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Previous studies revealed extensive genetic introgression between Ovis species, which affects genetic adaptation and morphological traits. However, the exact evolutionary scenarios underlying the hybridization between sheep and allopatric wild relatives remain unknown. To address this problem, we here integrate the reference genomes of several ovine and caprine species: domestic sheep, argali, bighorn sheep, snow sheep, and domestic goats. Additionally, we use 856 whole genomes representing 169 domestic sheep populations and their six wild relatives: Asiatic mouflon, urial, argali, snow sheep, thinhorn sheep, and bighorn sheep. We implement a comprehensive set of analyses to test introgression among these species. We infer that the argali lineage originated ∼3.08 to 3.35 Mya and hybridized with the ancestor of Pachyceriforms (e.g. bighorn sheep and snow sheep) at ∼1.56 Mya. Previous studies showed apparent introgression from North American Pachyceriforms into the Bashibai sheep, a Chinese native sheep breed, despite of their wide geographic separation. We show here that, in fact, the apparent introgression from the Pachyceriforms into Bashibai can be explained by the old introgression from Pachyceriforms into argali and subsequent recent introgression from argali into Bashibai. Our results illustrate the challenges of estimating complex introgression histories and provide an example of how indirect and direct introgression can be distinguished.

The subfamily Murininae is renowned for its inherent taxonomic challenges associated with sampling difficulties and morphological similarities. At present, three genera are acknowledged within the subfamily; however, their phylogenetic interrelations and systematic classification remain debated. In this study, the separation of Harpiola at the genus level was robustly supported by our phylogenomic analyses based on the mitochondrial genome, coding sequences (CDSs) and ultraconserved elements (UCEs) from 12 individuals covering all three genera of Murininae. Notably, a distinctive mito‐nuclear discordance emerged, with the nuclear genealogy ((Harpiocephalus, Harpiola), Murina) contrasting with the mitochondrial genealogy (Harpiocephalus, (Harpiola, Murina)). The integration of these findings with inferences of demographic history reveals that dramatic environmental changes during the Pleistocene glacial and inter‐glacial cycles have shaped the current distribution of Murininae. Moreover, the detection of extensive gene flow between ancient lineages of Harpiola and Murina suggests that an ancestral ‘ghost’ Murina lineage may have contributed its mitochondrial DNA, along with a limited portion of nuclear DNA, to Harpiola in a bygone hybridization zone. In addition to molecular analyses, we employed traditional and geometric morphometric analyses of skulls to differentiate the three genera. Harpiocephalus is readily distinguishable, but Harpiola and certain species of Murina exhibit overlapping characteristics both morphometrically and geometrically which may be the outcome of ancient introgression events. This finding highlights the importance of fine‐scale morphological distinctions within the latter genera, which may be the outcome of ancient introgression events. [ABSTRACT FROM AUTHOR]

AbstractThe Ribbontail stingray Taeniura lymma is an economically important fish and attractive species for the aquarium trade industry. Overfishing, habitat degradation, and pollution, however, pose a threat to this species. This study used partial mitochondrial cytochrome oxidase subunit I (COI) sequences (603 base pairs long) from 96 samples of T. lymma collected at five fish-landing sites (Deep Sea-Tanga, Malindi-Unguja, Kaole-Bagamoyo, Kivukoni-Dar es Salaam, and Bandarini-Mtwara) located along the coast of Tanzania to determine the species’ genetic diversity, population genetic structure, and demographic history. The findings revealed an average nucleotide diversity of 0.24 ± 0.16% and a haplotype diversity of 0.75 ± 0.04. Nucleotide and haplotype diversities were relatively low at Kaole-Bagamoyo compared to the other studied localities. An Analysis of Molecular Variance (AMOVA) indicated limited but statistically significant genetic differences among populations (Overall FST = 0.09, p < 0.01). Pairwise AMOVA revealed genetic difference between the Deep Sea-Tanga population and all other populations studied with exception of Malindi-Unguja. Analyses of mismatch distribution, demographic history, and a haplotype network support a scenario of historical population expansion in the studied species. Immediate effort is required to protect population exhibiting low genetic diversity in this commercially important ray. [ABSTRACT FROM AUTHOR]

Demographic processes can substantially affect a species' response to changing ecological conditions, necessitating the combined consideration of genetic responses to environmental variables and neutral genetic variation. Using a seascape genomics approach combined with population demographic modelling, we explored the interplay of demographic and environmental factors that shaped the current population structure in Indo‐Pacific bottlenose dolphins (Tursiops aduncus) along the Western Australian coastline. We combined large‐scale environmental data gathered via remote sensing with RADseq genomic data from 133 individuals at 19 sampling sites. Using population genetic and outlier detection analyses, we identified three distinct genetic clusters, coinciding with tropical, subtropical and temperate provincial bioregions. In contrast to previous studies, our demographic models indicated that populations occupying the paleo‐shoreline split into two demographically independent lineages before the last glacial maximum (LGM). A subsequent split after the LGM 12—15 kya gave rise to the Shark Bay population, thereby creating the three currently observed clusters. Although multi‐locus heterozygosity declined from north to south, dolphins from the southernmost cluster inhabiting temperate waters had higher heterozygosity in potentially adaptive loci compared to dolphins from subtropical and tropical waters. These findings suggest ongoing adaptation to cold‐temperate waters in the southernmost cluster, possibly linked to distinct selective pressures between the different bioregions. Our study demonstrated that in the marine realm, without apparent physical boundaries, only a combined approach can fully elucidate the intricate environmental and genetic interactions shaping the evolutionary trajectory of marine mammals. [ABSTRACT FROM AUTHOR]

The subtropical forests of East Asia are renowned for their high plant diversity, particularly the abundance of ancient relict species. However, both the evolutionary history of these relict species and their capacity for resilience in the face of impending climatic changes remain unclear. Using whole‐genome resequencing data, we investigated the lineage differentiation and demographic history of the relict and endangered tree, Bretschneidera sinensis (Akaniaceae). We employed a combination of population genomic and landscape genomic approaches to evaluate variation in mutation load and genomic offset, aiming to predict how different populations may respond to climate change. Our analysis revealed a profound genomic divergence between the East and West lineages, likely as the result of recurrent bottlenecks due to climatic fluctuations during the glacial period. Furthermore, we identified several genes potentially linked to growth characteristics and hypoxia response that had been subjected to positive selection during the lineage differentiation. Our assessment of genomic vulnerability uncovered a significantly higher mutation load and genomic offset in the edge populations of B. sinensis compared to their core counterparts. This implies that the edge populations are likely to experience the most significant impact from the predicted climate conditions. Overall, our research sheds light on the historical lineage differentiation and contemporary genomic vulnerability of B. sinensis. Broadening our understanding of the speciation history and future resilience of relict and endangered species such as B. sinensis, is crucial in developing effective conservation strategies in anticipation of future climatic changes. [ABSTRACT FROM AUTHOR]

Uncovering the fundamental processes that shape genomic variation in natural populations is a primary objective of population genetics. These processes include demographic effects such as past changes in effective population size or gene flow between structured populations. Furthermore, genomic variation is affected by selection on nonneutral genetic variants, for example, through the adaptation of beneficial alleles or balancing selection that maintains genetic variation. In this article, we discuss the characterization of these processes using population genetic models, and we review methods developed on the basis of these models to unravel the underlying processes from modern population genomic data sets. We briefly discuss the conditions in which these approaches can be used to infer demography or identify specific nonneutral genetic variants and cases in which caution is warranted. Moreover, we summarize the challenges of jointly inferring demography and selective processes that affect neutral variation genome-wide. [ABSTRACT FROM AUTHOR]

Social Impact Statement: For hundreds of years, Agave marmorata plants have been used in the production of alcoholic beverages in Mexico. This species is very important in small‐scale rural economies because it is a large plant, yielding five liters of mezcal. However, the production of these beverages takes place when it reaches its reproductive stage, which takes up to 35 years. Due to its slow maturation and high demand, it is considered an endangered species. Therefore, as a conservation strategy, this study proposes the creation of nurseries, genetic breeding programs, and demographic monitoring of wild populations to counteract the extraction of wild plants and, the conservation of the genetic diversity. Summary: Agave marmorata Roezl., is an endemic species distributed in the states of Oaxaca and Puebla, Mexico, and locally is widely used to produce mezcal.We assessed the genomic diversity and differentiation using the RADseq method and 29,101 high‐quality single nucleotide polymorphisms (SNPs) in wild plants and grown under three different management types (cultivated, plants used as live fences, and young plants growing in nurseries). We examined the demographic history and used species distribution modeling to understand the future of A. marmorata under scenarios of climate change.We found high levels of genomic diversity (HS = 0.229) and moderate levels of inbreeding (FIS = 0.106 and Fhat3 = 0.190). The cultivated samples harbored less genetic diversity than the wild plants. Furthermore, we estimated low differentiation between cultivated and wild localities (FST = 0.037). In the wild samples, we identified two main genetic groups, one in the East and another in the West of its distribution area. This genetic structure possibly derived from a population contraction during the Pleistocene (~216,879.75 BP) and the formation of two refugia in small areas with climatic stability. Furthermore, the demographic reconstruction indicated that A. marmorata went through a recent population expansion event, with a large current Ne (Ne = 8,009). The future climate change models indicated contrasting possible changes in its distribution range, from an increase to the reduction of its suitable habitat, differences related to model parametrization, and future levels of CO2 production.We propose conservation measures for the different management types of the species while also considering the biotic and abiotic interactions of Agave marmorata. [ABSTRACT FROM AUTHOR]

Habitat fragmentation reduces gene flow, causing genetic differentiation and diversity loss in endangered species through genetic drift and inbreeding. However, the impact of habitat fragmentation on ectomycorrhizal (ECM) fungi remains unexplored, despite their critical roles in forest ecosystems. Here, we investigated the population genetic structure and the demographic history of Rhizopogon togasawarius, the ECM fungus specifically colonizing the host tree Pseudotsuga japonica, across its entire distribution range (>200 km). These two species are designated as endangered species on the IUCN Red List since they are found only in small, fragmented forests in Japan. We analysed 236 R. togasawarius individuals from five remaining populations across the Kii Peninsula and the Shikoku Island, separated by a sea channel. Simple sequence repeat analyses using 20 loci revealed strong genetic differentiation among populations (FST = 0.255), even significant in the nearest population pair separated by a distance of only 8 km (FST = 0.075), indicating extremely limited gene flow between populations. DIYABC‐RF analyses implied that population divergence occurred approximately 6000 generations ago between the two regions, and nearly 1500 generations ago between the nearest populations within Shikoku Island, related to past climate events. Because of prolonged genetic isolation, significant inbreeding was confirmed in four of five populations, where effective population sizes became very small (Ne = 9.0–58.0). Although evaluation of extinction risks for microorganisms is challenging, our conservation genetic results indicated that habitat fragmentation increases extinction risk through population genetic mechanisms, and therefore should not be overlooked in biodiversity conservation efforts. [ABSTRACT FROM AUTHOR]

ABSTRACT Genomic resources are valuable to examine historical demographic patterns and their effects to better inform management and conservation of threatened species. We evaluated population trends and genome‐wide variation in the near‐threatened Orange‐breasted Falcon (Falco deiroleucus) and its more common sister species, the Bat Falcon (F. rufigularis), to explore how the two species differ in genomic diversity as influenced by their contrasting long‐term demographic histories. We generated and aligned whole genome resequencing data for 12 Orange‐breasted Falcons and 9 Bat Falcons to an annotated Gyrfalcon (F. rusticolus) reference genome that retained approximately 22.4 million biallelic autosomal SNPs (chromosomes 1–22). Our analyses indicated much lower genomic diversity in Orange‐breasted Falcons compared to Bat Falcons. All sampled Orange‐breasted Falcons were significantly more inbred than the sampled Bat Falcons, with values similar to those observed in island‐mainland species comparisons. The distribution of runs of homozygosity showed variation suggesting long‐term low population size and the possibility of bottlenecks in Orange‐breasted Falcons contrasting with consistently larger populations in Bat Falcons. Analysis of genetic load suggests that Orange‐breasted Falcons are less likely to experience inbreeding depression than Bat Falcons due to reduced inbreeding load but are at elevated risk from fixation of deleterious gene variants and perhaps a reduced adaptive potential. These genomic analyses highlight differences in the historical demography of two closely related species that have influenced their current genomic diversity and should result in differing strategies for their continued conservation. [ABSTRACT FROM AUTHOR]

Biscogniauxia mediterranea is a pathogenic fungus associated with Quercus species causing charcoal canker disease in forests. Its phenotypic and genetic variability has been well studied in Tunisia but little is known about its demographic history. Population dynamic of B. mediterranea was evaluated among 30 isolates from different cork oak forests in Northwestern Tunisia. The genetic structure analyzed with two DNA markers (ITS and tef-1α) showed low genetic differentiation associated with high genetic flow among populations. The polymorphism analysis showed low nucleotide diversity but high haplotypic diversity among and within B. mediterranea populations which could be due to rapid growth from a small ancestral population. This hints at recent population growth after a period of decline likely due to a catastrophic event involving fires and human-induced tree cutting. The resulting genetic diversity within populations primarily arises from the emergence of new haplotypes. Overall, this study provides insights into the polymorphism of B. mediterranea and its potential adaptive strategy. [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]

Right whales (genus Eubalaena) were among the first, and most extensively pursued, targets of commercial whaling. However, understanding the impacts of this persecution requires knowledge of the demographic histories of these species prior to exploitation. We used deep whole genome sequencing (~40×) of 12 North Atlantic (E. glacialis) and 10 Southwest Atlantic southern (E. australis) right whales to quantify contemporary levels of genetic diversity and infer their demographic histories over time. Using coalescent‐ and identity‐by‐descent–based modelling to estimate ancestral effective population sizes from genomic data, we demonstrate that North Atlantic right whales have lived with smaller effective population sizes (Ne) than southern right whales in the Southwest Atlantic since their divergence and describe the decline in both populations around the time of whaling. North Atlantic right whales exhibit reduced genetic diversity and longer runs of homozygosity leading to higher inbreeding coefficients compared to the sampled population of southern right whales. This study represents the first comprehensive assessment of genome‐wide diversity of right whales in the western Atlantic and underscores the benefits of high coverage, genome‐wide datasets to help resolve long‐standing questions about how historical changes in effective population size over different time scales shape contemporary diversity estimates. This knowledge is crucial to improve our understanding of the right whales' history and inform our approaches to address contemporary conservation issues. Understanding and quantifying the cumulative impact of long‐term small Ne, low levels of diversity and recent inbreeding on North Atlantic right whale recovery will be important next steps. [ABSTRACT FROM AUTHOR]

The Chinese pangolin (Manis pentadactyla, MP) has been extensively exploited and is now on the brink of extinction, but its population structure, evolutionary history, and adaptive potential are unclear. Here, we analyzed 94 genomes from three subspecies of the Chinese pangolin and identified three distinct genetic clusters (MPA, MPB, and MPC), with MPB further divided into MPB1 and MPB2 subpopulations. The divergence of these populations was driven by past climate change. For MPB2 and MPC, recent human activities have caused dramatic population decline and small population size as well as increased inbreeding, but not decrease in genomic variation and increase in genetic load probably due to strong gene flow; therefore, it is crucial to strengthen in situ habitat management for these two populations. By contrast, although human activities have a milder impact on MPA, it is at high risk of extinction due to long-term contraction and isolation, and genetic rescue is urgently needed. MPB1 exhibited a relatively healthy population status and can potentially serve as a source population. Overall, our findings provide novel insights into the conservation of the Chinese pangolin and biogeography of the mammals of eastern Asia. [ABSTRACT FROM AUTHOR]

As evidence of global insect declines continues to mount, insect conservationists are becoming increasingly interested in modeling the demographic history of at-risk species from long-term survey data. However, certain entomological survey methods may be susceptible to temporal biases that will complicate these efforts. Entomological light traps, in particular, may catch fewer insects today than they once did due solely to increases in anthropogenic light pollution. Here we investigate this possibility by comparing the demographic histories of corn earworm moths (Helicoverpa zea) estimated from pairs of blacklight and pheromone traps monitored at the same farms. We find a stark decline in blacklight trap efficacy over 25 years of monitoring in Delaware, USA, mirrored over 10 years of monitoring in New Jersey, USA. While the precise causes of this decline remain a subject for discussion, the practical consequences are clear: insect conservationists cannot fully rely on long-term trends from entomological light traps. Implications for insect conservation: H. zea populations appear to have remained largely stable over the past 25 years when assessed using pheromone trap data; when assessed using blacklight trap data, however, they appear to have declined precipitously. This disparity is consistent with a gradual loss in light trap efficacy due to concomitant increases in anthropogenic light pollution. Unfortunately, many nocturnal insects of conservation concern have historically been monitored via light traps alone. Going forward, insect conservationists should seek out alternative sources of monitoring data against which to calibrate estimates of demographic history obtained from light traps. [ABSTRACT FROM AUTHOR]

Social Impact Statement For hundreds of years, Agave marmorata plants have been used in the production of alcoholic beverages in Mexico. This species is very important in small‐scale rural economies because it is a large plant, yielding five liters of mezcal. However, the production of these beverages takes place when it reaches its reproductive stage, which takes up to 35 years. Due to its slow maturation and high demand, it is considered an endangered species. Therefore, as a conservation strategy, this study proposes the creation of nurseries, genetic breeding programs, and demographic monitoring of wild populations to counteract the extraction of wild plants and, the conservation of the genetic diversity. Summary Agave marmorata Roezl., is an endemic species distributed in the states of Oaxaca and Puebla, Mexico, and locally is widely used to produce mezcal. We assessed the genomic diversity and differentiation using the RADseq method and 29,101 high‐quality single nucleotide polymorphisms (SNPs) in wild plants and grown under three different management types (cultivated, plants used as live fences, and young plants growing in nurseries). We examined the demographic history and used species distribution modeling to understand the future of A. marmorata under scenarios of climate change. We found high levels of genomic diversity (HS = 0.229) and moderate levels of inbreeding (FIS = 0.106 and Fhat3 = 0.190). The cultivated samples harbored less genetic diversity than the wild plants. Furthermore, we estimated low differentiation between cultivated and wild localities (FST = 0.037). In the wild samples, we identified two main genetic groups, one in the East and another in the West of its distribution area. This genetic structure possibly derived from a population contraction during the Pleistocene (~216,879.75 BP) and the formation of two refugia in small areas with climatic stability. Furthermore, the demographic reconstruction indicated that A. marmorata went through a recent population expansion event, with a large current Ne (Ne = 8,009). The future climate change models indicated contrasting possible changes in its distribution range, from an increase to the reduction of its suitable habitat, differences related to model parametrization, and future levels of CO2 production. We propose conservation measures for the different management types of the species while also considering the biotic and abiotic interactions of Agave marmorata.

Abstract Background High-quality genomic datasets from under-representative populations are essential for population genetic analysis and medical relevance. Although the Tujia are the most populous ethnic minority in southwestern China, previous genetic studies have been fragmented and only partially reveal their genetic diversity landscape. The understanding of their fine-scale genetic structure and potentially differentiated biological adaptive features remains nascent. Objectives This study aims to explore the demographic history and genetic architecture related to the natural selection of the Tujia people, focusing on a meta-Tujia population from the central regions of the Yangtze River Basin. Results Population genetic analyses conducted on the meta-Tujia people indicate that they occupy an intermediate position in the East Asian North-South genetic cline. A close genetic affinity was identified between the Tujia people and neighboring Sinitic-speaking populations. Admixture models suggest that the Tujia can be modeled as a mixture of northern and southern ancestries. Estimates of f 3 /f 4 statistics confirmed the presence of ancestral links to ancient Yellow River Basin millet farmers and the BaBanQinCen-related groups. Furthermore, population-specific natural selection signatures were explored, revealing highly differentiated functional variants between the Tujia and southern indigenous populations, including genes associated with hair morphology (e.g., EDAR) and skin pigmentation (e.g., SLC24A5). Additionally, both shared and unique selection signatures were identified among ethnically diverse but geographically adjacent populations, highlighting their extensive admixture and the biological adaptations introduced by this admixture. Conclusions The study unveils significant population movements and genetic admixture among the Tujia and other ethno-linguistically diverse East Asian groups, elucidating the differentiated adaptation processes across geographically diverse populations from the current genetic landscape.

Understanding genome-wide diversity, inbreeding, and the burden of accumulated deleterious mutations in small and isolated populations is essential for predicting and enhancing population persistence and resilience. However, these effects are rarely studied in limestone karst plants. Here, we re-sequenced the nuclear genomes of 62 individuals of the Begonia masoniana complex (B. liuyanii, B. longgangensis, B. masoniana and B. variegata) and investigated genomic divergence and genetic load for these four species. Our analyses revealed four distinct clusters corresponding to each species within the complex. Notably, there was only limited admixture between B. liuyanii and B. longgangensis occurring in overlapping geographic regions. All species experienced historical bottlenecks during the Pleistocene, which were likely caused by glacial climate fluctuations. We detected an asymmetric historical gene flow between group pairs within this timeframe, highlighting a distinctive pattern of interspecific divergence attributable to karst geographic isolation. We found that isolated populations of B. masoniana have limited gene flow, the smallest recent population size, the highest inbreeding coefficients, and the greatest accumulation of recessive deleterious mutations. These findings underscore the urgency to prioritize conservation efforts for these isolated population. This study is among the first to disentangle the genetic differentiation and specific demographic history of karst Begonia plants at the whole-genome level, shedding light on the potential risks associated with the accumulation of deleterious mutations over generations of inbreeding. Moreover, our findings may facilitate conservation planning by providing critical baseline genetic data and a better understanding of the historical events that have shaped current population structure of rare and endangered karst plants.

Abstract Background Silkie is a traditional Chinese chicken breed characterized by its unique combination of specialized morphological traits. While previous studies have focused on the genetic basis of these traits, the overall genomic characteristics of the Silkie breed remain largely unexplored. In this study, we employed whole genome resequencing data to examine the genetic diversity, selective signals and demographic history of the Silkie breed through comparative analyses with seven other Chinese indigenous breeds (IDGBs), a commercial breed, and the wild ancestor Red Jungle Fowl. Results In total, 20.8 million high-quality single nucleotide polymorphisms and 86 large structural variations were obtained. We discovered that Silkie exhibits a relatively high level of inbreeding and is genetically distinct from other IDGBs. Furthermore, our analysis indicated that Silkie has experienced a stronger historical population bottleneck and has a smaller effective population size compared with other IDGBs. We identified 45 putatively selected genes that are enriched in the melanogenesis pathway, which probably is related to the feather color. Among these genes, LMBR1 and PDSS2 have been previously associated with the extra toe and the hookless feathers, respectively. Six of the selected genes (KITLG, GSK3B, SOBP, CTBP1, ELMO2, SNRPN) are known to be associated with neurodevelopment and mental diseases in human, and are possibly related to the distinct behavior of Silkie. We further identified structural variants in Silkie and found previously reported variants linked to hyperpigmentation (END3), muff and beard (HOXB8), and Rose-comb phenotype (MNR2). Additionally, we found a 0.61 Mb inversion overlapping with the GMDS gene, which was previously linked to neurodevelopmental defects in zebrafish and humans. This may also be related to the behavior distinctiveness of Silkie. Conclusions Our study revealed that Silkie is genetically distinct and relatively highly inbred compared to other IDGB chicken populations, possibly attributed to more prolong population bottlenecks and selective breeding practice. These results enhance our understanding of how domestication and selective breeding have shaped the genome of Silkie. These findings contribute to the broader field of domestication and avian genomics, and have implications for the future conservation and breeding efforts.

Abstract Background North African human populations present a complex demographic scenario due to the presence of an autochthonous genetic component and population substructure, plus extensive gene flow from the Middle East, Europe, and sub-Saharan Africa. Results We conducted a comprehensive analysis of 364 genomes to construct detailed demographic models for the North African region, encompassing its two primary ethnic groups, the Arab and Amazigh populations. This was achieved through an Approximate Bayesian Computation with Deep Learning (ABC-DL) framework and a novel algorithm called Genetic Programming for Population Genetics (GP4PG). This innovative approach enabled us to effectively model intricate demographic scenarios, utilizing a subset of 16 whole genomes at > 30X coverage. The demographic model suggested by GP4PG exhibited a closer alignment with the observed data compared to the ABC-DL model. Both point to a back-to-Africa origin of North African individuals and a close relationship with Eurasian populations. Results support different origins for Amazigh and Arab populations, with Amazigh populations originating back in Epipaleolithic times, while GP4PG supports Arabization as the main source of Middle Eastern ancestry. The GP4PG model includes population substructure in surrounding populations (sub-Saharan Africa and Middle East) with continuous decaying gene flow after population split. Contrary to ABC-DL, the best GP4PG model does not require pulses of admixture from surrounding populations into North Africa pointing to soft splits as drivers of divergence in North Africa. Conclusions We have built a demographic model on North Africa that points to a back-to-Africa expansion and a differential origin between Arab and Amazigh populations.

Background: High-quality genomic datasets from under-representative populations are essential for population genetic analysis and medical relevance. Although the Tujia are the most populous ethnic minority in southwestern China, previous genetic studies have been fragmented and only partially reveal their genetic diversity landscape. The understanding of their fine-scale genetic structure and potentially differentiated biological adaptive features remains nascent. Objectives: This study aims to explore the demographic history and genetic architecture related to the natural selection of the Tujia people, focusing on a meta-Tujia population from the central regions of the Yangtze River Basin. Results: Population genetic analyses conducted on the meta-Tujia people indicate that they occupy an intermediate position in the East Asian North-South genetic cline. A close genetic affinity was identified between the Tujia people and neighboring Sinitic-speaking populations. Admixture models suggest that the Tujia can be modeled as a mixture of northern and southern ancestries. Estimates of f3/f4 statistics confirmed the presence of ancestral links to ancient Yellow River Basin millet farmers and the BaBanQinCen-related groups. Furthermore, population-specific natural selection signatures were explored, revealing highly differentiated functional variants between the Tujia and southern indigenous populations, including genes associated with hair morphology (e.g., EDAR) and skin pigmentation (e.g., SLC24A5). Additionally, both shared and unique selection signatures were identified among ethnically diverse but geographically adjacent populations, highlighting their extensive admixture and the biological adaptations introduced by this admixture. Conclusions: The study unveils significant population movements and genetic admixture among the Tujia and other ethno-linguistically diverse East Asian groups, elucidating the differentiated adaptation processes across geographically diverse populations from the current genetic landscape. [ABSTRACT FROM AUTHOR]

Large mitochondrial DNA fragments and nearly complete mitogenomes were obtained from nextera-tagmented reductively amplified DNA (nextRAD) data from the Rio Grande silvery minnow (Hybognathus amarus). We used these data to characterize variation across the mitogenome and to evaluate changes in mitochondrial diversity across a 20 year time series punctuated by marked species decline. We observed different evolutionary rates among protein-coding genes and inflated values of the ratio of non-synonymous change to non-synonymous sites to synonymous changes per synonymous site for several protein-coding genes, violating assumptions of selective neutrality. Analyses suggested that non-synonymous substitutions are effectively neutral, and our results were not consistent with genetic draft. Mitogenomes revealed large long-term effective population size for Rio Grande silvery minnow, and time-series data indicated recent reductions in mitochondrial diversity via genetic drift associated with population bottlenecks. The results presented in this study show that in some cases, nextRAD sequences contain informative mitochondrial DNA data. [ABSTRACT FROM AUTHOR]

Fish provide food and income opportunities for millions of people in Lake Nyasa, also known as Lake Malawi in Malawi and Lake Niassa in Mozambique. Oreochromis karongae (Trewavas, 1941), which is native to Lake Nyasa, Lake Malombe and the Shire River, is at the verge of extinction and has been listed as critically endangered species by the International Union for Conservation of Nature (IUCN), primarily due to overfishing. Using 632 bp of partial mitochondrial cytochrome oxidase subunit I (COI) sequences from 115 samples, this work aims to assess the population genetic status and demographic history of this species to better manage and advance its conservation. The analysis of molecular variance (AMOVA) revealed a low and non‐significant genetic differentiation index across the populations under study (ΦST = 0.003, p = 0.278), indicating a lack of population genetic structure. Phylogenetic analysis, grouped together all COI haplotypes of O. karongae from the six sampled sites. Nonetheless, the results showed signs of population expansion from a historic bottleneck, consistent with most data from the Western Indian Ocean Fauna. The findings from this study could be used to improve management and conservation strategies for critically endangered O. karongae in Lake Nyasa. [ABSTRACT FROM AUTHOR]

Anthropogenic impact has transitioned from threatening already rare species to causing significant declines in once numerous organisms. Long‐tailed duck (Clangula hyemalis) and velvet scoter (Melanitta fusca) were once important quarry sea duck species in NW Europe, but recent declines resulted in their reclassification as vulnerable on the IUCN Red List. We sequenced and assembled genomes for both species and resequenced 15 individuals of each. Using analyses based on site frequency spectra and sequential Markovian coalescence, we found C. hyemalis to show more historical demographic stability, whereas M. fusca was affected particularly by the Last (Weichselian) Glaciation. This likely reflects C. hyemalis breeding continuously across the Arctic, with cycles of glaciation primarily shifting breeding areas south or north without major population declines, whereas the more restricted southern range of M. fusca would lead to significant range contraction during glaciations. Both species showed evidence of declines over the past thousands of years, potentially reflecting anthropogenic pressures with the recent decline indicating an accelerated process. Analysis of runs of homozygosity (ROH) showed low but nontrivial inbreeding, with FROH from 0.012 to 0.063 in C. hyemalis and ranging from 0 to 0.047 in M. fusca. Lengths of ROH suggested that this was due to ongoing background inbreeding rather than recent declines. Overall, despite demographically important declines, this has not yet led to strong inbreeding and genetic erosion, and the most pressing conservation concern may be the risk of density‐dependent (Allee) effects. We recommend monitoring of inbreeding using ROH analysis as a cost‐efficient method to track future developments to support effective conservation of these species. [ABSTRACT FROM AUTHOR]

Aim: Genetic diversity is crucial for species adaptability. Understanding the mechanisms behind its formation and maintenance is essential for effective conservation. Recent studies have demonstrated that despite experiencing severe population bottlenecks, Muntiacus reevesi retains high genetic diversity and continues its northward migration, indicative of ongoing adaptive evolution. However, our comprehension of this phenomenon remains incomplete. The objective of this study is to explore the mechanisms underlying the formation of high genetic diversity and the genomic characteristics associated with local adaptation, using M. reevesi as a case study. Location: Southern China. Methods: We analysed resequencing data from 62 genomes and identified 29,124,081 high‐quality single‐nucleotide polymorphisms (SNPs). We used population genetics, demographic history, population differentiation, gene flow analysis software, and genotype‐environment association (GEA) models to assess the factors that have contributed to high genetic diversity and environmental adaptability in the historical climate and geographical context. Results: The study identified that during Pleistocene climatic fluctuations, M. reevesi diverged into eastern (DB and WJW populations) and western lineages (WL, BA, and QL populations), all displayed high genetic diversity. Historically, M. reevesi maintained large effective populations, but contemporary human‐induced threats have led to a significant decline. Population differentiation models suggest distinct expansion pathways for eastern and western lineages, resulting in population admixture, with mountain corridors facilitating gene flow and maintaining high genetic diversity. Additionally, environmental‐genotype analysis revealed local adaptation in the QL‐BA population, highlighting candidate adaptive genes (ME3 and PRKG1) potentially linked to cold adaptation and foraging behaviour. Conclusion: This study enhances our understanding of the mechanisms behind the high genetic diversity and environmental adaptability of M. reevesi, offering insights into how bottleneck populations maintain diversity, crucial for biogeographic research and conservation strategies for similar species. [ABSTRACT FROM AUTHOR]

The last glacial period is known to have greatly influenced the demographic history of temperate forest trees, with important range contractions and post‐glacial expansions that led to the formation of multiple genetic lineages and secondary contact zones in the Northern Hemisphere. These dynamics have been extensively studied for European and North American species but are still poorly understood in other temperate regions of rich biodiversity such as the Caucasus. Our study helps filling that gap by deciphering the genomic landscapes of F. orientalis across the South Caucasus. The use of genome‐wide data confirmed a past demographic history strongly influenced by the Last Glacial Maximum, revealing two disjunct glacial refugia in the Colchis and Hyrcanian regions. The resulting patterns of genetic diversity, load and differentiation are not always concordant across the region, with genetic load pinpointing the location of the glacial refugia more efficiently than genetic diversity alone. The Hyrcanian forests show depleted genetic diversity and substantial isolation, even if long‐distance gene flow is still present with the main centre of diversity in the Greater Caucasus. Finally, we characterize a strong heterogeneity of genetic diversity and differentiation along the species chromosomes, with noticeably a first chromosome showing low diversity and weak differentiation. [ABSTRACT FROM AUTHOR]

Myotis septentrionalis (Northern Long-eared Bat) has recently suffered a >90% decline in population size in North America due to white-nose syndrome (WNS). We assessed genetic diversity, population structure, current effective population size, and demographic history of M. septentrionalis distributed across the United States to determine baseline levels pre-WNS. We analyzed RADseq data from 81 individuals from Kentucky, Louisiana, Michigan, Minnesota, North Carolina, Oklahoma, and Wisconsin. Additionally, we examined population genetic structure using discriminant analysis of principal components, fastStructure, and STRUCTURE. We then estimated effective population size and demographic history using fastsimcoal2. Similar levels of genetic diversity were found across all samples. We found no population genetic structure in the varied analyses from these contemporary samples. The best model for demographic history estimated a rapid population expansion followed by a slower expansion approximately 340,000 years ago. The vagility of M. septentrionalis , along with male dispersal and random mating, may provide a buffer against serious bottleneck effects stemming from rapid population declines due to WNS. This research provides a baseline for tracking and monitoring the influence of WNS on genetic diversity such as potential reduced diversity or increased population structuring in the future. [ABSTRACT FROM AUTHOR]

Background: Silkie is a traditional Chinese chicken breed characterized by its unique combination of specialized morphological traits. While previous studies have focused on the genetic basis of these traits, the overall genomic characteristics of the Silkie breed remain largely unexplored. In this study, we employed whole genome resequencing data to examine the genetic diversity, selective signals and demographic history of the Silkie breed through comparative analyses with seven other Chinese indigenous breeds (IDGBs), a commercial breed, and the wild ancestor Red Jungle Fowl. Results: In total, 20.8 million high-quality single nucleotide polymorphisms and 86 large structural variations were obtained. We discovered that Silkie exhibits a relatively high level of inbreeding and is genetically distinct from other IDGBs. Furthermore, our analysis indicated that Silkie has experienced a stronger historical population bottleneck and has a smaller effective population size compared with other IDGBs. We identified 45 putatively selected genes that are enriched in the melanogenesis pathway, which probably is related to the feather color. Among these genes, LMBR1 and PDSS2 have been previously associated with the extra toe and the hookless feathers, respectively. Six of the selected genes (KITLG, GSK3B, SOBP, CTBP1, ELMO2, SNRPN) are known to be associated with neurodevelopment and mental diseases in human, and are possibly related to the distinct behavior of Silkie. We further identified structural variants in Silkie and found previously reported variants linked to hyperpigmentation (END3), muff and beard (HOXB8), and Rose-comb phenotype (MNR2). Additionally, we found a 0.61 Mb inversion overlapping with the GMDS gene, which was previously linked to neurodevelopmental defects in zebrafish and humans. This may also be related to the behavior distinctiveness of Silkie. Conclusions: Our study revealed that Silkie is genetically distinct and relatively highly inbred compared to other IDGB chicken populations, possibly attributed to more prolong population bottlenecks and selective breeding practice. These results enhance our understanding of how domestication and selective breeding have shaped the genome of Silkie. These findings contribute to the broader field of domestication and avian genomics, and have implications for the future conservation and breeding efforts. [ABSTRACT FROM AUTHOR]

Cave burial has been prevalent in southern China for thousands of years since the Shang and Zhou Dynasties (3600 − 2200 BP). The population history and the genetic contribution of cave burial groups to the formation of present-day southern minorities are largely unknown due to the lack of ancient genomic data. Here, we present the genomic data from four ancient individuals from cave burial sites Baitaishan and Huatudong from the Late Yuan to Ming Dynasties (650 − 300 BP) in Guangxi. We observed a close genetic affinity between the four individuals and published contemporaneous cave burial samples. However, our studied individuals received gene flows from northern East Asians compared to the cave burial groups around 1600 − 1400 years ago. We identified a strong genetic link between these ancient cave burial groups and present-day Hmong-Mien-speaking populations, particularly the geographically adjacent Baiku Yao population, indicating population stability in the mountainous region of southern China over the past few centuries. [ABSTRACT FROM AUTHOR]

Small and isolated populations are at risk of local extinction, either due to the reduction of genetic diversity or due to stochastic events. We assessed genetic diversity in populations of the red-spotted (Luscinia svecica svecica) and white-spotted bluethroat (L. s. cyanecula) subspecies from six European sites, focusing on a peripheral and declining, red-spotted population from Central Europe (Krkonoše Mountains, Czech Republic). Analysis of population structure using mitochondrial sequences (cytochrome b) and ddRAD genomic data revealed that the two subspecies form clearly defined clusters, but traces of possible admixture were found in three populations of the white-spotted bluethroat. Demographic history reconstruction indicates past population range expansion in both subspecies, while the occurrence of short (0.4 Mbp) runs of homozygosity (ROH) segments suggests possible inbreeding 50 to 200 generations ago. Interestingly, although established by a small number of individuals, the Krkonoše population show reduced genetic diversity in only one measure of summary statistics, possibly due to sustained gene flow. Correspondingly, nine highly homozygous genes were recovered within a 2.6-Mbp long ROH region on the Chr 5. Thus, we found only a small reduction of genetic diversity in a population facing extinction, contrary to the expectations for a geographically distant and small population. [ABSTRACT FROM AUTHOR]

Understanding population genetic structure and its possible causal factors is critical for utilizing genetic resources and genetic breeding of economically important plants. Although Torreya grandis is an important conifer producing nuts in China, little is known about its population structure, let alone the causal factors that shaped its genetic variation pattern and population structure. In this work, we intended to characterize the genetic variation pattern and population structure of the nut-yielding conifer T. grandis throughout its whole geographical distribution and further explore the potentially causal factors for the population structure using multiple approaches. A moderate level of genetic diversity and a novel population structure were revealed in T. grandis based on eleven robust EST-SSR loci and three chloroplast fragments. Alien genetic composition derived from the closely related species T. nucifera endemic to Japan was detected in the Kuaiji Mountain area, where the seed quality of T. grandis is considered the best in China. Demography history and niche modeling were inferred and performed, and the contribution of geographic isolation to its population structure was compared with that of environmental isolation. Significant demographic changes occurred, including a dramatic population contraction during the Quaternary, and population divergence was significantly correlated with geographic distance. These results suggested that early breeding activities and demographic changes significantly contributed to the population structure of T. grandis. In turn, the population structure was potentially associated with the excellent variants and adaptation of cultivars of T. grandis. The findings provide important information for utilizing genetic resources and genetic breeding of T. grandis in the future. [ABSTRACT FROM AUTHOR]

Inbred populations often suffer from increased mutational load and reduced fitness due to lower efficacy of purifying selection in groups with small effective population sizes. Genetic rescue (GR) is a conservation tool that is studied and deployed with the aim of increasing the fitness of such inbred populations by assisted migration of individuals from closely related outbred populations. The success of GR depends on several factors—such as their demographic history and distribution of dominance effects of mutations—that may vary across populations. While we understand the impact of these factors on the dynamics of GR, their impact on local adaptations remains unclear. To this end, we conduct a population genetics simulation study to evaluate the impact of trait complexity (Mendelian vs. polygenic), dominance effects, and demographic history on the efficacy of GR. We find that the impact on local adaptations depends highly on the mutational load at the time of GR, which is in turn shaped dynamically by interactions between demographic history and dominance effects of deleterious variation. Over time local adaptations are generally restored post-GR, though in the short term they are often compromised in the process of purging deleterious variation. We also show that while local adaptations are almost always fully restored, the degree to which ancestral genetic variation affecting the trait is replaced by donor variation can vary drastically and is especially high for complex traits. Our results provide insights on the impact of GR on trait evolution and considerations for the practical implementation of GR. [ABSTRACT FROM AUTHOR]

Runs of homozygosity (ROHs) are indicative of elevated homozygosity and inbreeding due to mating of closely related individuals. Self-fertilization can be a major source of inbreeding which elevates genome-wide homozygosity and thus should also create long ROHs. While ROHs are frequently used to understand inbreeding in the context of conservation and selective breeding, as well as for consanguinity of populations and their demographic history, it remains unclear how ROH characteristics are altered by selfing and if this confounds expected signatures of inbreeding due to demographic change. Using simulations, we study the impact of the mode of reproduction and demographic history on ROHs. We apply random forests to identify unique characteristics of ROHs, indicative of different sources of inbreeding. We pinpoint distinct features of ROHs that can be used to better characterize the type of inbreeding the population was subjected to and to predict outcrossing rates and complex demographic histories. Using additional simulations and four empirical datasets, two from highly selfing species and two from mixed-maters, we predict the selfing rate and validate our estimations. We find that self-fertilization rates are successfully identified even with complex demography. Population genetic summary statistics improve algorithm accuracy particularly in the presence of additional inbreeding, e.g. from population bottlenecks. Our findings highlight the importance of ROHs in disentangling confounding factors related to various sources of inbreeding and demonstrate situations where such sources cannot be differentiated. Additionally, our random forest models provide a novel tool to the community for inferring selfing rates using genomic data. [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]

As climatic variation re‐shapes global biodiversity, understanding eco‐evolutionary feedbacks during species range shifts is of increasing importance. Theory on range expansions distinguishes between two different forms: "pulled" and "pushed" waves. Pulled waves occur when the source of the expansion comes from low‐density peripheral populations, while pushed waves occur when recruitment to the expanding edge is supplied by high‐density populations closer to the species' core. How extreme events shape pushed/pulled wave expansion events, as well as trailing‐edge declines/contractions, remains largely unexplored. We examined eco‐evolutionary responses of a marine invertebrate (the owl limpet, Lottia gigantea) that increased in abundance during the 2014–2016 marine heatwaves near the poleward edge of its geographic range in the northeastern Pacific. We used whole‐genome sequencing from 19 populations across >11 degrees of latitude to characterize genomic variation, gene flow, and demographic histories across the species' range. We estimated present‐day dispersal potential and past climatic stability to identify how contemporary and historical seascape features shape genomic characteristics. Consistent with expectations of a pushed wave, we found little genomic differentiation between core and leading‐edge populations, and higher genomic diversity at range edges. A large and well‐mixed population in the northern edge of the species' range is likely a result of ocean current anomalies increasing larval settlement and high‐dispersal potential across biogeographic boundaries. Trailing‐edge populations have higher differentiation from core populations, possibly driven by local selection and limited gene flow, as well as high genomic diversity likely as a result of climatic stability during the Last Glacial Maximum. Our findings suggest that extreme events can drive poleward range expansions that carry the adaptive potential of core populations, while also cautioning that trailing‐edge extirpations may threaten unique evolutionary variation. This work highlights the importance of understanding how both trailing and leading edges respond to global change and extreme events. [ABSTRACT FROM AUTHOR]

A genetic analysis was conducted on Anguilla bicolor from Tanzania using the mitochondrial COI region. The study aimed to understand the population genetic structure and demographic history of A. bicolor. In this study, 42 samples of A. bicolor were collected from the Lower Rufiji River Basin and Pangani River in Tanzania between January and June 2023. The mtDNA COI sequences of 65 A. bicolor from various Indo‐Pacific countries were retrieved from GenBank. 2.The findings revealed an overall high haplotype diversity (0.83 ± 0.033) and moderate nucleotide diversity (0.63% ± 0.000).A limited genetic differentiation between populations was observed (FST = −0.00322, p = 0.0494), indicating gene flow, leading to an absence of population structure. The haplotype network tree also supported a panmictic stock in the Indo‐Pacific region with 44 haplotypes clustered around three principal haplotypes.Furthermore, the significantly overall negative values of both Tajima's D (−2.27, p = 0.002) and Fu's Fs (−26.36, p = 0.000) and the multimodal mismatch distribution suggested the presence of multiple demographic events in A. bicolor populations.Given the lack of substantial genetic structure among populations, managing the fishery as a single‐stock unit is advised, aligning with the current fisheries management practices in Tanzania. It is also crucial to ensure habitat quality along migratory paths to facilitate genetic exchange and long‐term species viability. [ABSTRACT FROM AUTHOR]

ABSTRACT The subtropical forests of East Asia are renowned for their high plant diversity, particularly the abundance of ancient relict species. However, both the evolutionary history of these relict species and their capacity for resilience in the face of impending climatic changes remain unclear. Using whole‐genome resequencing data, we investigated the lineage differentiation and demographic history of the relict and endangered tree, Bretschneidera sinensis (Akaniaceae). We employed a combination of population genomic and landscape genomic approaches to evaluate variation in mutation load and genomic offset, aiming to predict how different populations may respond to climate change. Our analysis revealed a profound genomic divergence between the East and West lineages, likely as the result of recurrent bottlenecks due to climatic fluctuations during the glacial period. Furthermore, we identified several genes potentially linked to growth characteristics and hypoxia response that had been subjected to positive selection during the lineage differentiation. Our assessment of genomic vulnerability uncovered a significantly higher mutation load and genomic offset in the edge populations of B. sinensis compared to their core counterparts. This implies that the edge populations are likely to experience the most significant impact from the predicted climate conditions. Overall, our research sheds light on the historical lineage differentiation and contemporary genomic vulnerability of B. sinensis. Broadening our understanding of the speciation history and future resilience of relict and endangered species such as B. sinensis, is crucial in developing effective conservation strategies in anticipation of future climatic changes.

ObjectiveTo genotype Oncomelania hupensis， based on microsatellites， in different snail-bearing environments in Jiaxing City， Zhejiang Province， for population genetics analysis in order to explore the reasons and influencing factors for the existence or proliferation of snails and to provide scientific basis for effective monitoring and control of snails.MethodsA total of 90 snail samples from three populations were collected in Yaobang Village （YB） and Sanxing Village （SX） in Pinghu City， and Yunhe Farm （YH） in Xiuzhou District， all were selected for snail checking in key snail habitats of Jiaxing City in 2022. DNA of the snails was genotyped and analyzed for population genetics using nine microsatellite loci.ResultsA total of 84 alleles were observed， and the mean number of alleles （Na） was 7.889， 5.667， and 3.778 for YB， SX， and YH respectively； the number of effective alleles （NeA） was 4.807， 3.329， and 2.294， respectively； and the coefficients of inbreeding （FIS） were 0.400， 0.377， and 0.493， respectively. Under the Infinite Allele Model （IAM）， the SX and YH might have a recent bottleneck. The NEstimator and LDNe software calculated effective population sizes （Ne） were above 31.9. AMOVA analysis showed that the variation of snails in the three populations mainly existed among individuals， accounting for 41.4% of the total variation. The value of the index of genetic differentiation between populations （FST） was 0.286， indicating a high degree of genetic differentiation. The results of the principal component analysis and phylogenetic tree were consistent， and the three populations were divided into two lineages， YB and SX were one lineage， and YH belonged to another independent lineage. Population history and dynamics analysis showed that the gene flow of the three populations was insufficient， population divergence history indicated that YH might have diverged from SX first， and YB was produced by the contact fusion of SX and YH.ConclusionThe genetic diversity of snail populations in Jiaxing City is generally low， and the snail populations are unstable， with a great degree of genetic differentiation and insufficient gene flow among populations. This study can provide a basis for evaluating the effectiveness of the control of the snail as well as monitoring the trend of the spread of the snail.

Abstract The white-bellied pangolin is subject to intense trafficking, feeding both local and international trade networks. In order to assess its population genetics and trace its domestic trade, we genotyped 562 pangolins from local to large bushmeat markets in western central Africa. We show that the two lineages described from the study region (WCA and Gab) were overlapping in ranges, with limited introgression in southern Cameroon. There was a lack of genetic differentiation across WCA and a significant signature of isolation-by-distance possibly due to unsuspected dispersal capacities involving a Wahlund effect. We detected a c. 74.1–82.5% decline in the effective population size of WCA during the Middle Holocene. Private allele frequency tracing approach indicated up to 600 km sourcing distance by large urban markets from Cameroon, including Equatorial Guinea. The 20 species-specific microsatellite loci provided individual-level genotyping resolution and should be considered as valuable resources for future forensic applications. Because admixture was detected between lineages, we recommend a multi-locus approach for tracing the pangolin trade. The Yaoundé market was the main hub of the trade in the region, and thus should receive specific monitoring to mitigate pangolins’ domestic trafficking. Our study also highlighted the weak implementation of CITES regulations at European borders.

Global climate change has increased concerns regarding biodiversity loss. However, many key conservation issues still required further research, including demographic history, deleterious mutation load, adaptive evolution, and putative introgression. Here we generated the first chromosome-level genome of the endangered Chinese hazelnut, Corylus chinensis, and compared the genomic signatures with its sympatric widespread C. kwechowensis–C. yunnanensis complex. We found large genome rearrangements across all Corylus species and identified species-specific expanded gene families that may be involved in adaptation. Population genomics revealed that both C. chinensis and the C. kwechowensis–C. yunnanensis complex had diverged into two genetic lineages, forming a consistent pattern of southwestern-northern differentiation. Population size of the narrow southwestern lineages of both species have decreased continuously since the late Miocene, whereas the widespread northern lineages have remained stable (C. chinensis) or have even recovered from population bottlenecks (C. kwechowensis–C. yunnanensis complex) during the Quaternary. Compared with C. kwechowensis–C. yunnanensis complex, C. chinensis showed significantly lower genomic diversity and higher inbreeding level. However, C. chinensis carried significantly fewer deleterious mutations than C. kwechowensis–C. yunnanensis complex, as more effective purging selection reduced the accumulation of homozygous variants. We also detected signals of positive selection and adaptive introgression in different lineages, which facilitated the accumulation of favorable variants and formation of local adaptation. Hence, both types of selection and exogenous introgression could have mitigated inbreeding and facilitated survival and persistence of C. chinensis. Overall, our study provides critical insights into lineage differentiation, local adaptation, and the potential for future recovery of endangered trees.

Abstract The common dolphin (Delphinus delphis) is widely distributed worldwide and well adapted to various habitats. Animal genomes store clues about their pasts, and can reveal the genes underlying their evolutionary success. Here, we report the first high-quality chromosome-level genome of D. delphis. The assembled genome size was 2.56 Gb with a contig N50 of 63.85 Mb. Phylogenetically, D. delphis was close to Tursiops truncatus and T. aduncus. The genome of D. delphis exhibited 428 expanded and 1,885 contracted gene families, and 120 genes were identified as positively selected. The expansion of the HSP70 gene family suggested that D. delphis has a powerful system for buffering stress, which might be associated with its broad adaptability, longevity, and detoxification capacity. The expanded IFN-α and IFN-ω gene families, as well as the positively selected genes encoding tripartite motif-containing protein 25, peptidyl-prolyl cis-trans isomerase NIMA-interacting 1, and p38 MAP kinase, were all involved in pathways for antiviral, anti-inflammatory, and antineoplastic mechanisms. The genome data also revealed dramatic fluctuations in the effective population size during the Pleistocene. Overall, the high-quality genome assembly and annotation represent significant molecular resources for ecological and evolutionary studies of Delphinus and help support their sustainable treatment and conservation.

The white-bellied pangolin is subject to intense trafficking, feeding both local and international trade networks. In order to assess its population genetics and trace its domestic trade, we genotyped 562 pangolins from local to large bushmeat markets in western central Africa. We show that the two lineages described from the study region (WCA and Gab) were overlapping in ranges, with limited introgression in southern Cameroon. There was a lack of genetic differentiation across WCA and a significant signature of isolation-by-distance possibly due to unsuspected dispersal capacities involving a Wahlund effect. We detected a c. 74.1–82.5% decline in the effective population size of WCA during the Middle Holocene. Private allele frequency tracing approach indicated up to 600 km sourcing distance by large urban markets from Cameroon, including Equatorial Guinea. The 20 species-specific microsatellite loci provided individual-level genotyping resolution and should be considered as valuable resources for future forensic applications. Because admixture was detected between lineages, we recommend a multi-locus approach for tracing the pangolin trade. The Yaoundé market was the main hub of the trade in the region, and thus should receive specific monitoring to mitigate pangolins' domestic trafficking. Our study also highlighted the weak implementation of CITES regulations at European borders. [ABSTRACT FROM AUTHOR]

Summary: Evolutionary radiation, a pivotal aspect of macroevolution, offers valuable insights into evolutionary processes. The genus Pinus is the largest genus in conifers with c. 90% of the extant species emerged in the Miocene, which signifies a case of rapid diversification. Despite this remarkable history, our understanding of the mechanisms driving radiation within this expansive genus has remained limited.Using exome capture sequencing and a fossil‐calibrated phylogeny, we investigated the divergence history, niche diversification, and introgression among 13 closely related Eurasian species spanning climate zones from the tropics to the boreal Arctic.We detected complex introgression among lineages in subsection Pinus at all stages of the phylogeny. Despite this widespread gene exchange, each species maintained its genetic identity and showed clear niche differentiation. Demographic analysis unveiled distinct population histories among these species, which further influenced the nucleotide diversity and efficacy of purifying and positive selection in each species.Our findings suggest that radiation in the Eurasian pines was likely fueled by interspecific recombination and further reinforced by their adaptation to distinct environments. Our study highlights the constraints and opportunities for evolutionary change, and the expectations of future adaptation in response to environmental changes in different lineages. [ABSTRACT FROM AUTHOR]

Biological invasion consists of spatially and temporally varying stages, accompanied by ecological and evolutionary changes. Understanding the genomics underlying invasion dynamics provides critical insights into the geographic sources and genetic diversity, contributing to successful invasions across space and time. Here, we used genomic data and model‐based approaches to characterize the invasion dynamics of Hypochaeris radicata L., a noxious weed in Korea. Genetic diversity and assignment patterns were investigated using 3563 SNPs of 283 individuals sampled from 22 populations. We employed a coalescent‐based simulation method to estimate demographic changes for each population and inferred colonization history using both phylogenetic and population genetic model‐based approaches. Our data suggest that H. radicata has been repeatedly been introduced to Korea from multiple genetic sources within the last 50 years, experiencing weak population bottlenecks followed by subsequent population expansions. These findings highlight the potential for further range expansion, particularly in the presence of human‐mediated dispersal. Our study represents the first population‐level genomic research documenting the invasion dynamics of the successful worldwide invader, H. radicata, outside of Europe. [ABSTRACT FROM AUTHOR]

Understanding the genetic basis of local adaption is crucial in the context of global climate change. Mangroves, as salt-tolerant trees and shrubs in the intertidal zone of tropical and subtropical coastlines, are particularly vulnerable to climate change. Kandelia obovata, the most cold-tolerant mangrove species, has undergone ecological speciation from its cold-intolerant counterpart, Kandelia candel, with geographic separation by the South China Sea. In this study, we conducted wholegenome re-sequencing of K. obovata populations along China's southeast coast, to elucidate the genetic basis responsible for mangrove local adaptation to climate. Our analysis revealed a strong population structure among the three K. obovata populations, with complex demographic histories involving population expansion, bottleneck, and gene flow. Genome-wide scans unveiled pronounced patterns of selective sweeps in highly differentiated regions among pairwise populations, with stronger signatures observed in the northern populations compared to the southern population. Additionally, significant genotype-environment associations for temperature-related variables were identified, while no associations were detected for precipitation. A set of 39 high-confidence candidate genes underlying local adaptation of K. obovata were identified, which are distinct from genes under selection detected by comparison between K. obovata and its cold-intolerant relative K. candel. These results significantly contribute to our understanding of the genetic underpinnings of local adaptation in K. obovata and provide valuable insights into the evolutionary processes shaping the genetic diversity of mangrove populations in response to climate change. [ABSTRACT FROM AUTHOR]

Pleistocene climatic oscillations exerted significant influences on the genetic structure and demography of rhesus macaque (Macaca mulatta) in eastern China. However, the evolutionary history of rhesus macaques in subtropical and temperate China remained unclear and/or controversial. Herein, we analyzed the autosomes, mitochondrial genomes, and Y‐chromosomes from 84 individuals of Chinese rhesus macaque. The results revealed that (1) all individuals were clustered into pan‐west and pan‐east genetic groups, which exhibited Shaanxi Province as the northernmost region of western dispersal route of rhesus macaques in China; (2) in subtropical and temperate China, rhesus macaques were divided into four lineages (TH, DB, HS, and QL), and their divergence times corresponded to the Penultimate Glaciation (300–130 kya) and Last Glaciation (70–10 kya), respectively; (3) the individuals from Mt. Taihangshan (TH) are closely related to individuals from Mt. Dabashan (DB) in the autosomal tree, rather than individuals from Mt. Huangshan (HS) as indicated by the mitogenome tree, which supports the hypothesis that the ancestral rhesus macaques radiated into Mt. Taihangshan from Mt. Huangshan via Mt. Dabashan; and (4) the demographic scenario of the four lineages showed the ancestral rhesus macaques bottleneck and expansion corresponding to the suitable habitat reduction and expansion, which confirmed they had experienced northward recolonization and southward retreat events from Mt. Huangshan area via Northern China Plain to Northernmost China along with Pleistocene glacial cycles. This study provides a new insight into understanding how Pleistocene glaciation has influenced faunal diversity in subtropical and temperate China, especially for those exhibiting differential patterns of sex dispersal. [ABSTRACT FROM AUTHOR]

The Mediterranean Sea is a semi-enclosed oceanic basin that communicates with the Atlantic Ocean and can be subdivided into seven geographical regions. It is considered a hotspot of biodiversity and is characterised by high rates of endemism. Over the past decades, many studies showed the presence of potential geographical breaks both across the Atlanto-Mediterranean transition and within the Mediterranean Sea. These investigations led to the identification of three distinct types of population genetic structures: (1) populations characterized by panmixia; (2) Atlanto-Mediterranean geographical partitioning; and (3) possible further subdivision between East and West Mediterranean basins. In this review, mainly focused on Christoph Schubart's works and interests, we summarize the different patterns of gene flows across the Atlanto-Mediterranean transition and within the Mediterranean Sea, recorded for decapod species living in littoral zones. Although some species share similar biological traits, larval dispersal mechanisms and habitat preferences, differences in their phylogeographic and population genetic structures do emerge. These findings confirm the complex nature of gene flows across the Atlanto-Mediterranean transition and within the Mediterranean basin and how difficult it is to achieve a generalised picture of the phylogeographical patterns of Atlantic-Mediterranean species. [ABSTRACT FROM AUTHOR]