal fungus, Tricholoma populinum

The ectomycorrhizal fungus Tricholoma populinum is host-specific with Populus species. T. populinum has wind-dispersed progagules and may be capable of long-distance dispersal. In this study, we tested the hypothesis of a panmictic population between Scandinavia and North America. DNA sequences from five nuclear loci were used to assess phylogeographic structure and nucleotide divergence between continents. Tricholoma populinum was composed of Scandinavian and North American lineages with complete absence of shared haplotypes and only one shared nucleotide mutation. Divergence of these lineages was estimated at approx. 1.7-1.0 million yr ago (Ma), which occurred after the estimated divergence of host species Populus tremula and Populus balsamifera/Populus trichocarpa at 5 Ma. Phylogeographic structure was not observed within Scandinavian or North American lineages of T. populinum. Intercontinental divergence appears to have resulted from either allopatric isolation; a recent, rare long-distance dispersal founding event followed by genetic drift; or the response in an obligate mycorrhizal fungus with a narrow host range to contractions and expansion of host distribution during glacial and interglacial episodes within continents. Understanding present genetic variation in populations is important for predicting how obligate symbiotic fungi will adapt to present and future changing climatic conditions.

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.

Present and past genetic connectivity of the Indo‐Pacific tropical eel Anguilla bicolor

AbstractAim The objective of this study was to reveal the present population structure and infer the gene‐flow history of the Indo‐Pacific tropical eel Anguilla bicolor.Location The Indo‐Pacific region.Methods The entire mitochondrial control region sequence and the genotypes at six microsatellite loci were analysed for 234 specimens collected from eight representative localities where two subspecies have been historically designated. In order to infer the population structure, genetic differentiation estimates, analysis of molecular variance and gene‐tree reconstruction were performed. The history of migration events and population growth was assessed using neutrality tests based on allelic frequency spectrum, coalescent‐based estimation of gene flow and Bayesian demographic analysis using control region sequences.Results Population structure analysis showed genetic divergence between eels from the Indian and Pacific oceans (FST = 0.0174–0.0251, P < 0.05 for microsatellites; ΦST = 0.706, P < 0.001 for control region), while no significant variation was observed within each ocean. Two mitochondrial sublineages that do not coincide with geographical regions were found in the Indian Ocean clade of a gene tree. However, these two sublineages were not differentiated at the microsatellite markers. The estimation of mitochondrial gene‐flow history suggested allopatric isolation between the Indian and Pacific oceans, and a possible secondary contact within the Indian Ocean after an initial population splitting. Bayesian demographic history reconstruction and neutrality tests indicated population growth in each ocean after the Indo‐Pacific divergence.Main conclusions Anguilla bicolor has diverged between the Indian and Pacific oceans, which is consistent with the classical subspecies designation, but is apparently genetically homogeneous in the Indian Ocean. The analysis of gene‐flow and demographic history indicated that the two mitochondrial sublineages observed in the Indian Ocean probably represent the haplotype groups of relict ancestral populations. A comparison with a sympatric congener suggested that absolute physical barriers to gene flow may not be necessary for population divergence in eels.

Genetic and geographic structure of an insect resistant and a susceptible type of Barbarea vulgaris in western Europe

Interactions between herbivores and plants are believed to have been important drivers of biodiversity. However, to drive an initial resistance divergence into different evolutionary lineages and taxa, these interactions have probably been embedded in other processes of divergence, like allopatric isolation. The cruciferous plant Barbarea vulgaris ssp. arcuata occurs in Denmark in two types: one (G) is resistant to most genotypes of the flea beetle Phyllotreta nemorum, the other (P) is susceptible. The two types additionally differ in hairiness and glucosinolates, they are genetically strongly divergent, and reproduction between them is reduced. To determine whether the two plant types and their resistance polymorphisms are also present outside Denmark, and to understand how they have evolved, we analysed 33 European populations of B. vulgaris for resistance, hairiness, glucosinolates, and microsatellite markers. Most populations had traits indicative of the G type, including the already characterized Danish G populations. In contrast, only two populations outside Denmark were of the P type; one from northern Sweden and one from Estonia. Genetically, the G populations formed two genetic clusters that were strongly divergent from a genetic cluster containing P populations. A fourth genetic cluster, which contained only a single population and no Danish plants, belonged morphologically to the subspecies ssp. vulgaris. The divergence found in Denmark between a resistant G and a susceptible P type is thus part of a larger divergence in Europe. Judging from the trait correlations, genetic divergence, and partial reproductive incompatibility, the plant types must have been isolated from each other for quite some time. The two P populations outside Denmark came from the north and east, suggesting a more eastern distribution. If so, resistant and susceptible types could have diverged during the ice age and later met in Scandinavia. However, more samples from Eastern Europe are needed to clarify this.