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BACKGROUND: Human-commensal species often display deep ancestral genetic structure within their native range and founder-effects and/or evidence of multiple introductions and admixture in newly established areas. We investigated the phylogeography of Eutropis multifasciata, an abundant human-commensal scincid lizard that occurs across Southeast Asia, to determine the extent of its native range and to assess the sources and signatures of human introduction outside of the native range. We sequenced over 350 samples of E. multifasciata for the mitochondrial ND2 gene and reanalyzed a previous RADseq population genetic dataset in a phylogenetic framework. RESULTS: Nuclear and mitochondrial trees are concordant and show that E. multifasciata has retained high levels of genetic structure across Southeast Asia despite being frequently moved by humans. Lineage boundaries in the native range roughly correspond to several major biogeographic barriers, including Wallaces Line and the Isthmus of Kra. Islands at the outer fringe of the range show evidence of founder-effects and multiple introductions. CONCLUSIONS: Most of enormous range of E. multifasciata across Southeast Asia is native and it only displays signs of human-introduction or recent expansion along the eastern and northern fringe of its range. There were at least three events of human-introductions to Taiwan and offshore islands, and several oceanic islands in eastern Indonesia show a similar pattern. In Myanmar and Hainan, there is a founder-effect consistent with post-warming expansion after the last glacial maxima or human introduction.

Understanding the source of non-native introduced populations is crucial for forecasting geographic invasion potential and understanding the ecological consequences of potential establishment. Here we use genomics to identify the source populations and invasion dynamics of two non-native introduced populations from the iconic avian lineage of ‘great speciators’ known as white-eyes (genus Zosterops). We established confidently for the first time that introduced Zosterops populations in Hawaii and southern California are completely unrelated and derived from independent introductions of the species Z. japonicus and Z. simplex, respectively. We used descriptive population genetic statistics to identify a reduction in genetic diversity and increase in private alleles in the southern California population supporting a recent, potentially ongoing, genetic bottleneck in this population. In contrast, the introduced population in Hawaii showed no such characteristics, likely due to a larger founding population size and repeated introductions in this intentionally introduced population. Ecological niche modeling indicated that there is little environmentally suitable habitat for Z. simplex across the continent of North America, suggesting limited invasion potential, assuming niche conservatism. Yet, portions of the introduced Z. simplex population have already surpassed areas projected as suitable, likely because the urbanized environment of southern California offers biotic resources and microhabitats not captured by our model. Because Z. simplex appears to have overcome both the ‘invasion paradox’ of low founding genetic diversity and relatively unfamiliar environmental conditions in southern California, we suggest that this population may continue expanding beyond our environmental niche model projections in other temperate, urban regions.

Large structural variants in the genome, such as inversions, may play an important role in producing population structure and local adaptation to the environment through suppression of recombination. However, relatively few studies have linked inversions to phenotypic traits that are sexually selected and may play a role in reproductive isolation. Here, we found that geographic differences in the sexually selected plumage of a warbler, the common yellowthroat (Geothlypis trichas), are largely due to differences in the Z (sex) chromosome (males are ZZ), which contains at least one putative inversion spanning 40% (31/77 Mb) of its length. The inversions on the Z chromosome vary dramatically east and west of the Appalachian Mountains, which provides evidence of cryptic population structure within the range of the most widespread eastern subspecies (G. t. trichas). In an eastern (New York) and western (Wisconsin) population of this subspecies, female prefer different male ornaments; larger black facial masks are preferred in Wisconsin and larger yellow breasts are preferred in New York. The putative inversion also contains genes related to vision, which could influence mating preferences. Thus, structural variants on the Z chromosome are associated with geographic differences in male ornaments and female choice, which may provide a mechanism for maintaining different patterns of sexual selection in spite of gene flow between populations of the same subspecies. [ABSTRACT FROM AUTHOR]

Genetic analyses of host‐specific parasites can elucidate the evolutionary histories and biological features of their hosts. Here, we used population‐genomic analyses of ectoparasitic seal lice (Echinophthirius horridus) to shed light on the postglacial history of seals in the Arctic Ocean and the Baltic Sea region. One key question was the enigmatic origin of relict landlocked ringed seal populations in lakes Saimaa and Ladoga in northern Europe. We found that that lice of four postglacially diverged subspecies of the ringed seal (Pusa hispida) and Baltic gray seal (Halichoerus grypus), like their hosts, form genetically differentiated entities. Using coalescent‐based demographic inference, we show that the sequence of divergences of the louse populations is consistent with the geological history of lake formation. In addition, local effective population sizes of the lice are generally proportional to the census sizes of their respective seal host populations. Genome‐based reconstructions of long‐term effective population sizes revealed clear differences among louse populations associated with gray versus ringed seals, with apparent links to Pleistocene and Holocene climatic variation as well as to the isolation histories of ringed seal subspecies. Interestingly, our analyses also revealed ancient gene flow between the lice of Baltic gray and ringed seals, suggesting that the distributions of Baltic seals overlapped to a greater extent in the past than is the case today. Taken together, our results demonstrate how genomic information from specialized parasites with higher mutation and substitution rates than their hosts can potentially illuminate finer scale population genetic patterns than similar data from their hosts. [ABSTRACT FROM AUTHOR]

Earlier studies on Isothecium s.l. suggested potential interchange of genetic material between species that are nowadays known to belong to separate genera. In this study, we analyse the variation in three molecular markers (nuclear gpd ; mitochondrial nad 5; and plastid trn G) in a wide selection of Isothecium alopecuroides and Pseudisothecium myosuroides specimens to infer whether this potential exchange of genetic material is frequent. In addition, we explore the phylogeographic structure of these two species in Europe. Our results seem to show repeated genetic interchange for the nuclear and mitochondrial markers in both species, suggesting intergeneric hybridization, although horizontal gene transfer and/or incomplete lineage sorting could also explain the detected incongruences. The genetic lineages found indicate a complex biogeographical history for I. alopecuroides , including both post-glacial immigration from different glacial refugia and developing haplotypes potentially adapted to cold climates. As for P. myosuroides , genetic variants could either indicate a post-glacial immigration history or adaptation to oceanic conditions. Further studies including a larger set of more variable molecular markers could help to reach final conclusions on the results here presented. [ABSTRACT FROM AUTHOR]

The Antarctic benthos is rich in biodiversity, with many species being endemic to the Southern Ocean. Multiple factors such as oceanic currents, glacial cycles and reproductive life stages have been attributed to the distribution of benthic dwelling invertebrates around the continent. The sea spider (Pycnogonida) Nymphon australe is a paternal brooder, which lacks a pelagic planktonic life stage. Typically brooding is assumed to suggest limited dispersal capabilities. Here we investigated the genetic structure of N. australe, a highly abundant pycnogonid species in the Southern Ocean to test assumptions of a documented circumpolar distribution. Previous studies with mitochondrial data have revealed that N. australe has high genetic diversity, limited gene flow, as well as distinct geographic structure. To resolve the phylogeographic structure of the circumpolar N. australe from the Antarctic continental shelf, we used 3RAD single nucleotide polymorphism (SNP) data from 111 individuals sampled from ten different, circumpolar geographic regions including the Western Antarctic Peninsula, Ross Sea, Weddell Sea, and Eastern Antarctica. Analyses revealed populations to have distinct regional populations with strong geographic structuring observed by locality and suggest the possibility that N. australe may be a species complex in the Southern Ocean. [ABSTRACT FROM AUTHOR]

Binturong (Arctictis binturong) is a threatened carnivore that inhabits the forests of South and Southeast Asia. Despite its wide range, binturong is relatively scarce across its habitat distribution and is currently under the threat of poaching and illegal trade. Captive breeding has unfortunately been conducted rather haphazardly with a lack of origin record maintained, implicating potential risks to the management such as inbreeding or genetic swamping. This study thus aims to characterise the phylogenetic relationship of Indonesian binturong within the context of Southeast Asian binturong and further probe the distinctness of lineages originating from Java, Sumatra, Indonesian Borneo, and Bangka using Cytochrome B (CytB) and Cytochrome C Oxidase Subunit 1 (CO1). Genetic distance, phylogram topology, and haplotype analysis of both encoding genes further corroborate the distinctness of Java, Borneo, and Bangka binturong from other binturong from Indochinese regions such as India, Laos, and Myanmar. Search for prospective single nucleotide polymorphism markers to discriminate island lineages consistently found that each Java, Bangka, and Bornean binturong be distinct from each other and other lineages, especially when assessed using haplotype-based clustering. Assigning binturong originated from Sumatra is nonetheless more complicated, suggesting the possibility. Our findings substantiated the much-needed systematic research of Southeast Asian binturong as ex-situ insurance population management grows in Indonesia and other parts of the world to protect the diversity of binturong lineages and their corresponding unique evolutionary history. [ABSTRACT FROM AUTHOR]

Aim: In 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. Location: North America. Taxon: Atlantic salmon, Salmo salar. Methods: Samples 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. Results: Spatial 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 Conclusions: These 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. [ABSTRACT FROM AUTHOR]

Aim: Various species distributed in the Alps have their disjunct occurrences in the Carpathians. Fossil evidence for some woodland snails of Alpine distribution suggests that they colonized the Carpathians during the Holocene forest optimum or later. Here, we focus on disjunct Carpathian populations of the rock‐dwelling alpine snail Pyramidula saxatilis. As it occupies very stable habitats, that is, high‐elevation limestone rocks, one can assume its potential survival in Carpathian refugia over the glacial period(s). For comparison, the more widespread and warm‐climate P. pusilla is analysed. Location: Europe. Taxon: Pyramidula saxatilis and P. pusilla. Methods: We analysed the genetic diversity of P. saxatilis and P. pusilla populations across their entire ranges using mitochondrial DNA and nuclear DNA markers. Seven fossil mollusc successions from the area where P. saxatilis occurs in the Carpathians were analysed and dated using the radiocarbon method. Habitat suitability models of both species were calculated for selected time periods since the Last Glacial Maximum. Results: All Carpathian P. saxatilis populations were genetically homogeneous and similar to those from the Eastern Alps. In P. pusilla, we found a genetically distinct lineage in the southern Western Carpathians. Both species were found in three fossil profiles since the Middle Holocene, and in one already in the Late Glacial. Habitat suitability models suggested the fluctuations of suitable conditions in the Carpathians driven by summer precipitation, especially for P. saxatilis. Main Conclusions: Our results suggest that the Carpathian populations of P. saxatilis represent a post‐LGM colonization from the Eastern Alps triggered by climatic changes, mainly by the increase in summer precipitation during the Late Glacial interstadials and Middle Holocene. The evidence for P. pusilla is similar, but also suggests rare long‐term survival in the Carpathian microrefugia. The palaeoecological evidence indicates a possible threat to high‐elevation species from future fluctuations in precipitation regimes. [ABSTRACT FROM AUTHOR]

An intricate interplay between evolutionary and demographic processes has frequently resulted in complex patterns of genetic and phenotypic diversity in alpine lineages, posing serious challenges to species delimitation and biodiversity conservation planning. Here we integrate genomic data, geometric morphometric analyses and thermal tolerance experiments to explore the role of Pleistocene climatic changes and adaptation to alpine environments on patterns of genomic and phenotypic variation in diving beetles from the taxonomically complex Agabus bipustulatus species group. Genetic structure and phylogenomic analyses revealed the presence of three geographically cohesive lineages, two representing trans‐Palearctic and Iberian populations of the elevation‐generalist A. bipustulatus and another corresponding to the strictly‐alpine A. nevadensis, a narrow‐range endemic taxon from the Sierra Nevada mountain range in southeastern Iberia. The best‐supported model of lineage divergence, along with the existence of pervasive genetic introgression and admixture in secondary contact zones, is consistent with a scenario of population isolation and connectivity linked to Quaternary climatic oscillations. Our results suggest that A. nevadensis is an alpine ecotype of A. bipustulatus, whose genotypic, morphological and physiological differentiation likely resulted from an interplay between population isolation and local altitudinal adaptation. Remarkably, within the Iberian Peninsula, such ecotypic differentiation is unique to Sierra Nevada populations and has not been replicated in other alpine populations of A. bipustulatus. Collectively, our study supports fast ecotypic differentiation and incipient speciation processes within the study complex and points to Pleistocene glaciations and local adaptation along elevational gradients as key drivers of biodiversity generation in alpine environments. [ABSTRACT FROM AUTHOR]

The phylogeography of economically important forest pests is important for understanding their demographic and evolutionary history. Linking the genetic data obtained with the bioclimatic models helps reveal future demographic trends of the pest species studied. Lymantria monacha is a polyphagous species that feeds on numerous coniferous and deciduous trees throughout the Palaearctic and is known to cause catastrophic defoliation, particularly in Europe. In addition, data from various mapping programmes over the last decade have revealed changes in the distribution of L. monacha. Therefore, in this study, we decided to clarify the evolutionary and demographic history of this important forest species using genetic data complemented by bioclimatic modelling. Our results confirmed the systematic status and monophyly of L. monacha. However, the lack of a geographical pattern between the studied regions suggests that the current genetic structure may be the result of recent dispersal events. Moreover, we found that the areas of high genetic diversity are consistent with potential past range shifts and survival of changes in climate and host plant availability. These two main variables also seem to determine the future range of L. monacha. Also, our modelling confirmed a poleward shift in its range and with a significant retraction from its current southern edge of distribution. [ABSTRACT FROM AUTHOR]

Neglected cryptic diversity can lead to the permanent loss of locally adapted alleles, which can reduce resilience to rapid environmental change. It can also result in overestimation of fisheries stock sizes that can result from treating different species as if they belonged to one. Bluefish (Pomatomus saltatrix) is considered a circumtropical and subtropical species and an important fishery resource all over the world. Differences in ecologically relevant traits are observed among isolated populations. Also, in the Southwestern Atlantic, molecular data suggest multiple populations, but these are treated as a single fish stock by regulatory agencies due to a lack of definitive information. We used whole mitogenome sequences, nuclear (rho) and mitochondrial (coxI and cytb) genes, as well as microsatellites to investigate historical and current genetic population structure and parameters of bluefish in the Western Atlantic. A total of 263 samples were collected along the Brazilian coast and in the USA (New Jersey, Northwest Atlantic). Data revealed the existence of two evolutionarily significant units (ESU) of bluefish along the South American coast, later confirmed by whole mitogenome sequencing of both haplogroups. These two ESUs have a mostly parapatric distribution, with some areas of overlap, which vary along the year. We also conducted seasonal sampling in Brazil to investigate migration patterns. ESUs occur mostly north and south of parallel 23° 40′ S, with an overlap area that varied seasonally. The level of differentiation between those two ESUs in the SW Atlantic, even in sympatry, is as high as that found between them and those from the NW Atlantic and Europe. Parapatric distribution and restricted gene flow suggest the existence of ecological barriers and local adaptation. The splitting of an ancient population from the Southwestern Atlantic into two putative species is important to understand bluefish evolutionary diversification and has implications for fishery regulatory measures in Brazil. [ABSTRACT FROM AUTHOR]

The terrestrial isopod genus Ligidium includes 58 species from Europe, Asia, and North America. In Eastern North America four species are recognized: L. floridanum and L. mucronatum, known just from their type localities in Florida and Louisiana respectively, L. blueridgensis, endemic to the southern Appalachians, and L. elrodii, widespread from Georgia to Ontario. The genus shows a marked morphological conservatism, and species are differentiated mostly by small morphological differences; it is not always easy to determine if such variability represents inter‐ or intraspecific variation. Here, we explore the diversity of Ligidium from the southern Appalachian Mountains, exploring the congruence of morphologically defined groups with multilocus phylogenetic reconstructions and molecular species delimitation methods. We have studied a total of 130 specimens from 37 localities, mostly from the southern Appalachians, and analysed mtDNA (Cox1) and nuclear (28S, NaK) sequences. Morphologically, we recognized eight morphotypes, most of them assignable to current concepts of L. elrodii and L. blueridgensis. Phylogenetic analyses supported the evolutionary independence of all morphotypes, and suggest the existence of 8–9 species, including limited cryptic diversity. Single‐locus delimitation analyses based on mtDNA data suggest the existence of a much higher number of species than the multilocus analyses. The estimated age of the ancestors of sampled lineages indicates a long presence of the genus in eastern North America and old speciation events through the Miocene. Our results indicate a higher diversity than previously thought among the Ligidium populations present in the southern Appalachian Mountains, with several species to be described. [ABSTRACT FROM AUTHOR]

The evolutionary dynamics of the ecoregions of southern South America and the species that inhabit them have been poorly studied, and few biogeographic hypotheses have been proposed and tested. Quaternary climatic oscillations are among the most important processes that have led to the current distribution of genetic variation in different regions of the world. In this work, we studied the evolutionary history and distribution of the Córdoba vesper mouse (Calomys venustus), a characteristic rodent of the region of which little is known about its natural history. Since the population dynamics of this species are influenced by climatic factors, this rodent is a suitable model to study the effects of Quaternary climatic oscillations in central Argentina. The mitochondrial cytochrome b gene was sequenced to analyze the phylogeography of C. venustus, and ecological niche modeling tools were used to map its potential distributions. The results of these approaches were combined to provide additional spatially explicit information about this species' past. Our results suggest that the Espinal was the area of origin of this species, which expanded demographically and spatially during the last glacial period. A close relationship was found between the Espinal and the Mountain Chaco. These results are consistent with previous studies and emphasize the role of the Espinal in the biogeographic history of southern South America as an area of origin of several species. [ABSTRACT FROM AUTHOR]

Global climate change is expected to have a profound effect on species distribution. Due to the temperature constraints, some narrow niche species could shift their narrow range to higher altitudes or latitudes. In this study, we explored the correlation between species traits, genetic structure, and geographical range size. More specifically, we analyzed how these variables are affected by differences in fundamental niche breadth or dispersal ability in the members of two sympatrically distributed stream‐dwelling amphibian species (frog, Quasipaa yei; salamander, Pachyhynobius shangchengensis), in Dabie Mountains, East China. Both species showed relatively high genetic diversity in most geographical populations and similar genetic diversity patterns (JTX, low; BYM, high) correlation with habitat changes and population demography. Multiple clustering analyses were used to disclose differentiation among the geographical populations of these two amphibian species. Q. yei disclosed the relatively shallow genetic differentiation, while P. shangchengensis showed an opposite pattern. Under different historical climatic conditions, all ecological niche modeling disclosed a larger suitable habitat area for Q. yei than for P. shangchengensis; these results indicated a wider environment tolerance or wider niche width of Q. yei than P. shangchengensis. Our findings suggest that the synergistic effects of environmental niche variation and dispersal ability may help shape genetic structure across geographical topology, particularly for species with extremely narrow distribution. [ABSTRACT FROM AUTHOR]

The article "Molecular phylogeography of Hipposideros pratti in China" discusses the genetic diversity and population dynamics of the bat species Hipposideros pratti in China. The study found that H. pratti has low genetic diversity and is divided into two clades, the central-western clade and the eastern clade. The research did not detect a clear east-to-west dispersal route, and the eastern clade spread outward from one population to another while the central-western clade spread gradually. The study also highlighted the importance of preserving bat populations and the need for in situ conservation measures. [Extracted from the article]

Brachypodium stacei is the most ancestral lineage in the genus Brachypodium, a model system for grass functional genomics. B. stacei shows striking and sometimes contradictory biological and evolutionary features, including a high selfing rate yet extensive admixture, an ancient Miocene origin yet with recent evolutionary radiation, and adaptation to different dry climate conditions in its narrow distribution range. Therefore, it constitutes an ideal system to study these life history traits. We studied the phylogeography of 17 native circum‐Mediterranean B. stacei populations (39 individuals) using genome‐wide RADseq SNP data and complete plastome sequences. Nuclear SNP data revealed the existence of six distinct genetic clusters, low levels of intra‐population genetic diversity and high selfing rates, albeit with signatures of admixture. Coalescence‐based dating analysis detected a recent split between crown lineages in the Late Quaternary. Plastome sequences showed incongruent evolutionary relationships with those recovered by the nuclear data, suggesting interbreeding and chloroplast capture events between genetically distant populations. Demographic and population dispersal coalescent models identified an ancestral origin of B. stacei in the western‐central Mediterranean islands, followed by an early colonization of the Canary Islands and two independent colonization events of the eastern Mediterranean region through long‐distance dispersal and bottleneck events as the most likely evolutionary history. Climate niche data identified three arid niches of B. stacei in the southern Mediterranean region. Our findings indicate that the phylogeography of B. stacei populations was shaped by recent radiations, frequent extinctions, long‐distance dispersal events, occasional interbreeding, and adaptation to local climates. [ABSTRACT FROM AUTHOR]

Genome‐wide technologies open up new possibilities to clarify questions on genetic structure and phylogeographic history of taxa previously studied with microsatellite loci and mitochondrial sequences. Here, we used 736 individual red deer (Cervus elaphus) samples genotyped at 35,701 single nucleotide polymorphism loci (SNPs) to assess the population structure of the species throughout Europe. The results identified 28 populations, with higher degrees of genetic distinction in peripheral compared to mainland populations. Iberian red deer show high genetic differentiation, with lineages in Western and Central Iberia maintaining their distinctiveness, which supports separate refugial ranges within Iberia along with little recent connection between Iberian and the remaining Western European populations. The Norwegian population exhibited the lowest variability and the largest allele frequency differences from mainland European populations, compatible with a history of bottlenecks and drift during post‐glacial colonization from southern refugia. Scottish populations showed high genetic distance from the mainland but high levels of diversity. Hybrid zones were found between Eastern and Western European lineages in Central Europe as well as in the Pyrenees, where red deer from France are in close contact with Iberian red deer. Anthropogenic restocking has promoted the Pyrenean contact zone, admixture events in populations on the Isle of Rum and in the Netherlands, and at least partly the admixture of the two main lineages in central‐eastern Europe. Our analysis enabled detailed resolution of population structure of a large mammal widely distributed throughout Europe and contributes to resolving the evolutionary history, which can also inform conservation and management policies. [ABSTRACT FROM AUTHOR]

Historical periods of rapid climate change and associated direct and indirect impacts such as glaciation and restructuring of drainage systems are important in shaping biodiversity, lineage divergence, and contemporary genetic variation amongst many aquatic taxa. Through an understanding of the impacts of these ancient changes in land‐ and waterscapes on current diversity, practitioners can account for a species' unique evolutionary history when developing conservation strategies. We investigated intraspecific genetic diversity of the critically endangered freshwater mussel, Lampsilis rafinesqueana, endemic to the interior region of the U.S.A. Our study (1) characterises genetic variation within and amongst populations to infer biogeographic history and (2) applies genetic information to potential conservation strategies. We applied restriction‐site associated DNA sequencing and mitochondrial DNA sequencing to investigate genetic diversity within and amongst populations of L. rafinesqueana from across the species' distribution. We then considered this information in the context of historical riverscape processes and applicability to conservation. Variation within rivers was similar, but we found different genetic populations associated with two major ecoregions, the Central Interior Highlands and Osage Plains. The plains population displayed an Ne value approximately 10‐fold lower than the highlands population. Historical demographic modelling suggests the two populations diverged approximately 1.2 million years ago and then both populations underwent a substantial decrease in population size around 19,700 years ago. These two major events are each correlated with known periods of historic rapid climate change. We identified two distinct populations of a federally endangered mussel, L. rafinesqueana. Contemporary genetic diversity of this species was strongly influenced by direct and indirect impacts of rapid historic shifts in climate. The highlands population has undergone a recent expansion, typical of post‐Pleistocene climate change, while also having a much larger Ne value than the plains population. Our results suggest low levels of gene flow amongst the two distinct populations across generations. We recommend that conservation managers for this species take into account relative difference in diversity between populations when developing management strategies. In many species, assisted gene flow amongst genetically unique populations should only be considered in extreme circumstances; however, in L. rafinesqueana, low levels of assisted migration amongst populations may be a valuable tactic to maintain natural levels of genetic variation. Our study shows that biogeographical frameworks can be useful for developing conservation strategies that serve to retain important genomic variation that represents the evolutionary potential of target freshwater species. [ABSTRACT FROM AUTHOR]

Aim Location Taxon Methods Results Main Conclusions We examined range‐wide genetic variation in a widespread white oak species in western North America to determine phylogeographic patterns (including possible latitudinal gradients) and investigate their underlying causes.Western North America.Quercus garryana (Fagaceae).We sampled Q. garryana at 117 locations throughout its range and related species of white oaks in 8 additional populations. We sequenced DNA from four variable intergenic plastid spacers and the ribosomal nuclear ITS region. We constructed haplotype networks and phylogenetic trees, mapped the geographical distributions of plastid haplotypes, and analysed genetic diversity patterns.We identified 25 plastid haplotypes that clustered in two major groups, each showing pronounced genetic variation with latitude. In contrast, ITS showed little or no geographical or phylogenetic variation. Quercus garryana shared several plastid haplotypes with related white oaks and was not differentiated from these species by ITS. Plastid haplotype diversity in Q. garryana was highest in the central part of its range and sharply reduced to the north. Two haplotypes (one from each haplotype group) occurred in the northern third of the range, with only one at the northern range limit. Populations at the southern range limit were characterised by distinct haplotypes.Genetic patterns of Q. garryana have been shaped both by post‐Pleistocene climate change, interacting with features of the landscape, and by hybridisation with other white oaks. The species contains substantial genetic variation with strong spatial structuring of plastid haplotypes, indicating (1) early divergence of southern (Sierra Nevada) and northern populations, and (2) northward dispersal during the Holocene resulting in greatly reduced genetic diversity in its northern range. Species that can adjust their ranges with changing climates may remain susceptible to loss of genetic variation, potentially affecting their ability to persist in novel conditions at northern range margins. [ABSTRACT FROM AUTHOR]

Gall‐forming insects induce various types of galls on their host plants by altering gene expression in host plant organs, and recent studies have been conducted for gene expression in galls. However, the evolutionary trajectories of gene expression patterns and the resulting phenotypes have not yet been studied using multiple related species. We investigated the speciation and the diversification process of galls induced by four closely related aphid species (Hormaphidini) on a host plant species (Hamamelis japonica) by examining the phylogenetic congruence between the geographical divergences of aphids and the host plant, and by comparing their gene expression patterns and resulting phenotypes. Phylogenetic analysis of aphids and the host plant showed that geographical isolation among host plant populations has interrupted gene flow in aphids and accelerated the speciation process. The concentration of phenolics and the complexity of the internal structure of galls were correlated with the expression levels of genes for the biosynthesis of phenolics and morphogenesis respectively. These results suggest that the expression levels of genes for the biosynthesis of phenolics and morphogenesis have evolutionarily increased in galls accelerated by the speciation process of aphids due to the distribution change of the host plant, leading to the related phenotypic evolution. Our study showed the evolutionary process of phenotypic traits in galls in the wild from both gene expression and actual phenotype levels. [ABSTRACT FROM AUTHOR]

This article explores the human-mediated dispersal of snake species in the Aegean Islands. The region's diverse herpetofauna is a result of its geographical location and historical factors. Human activities, particularly trade routes, have played a role in the movement of snakes in the area. The study focuses on two snake species, Telescopus fallax and Natrix tessellata, and uses DNA sequences to examine the genetic relationships and biogeographic history of specific island populations. The findings reveal distinct genetic groups and differences between populations in different parts of the Aegean. The article emphasizes the importance of further research to better understand the impact of human-mediated snake dispersal in the region. [Extracted from the article]

The European Roller (Coracias garrulus), a long-distance migratory bird, faced a considerable decline in breeding pairs throughout Europe at the end of the 20th century. Due to conservation efforts and the installation of nesting boxes, the population of the European Roller in Serbia has made a remarkable recovery. Here, we used the variability of nucleotide sequences of the mitochondrial DNA (mtDNA) control region and 10 microsatellite loci to assess the genetic diversity and structuring, phylogeographic patterns and demographic history of this species using 224 individuals from Serbia. Our results showed moderate level of genetic diversity (HO = 0.392) and a slightly elevated level of inbreeding and homozygosity (FIS = 0.393). Genetic structuring based on microsatellite data indicated three genetic clusters, but without a clear spatial pattern. High haplotype diversity (Hd = 0.987) of the mtDNA control region sequences was detected, and neutrality tests indicated a recent demographic expansion. The phylogeographic analysis, which also included previously published sequences of the mtDNA control region, supported the subdivision into two distinct European and Asian haplogroups (ΦST = 0.712). However, the results of our study showed that a larger number of haplotypes sampled in Serbia are clustered in the Asian haplogroup as compared to previous studies, indicating a historically continuous distribution of this species and possibly a wider distribution of the subspecies Coracias garrulus semenovwi. Our results suggest that the European Roller population in Serbia is genetically stable, with no evidence of recent bottlenecks, and emphasize the importance of artificial nest boxes for promoting and maintaining population dynamics of European Rollers. [ABSTRACT FROM AUTHOR]

Aim Location Methods Results Main Conclusion Glaciers cover considerable portion of land and host diverse life forms from single‐celled organisms to invertebrates. However, the determinants of diversity and community composition of these organisms remain underexplored. This study addresses the biogeography, population connectivity and dispersal of these organisms, especially critical in understanding during the rapid recession of glaciers and increased extinction risk for isolated populations. By reconstructing the Quaternary biogeographic history of Fontourion glacialis, a widespread in Northern Hemisphere glacier obligate species of Tardigrada, we aim to understand how populations of glacier‐dwelling metazoans receive immigrants, respond to disappearing glaciers and to what extent remaining glaciers can serve as refugia.Glaciers across Svalbard, Scandinavia, Greenland and Iceland.We analysed mtDNA (COI gene) variability of 263 F. glacialis specimens collected across the distribution range. Phylogeographic and coalescent‐based approaches were used to detect population differentiation patterns, investigate most likely models of gene flow and test the influences of geographical and climatic factors on the distribution of F. glacialis genetic variants.Our findings indicate that the distribution of F. glacialis genetic variants is primarily influenced by geographical rather than climatic factors. Populations exhibit a dispersal‐limited distribution pattern, influenced by geographical distance and local barriers, even between neighbouring glaciers. Significantly, the genetic structure within Scandinavia suggests the existence of “southern” glacial or low‐temperature refugia, where F. glacialis may have survived a period of extensive deglaciation during the Holocene climatic optimum (8–5 kyr ago).The study uncovers complex metapopulation structures in F. glacialis, with impacts of local barriers, population bottlenecks as well as historical ice sheet fluctuations. It suggests that such populations can endure extended periods of deglaciation, highlighting the resilience of glacial refugia. The study highlights the necessity of understanding the diversity and population structure of ice‐dwelling fauna in both spatial and temporal contexts. [ABSTRACT FROM AUTHOR]

Key message: Populations 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. Context: In 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. Aims: The 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. Methods: We 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. Conclusion: Moderate 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. [ABSTRACT FROM AUTHOR]

Premise Methods Results Conclusions Globally, barriers triggered by climatic changes have caused habitat fragmentation and population allopatric divergence. Across North America, oscillations during the Quaternary have played important roles in the distribution of wildlife. Notably, diverse plant species from the Baja California Peninsula in western North America, isolated during the Pleistocene glacial–interglacial cycles, exhibit strong genetic structure and highly concordant divergent lineages across their ranges. A representative plant genus of the peninsula is Yucca, with Y. valida having the widest range. Although a dominant species, it has an extensive distribution discontinuity between 26° N and 27° N, suggesting restricted gene flow. Moreover, historical distribution models indicate the absence of an area with suitable conditions for the species during the Last Interglacial, making it an interesting model for studying genetic divergence.We assembled 4411 SNPs from 147 plants of Y. valida throughout its range to examine its phylogeography to identify the number of genetic lineages, quantify their genetic differentiation, reconstruct their demographic history and estimate the age of the species.Three allopatric lineages were identified based on the SNPs. Our analyses support that genetic drift is the driver of genetic differentiation among these lineages. We estimated an age of less than 1 million years for the common ancestor of Y. valida and its sister species.Habitat fragmentation caused by climatic changes, low dispersal, and an extensive geographical range gap acted as cumulative mechanisms leading to allopatric divergence in Y. valida. [ABSTRACT FROM AUTHOR]

Global biodiversity loss continues unabated, and in Australia, the rate of recent mammal extinctions is among the worst in the world. Meanwhile, the diversity among and within many endemic mammal species remains undescribed. This information is crucial to delineate species boundaries and thus inform decision‐making for conservation. Sminthopsis virginiae (the red‐cheeked dunnart) is a small, dasyurid marsupial found in four disjunct populations around the northern coast of Australia and New Guinea. There are three currently recognized subspecies, each occupying a distinct geographic location. Sminthopsis v. virginiae occurs in Queensland, S. v. rufigenis is distributed across New Guinea and the Aru Islands, and S. v. nitela has populations in the Top End of the Northern Territory and the Kimberley region of Western Australia. Previous molecular work has suggested the current subspecies definitions are not aligned with DNA sequence data, though the sampling was limited. We undertook a comprehensive genetic and morphological review of S. virginiae to clarify relationships within the species. This included mitochondrial (CR, 12S, and cytb) and nuclear (omega‐globin, IRBP, and bfib7) loci, and morphometric analysis of skulls and whole wet‐preserved specimens held in museums. Maximum Likelihood and Bayesian phylogenetic analyses resolved samples into two distinct clades, demarcated by the Gulf of Carpentaria in Australia's north. Sminthopsis. v. nitela was consistently separated from S. v. virginiae and S. v. rufigenis, based on the overall body and skull size and craniodental features, while S. v. virginiae and S. v. rufigenis were more difficult to distinguish from each other. Thus, we redescribed S. virginiae, recognizing two species, S. nitela (raised from subspecies) and S. virginiae (now comprising the subspecies S. v. virginiae and S. v. rufigenis). This study highlights the importance of recognizing cryptic mammal fauna to help address the gap in our knowledge about diagnosing diversity during a time of conservation crisis. [ABSTRACT FROM AUTHOR]

This study explores how climate variables influenced the evolution and diversification of Neurergus newts within the Irano‐Anatolian biodiversity hotspot. We use a dated phylogenetic tree and climatic niche models to analyze their evolutionary history and ecological preferences. Using genetic data from nuclear (KIAA) and mitochondrial (16s and 12s) genes, we estimate divergence times and identify four major Neurergus clades. The initial speciation event occurred approximately 11.3 million years ago, coinciding with the uplift of the Zagros and Anatolian mountains. This geological transformation isolated newt populations, likely triggering the first speciation event. By integrating potential geographic distribution with climate variables, we reconstruct ancestral niche occupancy profiles. This highlights the critical roles of temperature and precipitation in shaping Neurergus habitat preferences and distribution. We observe both phylogenetic niche conservatism and divergence, with niche divergence playing a dominant role in diversification. This research emphasizes the complex interplay of geography, climate, and ecology in speciation and the vulnerability of isolated mountain newt populations to environmental changes. [ABSTRACT FROM AUTHOR]

Barley is one of the founder crops of the Neolithic transition in West Asia. While recent advances in genomics have provided a rather detailed picture of barley domestication, there are contradictory views on how the domestication process affected genetic diversity. We set out to revisit this question by integrating public DNA sequencing data from ancient barley and wide collections of extant wild and domesticated accessions. Using two previously overlooked approaches – analyses of chloroplast genomes and genome‐wide proportions of private variants – we found that the barley cultivated six millennia ago was genetically unique and more diverse when compared to extant landraces and cultivars. Moreover, the chloroplast genomes revealed a link between the ancient barley, an obscure wild genotype from north‐eastern Libya, and a distinct population of barley cultivated in Ethiopia/Eritrea. Based on these results, we hypothesize past existence of a wider North African population that included both wild and cultivated types and suffered from genetic erosion in the past six millennia, likely due to a rapid desertification that ended the Holocene African humid period. Besides providing clues about the origin of Ethiopian landraces, the hypothesis explains the post‐domestication loss of diversity observed in barley. Analyses of additional samples will be necessary to resolve the history of African barley and its contribution to the extant cultivated gene pool. [ABSTRACT FROM AUTHOR]

Genetic management is a critical component of threatened species conservation. Understanding spatial patterns of genetic diversity is essential for evaluating the resilience of fragmented populations to accelerating anthropogenic threats. Nowhere is this more relevant than on the Australian continent, which is experiencing an ongoing loss of biodiversity that exceeds any other developed nation. Using a proprietary genome complexity reduction‐based method (DArTSeq), we generated a data set of 3239 high quality Single Nucleotide Polymorphisms (SNPs) to investigate spatial patterns and indices of genetic diversity in the koala (Phascolarctos cinereus), a highly specialised folivorous marsupial that is experiencing rapid and widespread population declines across much of its former range. Our findings demonstrate that current management divisions across the state of New South Wales (NSW) do not fully represent the distribution of genetic diversity among extant koala populations, and that care must be taken to ensure that translocation paradigms based on these frameworks do not inadvertently restrict gene flow between populations and regions that were historically interconnected. We also recommend that koala populations should be prioritised for conservation action based on the scale and severity of the threatening processes that they are currently faced with, rather than placing too much emphasis on their perceived value (e.g., as reservoirs of potentially adaptive alleles), as our data indicate that existing genetic variation in koalas is primarily partitioned among individual animals. As such, the extirpation of koalas from any part of their range represents a potentially critical reduction of genetic diversity for this iconic Australian species. [ABSTRACT FROM AUTHOR]

The sub-Antarctic terrestrial ecosystems survive on isolated oceanic islands in the path of circumpolar currents and winds that have raged for more than 30 million years and are shaped by climatic cycles that surpass the tolerance limits of many species. Surprisingly little is known about how these ecosystems assembled their native terrestrial fauna and how such processes have changed over time. Here, we demonstrate the patterns and timing of colonization and speciation in the largest and dominant arthropod predators in the eastern sub-Antarctic: spiders of the genus Myro. Our results indicate that this lineage originated from Australia before the Plio-Pleistocenic glacial cycles and underwent an adaptive radiation on the Crozet archipelago, from where one native species colonized multiple remote archipelagos via the Antarctic circumpolar current across thousands of kilometers. The results indicate limited natural connectivity between terrestrial macroinvertebrate faunas in the eastern sub-Antarctic and partial survival of repeated glaciations in the Plio-Pleistocene. Furthermore, our findings highlight that by integrating arthropod taxa from multiple continents, the climatically more stable volcanic Crozet archipelago played a critical role in the evolution and distribution of arthropod life in the sub-Antarctic. [ABSTRACT FROM AUTHOR]

The complex topography of mountainous landscapes can create biogeographical barriers and promote allopatric speciation—even among morphologically cryptic species. However, these biogeographical barriers may not be permanent, and secondary contact between previously independently evolving populations can result in hybridization and introgression. In this study, we used genome-wide single nucleotide polymorphism data to re-examine a classic example of cryptic species in the Appalachian Mountains: the slimy salamander (Plethodon glutinosus) species complex. This group of morphologically similar terrestrial salamanders includes 14 species with parapatric distributions across the eastern USA. We focused on the Chattahoochee slimy salamander (P. chattahoochee) in northern Georgia and used a series of complementary phylogenomic and population genomic analyses to evaluate spatial genetic structure within this species and admixture with at least four other species of parapatric woodland salamanders. Our results highlight the utility of genomic data in clarifying species boundaries and underline the difficulty of species delimitation in organisms with complex evolutionary histories. [ABSTRACT FROM AUTHOR]

Aim: The distribution of within‐species lineages has been affected by Quaternary climate changes, and population differentiation has been influenced by species life history traits. We investigated whether the distribution of individual mitochondrial genetic lineages reflects the constituent species' traits. Using the functionally diverse group of butterflies, we examined which lineages are present in Central Europe, an important suture zone. Location: Czech Republic and Western Palearctic. Taxon: A total of 140 butterfly species. Methods: We sequenced DNA barcodes (cytochrome c oxidase 1) (959 sequences) of the entire Czech Republic butterfly fauna and used Barcoding of Life Data System to visualise the species' biogeographic patterns across Europe. We categorised the distribution patterns of lineages inhabiting the Czech Republic, and used multivariate statistics to interpret these categories by the butterflies' habitats, life history traits and threat levels. Results: Open habitat dwellers with specialist traits belonged to Eastern, Southern and temperate lineages. Habitat generalists and woodland dwellers belonged to the Western lineage, formed several lineages or displayed low genetic diversity; they often developed on woody plants, were large‐winged and had long flight periods. The most threatened species were the specialists of Southern, Eastern and temperate lineages. Main Conclusions: The distribution of lineages in Central Europe reflects the history of Quaternary ecosystems: during cold periods of the Pleistocene, the diverse open habitats prevailed and species could expand westwards. Such species also suffer the most under the current anthropogenic habitat alteration. On the other hand, the mobile generalists and woodland dwellers expanded to Central Europe during the Holocene. Our approach of linking the distribution of lineages with species traits can be transferred to other study systems, and we show that DNA barcoding of under‐sampled areas represents a powerful tool for discovering the driving forces of biogeography. [ABSTRACT FROM AUTHOR]

Aim: The factors that influence the diversity of Yungas Andean forest remain unexplored. Our study seeks to investigate the impact of key isolating factors on the genetic structure of multiple taxa, testing for four hypotheses: isolation by distance (IBD), isolation by resistance due to topography (IBRtopo), isolation by resistance due to habitat suitability (IBRsuit) and isolation by environmental dissimilarity (IBE). Location: Yungas Andean forest. Taxon: Tetrapoda. Methods: We analysed a dataset consisting of 477 Cyt‐b sequences from 138 localities, encompassing 13 species. Through multiple matrix regression, Moran Spectral Randomization of Mantel and GDM analyses, we tested the impact of each extrinsic predictor on observed genetic variation and determined the effect size of environmental variation on genetic divergence. Additionally, we investigated the spatial distribution of lineages within the study species. Results: The genetic variation within the Yungas exhibited varied responses that correspond to the regional landscape heterogeneity. We identified different isolating factors as the main predictor for specific species: IBD for Akodon spegazzinii; IBRtopo for certain small mammals' species; IBE for Thylamys cinderella and Oligoryzomys brendae; and IBRsuit for Calomys fecundus, Oreobates barituensis and Melanophryniscus rubriventris with some considerations. Furthermore, our results support the presence of a latitudinal pattern in the distribution of genetic lineages. Main Conclusions: The heterogeneous landscape of the Yungas Andean forest posed varied effects on genetic variation. The effect of topography and continuity of suitable habitats over vertebrate dispersal shapes the genetic diversity, in particular topography acts either as a barrier or as corridor, while habitat suitability resistance mainly shapes endemism genetic structure; local climate represents a strong genetic promoter in transition zones; and the effect of geographic distance is less evident when considering other landscape promoter of genetic divergence. This reinforces the understanding that the complex interplay of environmental and historical factors contributes to the observed patterns of genetic diversity in this region. [ABSTRACT FROM AUTHOR]

Aim: Ecological niche‐based models (ENM) frequently rely on bioclimatic variables (BioV) to reconstruct biogeographic scenarios for species evolution, ignoring mechanistic relations. We tested if climatic predictors relevant to species hydric and thermal physiology better proximate distribution patterns and support location of Pleistocene refugia derived from phylogeographic studies. Location: The Western Palaearctic. Taxon: Vipera berus and Zootoca vivipara, two cold‐adapted species. Methods: We used two sets of variables, that is physiologically meaningful climatic variables (PMV) and BioV, in a multi‐algorithm ENM approach, to compare their ability to predict current and Last Glacial Maximum (LGM) species ranges. We estimated current and LGM permafrost extent to address spatially the cold hardiness dissimilarity between both species. Results: PMV explained more accurately the current distribution of these two cold‐adapted species and identified the importance of summer temperature and solar radiation that constrain activity in cold habitats. PMV also provide a better insight than BioV predictors on LGM distribution. By including notably, the permafrost extent, PMV‐based models gave parsimonious putative arrangement and validity of refugia for each clade and subclade in accordance with phylogeographic data. Northern refugia were also identified from 48 to 52° N for V. berus and from 50 to 54° N for Z. vivipara. Main Conclusions: Our hybrid approach based on PMV generated more realistic predictions for both current (biogeographical validation) and past distributions (phylogeographic validation). By combining constraints during the activity period (summer climatic niche) and those inherent to the wintering period (freeze tolerance), we managed to identify glacial refuges in agreement with phylogeographic hypotheses concerning post‐glacial routes and colonization scenarios. [ABSTRACT FROM AUTHOR]

Aim: Knowledge of taxonomy and species distributions in highly diverse lineages of invertebrates remains too incomplete for the study of biogeographical patterns at the global scale. This limits the understanding of processes leading to the formation and maintenance of boundaries between major biogeographical realms. Site‐based metagenomic approaches may provide an alternative source of data for inference of historical processes of in situ speciation and interchange among biogeographical regions. We applied the methodology to explore the historical biogeography of the Qinling Mountains at the boundary of the Oriental and Palaearctic regions. Location: The focal area in the Qinling Mountains; sites in Borneo, Panama, and Spain, representing the Oriental, Neotropical and Palaearctic faunas. Time Period: Contemporary. Major Taxa Studied: Chrysomelidae, a group of ~40,000 species with worldwide distribution. Methods: Mass‐trapped insects were subjected to deep Illumina DNA sequencing and mitochondrial genome assembly, followed by phylogenetic analysis and historical biogeographical inference on a dated tree. The methodology produced 622 mitogenomes (304 newly sequenced) each representing a morphologically distinct species. Results: Ancestral area reconstruction revealed that the Qinling fauna is a composite of distinct clades that, respectively, have Oriental or Palaearctic ancient origins, while in situ speciation and local clade formation were limited. The global diversity of Chrysomelidae consists of regionalised deep clades at the level of the major zoogeographic realms, which remain recognisable where these realms abut in the Qinling mountains. Yet, the Qinling fauna is clearly distinct from the source areas although local lineage ages are generally <20 Ma. Main Conclusions: The Qinling fauna is a composite of clades that have either Oriental or Palaearctic origin, indicating the important role of immigration at the realm boundary. Global site‐based phylogenetic analyses based on metagenomic sequencing can address previously intractable questions about the historical biogeography of poorly studied groups even without a fully developed taxonomy. [ABSTRACT FROM AUTHOR]

Octopus insularis is a shallow‐water octopus distributed throughout the western Atlantic, the Gulf of Mexico and the Caribbean. To evaluate its phylogeographic pattern, mitochondrial markers (16S rRNA and COIII) and genome‐wide nuclear markers (SNP's) were analyzed in individuals from artisanal fishing in different locations of the Colombian Caribbean coast. Mitochondrial analyzes displayed novel haplotypes (16S = H2, H3 and H4; COIII = H2–H7) and haplotypes shared with distant geographic areas (16S = H1 COIII = H1). The COIII gene did not show genetic differentiation between the analyzed localities, while the 16S gene showed significant differences between Santa Marta and Isla Fuerte. COIII's demographic analysis indicated that the species' effective population size has remained constant. Inferences were made from next‐generation genomic data with restriction site‐associated DNA (ddRAD‐seq) and 6769 polymorphic loci. The pairwise FST test indicated that there are low but significant differences between localities; however, the general molecular analysis of variance (AMOVA) and the principal coordinate analysis showed a lack of spatial structure in the populations analyzed. The Mantel test found no correlation between genetic distance and geographic distance, and the genetic structure analyses showed the presence of one genetic stock. The information obtained in this study indicates the genetic connectivity of O. insularis in the southwestern Caribbean, the absence of putative biogeographic barriers that affect its gene flow, and the crucial role played by life history strategies (planktonic paralarvae) and oceanographic factors to define the current distribution of its genetic diversity in this region. [ABSTRACT FROM AUTHOR]

Mycobacterium tuberculosis is considered by many to be the deadliest microbe, with the estimated annual cases numbering more than 10 million. The bacteria, including Mycobacterium africanum, are classified into nine major lineages and hundreds of sublineages, each with different geographical distributions and levels of virulence. The phylogeographic patterns can be a result of recent and early human migrations as well as coevolution between the bacteria and various human populations, which may explain why many studies on human genetic factors contributing to tuberculosis have not been replicable in different areas. Moreover, several studies have revealed the significance of interactions between human genetic variations and bacterial genotypes in determining the development of tuberculosis, suggesting coadaptation. The increased availability of whole-genome sequence data from both humans and bacteria has enabled a better understanding of these interactions, which can inform the development of vaccines and other control measures. [ABSTRACT FROM AUTHOR]

The introduction of the spatial Lambda-Fleming–Viot model (Λ V) in population genetics was mainly driven by the pioneering work of Alison Etheridge, in collaboration with Nick Barton and Amandine Véber about ten years ago (Barton et al., 2010; Barton et al., 2013). The Λ V model provides a sound mathematical framework for describing the evolution of a population of related individuals along a spatial continuum. It alleviates the "pain in the torus" issue with Wright and Malécot's isolation by distance model and is sampling consistent, making it a tool of choice for statistical inference. Yet, little is known about the potential connections between the Λ V and other stochastic processes generating trees and the spatial coordinates along the corresponding lineages. This work focuses on a version of the Λ V whereby lineages move rapidly over small distances. Using simulations, we show that the induced Λ V tree-generating process is well approximated by a birth–death model. Our results also indicate that Brownian motions modelling the movements of lines of descent along birth–death trees do not generally provide a good approximation of the Λ V due to habitat boundaries effects that play an increasingly important role in the long run. Accounting for habitat boundaries through reflected Brownian motions considerably increases the similarity to the Λ V model however. Finally, we describe efficient algorithms for fast simulation of the backward and forward in time versions of the Λ V model. [ABSTRACT FROM AUTHOR]

Species of the genus Eubranchus Forbes, 1838 (Mollusca: Gastropoda: Nudibranchia) are common faunistic elements of boreal benthic ecosystems, associated with hydroid communities. Recent studies have suggested that the widely distributed trans-Arctic E. rupium (Møller, 1842) constitutes a complex of at least three candidate species, but the detailed taxonomy of the complex remains unresolved. The purpose of the present paper is to conduct an integrative taxonomic study including molecular genetic methods (a phylogenetic analysis using COI , 16S rRNA and histone H3 with application of species delimitation methods) and morphological study (light and scanning electron microscopy) of E. rupium and closely related species. The specific aims of this study were to establish the species boundaries, morphological variability, and the phylogeographic structure within this group. The phylogeographic analysis included a TCS -based network analysis, an analysis of molecular variance (AMOVA), divergence time estimations, and ancestral area reconstructions. We demonstrate that specimens initially identified as E. rupium included three distinctive species: the nominal E. rupium with an amphiboreal range, the new species Eubranchus novik sp. nov. from the Sea of Japan, for which a taxonomic description is provided in this paper, and Eubranchus sp. from the northern Kuril Islands, which requires the collection and study of additional material for formal description. Our results confirm the amphiboreal distribution of E. rupium , as no geographic structure was found across Pacific, Arctic and Atlantic populations, and the results of the AMOVA analysis showed no differences between groups of samples from different geographic regions. The divergence of the ' Eubrancus rupium species complex' is estimated from the late Miocene or the Miocene–Pliocene boundary to the late Pliocene. It is hypothesised that the most probable ancestral region for the Eubranchus rupium species complex is the north-western Pacific, and the subsequent speciation likely occurred due to dispersal followed by allopatric speciation. ZooBank: Species of the genus Eubranchus Forbes, 1838 are common in boreal benthic ecosystems. Recent studies suggest the trans-Arctic Eubranchus rupium (Møller, 1842) is a species complex. This paper conducts an integrative taxonomic study of Eubranchus rupium and related species, confirming its amphiboreal distribution. The divergence of the species complex is estimated from the late Miocene or the Miocene–Pliocene boundary to the late Pliocene with the north-western Pacific as the probable ancestral region, followed by dispersal and allopatric speciation. (Image credit: Darya Grishina.) [ABSTRACT FROM AUTHOR]

In migratory animals, high mobility may reduce population structure through increased dispersal and enable adaptive responses to environmental change, whereas rigid migratory routines predict low dispersal, increased structure, and limited flexibility to respond to change. We explore the global population structure and phylogeographic history of the bar‐tailed godwit, Limosa lapponica, a migratory shorebird known for making the longest non‐stop flights of any landbird. Using nextRAD sequencing of 14,318 single‐nucleotide polymorphisms and scenario‐testing in an Approximate Bayesian Computation framework, we infer that bar‐tailed godwits existed in two main lineages at the last glacial maximum, when much of their present‐day breeding range persisted in a vast, unglaciated Siberian‐Beringian refugium, followed by admixture of these lineages in the eastern Palearctic. Subsequently, population structure developed at both longitudinal extremes: in the east, a genetic cline exists across latitude in the Alaska breeding range of subspecies L. l. baueri; in the west, one lineage diversified into three extant subspecies L. l. lapponica, taymyrensis, and yamalensis, the former two of which migrate through previously glaciated western Europe. In the global range of this long‐distance migrant, we found evidence of both (1) fidelity to rigid behavioural routines promoting fine‐scale geographic population structure (in the east) and (2) flexibility to colonise recently available migratory flyways and non‐breeding areas (in the west). Our results suggest that cultural traditions in highly mobile vertebrates can override the expected effects of high dispersal ability on population structure, and provide insights for the evolution and flexibility of some of the world's longest migrations. [ABSTRACT FROM AUTHOR]

Replicability of divergence after contact is a poorly characterized process, particularly in the contexts of phylogeography and postglacial range dynamics within species. Using contact zones located at the leading‐, mid‐ and rear‐edges of a species' range, we examined variation in outcomes to contact between divergent lineages of Campanula americana. We investigated whether contact zones vary in quantity and directionality of gene flow, how phylogeographic structure differs between contact zones, and how historic range dynamics may affect outcomes to contact. We found that all contact zones formed at similar times via primary contact yet detected significant admixture in only the rear‐edge (RE) contact zone. In the northern leading‐edge contact zone and the mid‐range Virginia contact zone, gene flow was minimal and asymmetric. In the southern RE contact zone, gene flow was strong and symmetric. Asymmetric admixture in the leading‐edge and Virginia contact zones matches the directionality of a known cosmopolitan cytonuclear incompatibility between lineages of C. americana. Our results emphasize the dependence of speciation processes on phylogeographic structure, evolutionary history and range dynamics. [ABSTRACT FROM AUTHOR]

Simple Summary: Grasshopper species of the Stenobothrini tribe are known by the wide diversity of their premating traits, such as acoustic behavior and morphological characters. However, the phylogenetic relationships, divergence time, and phylogeography of these species inferred with the mtDNA markers (the control region and the COI gene) did not reflect the species divergence. The analysis of interspecific and intraspecific variability in the control region in two hybridizing species of this genus, S. eurasius and S. hyalosuperficies, supports the hypothesis of putative hybridization between the species and shows the direction of the mtDNA introgression. The two cryptic grasshopper species of the genus Stenobothrus, S. eurasius and S. hyalosuperficies, demonstrate different acoustic behavior despite a strong similarity in morphology. A hybridization between these species is possible in the contact zone; however, there are little molecular data about the relationships of these species. The analysis of the mtDNA control region (CR) reveals that haplotypes of S. hyalosuperficies have more in common with the more distant Stenobothrus species than with the closely related S. eurasius. In the contact zone, S. eurasius has mt-haplotypes shared with S. hyalosuperficies, which might indicate an introgression of mtDNA from S. hyalosuperficies to the S. eurasius gene pool. We also analyze the structure and evolutionary rate of the mtDNA CR for the Stenobothrus genus and estimate the time of divergence of the species within the genus. The phylogenetic tree of the tribe Stenobothrini reconstructed with either the CR or COI gave the same four groups. The phylogenetic tree of the Stenobothrus genus has a star-like topology with each mtDNA haplotype found in any analyzed species, except S. eurasius, which forms a separate branch. The maximum degree of incomplete lineage sorting can demonstrate either ancestral polymorphism or introgression. [ABSTRACT FROM AUTHOR]

The heteroplasmic mitogenome of the stingless bee Tetragonula laeviceps from Peninsular Malaysia consists of two variants (TL1-1 and TL1-2), both with 29,084 bp consisting of two segments: the “canonical” segment contains 36 genes—13 protein-coding genes (PCGs), 2 rRNA, and 21 tRNA genes; and the inverted repeat segment consists of 31 genes (11 PCGs, 2 rRNAs, and 18 tRNAs). In the TL1-2 variant, the (nad4-nad4L-trnP-trnS1) gene segment in the “canonical” genome of the TL1-1 variant was inverted to (trnS1-trnP-nad4-nad4L). Phylogenetic analyses based on 13 PCGs and 15 mt-genes reveal that T. laeviceps from Peninsular Malaysia and China form a lineage in the subclade consisting also of the Tetragonula lineage of T. mellipes, T. davenporti, T. carbonaria, and T. hockingsi. The genetic distances of 13 PCGs and 15 mt-genes between T. laeviceps of Peninsular Malaysia and China (p = over 10%) and between the taxa of China (p = about or over 10%) indicate that these three taxa are genetically distinct, reflecting the presence of a species complex. The large genetic distances, based on COX1 sequences, of p = over 10% among the taxa of T. laeviceps of China, Peninsular Malaysia, Sabah, Indonesia, and India indicate beyond reasonable doubt that they are not conspecific. Assuming that the Peninsular Malaysian taxon is T. laeviceps s.str., the taxa of China, Sabah, Indonesia, and India (as well as Thailand based on the 16S rRNA gene) warrant to be accorded as distinct cryptic species. Likewise, the taxonomic status of some taxa (e.g., Tetragonula fuscobalteata of Sabah and Sulawesi) needs clarification. [ABSTRACT FROM AUTHOR]

Aim: Synthesize literature on genetic structure within species to understand how geographic features and species traits influence past responses to climate change. Location: North America. Time Period: We synthesized phylogeographic studies from 1978 to 2023, which describe genetic lineages that diverged during the Pleistocene (≥11,700 years ago). Major Taxa Studied: Mammals. Methods: We conducted a literature review to map genetic breaks in species distributions, then tested a set of geographic hypotheses (e.g., mountains, rivers) to explain their position by comparing break locations to a grid within each species' sampled range using logistic regression. We then conducted a meta‐analysis using species‐specific model estimates to ask if life‐history traits explained variation in which barriers were most important in species' past response to climate change. Results: Our findings reveal heterogeneity in both where North American mammal phylogeography has been studied and the density of genetic breaks across 229 species. We found relatively high concordance among carnivores, ungulates and lagomorphs, where breaks were associated with mountains, major water bodies and relatively even terrain. In contrast, we found high variability within rodents and shrews, and no evidence that intrinsic factors related to dispersal ability explained the importance of hypothesized barriers across all species. Main Conclusions: Southern Mexico is a hotspot for genetic breaks that has yet to be integrated into the broader story of North American phylogeography. We show that mountains and major water bodies play particularly important roles as barriers, but substantial variation across species within orders suggests that there is more to the story besides shared climatic or phylogenetic histories. Thus, understanding the phylogeography of individual species will continue to be important given that our results suggest high variability in how species may respond to future global change. [ABSTRACT FROM AUTHOR]

Coastal dunes are unique habitats, threatened by human activities. In biogeographical terms, coastal dunes are habitat islands, being discrete and distinct patches of similar habitat among themselves, separated from each other by a different type of habitat. Furthermore, coastal dunes harbor endemic species, adapted to living solely in the habitats found on specific dune systems. For example, the honeypot ant Myrmecocystus baja is endemic and restricted to coastal dunes of Mexico's Baja California Pacific coast. This ecological and biogeographical scenario led to the questions whether their geographical isolation is reflected in their genetic diversity and structuring, and how their demographic history is related with the formation of the dune system habitats. To answer these questions, population genetic, isolation-with-migration, and phylogeographical analyses were carried out, based on mitochondrial and five nuclear intronic markers. Minimal gene flow was detected only between two of the dune systems sampled; otherwise, the M. baja populations were found to be isolated and genetically structured, and their divergence generally pre-dated the modern-day dune systems. It is therefore highly likely that these ants were already present in paleodunes and that each of the populations was established from founder populations as the dunes formed. These findings highlight the importance of coastal dunes for species such as the honeypot ant from Baja California, in promoting genetic differentiation. [ABSTRACT FROM AUTHOR]

This article discusses the observation of the critically endangered soupfin shark in the Changing Salish Sea. The study confirms the presence of soupfin sharks in Hammersley Inlet through fishing efforts and sampling. The findings suggest that the presence of soupfin sharks may have implications for trophic dynamics and fisheries management in the region. The article also provides a list of references for further research on marine ecosystems in the Salish Sea and surrounding areas. [Extracted from the article]

Prosorhochmidae, known as smiling worms, are hoplonemerteans of great interest to nemertologists, since some species display viviparity and hermaphroditism, both rare traits in this phylum, and can be found in terrestrial and marine environments. Prosorhochmus is a predominantly marine genus and was never recorded on the Brazilian coast. The present study documents the first record of the oviparous Prosorhochmus belizeanus, along with population genetic diversity analyses. Here, we sequenced cytochrome c oxidase subunit 1 (COI) and 16S ribosomal RNA (16SrRNA) regions from individuals of three localities along the Brazilian Northeast coast. From these analyses, we found moderate genetic diversity, no genetic structuring, and no clear geographical pattern. In addition, migration analysis evidenced some influence of the Brazilian Current in the species’ dispersion. Those findings indicate colonization by a small number of mtDNA lineages followed by population stability and shed light into the importance of deepening the knowledge about those organisms to elucidate genetic and dispersion patterns of oviparous invertebrates of rocky shores. [ABSTRACT FROM AUTHOR]

This article reports on the discovery of a complete male skull of the marsh deer in Uruguay, marking the southernmost limit of its range. The skull was found in the departments of Canelones and Maldonado and was estimated to be around 294 years old through radiocarbon dating. Genetic analysis revealed significant genetic diversity and past population dynamics of marsh deer in the region. These findings highlight the need for habitat restoration and future rewilding strategies to protect this species. [Extracted from the article]