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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.

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]

Prunus discoidea is a unique cherry blossom germplasm resource native to China. It is widely distributed across the provinces of Anhui, Zhejiang, Jiangxi, Jiangsu, and Henan, with significant variation. We employed phylogeographic analysis to reveal the evolutionary history of P. discoidea to better understand its genetic diversity and structure. This study provides more accurate molecular insights for the effective conservation and utilization of this germplasm resource. We conducted a phylogeographic analysis of 348 individual plants from 13 natural populations using three fragments (rpoB, rps16, and trnD–E) of chloroplast DNA (cpDNA) and one fragment (ITS) of ribosomal DNA. The results revealed that P. discoidea demonstrates a significant level of genetic diversity (Hd = 0.782; Rd = 0.478). Gene flow among populations was limited, and the variation within populations was the main source of genetic diversity in P. discoidea (among populations: 34.26%, within populations: 65.74%). Regarding genetic differences among populations, Nst (0.401) showed greater differences than Gst (0.308; p < 0.05), demonstrating that there was a significant geographical structure of lineage. One lineage was the central region of Anhui and the western region of Hubei. The other lineage was the Jiangsu region and the Zhejiang region. P. discoidea diverged from Prunus campanulata approximately 1.5 million years ago, during the Pleistocene epoch. This study provides a scientific theoretical basis for the conservation and utilization of germplasm resources of P. discoidea. [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]

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]

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]

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]

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]

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]

The terrestrial fauna of Antarctica consists of a limited number of species, notably insects, small crustaceans and other micro-invertebrates. Over long periods of evolutionary isolation, these organisms have developed varying degrees of tolerance to multifaceted environmental stresses. Recent molecular biogeographical research highlights the enduring persistence of much of Antarctica's current terrestrial fauna, with estimates spanning from hundreds of thousands to millions of years. Parochlus steinenii, commonly known as the Antarctic winged midge, stands out as one of the only two insect species native to Antarctica. Distributed across three biogeographic regions, southern South America and the Falkland/Malvinas Islands, sub-Antarctic South Georgia and the Maritime Antarctic South Shetland Islands, this midge raises questions about the temporal isolation of its populations and their divergence. Employing mitochondrial and nuclear genetic markers, we conducted phylogeographic and demographic analyses on 151 individuals of P. steinenii obtained across the three main biogeographic regions including the Magellanic sub-Antarctic Ecoregion (MSE) of southern South America, the sub-Antarctic Island of South Georgia (SG) and the South Shetland Islands (SSI) within the Maritime Antarctic (MA). Our data support the diversification of P. steinenii during the midPleistocene around 1.46 Mya. This period included a branching event between a clade containing only specimens from the MSE and a clade containing individuals from a broader range of locations including the SSI and SG. Based on intraspecific phylogeographic and demographic inferences, we detected strong evolutionary divergence between the three main biogeographic regions. We also detected a signal of population growth during the deglaciation process in SSI and SG, contrary to the pattern seen in the MSE. The different demographic and phylogeographic histories between the sampled biogeographic regions could result from the MA and SG experiencing a strong genetic bottleneck due to a reduction in population size during the Last Glacial Maximum, while the MSE maintained a significant effective population size. The high level of divergence detected between individuals from the MSE and the remaining biogeographic regions supports the hypothesis of a speciation process taking place in P. steinenii. [ABSTRACT FROM AUTHOR]

Many studies suggest that aside from environmental variables, such as topography and climate, species‐specific ecological traits are relevant to explain the geographic distribution of intraspecific genetic lineages. Here, we investigated whether and to what extent incorporating such traits systematically improves the accuracy of random forest models in predicting genetic differentiation among pairs of localities. We leveraged available ecological datasets for birds and tested the inclusion of two categories of ecological traits: dispersal‐related traits (i.e. morphology and foraging ecology) and demographic traits (such as species survival rate and generation length). We estimated genetic differentiation from published mitochondrial DNA sequences for 28 species of birds (1578 total genetic samples, 391 localities) in the Atlantic Forest of South America. Aside from the aforementioned ecological traits, we included geographic, topographic and climatic distances between localities as environmental predictors. We then created models using all available data to evaluate model uncertainty both across space and across the different categories of predictors. Finally, we investigated model uncertainty in predicting genetic differentiation individually for each species (a common challenge in conservation biology). Our results show that while environmental conditions are the most important predictors of genetic differentiation, model accuracy largely increases with the addition of ecological traits. Additionally, the inclusion of dispersal traits improves model accuracy to a larger extent than the inclusion of demographic traits. Similar results are observed in models for individual species, although model accuracy is highly variable. We conclude that ecological traits improve predictive models of genetic differentiation, refining our ability to predict phylogeographic patterns from existing data. Additionally, demographic traits may not be as informative as previously hypothesized. Finally, prediction of genetic differentiation for species with conservation concerns may require further careful assessment of the environmental and ecological variation within the species range. [ABSTRACT FROM AUTHOR]

Wind is expected to be one of the main vectors of passive dispersal for small zooplankters between discrete, unconnected habitats. However, little is known about the differences in the dispersal capacity of species in relation to their propagule traits. Here we assessed the effect of volume and weight of diapausing eggs and substrate granulometry on the dispersal departure propensity of two differently body-sized rotifer species belonging to the Brachionus plicatilis complex using a wind tunnel experiment. Diapausing eggs of the larger species were also larger but, counterintuitively, were lifted by the wind to a greater extent than those of the smaller one. Further, diapausing eggs on the finer substrate were more exposed to the wind than those over the coarser one, and therefore higher departure rates were observed in the former. Overall, results show that wind is a relevant dispersal vector for the rotifers of the B. plicatilis species complex, with egg morphological traits and substrate granulometry being important factors modulating their dispersal. This study is a proof of concept for the departure phase of dispersal. Further studies on transfer and settlement phases are needed to get a complete picture of the dispersal potential of these organisms. [ABSTRACT FROM AUTHOR]

Background: Engelhardia (Juglandaceae) is a genus of significant ecological and economic importance, prevalent in the tropics and subtropics of East Asia. Although previous efforts based on multiple molecular markers providing profound insights into species delimitation and phylogeography of Engelhardia, the maternal genome evolution and phylogeny of Engelhardia in Juglandaceae still need to be comprehensively evaluated. In this study, we sequenced plastomes from 14 samples of eight Engelhardia species and the outgroup Rhoiptelea chiliantha, and incorporated published data from 36 Juglandaceae and six outgroup species to test phylogenetic resolution. Moreover, comparative analyses of the plastomes were conducted to investigate the plastomes evolution of Engelhardia and the whole Juglandaceae family. Results: The 13 Engelhardia plastomes were highly similar in genome size, gene content, and order. They exhibited a typical quadripartite structure, with lengths from 161,069 bp to 162,336 bp. Three mutation hotspot regions (TrnK-rps16, ndhF-rpl32, and ycf1) could be used as effective molecular markers for further phylogenetic analyses and species identification. Insertion and deletion (InDels) may be an important driving factor for the evolution of plastomes in Juglandoideae and Engelhardioideae. A total of ten codons were identified as the optimal codons in Juglandaceae. The mutation pressure mostly contributed to shaping codon usage. Seventy-eight protein-coding genes in Juglandaceae experienced relaxed purifying selection, only rpl22 and psaI genes showed positive selection (Ka/Ks > 1). Phylogenetic results fully supported Engelhardia as a monophyletic group including two sects and the division of Juglandaceae into three subfamilies. The Engelhardia originated in the Late Cretaceous and diversified in the Late Eocene, and Juglandaceae originated in the Early Cretaceous and differentiated in Middle Cretaceous. The phylogeny and divergence times didn't support rapid radiation occurred in the evolution history of Engelhardia. Conclusion: Our study fully supported the taxonomic treatment of at the section for Engelhardia species and three subfamilies for Juglandaceae and confirmed the power of phylogenetic resolution using plastome sequences. Moreover, our results also laid the foundation for further studying the course, tempo and mode of plastome evolution of Engelhardia and the whole Juglandaceae family. [ABSTRACT FROM AUTHOR]

Introduction: Several studies of MADS-box transcription factors in flowering plants have been conducted, and these studies have indicated that they have conserved functions in floral organ development; MIKC-type MADS-box genes has been proved to be expanded in ferns, however, few systematic studies of these transcription factors have been conducted in non-seed plants. Although ferns and seed plants are sister groups, they exhibit substantial morphological differences. Methods: Here, we clarified the evolution of MADS-box genes across 71 extant fern species using available transcriptome, genome, and gene expression data. Results: We obtained a total of 2,512 MADS-box sequences, ranging from 9 to 89 per species. The most recent common ancestor (MRCA) of ferns contained approximately three type I genes and at least 5-6 type II MADS-box genes. The domains, motifs, expression of type I and type II proteins, and the structure of the both type genes were conserved in ferns as to other land plants. Within type II genes, MIKC*-type proteins are involved in gametophyte development in ferns; MIKCC-type proteins have broader expression patterns in ferns than in seed plants, and these protein sequences are likely conserved in extant seed plants and ferns because of their diverse roles in diploid sporophyte development. More than 90% of MADS-box genes are type II genes, and MIKCC genes, especially CRM1 and CRM6-like genes, have undergone a large expansion in leptosporangiate ferns; the diverse expression patterns of these genes might be related to the fuctional diversification and increased complexity of the plant body plan. Tandem duplication of CRM1 and CRM6-like genes has contributed to the expansion of MIKCC genes. Conclusion or Discussion: This study provides new insights into the diversity, evolution, and functions of MADS-box genes in extant ferns. [ABSTRACT FROM AUTHOR]

Agaves are an outstanding arid‐adapted group of species that provide a unique chance to study the influence of multiple potential factors (i.e., geological and ecological) on plant population structure and diversification in the heterogeneous environment of the Baja California Peninsula. However, relatively little is known about the phylogeography of the endemic agave species of this region. Herein, we used over 10,000 single‐nucleotide polymorphisms (SNPs) and spatial data from the Agave aurea species complex (i.e., A. aurea ssp. aurea, A. aurea ssp. promontorii, and A. aurea var. capensis) to resolve genetic relationships within this complex and uncover fine‐scale population structure, diversity patterns, and their potential underlying drivers. Analyses resolved low genetic structure within this complex, suggesting that A. aurea is more likely to represent several closely related populations than separate species or varieties/subspecies. We found that geographical and historical ecological characteristics—including precipitation, latitude, and past climatic fluctuations—have played an important role in the spatial distribution of diversity and structure in A. aurea. Finally, species distribution modeling results suggested that climate change will become critical in the extinction risk of A. aurea, with the northernmost population being particularly vulnerable. The low population genetic structure found in A. aurea is consistent with agave's life history, and it is probably related to continuity of distribution, relatively low habitat fragmentation, and dispersion by pollinators. Together, these findings have important implications for management and conservation programs in agave, such as creating and evaluating protected areas and translocating and augmentation of particular populations. [ABSTRACT FROM AUTHOR]

The mountains in the Atlantic Forest domain are environments that harbor a high biodiversity, including species adapted to colder climates that were probably influenced by the climatic variations of the Pleistocene. To understand the phylogeographic pattern and assess the taxonomic boundaries between two sister montane species, a genomic study of the butterflies Actinote mantiqueira and A. alalia (Nymphalidae: Acraeini) was conducted. Analyses based on partial sequences of the mitochondrial gene COI (barcode region) failed to recover any phylogenetic or genetic structure discriminating the two species or sampling localities. However, single nucleotide polymorphisms gathered using Genotyping‐by‐Sequencing provided a strong isolation pattern in all analyses (genetic distance, phylogenetic hypothesis, clustering analyses, and FST statistics) which is consistent with morphology, separating all individuals of A. alalia from all populations of A. mantiqueira. The three sampled mountain ranges where A. mantiqueira populations occur—Serra do Mar, Serra da Mantiqueira, and Poços de Caldas Plateau—were identified as three isolated clusters. Paleoclimate simulations indicate that both species' distributions changed according to climatic oscillations in the Pleistocene period, with the two species potentially occurring in areas of lower altitude during glacial periods when compared to the interglacial periods (as the present). Besides, a potential path between their distribution through the Serra do Mar Mountain range was inferred. Therefore, the Pleistocene climatic fluctuation had a significant impact on the speciation process between A. alalia and A. mantiqueira, which was brought on by isolation at different mountain summits during interglacial periods, as shown by the modeled historical distribution and the observed genetic structure. [ABSTRACT FROM AUTHOR]

Astydamia latifolia is the only species of the genus Astydamia, which forms an early‐diverging lineage of Apiaceae, subfamily Apioideae. This species is subendemic to the Canary Islands and one of the most representative species of the coastal environments of this archipelago. Astydamia displays diplochory, that is, diaspores with two long‐distance dispersal (LDD) syndromes. In particular, A. latifolia has both anemochorous and thalassochorous fruit traits (corky and winged mericarps). Although we expect this species to have a high dispersal capacity, there is no genetic study addressing it. The divergence time of this species from its sister taxon is also unknown. In this study, we aimed (i) to unveil the phylogenetic relationships and divergence times of A. latifolia; (ii) to reconstruct its phylogeographic structure across the Canary Islands; and (iii) to estimate the number of inter‐island colonization events. To these ends, we first sequenced the internal transcribed spacer (ITS) region for A. latifolia, reconstructed the phylogenetic relationships of Astydamia and Apiaceae relatives and estimated divergence times. Then, two plastid DNA regions (psaI‐aacD and psbK‐trnS) were sequenced for 158 individuals (from 36 Canarian population and one NW African population) to reconstruct a haplotype network. The recently developed method Phylogeographic Analysis of Island Colonization Events (PAICE) was used to estimate the number of inter‐island colonization events. Results show that A. latifolia is a phylogenetically isolated lineage that diverged from the most closely related genus (Molopospermum) in the Eocene–Miocene. It displays a low plastid DNA diversity (only four haplotypes detected), which is accompanied by a high degree of haplotype sharing between islands and highly linear rarefaction curves of colonization obtained in PAICE. These findings suggest a high colonization ability for this species, most likely related to the availability of two LDD syndromes. [ABSTRACT FROM AUTHOR]

The Yunnan‐Guizhou Plateau (YGP) is characterized by the distinctive isolated habitat of the limestone Karst Islands and features the Wumeng Mountains, which divide the YGP into the two Plateaus of Yunnan and Guizhou. This study aimed to assess the effects of geographic isolation and past climate fluctuation on the distribution of flora in the YGP. To achieve this, we carried out the phylogeographical pattern and genetic structure based on chloroplast and nuclear ribosomal DNA sequence in relation to past (Last Glacial Maximum) and present distributions based on ecological niche modeling for Morella nana, an important wild plant resource and endemic to the YGP once considered a vulnerable species. The results suggest that the genetic and chlorotype network structures of M. nana are divided into at least two groups: cpDNA chlorotype H2 (or dominant nrDNA haplotypes h1 and h2), distributed primarily to the east of the Wumeng Mountains, and cpDNA chlorotypes H1 and H3–H10 (or dominant nrDNA haplotype h2 and h3), distributed to the west of the Wumeng Mountains. A deep genetic split was noted within the two groups to reach 25 steps, especially for the cpDNA fragment variation. This east–west divergence reveals the existence of a natural geographical isolation boundary in the form of the Wumeng Mountains, and supports the existence of at least two glacial refuges during the Quaternary glacial period, along with two genetic diversity center, and at least two large geographic protection units for the important species of M. nana. This study indicates that the phylogeographical pattern of M. nana can be attributed to geographic/environmental isolation caused by the Wumeng Mountains and climate fluctuation during the last glacial maximum, and proposes an effective strategy to protecting this important plant resource. [ABSTRACT FROM AUTHOR]

Swine acute diarrhoea syndrome coronavirus (SADS-CoV; Coronaviridae, Rhinacovirus) was detected in 2017 in Guangdong Province (China), where it caused high mortality rates in piglets. According to previous studies, SADS-CoV evolved from horseshoe bat reservoirs. Here, we report the first five Rhinacovirus genomes sequenced in horseshoe bats from Vietnam and their comparisons with data published in China. Our phylogenetic analyses provided evidence for four groups: rhinacoviruses from Rhinolphus pusillus bats, including one from Vietnam; bat rhinacoviruses from Hainan; bat rhinacoviruses from Yunnan showing a divergent synonymous nucleotide composition; and SADS-CoV and related bat viruses, including four rhinacoviruses from Vietnam sampled in Rhinolophus affinis and Rhinolophus thomasi. Our phylogeographic analyses showed that bat rhinacoviruses from Dien Bien (Vietnam) share more affinities with those from Yunnan (China) and that the ancestor of SADS-CoVs arose in Rhinolophus affinis circulating in Guangdong. We detected sequencing errors and artificial chimeric genomes in published data. The two SADS-CoV genomes previously identified as recombinant could also be problematic. The reliable data currently available, therefore, suggests that all SADS-CoV strains originate from a single bat source and that the virus has been spreading in pig farms in several provinces of China for at least seven years since the first outbreak in August 2016. [ABSTRACT FROM AUTHOR]

The impact of climate fluctuations on the genetic diversity and distribution of species is of particular concern for large mammals that are already at risk of extinction. In this study, we investigated the genetic status of populations, the evolutionary relationships, and the current and future state of population dispersion of the goitered gazelle, Gazella subgutturosa, using 109 mtDNA sequences (cytb) and species distribution modeling. We assessed the impact of past (Last Glacial Maximum [lgm: 21 Kya] and Mid-Holocene [6 Kya]), current, and future (2070) climate on the phylogeography and spatial distribution of the species. Our results indicate evidence of divergence of two main clades (G. subgutturosa subgutturosa, and G. subgutturosa yarkandensis) (1.052 Mya) and a further split between two clades of G. s. subgutturosa (Middle Eastern and Central Iranian) in the middle Pleistocene. Historical species distribution models suggest the species' range has not changed much across all periods examined, but there has been a decreasing trend from 21k to the current. Future climate projections (bcc-csm1 and ccsm4, rcp s 4.5 and 6 scenarios) predict a contraction of suitable habitat at the northern and southern edges of the species' current distribution, shifting the range to the center of the study area. Biogeographic analyses suggest that vicariance and dispersal events have shaped the genetic structure of G. subgutturosa. Our findings suggest that the current genetic structure of the species is potentially related to Pleistocene climatic fluctuations and refuges (Alborz, Zagros, and Kope Dagh Mountains) during cold periods. The study highlights the importance of understanding the genetic status of populations and their evolutionary relationships to effectively prevent further declines of species at risk of extinction. [ABSTRACT FROM AUTHOR]

The present distribution of Siberian boreal forests that are dominated by larches (Larix spp.) is influenced, to an unknown extent, by glacial history. Knowing the past treeline dynamics can improve our understanding of future treeline shifts under changing climate. Here, we study patterns in the genetic variability of Siberian Larix to help unravel biogeographic migration routes since the Last Glacial Maximum (LGM). We infer the spatial distribution and the postglacial demographic history of Larix using genome‐wide single nucleotide polymorphisms (SNPs) derived through genotyping by sequencing (GBS) from 130 individuals sampled across eastern Siberia. Our analysis gives statistical support for two or three clusters, spanning from western to eastern Siberia. These clusters reveal a genetic structure influenced by isolation resulting from geographical distance, barriers imposed by geographic features, and distinct glacial histories. Assuming three clusters, our demographic inference indicates that the common ancestor of the current Larix populations existed in northeast Siberia well before the LGM. This suggests that Larix persisted in the northern region throughout previous glacials. Our genetic studies suggest that Larix likely survived the cold LGM in northern refugia, enabling a fast colonization of Siberia. Instead of complete repopulation from southern areas postglacially, the northernmost Larix expansion during the Holocene seems to have benefitted from refugial populations ahead of the treeline. Present‐day migration is expected to be slow initially, due to the absence of current refugial populations in the far north, in contrast to the early‐Holocene situation. [ABSTRACT FROM AUTHOR]

It has been hypothesized that the Araucaria Forest in southern Brazil underwent expansions in the past, driven either by human groups or by climate fluctuations of the Holocene and Pleistocene. Fossil pollen records of the Paraná pine Araucaria angustifolia, a dominant tree in that forest, provide some insights into when those may have occurred. Still, the timing of those expansions has never been estimated. To infer past range shifts and shed light on their main drivers, we employed next‐generation DNA sequencing (ddRADseq), machine learning, and a comprehensive database of fossil pollen records into a study of historical demographic inference and paleo‐distribution modeling of the Paraná pine. We found that A. angustifolia comprises two populations expanding at different times: one in the Mantiqueira mountain chain, the other in the southern Brazilian plateau. The southern population began to expand during the Last Glacial Period ~ 70 kya, long before human arrival in South America. Still, genetic analyses support that humans later impacted this population, resulting in lower genetic diversity, higher inbreeding, and high levels of gene flow over large distances with a weak pattern of isolation‐by‐distance. It is possible this resulted from human influence on seed dispersal and germination on the southern Brazilian plateau. The Mantiqueira population, in contrast, expanded only recently (~ 3 kya). This timing coincides with Holocene climatic changes and human settlements established further south, although, to date, there is little archeological evidence of human impact in the Mantiqueira. In addition, multitemporal species distribution models built from a combination of present‐day and pollen records infer a range expansion of the Araucaria Forest during glacial times until the cold humid HS1 event (~ 16 kya), when the forest was most widespread, with no evidence of glacial refugia. The combination of genomic and spatial analyses suggests that both human and climatic controls played a role in the dynamics of the Araucaria Forest. [ABSTRACT FROM AUTHOR]

Aim: Our aim was to assess the population structure, genetic diversity and demographic history of the wolverine (Gulo gulo) throughout its entire Eurasian range. Additionally, we aimed to contextualize and put into perspective the state of the endangered Fennoscandian population by emphasizing its connectivity to other populations. Location: The main study area covered most of the Eurasian wolverine range, with samples from Finland, Russia, Kazakhstan and Mongolia. Methods: Using a 495 bp fragment of the mitochondrial DNA control region and a frequently used set of 14 microsatellite markers on an extensive dataset of samples, we assessed the population structure, genetic diversity, and demographic history of wolverines with a variety of population genetic analyses. Results: According to both nuclear and mitochondrial genetic markers, Eurasian wolverines exhibit substructure, with the most distinct population located in Fennoscandia. The Fennoscandian population has undergone a genetic bottleneck, likely influencing its genetic diversity, which is notably the lowest in Eurasia. Genetic diversity in the rest of Eurasia gradually rises towards the central part of the range and decreases again in the east, although not as significantly as in the west. Main Conclusions: This study reveals the population structure of wolverines across Eurasia and provides direction for allocating conservation efforts to sustain a diverse and connected wolverine population. While most of the Eurasian populations seem to be well‐connected and genetically diverse, the Fennoscandian wolverines may need better connectivity to the other Eurasian populations to ensure gene flow and long‐term persistence. Our study further highlights the importance of considering the population genetic structure and diversity of the entire species range when planning management strategies. [ABSTRACT FROM AUTHOR]

Renicolids are parasites of aquatic birds. Their species identification based on morphological characters is problematic. Here, we revised the composition of Renicola spp. parasitising anatids in nearshore areas of northern seas using integrated morphological and molecular data. We redescribed Renicola somateria and verified the diagnosis of R. mediovitellata. We established that the first intermediate host (FIH) of R. somateria is the mollusc Buccinum undatum, while the FIHs of R. mediovitellata are Nucella spp. molluscs. We described the intramolluscan stages of both species. Renicola somateria and R. mediovitellata formed a separate clade in the molecular trees of the Renicolidae. This finding confirms the existence of three main phylogenetic branches of renicolids, differing in the structure of adults, type of cercariae, and host range. Molecular data demonstrated an amphiboreal distribution of both R. somateria and R. mediovitellata. The former is represented by a single population in Europe and the North Pacific, while the latter forms separate populations in these regions. This may be because R. somateria actually uses not only B. undatum but also some other buccinid species with similar circum-Arctic ranges as the FIH. We discuss the roles played in the formation of digenean ranges by the vagility of the definitive host, the lifespan of the adults, and the distribution of the FIH. [ABSTRACT FROM AUTHOR]

In this unit, students explore the phylogeography of three-toed sloths (Bradypus pygmaeus and Bradypus variegatus) endemic to the Bocas del Toro islands off the Caribbean coast of Panama. After learning about the geologic history of this region, students measure model sloth skulls from each of the islands and compile that data into scatterplots. Students then analyze the scatterplots to make conclusions about which geographic factors best account for the regional variance in sloth body size. The sequence of activities was designed for high school life science classrooms using the Next Generation Science Standards (NGSS) framework and teaches the disciplinary core idea LS3.B Variation of Traits. This lesson was taught in an integrated co-teaching classroom, a special education classroom, and a ninth-grade general biology classroom. Students successfully answered the overarching research question and gained a deeper knowledge about natural selection and evolution in the process. [ABSTRACT FROM AUTHOR]

Cownose rays Rhinoptera bonasus and R. brasiliensis, are species distributed along the coastal waters from eastern United States, Gulf of Mexico to Brazil. This study represents the most extensive evaluation to date of the genetic diversity and population genetic structure of R. bonasus across its distribution, and it is the first to investigate the population genetics of R. brasiliensis. We analyzed sequences of COI and Cytb genes for Rhinoptera bonasus (COI: 230, Cytb: 108) and R. brasiliensis (COI: 181, Cytb: 105) to investigate the genetic diversity and their relationship with environmental variables, genetic structure, as well as demographic parameters. We found that benthic temperature and current velocity were the most important environmental variables in genetic diversity. The global population structure reveals the presence of significant population genetic structure in both species. Bayesian clusters in BAPS were consistent with the segregation pattern observed for haplotype networks based on COI and Cytb markers for both species, which may respond to philopatry and temperature. These results will further improve management and conservation efforts for these species of ecological and economic importance. [ABSTRACT FROM AUTHOR]

Modern phylogeography aims at reconstructing the geographic movement of organisms based on their genomic sequences and spatial information. Phylogeographic approaches are often applied to pathogen sequences and therefore tend to neglect the possibility of recombination, which decouples the evolutionary and geographic histories of different parts of the genome. Genomic regions of recombining or reassorting pathogens often originate and evolve at different times and locations, which characterize their unique spatial histories. Measuring the extent of these differences requires new methods to compare geographic information on phylogenetic trees reconstructed from different parts of the genome. Here we develop for the first time a set of measures of phylogeographic incompatibility, aimed at detecting differences between geographical histories in terms of distances between phylogeographies. We study the effect of varying demography and recombination on phylogeographic incompatibilities using coalescent simulations. We further apply these measures to the evolutionary history of human and livestock pathogens, either reassorting or recombining, such as the Victoria and Yamagata lineages of influenza B and the O/Ind-2001 foot-and-mouth disease virus strain. Our results reveal diverse geographical paths of migration that characterize the origins and evolutionary histories of different viral genes and genomic segments. These incompatibility measures can be applied to any phylogeography, and more generally to any phylogeny where each tip has been assigned either a continuous or discrete "trait" independent of the sequence. We illustrate this flexibility with an analysis of the interplay between the phylogeography and phylolinguistics of Uralic-speaking human populations, hinting at patrilinear language transmission. [ABSTRACT FROM AUTHOR]

Research studies on the conservation genetics of endangered plants play a crucial role in establishing management plans for biodiversity conservation. Phoebe chekiangensis is a precious and scarce tree species resource in the East China region. To comprehend the origin, evolutionary history, geographical, and historical factors that has contributed to the current distribution pattern of Phoebe chekiangensis in the East China region, we conducted a phylogeographic analysis that utilized intergenic spacers of chloroplast DNA (cpDNA). We amplified and sequenced three spacer regions of cpDNA (psbC-trnS, trnL-Intro, and Ycf3) intergenic spacer regions of 306 individuals from 11 populations, encompassing the majority of its geographical range in China. Our analysis revealed a total of 11 haplotypes. The research findings show that the spacer regions of the cpDNA genetic diversity of Phoebe chekiangensis was Hd = 0.423, and the nucleotide diversity was Pi × 10−3 = 0.400. At the species level, the population differentiation index Fst = 0.25610 (p < 0.05), and the gene flow Nm = 0.73. The genetic variation between populations was 29.14%, while within populations, it was 70.86%, with the inter-population genetic variation much lower than the within-population variation. The divergence time between the genera Phoebe and Machilus was estimated to be approximately 37.87 mya (PP = 1; 95%HPD: 25.63–44.54 mya), and the crown group time of the genus Phoebe was estimated to be 21.30 mya (PP = 1; 95%HPD: 9.76–34.94 mya). The common ancestor of the 11 Phoebe chekiangensis haplotypes was 7.85 mya, while the H7, H8, and H10 haplotypes of Phoebe chekiangensis (northern region) differentiated relatively late, with a divergence time of 1.90 mya. Neutrality tests (NTs) and mismatch distribution analysis (MDA) suggest that the time frame for Phoebe chekiangensis to expand southwestward along Wuyishan was relatively short and its adaptability to the environment was low, thereby limiting the formation of new haplotypes. These results suggest that Phoebe chekiangensis exhibited greater adaptation to the northern subtropics than to the central subtropics, offering valuable insights for the conservation and utilization of germplasm resources. [ABSTRACT FROM AUTHOR]

The genus Silurus, an important group of catfish, exhibits heterogeneous distribution in Eurasian freshwater systems. This group includes economically important and endangered species, thereby attracting considerable scientific interest. Despite this interest, the lack of a comprehensive phylogenetic framework impedes our understanding of the mechanisms underlying the extensive diversity found within this genus. Herein, we analyzed 89 newly sequenced and 20 previously published mitochondrial genomes (mitogenomes) from 13 morphological species to reconstruct the phylogenetic relationships, biogeographic history, and species diversity of Silurus. Our phylogenetic reconstructions identified eight clades, supported by both maximum-likelihood and Bayesian inference. Sequence-based species delimitation analyses yielded multiple molecular operational taxonomic units (MOTUs) in several taxa, including the Silurus asotus complex (four MOTUs) and Silurus microdorsalis (two MOTUs), suggesting that species diversity is underestimated in the genus. A reconstructed time-calibrated tree of Silurus species provided an age estimate of the most recent common ancestor of approximately 37.61 million years ago (Ma), with divergences among clades within the genus occurring between 11.56 Ma and 29.44 Ma, and divergences among MOTUs within species occurring between 3.71 Ma and 11.56 Ma. Biogeographic reconstructions suggested that the ancestral area for the genus likely encompassed China and the Korean Peninsula, with multiple inferred dispersal events to Europe and Central and Western Asia between 21.78 Ma and 26.67 Ma and to Japan between 2.51 Ma and 18.42 Ma. Key factors such as the Eocene-Oligocene extinction event, onset and intensification of the monsoon system, and glacial cycles associated with sea-level fluctuations have likely played significant roles in shaping the evolutionary history of the genus Silurus. [ABSTRACT FROM AUTHOR]

Prochlorococcus is the most numerically abundant photosynthetic organism in the surface ocean. The Prochlorococcus high-light and warm-water adapted ecotype (HLII) is comprised of extensive microdiversity, but specific functional differences between microdiverse sub-clades remain elusive. Here we characterized both functional and phylogenetic diversity within the HLII ecotype using Bio-GO-SHIP metagenomes. We found widespread variation in gene frequency connected to local environmental conditions. Metagenome-assembled marker genes and genomes revealed a globally distributed novel HLII haplotype defined by adaptation to chronically low P conditions (HLII-P). Environmental correlation analysis revealed different factors were driving gene abundances verses phylogenetic differences. An analysis of cultured HLII genomes and metagenome-assembled genomes revealed a subclade within HLII, which corresponded to the novel HLII-P haplotype. This work represents the first global assessment of the HLII ecotype's phylogeography and corresponding functional differences. These findings together expand our understanding of how microdiversity structures functional differences and reveals the importance of nutrients as drivers of microdiversity in Prochlorococcus.

To date, a number of studies have been published on the phylogenetics of woolly mammoths (Mammuthus primigenius), ranging from analyses of parts of the mitochondrial genome to studies of complete nuclear genomes. However, until recently nothing was known about the genetic diversity of woolly mammoths in southern Siberia, in the Minusinsk Depression in particular. Within the framework of this effort, libraries for high-throughput sequencing of seven bone samples of woolly mammoths were obtained, two-round enrichment using biotinylated probes of modern mtDNA of Elephas maximus immobilised on magnetic microspheres and sequencing with subsequent bioinformatic analysis were carried out. Phylogenetic reconstructions showed the presence of all studied mammoths in clade I, which expanded its range. The assignment of mammoth mitotypes in the Minusinsk Depression to different clusters within clade I may indicate a sufficiently high diversity of their gene pool. Phylogeographic reconstructions revealed a genetic proximity of mitochondrial lineages of Late Pleistocene mammoths of the Minusinsk Depression and other regions of eastern Siberia and estimated their divergence time in the range of 100–150 thousand years ago, which indicates active migrations of woolly mammoths over vast territories of eastern Siberia in the late Middle Pleistoceneearly Late Pleistocene.

Abstract 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.

Bent-toed Geckos, genus Cyrtodactylus, are one of the most diverse terrestrial vertebrate groups, and their range extends from South Asia into Australo-Papua and adjacent Pacific islands. Given the generally high faunal endemism on Wallacean islands, it is rather paradoxical that the diversity in these geckos appears to be so low (21 species in Wallacea, 15 in the Philippines) compared with continental shelf assemblages (>300 species on Sunda + Sahul Shelves + adjacent islands). To determine whether this shortfall was real or an artifact of historical undersampling, we analyzed mitochondrial DNA sequences of hundreds of southern Wallacean samples (Lesser Sundas + southern Maluku). After screening to guide sample selection for target capture data collection, we obtained a 1150-locus genomic dataset (1,476,505 bp) for 119 samples of southern Wallacean and closely related lineages. The results suggest that species diversity of Cyrtodactylus in southern Wallacea is vastly underestimated, with phylogenomic and clustering analyses suggesting as many as 25 candidate species, in contrast to the 8 currently described. Gene exchange between adjacent candidate species is absent or minimal across the archipelago with only one case of > 0.5 migrants per generation. Biogeographical analysis suggests that the hitherto unrecognized diversity is the result of at least three independent dispersals from Sulawesi or its offshore islands into southern Wallacea between 6 and 14 Ma, with one invasion producing small-bodied geckos and the other two or three producing larger-bodied geckos. The smaller-bodied laevigatus group appears to be able to coexist with members of either larger-bodied clade, but we have yet to find members of the two larger-bodied clades occurring in sympatry, suggesting that ecological partitioning or competitive exclusion may be shaping individual island assemblages.

The biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of in situ biological diversification. While the island's long period of isolation and dynamic tectonic history have been implicated as drivers of the regional diversification, this has rarely been tested in the context of an explicit geological framework. Here, we provide a tectonically informed biogeographical framework that we use to explore the diversification history of Sulawesi flying lizards (the Draco lineatus Group), a radiation that is endemic to Sulawesi and its surrounding islands. We employ a framework for inferring cryptic speciation that involves phylogeographic and genetic clustering analyses as a means of identifying potential species followed by population demographic assessment of divergence-timing and rates of bi-directional migration as means of confirming lineage independence (and thus species status). Using this approach, phylogenetic and population genetic analyses of mitochondrial sequence data obtained for 613 samples, a 50-SNP data set for 370 samples, and a 1249-locus exon-capture data set for 106 samples indicate that the current taxonomy substantially understates the true number of Sulawesi Draco species, that both cryptic and arrested speciations have taken place, and that ancient hybridization confounds phylogenetic analyses that do not explicitly account for reticulation. The Draco lineatus Group appears to comprise 15 species-9 on Sulawesi proper and 6 on peripheral islands. The common ancestor of this group colonized Sulawesi ~11 Ma when proto-Sulawesi was likely composed of two ancestral islands, and began to radiate ~6 Ma as new islands formed and were colonized via overwater dispersal. The enlargement and amalgamation of many of these proto-islands into modern Sulawesi, especially during the past 3 Ma, set in motion dynamic species interactions as once-isolated lineages came into secondary contact, some of which resulted in lineage merger, and others surviving to the present. [Genomics; Indonesia; introgression; mitochondria; phylogenetics; phylogeography; population genetics; reptiles.].

Currents are unique drivers of oceanic phylogeography and thus determine the distribution of marine coastal species, along with past glaciations and sea-level changes. Here we reconstruct the worldwide colonization history of eelgrass (Zostera marina L.), the most widely distributed marine flowering plant or seagrass from its origin in the Northwest Pacific, based on nuclear and chloroplast genomes. We identified two divergent Pacific clades with evidence for admixture along the East Pacific coast. Two west-to-east (trans-Pacific) colonization events support the key role of the North Pacific Current. Time-calibrated nuclear and chloroplast phylogenies yielded concordant estimates of the arrival of Z. marina in the Atlantic through the Canadian Arctic, suggesting that eelgrass-based ecosystems, hotspots of biodiversity and carbon sequestration, have only been present there for ~243 ky (thousand years). Mediterranean populations were founded ~44 kya, while extant distributions along western and eastern Atlantic shores were founded at the end of the Last Glacial Maximum (~19 kya), with at least one major refuge being the North Carolina region. The recent colonization and five- to sevenfold lower genomic diversity of the Atlantic compared to the Pacific populations raises concern and opportunity about how Atlantic eelgrass might respond to rapidly warming coastal oceans.

AbstractMarek’s disease virus (MDV) has become an increasingly virulent pathogen in the poultry industry despite vaccination efforts to control it. Brazil has experienced a significant rise of Marek’s disease (MD) outbreaks in recent years. Our study aimed to analyze the complete meq gene sequences to understand the molecular epidemiological basis of MD outbreaks in Brazilian vaccinated layer farms. We detected a high incidence rate of visceral MD (67.74%) and multiple circulating MDV strains. The most prevalent and geographically widespread genotype presented several clinical and molecular characteristics of a highly virulent strain and evolving under positive selective pressure. Phylogenetic and phylogeographic analysis revealed a closer relationship with strains from the USA and Japan. This study sheds light on the circulation of MDV strains capable of infecting vaccinated birds. We emphasize the urgency of adopting preventive measures to manage MDV outbreaks threatening the poultry farming industry.

Abstract The Middle Eastern endemic genus Asaccus comprises Southwest Asian leaf-toed geckos. To date, this genus includes 19 species of leaf-toed geckos (seven in Arabia and 12 in the Zagros Mountains). Despite a recent study on the taxonomy and phylogeny of Asaccus species in Iran, controversies still remain surrounding the phylogeny and phylogeography of the genus. Here, we used an integrative approach to determine the phylogeny and phylogeography of Asaccus species using two mitochondrial genes (12 S and Cyt b), and one nuclear gene (c-mos). Our results uncovered 22 distinct lineages, demonstrating a significant cryptic diversity that challenges the current morphological classifications of these species. Phylogenetic analyses reinforce the monophyly of the Asaccus group, positioning A. montanus as a basal lineage, which supports a deep evolutionary divergence dating back to the Late Oligocene, approximately 27.94 million years ago. This genetic diversity also highlights the impact of historical climatic and geographical changes on species diversification. The findings advocate for an integrative approach combining both molecular and morphological data to resolve species identities accurately, thereby enhancing conservation strategies to protect these genetically distinct lineages.

Abstract Background The strong invasiveness and rapid expansion of dengue virus (DENV) pose a great challenge to global public health. However, dengue epidemic patterns and mechanisms at a genetic scale, particularly in term of cross-border transmissions, remain poorly understood. Importation is considered as the primary driver of dengue outbreaks in China, and since 1990 a frequent occurrence of large outbreaks has been triggered by the imported cases and subsequently spread to the western and northern parts of China. Therefore, this study aims to systematically reveal the invasion and diffusion patterns of DENV-1 in Guangdong, China from 1990 to 2019. Methods These analyses were performed on 179 newly assembled genomes from indigenous dengue cases in Guangdong, China and 5152 E gene complete sequences recorded in Chinese mainland. The genetic population structure and epidemic patterns of DENV-1 circulating in Chinese mainland were characterized by phylogenetics, phylogeography, phylodynamics based on DENV-1 E-gene-based globally unified genotyping framework. Results Multiple serotypes of DENV were co-circulating in Chinese mainland, particularly in Guangdong and Yunnan provinces. A total of 189 transmission clusters in 38 clades belonging to 22 subgenotypes of genotype I, IV and V of DENV-1 were identified, with 7 Clades of Concern (COCs) responsible for the large outbreaks since 1990. The epidemic periodicity was inferred from the data to be approximately 3 years. Dengue transmission events mainly occurred from Great Mekong Subregion-China (GMS-China), Southeast Asia (SEA), South Asia Subcontinent (SASC), and Oceania (OCE) to coastal and land border cities respectively in southeastern and southwestern China. Specially, Guangzhou was found to be the most dominant receipting hub, where DENV-1 diffused to other cities within the province and even other parts of the country. Genome phylogeny combined with epidemiological investigation demonstrated a clear local consecutive transmission process of a 5C1 transmission cluster (5C1-CN4) of DENV-1 in Guangzhou from 2013 to 2015, while the two provinces of Guangdong and Yunnan played key roles in ongoing transition of dengue epidemic patterns. In contextualizing within Invasion Biology theories, we have proposed a derived three-stage model encompassing the stages of invasion, colonization, and dissemination, which is supposed to enhance our understanding of dengue spreading patterns. Conclusions This study demonstrates the invasion and diffusion process of DENV-1 in Chinese mainland within a global genotyping framework, characterizing the genetic diversities of viral populations, multiple sources of importation, and periodic dynamics of the epidemic. These findings highlight the potential ongoing transition trends from epidemic to endemic status offering a valuable insight into early warning, prevention and control of rapid spreading of dengue both in China and worldwide. Graphical Abstract

The objective is to determine the complete nucleotide sequence and conduct a phylogenetic analysis of genome variants of the Puumala virus isolated in the Saratov region. Materials and methods. The samples for the study were field material collected in the Gagarinsky (formerly Saratovsky), Engelssky, Novoburassky and Khvalynsky districts of the Saratov region in the period from 2019 to 2022. To specifically enrich the Puumala virus genome in the samples, were used PCR and developed a specific primer panel. Next, the resulting PCR products were sequenced and the fragments were assembled into one sequence for each segment of the virus genome. To construct phylogenetic trees, the maximum parsimony algorithm was used. Results. Genetic variants of the Puumala virus isolated in the Saratov region have a high degree of genome similarity to each other, which indicates their unity of origin. According to phylogenetic analysis, they all form a separate branch in the cluster formed by hantaviruses from other subjects of the Volga Federal District. The virus variants from the Republics of Udmurtia and Tatarstan, as well as from the Samara and Ulyanovsk regions, are closest to the samples from the Saratov region. Conclusion. The data obtained show the presence of a pronounced territorial confinement of strains to certain regions or areas that are the natural biotopes of their carriers. This makes it possible to fairly accurately determine the territory of possible infection of patients and/or the circulation of carriers of these virus variants based on the sequence of individual segments of their genome.

Abstract Background There is no consensus as to the origin of the domestic yak (Bos grunniens). Previous studies on yak mitochondria mainly focused on mitochondrial displacement loop (D-loop), a region with low phylogenetic resolution. Here, we analyzed the entire mitochondrial genomes of 509 yaks to obtain greater phylogenetic resolution and a comprehensive picture of geographical diversity. Results A total of 278 haplotypes were defined in 509 yaks from 21 yak breeds. Among them, 28 haplotypes were shared by different varieties, and 250 haplotypes were unique to specific varieties. The overall haplotype diversity and nucleotide diversity of yak were 0.979 ± 0.0039 and 0.00237 ± 0.00076, respectively. Phylogenetic tree and network analysis showed that yak had three highly differentiated genetic branches with high support rate. The differentiation time of clades I and II were about 0.4328 Ma, and the differentiation time of clades (I and II) and III were 0.5654 Ma. Yushu yak is shared by all haplogroups. Most (94.70%) of the genetic variation occurred within populations, and only 5.30% of the genetic variation occurred between populations. The classification showed that yaks and wild yaks were first clustered together, and yaks were clustered with American bison as a whole. Altitude had the highest impact on the distribution of yaks. Conclusions Yaks have high genetic diversity and yak populations have experienced population expansion and lack obvious phylogeographic structure. During the glacial period, yaks had at least three or more glacial refugia.

To address the phylogenetic and phylogeographic relationship between different lineages of Anopheles (An.) subpictus species complex in most parts of the Asian continent by maximum utilization of Internal Transcriber Spacer 2 (ITS2) and cytochrome C oxidase I (COI) sequences deposited at the GenBank. Seventy-five ITS2, 210 COI and 26 concatenated sequences available in the NCBI database were used. Phylogenetic analysis was performed using Bayesian likelihood trees, whereas median-joining haplotype networks and time-scale divergence trees were generated for phylogeographic analysis. Genetic diversity indices and genetic differentiation were also calculated. Two genetically divergent molecular forms of An. subpictus species complex corresponding to sibling species A and B are established. Species A evolved around 37-82 million years ago in Sri Lanka, India, and the Netherlands, and species B evolved around 22-79 million years ago in Sri Lanka, India, and Myanmar. Vietnam, Thailand, and Cambodia have two molecular forms: one is phylogenetically similar to species B. Other forms differ from species A and B and evolved recently in the above mentioned countries, Indonesia and the Philippines. Genetic subdivision among Sri Lanka, India, and the Netherlands is almost absent. A substantial genetic differentiation was obtained for some populations due to isolation by large geographical distances. Genetic diversity indices reveal the presence of a long-established stable mosquito population, at mutation-drift equilibrium, regardless of population fluctuations. An. subpictus species complex consists of more than two genetically divergent molecular forms. Species A is highly divergent from the rest. Sri Lanka and India contain only species A and B.

Abstract Background The eastern edge of the Qinghai‒Tibet Plateau (QTP) and subtropical China have various regions where plant species originate and thrive, but these regions have been the focus of very few integrative studies. Here, we elucidated the phylogeographic structure of a continuous and widespread Akebia trifoliata population across these two regions. Results Sixty-one populations consisting of 391 genotypes were examined to assess population diversity and structure via network distribution analysis, maximum likelihood phylogenetic tree reconstruction, divergence time estimation, demographic history inference, and ancestral area reconstruction of both conserved internal transcribed spacer (ITS) and chloroplast (rps16) DNA sequences. The results showed that the ITS region was more variable than the rps16 region and could be suitable for studying intraspecific phylogeography. The A. trifoliata population displayed high genetic diversity, genetic differentiation and obvious phylogeographical structure, possibly originating on the eastern QTP, expanding during the last glacial-interglacial cycle, diverging in the early Pleistocene and middle Pleistocene, and extensively migrating thereafter. The migration route from west to east along rivers could be largely responsible for the long-distance dispersal of this species, while three main refuges (Qinba Mountains, Nanling Mountains and Yunnan-Guizhou Plateau) with multiple ice shelters facilitated its wide distribution. Conclusions Our results suggested that the from west to east long migration accompanying with the minor short reciprocal migration in the south-north direction, and the three main refuges (the Qinba Mountains, Nanling Mountains and Yunnan-Guizhou Plateau) contributed to the extant geographical distribution of A. trifoliata. In addition, this finding also strongly reduced the discrepancy between glacial contraction and postglacial expansion and the in situ survival hypothesis by simultaneously considering the existence of many similar climate-related ecological niches and migration influences.

The orchid genus Dipodium R.Br. (Epidendroideae) comprises leafy autotrophic and leafless mycoheterotrophic species, with the latter confined to sect. Dipodium. This study examined plastome degeneration in Dipodium in a phylogenomic and temporal context. Whole plastomes were reconstructed and annotated for 24 Dipodium samples representing 14 species and two putatively new species, encompassing over 80% of species diversity in sect. Dipodium. Phylogenomic analysis based on 68 plastid loci including a broad outgroup sampling across Orchidaceae found that sect. Leopardanthus is the sister lineage to sect. Dipodium. Dipodium ensifolium, the only leafy autotrophic species in sect. Dipodium, was found to be a sister to all leafless, mycoheterotrophic species, supporting a single evolutionary origin of mycoheterotrophy in the genus. Divergence-time estimations found that Dipodium arose ca. 33.3 Ma near the lower boundary of the Oligocene and that crown diversification commenced in the late Miocene, ca. 11.3 Ma. Mycoheterotrophy in the genus was estimated to have evolved in the late Miocene, ca. 7.3 Ma, in sect. Dipodium. The comparative assessment of plastome structure and gene degradation in Dipodium revealed that plastid ndh genes were pseudogenised or physically lost in all Dipodium species, including in leafy autotrophic species of both Dipodium sections. Levels of plastid ndh gene degradation were found to vary among species as well as within species, providing evidence of relaxed selection for retention of the NADH dehydrogenase complex within the genus. Dipodium exhibits an early stage of plastid genome degradation, as all species were found to have retained a full set of functional photosynthesis-related genes and housekeeping genes. This study provides important insights into plastid genome degradation along the transition from autotrophy to mycoheterotrophy in a phylogenomic and temporal context. [ABSTRACT FROM AUTHOR]