Allopatric Isolation Research Articles

Post‐glacial recolonization and multiple scales of secondary contact contribute to contemporary Atlantic salmon (Salmo salar) genomic variation in North America

AbstractAimIn northern environments, periods of isolation during Pleistocene glaciations and subsequent recolonization and secondary contact have had a significant influence on contemporary diversity of many species. The recent advent of high‐resolution genomic analyses allows unprecedented power to resolve genomic signatures of such events in northern species. Here, we provide the highest resolution genomic characterization of Atlantic salmon in North America to date to infer glacial refugia and the geographic scales of post‐glacial secondary contact.LocationNorth America.TaxonAtlantic salmon, Salmo salar.MethodsSamples were collected for 5455 individuals from 148 populations, encompassing the majority of the Atlantic salmon's native range in North America, from Labrador to Maine. Individuals were genotyped using a 220K single nucleotide polymorphism array aligned to the Atlantic salmon (Salmo salar) genome. Spatial genetic structure (principal component analysis, k‐means clustering, admixture) was evaluated in conjunction with genomic comparisons of these identified lineages to infer the refugia during the last glacial maximum and regions of secondary contact following recolonization.ResultsSpatial genomic analyses identified three phylogeographic groups, consistent with the northward recolonization from two southern glacial refugia in North America (a western Maritime lineage and an eastern Newfoundland and Labrador lineage), with subsequent differentiation of the eastern lineage into two separate groups. Secondary contact among these North American groups was observed within the northern Gulf of St. Lawrence, and evidence of trans‐Atlantic secondary contact was detected within the eastern Newfoundland and Labrador lineage. Comparison of groups from insular Newfoundland with those from mainland Labrador suggests genomic regions displaying high differentiation were characterized by elevated European admixture, suggesting a possible role of European secondary contact in population divergence.Main ConclusionsThese findings present the first evidence suggesting that genomic diversity in extant North American Atlantic salmon populations has resulted from allopatric isolation in two glacial refugia followed by both regional and trans‐Atlantic recolonization and secondary contact and demonstrate the power of genomic tools to resolve historical drivers of diversity in wild populations.

Landscape Heterogeneity Explains the Genetic Differentiation of a Forest Bird across the Sino-Himalayan Mountains.

Mountains are the world's most important centers of biodiversity. The Sino-Himalayan Mountains are global biodiversity hotspot due to their extremely high species richness and endemicity. Ample research investigated the impact of the Qinghai-Tibet Plateau uplift and Quaternary glaciations in driving species diversification in plants and animals across the Sino-Himalayan Mountains. However, little is known about the role of landscape heterogeneity and other environmental features in driving diversification in this region. We utilized whole genomes and phenotypic data in combination with landscape genetic approaches to investigate population structure, demography, and genetic diversity in a forest songbird species native to the Sino-Himalayan Mountains, the red-billed leiothrix (Leiothrix lutea). We identified 5 phylogeographic clades, including 1 in the East of China, 1 in Yunnan, and 3 in Tibet, roughly consistent with differences in song and plumage coloration but incongruent with traditional subspecies boundaries. Isolation-by-resistance model best explained population differentiation within L. lutea, with extensive secondary contact after allopatric isolation leading to admixture among clades. Ecological niche modeling indicated relative stability in the extent of suitable distribution areas of the species across Quaternary glacial cycles. Our results underscore the importance of mountains in the diversification of this species, given that most of the distinct genetic clades are concentrated in a relatively small area in the Sino-Himalayan Mountain region, while a single shallow clade populates vast lower-lying areas to the east. This study highlights the crucial role of landscape heterogeneity in promoting differentiation and provides a deep genomic perspective on the mechanisms through which diversity hotspots form.

Apennine-Pyrenees disjunct distribution: an unusual biogeographic pattern revealed in flea beetles of the Longitarsus candidulus species-group (Coleoptera, Chrysomelidae).

European mountain systems have played a crucial role in shaping the distribution of species and of their genetic diversity during the Quaternary climatic changes, with the establishment of allopatric patterns across main mountain ranges. Here we investigated the evolutionary history of flea beetles of the Longitarsus candidulus species-group showing an uncommon disjunct biogeographic pattern across the Apennine and the Pyrenees. We applied a multilocus molecular approach and multispecies coalescent models to establish a phylogenetic and systematic framework for this morphologically homogeneous species-group and to estimate the time of main cladogenetic events underlying the origin of the Apennine-Pyrenees pattern. We found strong support for the monophyly of the candidulus group with a sister relationship between Longitarsus laureolae and L. leonardii endemic to the Apennine and the Pyrenees mountains respectively. The timing of speciation events in the candidulus species-group coincides with 2 major climatic transitions during the Early and Middle Pleistocene which resulted in significant environmental changes in Europe and suggest a scenario of allopatric isolation and divergence on distinct mountain ranges. The split between the thermophilic species L. candidulus and the ancestor of the temperate species L. laureolae and L. leonardii is estimated at ~3 Ma during the transition from Pliocene to Pleistocene and was probably triggered by their segregation in xerophilous and temperate habitats. The speciation between L. laureolae and L. leonardii, estimated at ~1 Ma during the Mid-Pleistocene Transition, can be explained by the establishment of unfavorable conditions in West Alps and Central Massif underlying the onset of the Apennine-Pyrenees disjunct pattern. Finally, the strict association between members of the candidulus group and distinct Thymelaeaceae plants suggests further studies to address the hypothesis that speciation in these flea beetles might have been also associated with Pleistocene range changes of their host plants.

Systematic reappraisal of marsh-orchids native to Scotland

SummaryThe intensively studied Eurasian orchid genus Dactylorhiza has become a model system for exploring allopolyploid evolution, yet determining the optimal circumscriptions of, and most appropriate ranks for, its constituent taxa remain highly controversial topics. Here, novel allozyme data and detailed morphometric data for 16 Scottish marsh-orchid populations are interpreted in the context of recent DNA sequencing studies. Despite being derived from the same pair of parental species, the two allopolyploid species that currently occur in Scotland can reliably be distinguished using allozymes, haplotypes, ribotypes or sequences of nuclear genes. A modest range of diverse morphological characters are shown to distinguish the two molecularly-circumscribed species, but they have in the past been obscured by equivalent levels of infraspecific variation in characters rooted in anthocyanin pigments; these characters are better employed for distinguishing infraspecific taxa. Dactylorhiza francis-drucei (formerly D. traunsteinerioides) is confirmed as being distinct from the continental D. traunsteineri/lapponica, probably originating through allopatric isolation once the continental lineage reached Britain. All Scottish populations are attributed to the comparatively small-flowered, anthocyanin-rich subsp. francis-drucei, which includes as a variety the former D. 'ebudensis'; the less anthocyanin-rich subsp. traunsteinerioides is confined to Ireland, North Wales and northern England. In contrast with D. francis-drucei, only a minority of Scottish populations of D. purpurella are attributed to the anthocyanin-rich race, var. cambrensis. This species most likely originated through an allopolyploidy event that occurred comparatively recently within the British Isles, as it contains allozyme alleles distinctive of British rather than continental D. incarnata (its diploid pollen-parent). In contrast, the rare Scottish population of D. incarnata subsp. cruenta shares with its Irish counterparts a continental genotype, and is most likely a recent arrival in Scotland through long-distance dispersal. Among all European allotetraploid dactylorchids, D. purpurella is the species that most closely resembles D. incarnata, both molecularly and morphologically.

Multiple introgression events during the diversification history of the edible Mexican grasshopper genus Sphenarium (Orthoptera: Pyrgomorphidae)

Speciation with gene flow often leads to ambiguous phylogenetic reconstructions, reticulate patterns of relatedness and conflicting nuclear versus mitochondrial (mt) lineages. Here we employed a fragment of the COI mtDNA gene and nuclear genome-wide data (3RAD) to assess the diversification history of Sphenarium, an orthopteran genus of great economic importance in Mexico that is presumed to have experienced hybridisation events in some of its species. We carried out separate phylogenetic analyses to evaluate the existence of mito-nuclear discordance in the species relationships, and also assessed the genomic diversity and population genomic structure and investigated the existence of interspecific introgression and species limits of the taxa involved based on the nuclear dataset. The species delineation analyses discriminated all the currently recognised species, but also supported the existence of four undescribed species. The mt and nuclear topologies had four discordant species relationships that can be explained by mt introgression, where the mt haplotypes of S. purpurascens appear to have replaced those of S. purpurascens A and B, S. variabile and S. zapotecum. Moreover, our analyses supported the existence of nuclear introgression events between four species pairs that are distributed in the Sierra Madre del Sur province in southeast Mexico, with three of them occurring in the Tehuantepec Isthmus region. Our study highlights the relevance of genomic data to address the relative importance of allopatric isolation versus gene flow in speciation.

Role of paleoclimatic and paleohydrological processes in lineage divergence in freshwater organisms: A snippet from lentic genus Pila

The Indian subcontinent is extremely diverse in terms of its flora and fauna. However, only a handful of studies have aimed to understand the diversity of freshwater invertebrates using multiple lines of evidence in recent times. Here we aimed to estimate the cryptic diversity of two widespread freshwater snail species within the genus Pila (Röding, 1798) and uncover the processes behind lineage diversification in these species. We sequenced mitochondrial and nuclear markers from a comprehensive sampling of specimens from different river basins in India. We implemented an integrative taxonomy approach to delimit the lineages in these groups, employing phylogenetic, geometric morphometric and niche modelling-based methods. Then, we investigated the drivers of lineage divergence in these species using population genetic tools in conjunction with divergence time estimation. We found that both species consist of several genetically and ecologically distinct lineages. The genetic data showed that several of these lineages are restricted to a single or a few river basins. The divergence time estimation analyses indicated that the time frame of divergence within the species coincided with paleohydrological and paleoclimatic events in the Miocene. The diversification was primarily driven by allopatric isolation into different river basins. To conclude, the study sheds light on the complex interaction between the habitat preference of the species and the environment in shaping the diversification patterns in this group.

Phylogenomics of arboreal alligator lizards shed light on the geographical diversification of cloud forest‐adapted biotas

AbstractAimThe proximate ecological and evolutionary processes underlying the high biodiversity of neotropical montane cloud forests are still very poorly understood. Climatic oscillations may have contributed to vicariance and cladogenesis, but also promoted secondary contact and erosion of genetic divergence. Here we tested whether geographical diversification – or its lack thereof – in a complex of arboreal alligator lizards is explained by range shifts during Quaternary climatic oscillations.LocationPine–oak and cloud forests, central Mexico.TaxonAbronia taeniata–gramineaspecies complex (Squamata: Anguidae: Gerrhonotinae).MethodsWe generated genomic data (ddRADseq) to infer patterns of geographical diversification in the complex, reconstruct its demographic history, estimate the timing of lineage split, and test for the presence of contemporary and/or historical hybridization. We evaluated whether the tempo and mode of diversification (i.e. strict isolation vs. secondary contact with introgression) are explained by the contemporary distribution of suitable habitats and/or range shifts experienced by the complex since the Last Glacial Maximum (LGM), as inferred from environmental niche modelling (ENM).ResultsGenomic data supported a marked genetic structure within the complex, and phylogenomic and dating analyses revealed cryptic lineage diversification starting at the onset of the Pleistocene followed by secondary contact with limited introgression. ENM pointed to considerable range expansions of the complex during the LGM and a marked fragmentation and scarce connectivity among contemporary populations, which was supported by genomic‐based demographic reconstructions.Main ConclusionsThe geographical diversification of the complex has been moulded by vicariant events promoted by Pleistocene geologic and climatic changes impacting the distribution of their pine–oak and cloud forest habitats. Our data supported a model of divergence with introgression, indicating that pulses of population fragmentation and expansion during the Quaternary have led to multiple opportunities for both allopatric isolation and secondary contact.

Community phylogeographic patterns reveal how a barrier filters and structures taxa in North American warm deserts

AbstractAimThe study of biogeographic barriers is instrumental in understanding the evolution and distribution of taxa. With the increasing availability of empirical datasets, emergent patterns can be inferred from communities by synthesizing how barriers filter and structure populations across species. We assemble phylogeographic data across a barrier and perform spatially explicit simulations, quantifying spatiotemporal patterns of divergence, the influence of traits on these patterns, and the statistical power needed to differentiate diversification modes.TaxonVertebrates, Invertebrates, PlantsLocationNorth AmericaMethodsWe incorporate published datasets, from papers that match relevant keywords, to examine taxa around the Cochise Filter Barrier, separating the Sonoran and Chihuahuan Deserts of North America, to synthesize phylogeographic structuring across the communities with respect to organismal functional traits. We then use simulation and machine learning to assess the power of phylogeographic model selection.ResultsTaxa distributed across the Cochise Filter Barrier show heterogeneous responses to the barrier in levels of gene flow, phylogeographic structure, divergence timing, barrier width, and divergence mechanism. These responses correlate with locomotor and thermoregulatory traits. Many taxa show a Pleistocene population genetic break, often with introgression after divergence. Allopatric isolation and isolation by environment are the primary mechanisms structuring genetic divergence within taxa. Simulations reveal that in spatially explicit isolation with migration models across the barrier, age of divergence, presence of gene flow, and presence of isolation by distance can confound the interpretation of evolutionary history and model selection by producing easily confusable results. We re‐analyze five empirical genetic datasets to illustrate the utility of these simulations despite these constraints.Main ConclusionsBy synthesizing phylogeographic data for the Cochise Filter Barrier, we show that barriers interact with species traits to differentiate taxa in communities over millions of years. Identifying diversification modes across the barrier for these taxa remains challenging because commonly invoked demographic models may not be identifiable across a range of likely parameter space.

Geographical disjunction and environmental conditions drive intraspecific differentiation in the chalk-hill blue butterfly

Abstract Drivers of evolution are often related to geographical isolation and/or diverging environmental conditions. Spatial variation in neutral genetic markers mostly reflects past geographical isolation, i.e. long-lasting allopatry, whereas morphology is often driven by local environmental conditions, resulting in more rapid evolution. In Europe, most thermophilic species persisted during the past glacial periods in geographically disjunct refugia, representing long-lasting isolates, frequently with diverging environmental conditions. This situation has driven the evolution of intraspecific signatures in species. Here, we analysed wing shape and wing pigmentation of the chalk-hill blue butterfly, Polyommatus coridon, across its entire distribution range restricted to the western Palaearctic. In addition, we compiled abiotic environmental parameters for each sampling site. Wing colour patterns differentiated a western and an eastern lineage. These lineages might represent two main Pleistocene refugia and differentiation centres, one located on the Italian Peninsula and the other in the Balkan region. The two lineages showed evidence of hybridization across Central Europe, from the Alps and across Germany. The intraspecific differentiation was strongest in the width of the brown band on the outer margin of the wings. The morphological structures obtained are in line with genetic signatures found in previous studies, but the latter are more fine-grained. Current environmental conditions, such as mean temperatures, were only marginally correlated with colour patterns. Our study underlines that Pleistocene range shifts, often resulting in allopatric isolation, shape intraspecific phenotypic structures within species; that pigmentation responds in a more sensitive manner to spatial disjunction than wing shape; and that morphometric and genetic structures in P. coridon provide concordant patterns and thus support identical biogeographical conclusions.

Experimental admixture among geographically disjunct populations of an invasive plant yields a global mosaic of reproductive incompatibility and heterosis

Abstract Invasive species have the ability to rapidly adapt in the new regions where they are introduced. Classic evolutionary theory predicts that the accumulation of genetic differences over time in allopatric isolation may lead to reproductive incompatibilities resulting in decreases in reproductive success and, eventually, to speciation. However, experimental evidence for this theoretical prediction in the context of invasive species is lacking. We aimed to test for the potential of allopatry to determine reproductive success of invasive plants, by experimentally admixing genotypes from six different native and non‐native regions of Centaurea solstitialis, an invasive forb for which preliminary studies have detected some degree of reproductive isolation between one native and non‐native region. We grew plants under common garden conditions and outcrossed individuals originating from different source populations in the native and introduced range to evaluate reproductive success in terms of seed to ovule ratio produced. We also assessed geographical and genetic isolation among C. solstitialis regions as a potential driving factor of reproductive success. Experimental admixture generated mixed fitness effects, including significant increases, decreases and no differences in reproductive success as compared to crosses within population (control). Centaurea solstitialis invasive populations in the Americas generated preponderantly negative fitness interactions, regardless of the pollen source, suggesting selection against immigrants and reinforcement. Other non‐native populations (Australia) as well as individuals from the native range of Spain demonstrated an increase in fitness for between‐region crosses, indicating inbreeding. These differences show an asymmetrical response to inter‐regional gene flow, but no evidence of isolation by distance. Synthesis. The speed of adaptation and the accumulation of reproductive incompatibilities among allopatric populations of invasive species might be more rapid than previously assumed. Our data show a global mosaic of reproductive outputs, showcasing an array of evolutionary processes unfolding during colonization at large biogeographical scales.

A revision of the shield-back katydid genus Neduba (Orthoptera: Tettigoniidae: Tettigoniinae: Nedubini).

The Nearctic shield-back katydid genus Neduba is revised. Species boundaries were demarcated by molecular phylogenetic analysis, morphology, quantitative analysis of calling songs, and karyotypes. Nine previously described species are redescribed: N. carinata, N. castanea, N. convexa, N. diabolica, N. extincta, N. macneilli, N. propsti, N. sierranus, and N. steindachneri, and twelve new species are described: N. ambagiosa sp. n., N. arborea sp. n., N. cascadia sp. n., N. duplocantans sp. n., N. inversa sp. n., N. longiplutea sp. n., N. lucubrata sp. n., N. oblongata sp. n., N. prorocantans sp. n., N. radicata sp. n., N. radocantans sp. n., and N. sequoia sp. n. We chose a lectotype for N. steindachneri and transferred N. picturata from a junior synonym of N. diabolica to a junior synonym of N. steindachneri. Diversification in this relict group reflects cycles of allopatric isolation and secondary contact amidst the tumultuous, evolving geography of western North America. The taxonomy and phylogenies presented in this revision lay the groundwork for studies of speciation, biogeography, hybrid zones, and behavioral evolution. Given that one Neduba species is already extinct from human environmental disturbance, we suggest conservation priorities for the genus.

The contribution of ancient admixture to reproductive isolation between European sea bass lineages.

Understanding how new species arise through the progressive establishment of reproductive isolation (RI) barriers between diverging populations is a major goal in Evolutionary Biology. An important result of speciation genomics studies is that genomic regions involved in RI frequently harbor anciently diverged haplotypes that predate the reconstructed history of species divergence. The possible origins of these old alleles remain much debated, as they relate to contrasting mechanisms of speciation that are not yet fully understood. In the European sea bass (Dicentrarchus labrax), the genomic regions involved in RI between Atlantic and Mediterranean lineages are enriched for anciently diverged alleles of unknown origin. Here, we used haplotype‐resolved whole‐genome sequences to test whether divergent haplotypes could have originated from a closely related species, the spotted sea bass (Dicentrarchus punctatus). We found that an ancient admixture event between D. labrax and D. punctatus is responsible for the presence of shared derived alleles that segregate at low frequencies in both lineages of D. labrax. An exception to this was found within regions involved in RI between the two D. labrax lineages. In those regions, archaic tracts originating from D. punctatus locally reached high frequencies or even fixation in Atlantic genomes but were almost absent in the Mediterranean. We showed that the ancient admixture event most likely occurred between D. punctatus and the D. labrax Atlantic lineage, while Atlantic and Mediterranean D. labrax lineages were experiencing allopatric isolation. Our results suggest that local adaptive introgression and/or the resolution of genomic conflicts provoked by ancient admixture have probably contributed to the establishment of RI between the two D. labrax lineages.

Low Spontaneous Mutation Rate and Pleistocene Radiation of Pea Aphids

Accurate estimates of divergence times are essential to understand the evolutionary history of species. It allows linking evolutionary histories of the diverging lineages with past geological, climatic, and other changes in environment and shed light on the processes involved in speciation. The pea aphid radiation includes multiple host races adapted to different legume host plants. It is thought that diversification in this system occurred very recently, over the past 8,000-16,000 years. This young age estimate was used to link diversification in pea aphids to the onset of human agriculture, and led to the establishment of the pea aphid radiation as a model system in the study of speciation with gene flow. Here, we re-examine the age of the pea aphid radiation, by combining a mutation accumulation experiment with a genome-wide estimate of divergence between distantly related pea aphid host races. We estimate the spontaneous mutation rate for pea aphids as 2.7×10-10 per haploid genome per parthenogenic generation. Using this estimate of mutation rate and the genome-wide genetic differentiation observed between pea aphid host races, we show that the pea aphid radiation is much more ancient than assumed previously, predating Neolithic agriculture by several hundreds of thousands of years. Our results rule out human agriculture as the driver of diversification of the pea aphid radiation, and call for re-assessment of the role of allopatric isolation during Pleistocene climatic oscillations in divergence of the pea aphid complex.

From seven to three: Integrative species delimitation supports major reduction in species number in Rhodiola section Trifida (Crassulaceae) on the Qinghai‐Tibetan Plateau

An essential component of biodiversity research and conservation is to accurately delimit species. Traditional morphology‐based taxonomy has faced great challenges in complex taxa. In the last few years, the focus of species delimitations has shifted from defining species using different species concepts to integrating multiple lines of evidence to characterize different aspects of the speciation process. This study employs an integrative taxonomic method to revise the species limits in Rhodiola sect. Trifida, based on multi‐locus sequence data from population‐level sampling, morphometric analyses, and ecological niche modeling. We surveyed 44 populations representing seven previously defined morphological species. We sequenced three plastid markers and three nuclear markers, and employed the coalescent‐based species delimitation method to assess the variational patterns from the molecular data. We also conducted a comprehensive morphological analysis, as well as ecological niche modeling for each species. The multidisciplinary data support Rhodiola liciae and R. sinuata as distinct species, which likely originated by allopatric isolation and ecological speciation. Rhodiola ovatisepala, R. sacra and R. sexifolia are suggested to be synonyms of R. chrysanthemifolia, and the status of R. alterna needs further verification. Our study suggests that the previous taxonomy of this group may depend on too many intra‐lineage variable traits, and showcases the importance of integrative taxonomy for species delimitations in morphologically complex plant groups.

Rapid Divergence Followed by Adaptation to Contrasting Ecological Niches of Two Closely Related Columbine Species Aquilegia japonica and A. oxysepala.

Elucidating the mechanisms underlying the genetic divergence between closely related species is crucial to understanding the origin and evolution of biodiversity. The genus Aquilegia L. has undergone rapid adaptive radiation, generating about 70 well-recognized species that are specialized to distinct habitats and pollinators. In this study, to address the underlying evolutionary mechanisms that drive the genetic divergence, we analyzed the whole genomes of two ecologically isolated Aquilegia species, A. oxysepala and A. japonica as well as their putative hybrid. Our comparative genomic analyses reveal that while the two species diverged only recently and experienced recurrent gene flow, a high level of genetic divergence is observed in their nuclear genomes. In particular, candidate genomic regions that show signature of selection differ dramatically between the two species. Given that the splitting time of the two species is broadly matched with the decrease in effective population sizes, we propose that allopatric isolation together with natural selection have preceded the interspecific gene flow in the process of speciation. The observed high genetic divergence is likely an outcome of combined effects of natural selection, genetic drift and divergent sorting of ancestral polymorphisms. Our study provides a genome-wide view of how genetic divergence has evolved between closely related species.

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.

Disentangling the genetic effects of refugial isolation and range expansion in a trans-continentally distributed species.

In wide-ranging taxa with historically dynamic ranges, past allopatric isolation and range expansion can both influence the current structure of genetic diversity. Considering alternate historical scenarios involving expansion from either a single refugium or from multiple refugia can be useful in differentiating the effects of isolation and expansion. Here, we examined patterns of genetic variability in the trans-continentally distributed painted turtle (Chrysemys picta). We utilized an existing phylogeographic dataset for the mitochondrial control region and generated additional data from nine populations for the mitochondrial control region (n = 302) and for eleven nuclear microsatellite loci (n = 247). We created a present-day ecological niche model (ENM) for C. picta and hindcast this model to three reconstructions of historical climate to define three potential scenarios with one, two, or three refugia. Finally, we employed spatially-explicit coalescent simulations and an approximate Bayesian computation (ABC) framework to test which scenario best fit the observed genetic data. Simulations indicated that phylogeographic and multilocus population-level sampling both could differentiate among refugial scenarios, although inferences made using mitochondrial data were less accurate when a longer coalescence time was assumed. Furthermore, all empirical genetic datasets were most consistent with expansion from a single refugium based on ABC. Our results indicate a stronger role for post-glacial range expansion, rather than isolation in allopatric refugia followed by range expansion, in structuring diversity in this species. To distinguish among complex historical scenarios, we recommend explicitly modeling the effects of range expansion and evaluating alternate refugial scenarios for wide-ranging taxa.

Origin and macroevolution of micro-moths on sunken Hawaiian Islands.

The origins and evolution of Hawaiian biodiversity are a matter of controversy, and the mechanisms of lineage diversification for many organisms on this remote archipelago remain unclear. Here we focus on the poorly known endemic leaf-mining moth genus Philodoria (Lepidoptera, Gracillariidae), whose species feed on a diversity of Hawaiian plant lineages, many of which are critically endangered. We use anchored hybrid enrichment to assemble the first phylogenomic dataset (507 loci) for any Hawaiian animal taxon. To uncover the timing and pattern of diversification of these moths, we apply two frequently used dating calibration strategies, biogeographic calibrations and secondary calibrations. Island calibrations on their own resulted in much younger and unrealistic dates compared to strategies that relied on secondary calibrations. Philodoria probably originated on the now partially sunken islands of Laysan or Lisianski, approximately 21 Ma, and were associated with host plants in the families Ebenaceae, Malvaceae or Primulaceae. Major feeding groups associated with specific host-plant families originated soon after the plants colonized the islands. Allopatric isolation and host shifts, in concert and independently, probably play major roles in the diversification of Philodoria Our dating results indicate that Philodoria is among the oldest known Hawaiian arthropod lineages, and that island calibrations alone can lead to unrealistically young dates.

Molecular phylogeny of the Palaearctic butterfly genus Pseudophilotes (Lepidoptera: Lycaenidae) with focus on the Sardinian endemic P. barbagiae

BackgroundThe Palaearctic butterfly genus Pseudophilotes Beuret, 1958 (Lycaenidae: Polyommatinae), that today occurs in North Africa and in Eurasia, includes ten described species with various distribution ranges, including endemics such as the Sardinian P. barbagiae. Phylogenetic relationships among these species are largely unresolved. In the present study, we analysed 158 specimens, representing seven species out of ten described in the genus, from widely distributed sites throughout the western Palaearctic region, using nuclear markers (28S rRNA, wingless, Internal Transcribed Spacer 2 and Elongation Factor 1α) and the barcoding region of the mitochondrial cytochrome c oxidase subunit 1 gene to investigate if the current taxonomic entities match the phylogenetic pattern. Further, we attempt to infer the geographic origin of the genus Pseudophilotes and estimate the timing of its radiations, including the split of the Sardinian endemic P. barbagiae.ResultsMaximum Likelihood and Bayesian inference analyses confirmed the monophyly of the genus Pseudophilotes and clearly supported the closer affinity of P. barbagiae to the species assemblage of P. baton, P. vicrama and P. panoptes as opposed to P. abencerragus. The currently accepted species P. baton, P. vicrama and P. panoptes turned out to be weakly differentiated from each other, while P. bavius and P. fatma emerged as highly distinct and formed a well supported clade. The split between the lineage comprising bavius and fatma (sometimes treated as a distinct genus, Rubrapterus) with Salvia species as larval host plants, and the remaining Pseudophilotes that utilize Thymus and other Lamiaceae (but not Salvia), dates back to about 4.9 million years ago (Mya).ConclusionsOur results show that the last common ancestor of the genus probably lived in the Messinian period (5.33–7.25 Mya). At species level, they support the current taxonomy of the genus, although P. panoptes, P. baton and P. vicrama display complex patterns based on phylogeographic relationships inferred from mtDNA. The Sardinian endemic P. barbagiae turned out to be a young endemic, but clearly with European instead of North African origin and evolved through allopatric isolation on the island of Sardinia only about 0.74 Mya.

Whole-genome analysis of Mustela erminea finds that pulsed hybridization impacts evolution at high\xa0latitudes

At high latitudes, climatic shifts hypothetically initiate recurrent episodes of divergence by isolating populations in glacial refugia—ice-free regions that enable terrestrial species persistence. Upon glacial recession, populations subsequently expand and often come into contact with other independently diverging populations, resulting in gene flow. To understand how recurrent periods of isolation and contact may have impacted evolution at high latitudes, we investigated introgression dynamics in the stoat (Mustela erminea), a Holarctic mammalian carnivore, using whole-genome sequences. We identify two spatio-temporally distinct episodes of introgression coincident with large-scale climatic shifts: contemporary introgression in a mainland contact zone and ancient contact ~200 km south of the contemporary zone, in the archipelagos along North America’s North Pacific Coast. Repeated episodes of gene flow highlight the central role of cyclic climates in structuring high-latitude diversity, through refugial divergence and introgressive hybridization. When introgression is followed by allopatric isolation (e.g., insularization) it may ultimately expedite divergence.