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Introduction: Fusarium is a very heterogeneous group of fungi, difficult to classify, with a wide range of living styles, acting as saprophytes, parasites of plants, or pathogens for humans and animals. Prevalence of clinical fusariosis and lack of effective treatments have increased the interest in the precise diagnosis, which implies a molecular characterization of Fusarium populations. Objective: We compared different genotyping markers in their assessment of the genetic variability and molecular identification of clinical isolates of Fusarium. Materials and methods: We evaluated the performance of the fingerprinting produced by two random primers: M13, which amplifies a minisatellite sequence, and (GACA)4, which corresponds to a simple repetitive DNA sequence. Using the Hunter Gaston Discriminatory Index (HGDI), an analysis of molecular variance (AMOVA), and a Mantel test, the resolution of these markers was compared to the reference sequencing-based and PCR genotyping methods. Results: The highest HGDI value was associated with the M13 marker followed by (GACA)4. AMOVA and the Mantel tests supported a strong correlation between the M13 classification and the reference method given by the partial sequencing of the transcription elongation factor 1-alpha (TEF1-α) and rDNA 28S. Conclusion: The strong correlation between the M13 classification and the sequencingbased reference together with its higher resolution demonstrates its adequacy for the characterization of Fusarium populations.

Background: Anemone shikokiana (Makino) Makino is a perennial herb of the genus Anemone in the family Ranunculaceae. Endemic to the Shandong Peninsula in China and Shikoku Island in Japan, it is a rare and endangered plant with a narrow, disjunct distribution. It is threatened with extinction and is in urgent need of conservation. Evaluating the genetic diversity of species, revealing the population genetic structure and gene flow, and inferring the population history are of great importance for species conservation, especially for rare and endangered plants., Results: In our study, 73 samples from eight wild populations in China were sequenced by Super-GBS, yielding a total of 40.59 G clean reads and 52,231 SNPs. Based on the obtained SNP data set, we evaluated the population genetic diversity, genetic structure, and gene flow of A. shikokiana. A low level of genetic diversity was found (He = 0.1925, Ho = 0.1422). The neighbor-joining (NJ) tree, principal component analysis and ADMIXTURE analysis suggested that these 73 A. shikokiana could be considered as two groups. Pairwise genetic differentiation coefficients (Fst) indicated that genetic differentiation was lower between adjacent populations and higher between geographically separated populations. The gene flow between Kunyu Mountain and Lao Mountain was very low. However, neither of the two regions showed evidence of Isolation by Distance., Conclusions: Here, we revealed the population genetic structure and gene flow of A. shikokiana from the Shandong Peninsula, China. This research provides valuable genetic resources for A. shikokiana and contributes to the scientific and effective conservation of the species., (© 2024. The Author(s).)

Sex-ratio meiotic drivers are selfish genes or gene complexes that bias the transmission of sex chromosomes resulting in skewed sex ratios. Existing theoretical models have suggested the maintenance of a four-chromosome equilibrium (with driving and standard X and suppressing and susceptible Y) in a cyclic dynamic, but studies of natural populations have failed to capture this pattern. Although there are several plausible explanations for this lack of cycling, interference from autosomal suppressors has not been studied using a theoretical population genetic framework even though autosomal suppressors and Y-linked suppressors coexist in natural populations of some species. In this study, we use a simulation-based approach to investigate the influence of autosomal suppressors on the cycling of sex chromosomes. Our findings demonstrate that the presence of an autosomal suppressor can hinder the invasion of a Y-linked suppressor under some parameter space, thereby impeding the cyclic dynamics, or even the invasion of Y-linked suppression. Even when a Y-linked suppressor invades, the presence of an autosomal suppressor can prevent cycling. Our study demonstrates the potential role of autosomal suppressors in preventing sex chromosome cycling and provides insights into the conditions and consequences of maintaining both Y-linked and autosomal suppressors., (© The Author(s) 2024. Published by Oxford University Press on behalf of The American Genetic Association. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Following glacial retreat after the last ice age, brown bears (Ursus arctos) recolonised Scandinavia. Previous research based on mitochondrial markers suggests that bears recolonised from both the north and the south, with a contact zone in central Scandinavia. More recently, the Scandinavian brown bear was subjected to a strong population decline with only ca. 130 remaining individuals, due to intense human persecution approximately 100 years ago. Here, we analyse 41 ancient, historical, and modern mitochondrial genomes, to examine the number of female lineages involved in the postglacial recolonisation event and temporal changes in the Scandinavian brown bears' mitochondrial genetic diversity. Our results support the bi-directional recolonisation hypothesis, indicating multiple mitochondrial lineages from clade 1a possibly followed a southern route, while only a single lineage from clade 3a appears to have followed a northern route. Furthermore, we found that the recent bottleneck had a strong impact on the southern subpopulation, resulting in only one remaining haplotype in the contemporary brown bears. For the northern subpopulation, the impact was moderate, and most haplotypes were retained throughout the bottleneck. By exploring the postglacial recolonisation and recent population pressures, our study enhances understanding of how these factors have influenced the genetic diversity of Scandinavian brown bears., (© 2024. The Author(s).)

The Norway lobster ( Nephrops norvegicus ) is one of the most important decapod crustacean seafood species in the Adriatic Sea. Previous research has identified significant differences in growth rates and maturation timing of Nephrops in the Pomo/Jabuka Pits area compared to other subpopulations in Adriatic fishing grounds. Here, we use 1,623 genome-wide single nucleotide polymorphisms (SNPs) to investigate whether the Pomo Pits subpopulation is genetically different from other sites in the Adriatic and neighbouring seas. We found no genetic differentiation among all sampled Adriatic sites, suggesting high gene flow between Pomo Pits Nephrops and those of surrounding areas. We also found genetic homogeneity between the Adriatic sites and single-site samples from the Aegean and Tyrrhenian Seas. However, we detected distinct genetic differentiation between all Mediterranean sites and an Atlantic site in western Scotland, which provides evidence for a phylogenetic break between the Atlantic and the Mediterranean. Our results indicate that Pomo Pits Nephrops are not genetically different from others sampled in the Adriatic and that key biological parameters in Pomo Pits Nephrops could be driven by spatial variation in fishing pressure and/or environmental factors rather than geographic isolation., Competing Interests: The authors declare there are no competing interests., (©2024 Jenkins et al.)

Physics describes reality through the understanding and elucidation of physical laws. From these laws, the universe is predictable. It has indeed been suggested that explanation of observable phenomena comes from our ability to predict these events, through our understanding of physical laws and causal processes. Biological entities operate, of course, through physical and chemical laws. But there exist biological processes that have emergent properties, notably the evolution of adaptation through natural selection, which add an extra dimension to the concept of the understanding of biological phenotypes. The population genetic theory of evolution is mathematically formulated, and contains elements of determinism, typified by the action of natural selection, and elements of randomness, typified by the action of genetic drift and by the randomness of mutation. But is the goal-directed property of natural selection sufficient to conclude that the deterministic elements of the evolutionary process make evolutionary change predictable? And to what extent can we expect 'adaptation' to function as an explanation of biological phenotypes?, Competing Interests: Declaration of interests The author is a member of the Current Biology advisory board. He is Professor Emeritus at the University of Nottingham, a member of the Genetics Society, a member of the Natural Environment Research Council Peer Review College, and a Fellow of the Royal Society of Biology., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Interview with C. Brandon Ogbunu, who studies evolutionary and population genetics, computational biology and epidemiology at Yale University and the Santa Fe Institute., Competing Interests: Declaration of interests The author declares no competing interests., (Copyright © 2024.)

Asian elephants (Elephas maximus) are the largest extant terrestrial megaherbivores native to Asia, with 60% of their wild population found in India. Despite ecological and cultural importance, their population genetic structure and diversity, demographic history, and ensuing implications for management/conservation remain understudied. We analyzed 34 whole genomes (between 11× and 32×) from most known elephant landscapes in India and identified five management/conservation units corresponding to elephants in Northern (Northwestern/Northeastern), Central, and three in Southern India. Our data reveal signatures of divergence and serial colonization and a potential dilution of genetic diversity from north to south of India. The northern populations diverged from others more than 70,000 years ago, have higher genetic diversity, and have low inbreeding (pi = 0.0016 ± 0.0001; F ROH > 1 MB  = 0.09 ± 0.03). Two of three populations in Southern India have low diversity and are inbred, with very low effective population sizes compared with census sizes (pi = 0.0014 ± 0.00009 and 0.0015 ± 0.0001; F ROH > 1 MB  = 0.25 ± 0.09 and 0.17 ± 0.02). Analyses of genetic load reveal the purging of potentially high-effect insertion/deletion (indel) deleterious alleles in the southern populations and a decreasing number of deleterious alleles from north to south in India. However, despite dilution and purging for the damaging mutation load in Southern India, the load that remains is homozygous. High homozygosity of deleterious alleles, coupled with low neutral genetic diversity, make southernmost populations high priority for conservation attention. Most surprisingly, our study suggests that patterns of genetic diversity and genetic load can correspond to genomic signatures of serial founding events, even in large, highly mobile, endangered mammals., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Sea cucumbers are deposit feeding members of marine benthic communities. The over-exploitation of sea cucumber natural stocks, especially in the Mediterranean basin, is having negative impacts on the marine ecosystem. This concerns had led the Italian government to take legal actions to preserve these important marine resources. The aim of this study was to evaluate the level of genetic diversity and population structures within two sympatric Holothuria sea cucumber species, H. polii and H. tubulosa, across ten Mediterranean areas along Italy. A 323 bp portion of the COI mitochondrial gene was sequenced in a total of 441 holothurians (251 H. polii, 177 H. tubulosa and 13 from other species). Genetic diversity analyses and analysis of molecular variance (AMOVA) suggest that H. polii and H. tubulosa species are distinct, but within and among populations are homogeneous, indicating active gene flows across the Mediterranean areas investigated. H. polii showed a lower genetic diversity than H. tubulosa, probably related to differences in life history traits. Phylogenetic analyses showed a clear differentiation between the two species, even if six specimens morphologically assigned to a species clustered within the other species, indicating a possible occurrence of hybridization events. These data will be useful in implementing conservation actions for these holothurian genetic resources., (© 2024. The Author(s).)

Background: Croatia is a geographically small country with a remarkable diversity of cultivated and spontaneous grapevines. Local germplasm has been characterised by microsatellite markers, but a detailed analysis based on single nucleotide polymorphisms (SNPs) is still lacking. Here we characterize the genetic diversity of 149 accessions from three germplasm repositories and four natural sites using 516,101 SNPs to identify complete parent-offspring trios and their relations with spontaneous populations, offering a proof-of-concept for the use of reduced-representation genome sequencing in population genetics and genome-wide association studies (GWAS)., Results: Principal component analysis revealed a clear discontinuity between cultivated (V. vinifera subsp. sativa) and spontaneous grapevines, supporting the notion that the latter represent local populations of the wild progenitor (V. vinifera subsp. sylvestris). ADMIXTURE identified three ancestry components. Two sativa components are alternatively predominant in cultivars grown either in northern Adriatic Croatia and Continental Croatia or in Dalmatia (i.e. central and southern Adriatic Croatia). A sylvestris component, which is predominant in accessions from spontaneous populations, is a minor ancestry component in cultivated accessions. TREEMIX provided evidence of unidirectional migration from the vineyards to natural sites, suggesting that gene flow has gone preferentially from the introduced domesticated germplasm into local wild populations rather than vice versa. Identity-by-descent analysis indicated an extensive kinship network, including 14 complete parent-offspring trios, involving only cultivated accessions, six full-sibling relationships and invalidated a presumed pedigree of one of the most important varieties in Croatia, 'Plavac Mali'. Despite this strong population structure, significant association was found between 143 SNPs and berry skin colour and between 2 SNPs and leaf hairiness, across two previously known genomic regions., Conclusions: The clear genetic separation between Croatian cultivars and sylvestris ruled out the hypothesis that those cultivars originated from local domestication events. On the other hand, the evidence of a crop-to-wild gene flow signals the need for an urgent adoption of conservation strategies that preserve the residual genetic integrity of wild relatives. The use of this reduced-representation genome sequencing protocol in grapevine enables an accurate pedigree reconstruction and can be recommended for GWAS experiments., (© 2024. The Author(s).)

The effect of past environmental changes on the demography and genetic diversity of natural populations remains a contentious issue and has rarely been investigated across multiple, phylogenetically distant species. Here, we perform comparative population genomic analyses and demographic inferences for seven widely distributed and ecologically contrasting European forest tree species based on concerted sampling of 164 populations across their natural ranges. For all seven species, the effective population size, N e , increased or remained stable over many glacial cycles and up to 15 million years in the most extreme cases. Surprisingly, the drastic environmental changes associated with the Pleistocene glacial cycles have had little impact on the level of genetic diversity of dominant forest tree species, despite major shifts in their geographic ranges. Based on their trajectories of N e over time, the seven tree species can be divided into three major groups, highlighting the importance of life history and range size in determining synchronous variation in genetic diversity over time. Altogether, our results indicate that forest trees have been able to retain their evolutionary potential over very long periods of time despite strong environmental changes., (© 2024. The Author(s).)

Background: Austroasiatic (AA)-speaking populations in northern Thailand are of significant interest due to their status as indigenous descendants and their location at the crossroads of AA prehistoric distribution across Southern China, the Indian Subcontinent, and Mainland Southeast Asia. However, the complexity of ethnic identification can result in inaccuracies regarding the origin and migration history of these populations. To address this, we have conducted a genome-wide SNP analysis of 89 individuals from two Lavue and three Lwa-endonym populations. We then combined our outcomes with previously published data to elucidate the genetic diversity and clustering of AA groups in northern Thailand., Results: Our findings align with existing linguistic classifications, revealing different genetic compositions among the three branches of the Mon-Khmer subfamily within the AA family: Monic, Khmuic, and Palaungic. Although the term "Lua" ethnicity is confusingly used to identify ethnic groups belonging to both Khmuic and Palaungic branches, our genomic data indicate that the Khmuic-speaking Lua living on the eastern side of the region are relatively distant from the Palaungic-speaking Lavue and Lwa populations living on the western side. The Lavue populations, primarily inhabiting mountainous areas, exhibit a genetic makeup unique to the AA family, with a close genetic relationship to the Karenic subgroup of the Sino-Tibetan language family. Conversely, the Lwa and Blang populations, residing in lowland river valleys, display genetic signatures resulting from admixture with Tai-Kadai-speaking ethnic groups., Conclusion: Utilizing genome-wide SNP markers, our findings indicate genetic heterogeneity among the Lua, Lavue, and Lwa ethnic groups. The intricate interplay of genetics, cultural heritage, and historical influences has shaped these ethnic communities. Our study underscores the importance of accurate ethnic classifications, emphasizing the use of self-identified endonyms, names created and used by the ethnic groups themselves. This approach respects the AA communities in northern Thailand and acknowledges their significant contributions to advancing our understanding of genetic anthropology., (© 2024. The Author(s).)

Background: Largemouth bass ( Micropterus salmoides ), a valuable freshwater fish species, has experienced significant genetic decline in China due to prolonged domestic breeding and limited introduction of new genetic material. It is necessary to have a comprehensive understanding of the genetic status of largemouth bass populations in China. Method: In this study, we conducted population genetic analyses on nine cultured largemouth bass populations using whole genome resequencing. Results: A total of 3.23 Tb of clean bases were generated, with average Q20 and Q30 values of 98.17% and 94.25%, respectively, and 2,140,534 high-quality SNPs were obtained. Relatively high genetic diversity was observed across all populations. Combined with linkage disequilibrium (LD) patterns, the Wanlu (WL) population possessed the highest genetic diversity, and the Longyou (LY) population possessed the lowest genetic diversity. Additionally, population structure analyses, including pairwise F-statistics, phylogenetic trees, PCA, and admixture analysis, revealed significant genetic differentiation, particularly between the WL, LY, and other 7 populations, while also indicating the occurrence of a common admixture event. Finally, TreeMix inferred migration events from the WL to the Chuanlu (CL) population and from the Taiwan breeding population (TWL) to the Guanglu (GL) population. Conclusions: These findings provide a critical foundation for developing conservation and breeding strategies for largemouth bass in China.

Range disjunctions appear to be common in nature, although they may be caused by various factors. They may simply be an artefact of inadequate sampling. If real, they may be the result of colonization events or habitat change. With natural habitats showing increasing fragmentation because of human activity, understanding the cause of a disjunction can have important conservation implications. We investigate the geographical range of the Plains spadefoot toad, Spea bombifrons , a widely distributed species in the midwestern and southwestern United States, with a putative disjunct population in southern Texas. We combine GIS mapping, species distribution modeling, and population genetic analysis to investigate this putative disjunction. We establish that this southern Texas population is truly geographically disjunct and genetically distinct. Further, using climate projections we show that this unique population is at high risk of local extinction., Competing Interests: The authors declare that they have no competing interests., (© 2024 Chunco et al.)

Background: In areas of low disease endemicity, highly sensitive diagnostic tools to identify, diagnose, and monitor intestinal schistosomiasis transmission are needed to reliably measure the burden and risk of infection. Here, we used highly sensitive molecular diagnostic methods to investigate Schistosoma mansoni prevalence and transmission along the southern shoreline of Lake Malawi, five years post-disease outbreak., Methodology and Principal Findings: Faecal and urine samples were provided by school-aged children situated along the southern shoreline of Lake Malawi. Kato-Katz faecal-egg microscopy and point-of-care circulating cathodic antigen (POC-CCA) rapid diagnostic tests were then performed to diagnose infection with S. mansoni. Urine-egg microscopy was also used to diagnose infection with Schistosoma haematobium. In addition, Schistosoma miracidia were isolated from faecal material using a standard miracidium hatching technique. A two-step real-time PCR approach was then used to diagnose infection with S. mansoni using DNA isolated from faecal samples. Furthermore, isolated miracidia were genotyped to species level through PCR and Sanger sequencing. Phylogenetic analyses were then carried out to identify which previously defined S. mansoni cox1 lineage group S. mansoni miracidia were most closely related to. The measured prevalence of S. mansoni infection varied considerably depending on which diagnostic assay was used. When compared to real-time PCR, faecal-egg microscopy had a sensitivity of 9% and a specificity of 100%. When POC-CCA 'trace' results were considered positive, POC-CCA had a sensitivity of 73% and a specificity of 81% when compared to real-time PCR. However, when considered negative, POC-CCA sensitivity was reduced to 56%, whereas specificity was increased to 90%. In addition, a high degree of S. haematobium DNA was detected in DNA isolated from faecal samples and motile S. haematobium miracidia were recovered from faecal samples. Schistosoma mansoni miracidia were closely related to two independent cox1 lineage groups, suggesting multiple recent introduction and colonisation events originating from surrounding east African countries., Conclusions and Significance: Intestinal schistosomiasis is now highly prevalent along the southern shoreline of Lake Malawi just five years post-disease outbreak. In addition, a high prevalence of urogenital schistosomiasis persists. The revision of ongoing schistosomiasis control programmes in this area is therefore recommended. Our study also highlights the need for reliable diagnostic assays capable of distinguishing between Schistosoma species in multispecies co-endemic areas., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Archer et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: The Csangos are an East-Central European ethnographic group living mainly in east of Transylvania in Romania. Traditionally, ethnography distinguishes three Csango subpopulations, the Moldavian, Gyimes and Burzenland Csangos. In our previous study we found that the Moldavian Csangos have East Asian/Siberian Turkic ancestry components that might be unique in the East-Central European region and might help to better understand the history of Hungarian speaking ethnic groups of the area. Since then, we obtained further Csango samples from Moldavia and from a distinct region of Gyimes, which two Csango subgroups are traditionally different since they live in a degree of isolation not only from other people but also from each other. Here we present the first genomic analysis of Gyimes Csangos, which intended to compare the genetic makeup of these two Csango subgroups using both allele-frequency and haplotype-based methods. The main goal of the study was to investigate the genetic isolation of the Csangos on a genome-wide SNP basis and to assess the isolation of Gyimes Csangos, which in contrast to the Moldavians was not yet studied., Results: Our results show that these two Csango groups show slight differences from each other. We confirmed the genetic isolation of Moldavian Csangos and revealed that Gyimes Csangos have a similar, but detectably weaker isolation. In the case of Gyimes Csangos we detected also a stronger East European or presumably Asian derived ancestry., Conclusion: The Gyimes Csangos show a degree of genetic isolation comparable to that of the Moldavians. The Asian ancestry that differentiates the Moldavian Csango people from the other East-Central European populations may be present in the Gyimes Csangos in an even higher degree, since Gyimes Csango individuals show a more significant share from that ancestry component., (© 2024. The Author(s).)

The Fraser River once supported massive salmon returns. However, over the last century, the largest returns have consistently been less than half of the recorded historical maximum. There is substantial interest from surrounding communities and governments to increase salmon returns for both human use and functional ecosystems. To generate resources for this endeavor, we resequenced genomes of Chinook (Oncorhynchus tshawytscha), coho (Oncorhynchus kisutch), and sockeye salmon (Oncorhynchus nerka) from the Fraser River at moderate coverage (∼16×). A total of 954 resequenced genomes were analyzed, with 681 collected specifically for this study from tissues sampled between 1997 and 2021. An additional 273 were collected from previous studies. At the species level, Chinook salmon appeared to have 1.6-2.1× more SNPs than coho or sockeye salmon, respectively. This difference may be attributable to large historical declines of coho and sockeye salmon. At the population level, 3 Fraser River genetic groups were identified for each species using principal component and admixture analyses. These were consistent with previous research and supports the continued use of these groups in conservation and management efforts. Environmental factors and a migration barrier were identified as major factors influencing the boundaries of these genetic groups. Additionally, 20 potentially adaptive loci were identified among the genetic groups. This information may be valuable in new management and conservation efforts. Furthermore, the resequenced genomes are an important resource for contemporary genomics research on Fraser River salmon and have been made publicly available., Competing Interests: Conflicts of interest The authors declare no conflicts of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

The northern pike Esox lucius is a freshwater fish with low genetic diversity but ecological success throughout the Northern Hemisphere. Here, we generate an annotated chromosome-level genome assembly of 941 Mbp in length with 25 chromosome-length scaffolds. We then genotype 47 northern pike from Alaska through New Jersey at a genome-wide scale and characterize a striking decrease in genetic diversity along the sampling range. Individuals west of the North American Continental Divide have substantially higher diversity than those to the east (e.g. Interior Alaska and St. Lawrence River have on average 181 and 64K heterozygous SNPs per individual, or a heterozygous SNP every 5.2 and 14.6 kbp, respectively). Individuals clustered within each population with strong support, with numerous private alleles observed within each population. Evidence for recent population expansion was observed for a Manitoba hatchery and the St. Lawrence population (Tajima's D = -1.07 and -1.30, respectively). Several chromosomes have large regions with elevated diversity, including LG24, which holds amhby, the ancestral sex determining gene. As expected amhby was largely male-specific in Alaska and the Yukon and absent southeast to these populations, but we document some amhby(-) males in Alaska and amhby(+) males in the Columbia River, providing evidence for a patchwork of presence of this system in the western region. These results support the theory that northern pike recolonized North America from refugia in Alaska and expanded following deglaciation from west to east, with probable founder effects resulting in loss of both neutral and functional diversity (e.g. amhby)., Competing Interests: Conflicts of interest Ben Sutherland is affiliated with Sutherland Bioinformatics. The author has no competing financial interests to declare. The other authors declare no conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

The genetic effective size (Ne) is arguably one of the most important characteristics of a population as it impacts the rate of loss of genetic diversity. Methods that estimate Ne are important in population and conservation genetic studies as they quantify the risk of a population being inbred or lacking genetic diversity. Yet there are very few methods that can estimate the Ne from data from a single population and without extensive information about the genetics of the population, such as a linkage map, or a reference genome of the species of interest. We present ONeSAMP 3.0, an algorithm for estimating Ne from single nucleotide polymorphism data collected from a single population sample using approximate Bayesian computation and local linear regression. We demonstrate the utility of this approach using simulated Wright-Fisher populations, and empirical data from five endangered Channel Island fox (Urocyon littoralis) populations to evaluate the performance of ONeSAMP 3.0 compared to a commonly used Ne estimator. Our results show that ONeSAMP 3.0 is broadly applicable to natural populations and is flexible enough that future versions could easily include summary statistics appropriate for a suite of biological and sampling conditions. ONeSAMP 3.0 is publicly available under the GNU General Public License at https://github.com/AaronHong1024/ONeSAMP_3., Competing Interests: Conflicts of interest The author(s) declare no conflicts of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

When adaptive phenotypic variation or quantitative trait loci map within an inverted segment of a chromosome, researchers often despair because the suppression of crossing over will prevent the discovery of selective target genes that established the rearrangement. If an inversion polymorphism is old enough, then the accumulation of gene conversion tracts offers the promise that quantitative trait loci or selected loci within inversions can be mapped. The inversion polymorphism of Drosophila pseudoobscura is a model system to show that gene conversion analysis is a useful tool for mapping selected loci within inversions. D. pseudoobscura has over 30 different chromosomal arrangements on the third chromosome (Muller C) in natural populations and their frequencies vary with changes in environmental habitats. Statistical tests of five D. pseudoobscura gene arrangements identified outlier genes within inverted regions that had potentially heritable variation, either fixed amino acid differences or differential expression patterns. We use genome sequences of the inverted third chromosome (Muller C) to infer 98,443 gene conversion tracts for a total coverage of 142 Mb or 7.2× coverage of the 19.7 Mb chromosome. We estimated gene conversion tract coverage in the 2,668 genes on Muller C and tested whether gene conversion coverage was similar among arrangements for outlier vs non-outlier loci. Outlier genes had lower gene conversion tract coverage among arrangements than the non-outlier genes suggesting that selection removes exchanged DNA in the outlier genes. These data support the hypothesis that the third chromosome in D. pseudoobscura captured locally adapted combinations of alleles prior to inversion mutation events., Competing Interests: Conflicts of interest The author(s) declare no conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

During the second third of last century, the Orinoco Crocodile (Crocodylus intermedius) underwent a hunting process driven by the demand from the North American, European, and Japanese leather industry, resulting in a sharp decline of its populations. Currently, only two known remaining populations of this Critically Endangered species persist in the Colombian Orinoquía: in the Guayabero-Duda-Lozada and the Cravo Norte-Ele-Lipa River Systems. The latter has been the only population subject of study, including recent surveys and local conservation initiatives such as egg and hatchling ranching. Despite suggestions for population recovery based on the observed increase in clutches in the area, information regarding its genetic status has been pending assessment. This research aims to provide a genetic characterization of this remaining population and to evaluate the diversity recovered during a period of the egg ranching initiative. For this purpose, we utilized variable molecular markers, specifically 17 microsatellite loci, nuclear DNA. Despite revealing intermediate levels of genetic diversity, we identified an effective population size of 11.5-17, well below the minimum values proposed for short-term subsistence. While no evidence of inbreeding was found, it is acknowledged as a potential risk based on the population's history. Additionally, we detected a historical bottleneck possibly influenced by arid periods affecting the region since the Pleistocene. While the evaluated population presents a unique opportunity for C. intermedius conservation, it also exposes a high risk of entering the extinction vortex. The primary action to be taken is to support the egg and hatchling ranching program, which successfully recovered most of the genetic diversity present in the population., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Castillo-Rodríguez et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The human reference genome (GRCh38), primarily sourced from individuals of European descent, falls short in capturing the vast genetic diversity across global populations. Efforts to diversify the reference genome face challenges in accessibility and representation, exacerbating the scarcity of African genomic data crucial for studying diseases prevalent in these populations. Sherman et al. proposed constructing reference genomes tailored to distinct human sub-populations. Their African Pan-Genome initiative highlighted substantial genetic variation missing from the GRCh38 human reference genome, emphasizing the necessity for population-specific genomes. In response, local initiatives like the Senegalese Genome project (SEN-GENOME) have emerged to document the genomes of historically overlooked populations. SEN-GENOME embodies community-driven decentralized research. With meticulous recruitment criteria and ethical practices, it aims to sequence 1,000 genomes from 31 ethnolinguistic groups, in the fourteen administrative regions of Senegal, fostering local genomic research tailored to the region. The key to SEN-GENOME's success is its commitment to local governance of data, capacity building, and integration with broader pan-genome projects in Africa. Despite the complexities of data harmonization and sharing, our collaborative efforts are aligned with common goals, ensuring steady progress toward a comprehensive human pan-genome. We invite and welcome collaboration with other research entities to achieve this shared vision. In summary, local initiatives such as SEN-GENOME are pivotal in bridging genomic disparities, offering pathways to equitable and inclusive genomic research. Collaborative endeavors guided by a collective vision for human health will propel us toward a more encompassing understanding of the human genome and better health through genomic medicine., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)

It is unclear how patterns of regional genetic differentiation in the UK and Ireland might impact the protein-coding fraction of the genome. We exploit UK Biobank (UKB) and Viking Genes whole exome sequencing data to study regional genetic differentiation across the UK and Ireland in protein coding genes, encompassing 44,696 unrelated individuals from 20 regions of origin. We demonstrate substantial exonic differentiation among Shetlanders, Orcadians, individuals with full or partial Ashkenazi Jewish ancestry and in several mainland regions (particularly north and south Wales, southeast Scotland and Ireland). With stringent filtering criteria, we find 67 regionally enriched (≥5-fold) variants likely to have adverse biomedical consequences in homozygous individuals. Here, we show that regional genetic variation across the UK and Ireland should be considered in the design of genetic studies and may inform effective genetic screening and counselling., (© 2024. The Author(s).)

Background: The butterfly assemblage of Ladakh Trans-Himalaya demands a thorough analysis of their population genetic structure owing to their typical biogeographic affinity and their adaptability to extreme cold-desert climates. No such effort has been taken till date, and in this backdrop, we created a COI barcode reference library of 60 specimens representing 23 species., Methods and Results: Barcodes were generated from freshly collected leg samples using the Sanger sequencing method, followed by phylogenetic clade analyses and divergence calculation. Our data represents 22% of Ladakh's Rhopaloceran fauna with the novel barcode submission for six species, including one Schedule II species, Paralasa mani. Contrary to the 3% threshold rule, the interspecific divergence between two species pairs of typical mountain genus Hyponephele and Karanasa was found to be 2.3% and 2.2%, respectively. The addition of conspecific global barcodes revealed that most species showed little increase in divergence value, while a two-fold increase was noted in a few species. Bayesian clade clustering outcomes largely aligned with current morphological classifications, forming monophyletic clades of conspecific barcodes, with only minor exceptions observed for the taxonomically complicated genus Polyommatus and misidentified records of Aulocera in the database. We also observed variations within the same phylogenetic clades forming nested lineages, which may be attributed to the taxonomic intricacies present at the subspecies level globally, mostly among Eurasian species., Conclusions: Overall, our effort not only substantiated the effectiveness of DNA Barcoding for the identification and conservation of this climatically vulnerable assemblage but also highlighted the significance of deciphering the unique genetic composition among this geographically isolated population of Ladakh butterflies., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Background: The shea tree is a well-known carbon sink in Africa that requires a sustainable conservation of its gene pool. However, the genetic structure of its population is not well studied, especially in Côte d'Ivoire. In this study, 333 superior shea tree genotypes conserved in situ in Côte d'Ivoire were collected and genotyped with the aim of investigating its genetic diversity and population structure to facilitate suitable conservation and support future breeding efforts to adapt to climate change effects., Results: A total of 7,559 filtered high-quality single nucleotide polymorphisms (SNPs) were identified using the genotyping by sequencing technology. The gene diversity (HE) ranged between 0.1 to 0.5 with an average of 0.26, while the polymorphism information content (PIC) value ranged between 0.1 to 0.5 with an average of 0.24, indicating a moderate genetic diversity among the studied genotypes. The population structure model classified the 333 genotypes into three genetic groups (GP1, GP2, and GP3). GP1 contained shea trees that mainly originated from the Poro, Tchologo, and Hambol districts, while GP2 and GP3 contained shea trees collected from the Bagoué district. Analysis of molecular variance (AMOVA) identified 55% variance within populations and 45% variance within individuals, indicating a very low genetic differentiation (or very high gene exchange) between these three groups (F ST  = 0.004, gene flow Nm = 59.02). Morphologically, GP1 displayed spreading tree growth habit, oval nut shape, higher mean nut weight (10.62 g), wide leaf (limb width = 4.63 cm), and small trunk size (trunk circumference = 133.4 cm). Meanwhile, GP2 and GP3 showed similar morphological characteristics: erect and spreading tree growth habit, ovoid nut shape, lower mean nut weight (GP2: 8.89 g; GP3: 8.36 g), thin leaf (limb width = 4.45 cm), and large trunk size ( GP2: 160.5 cm, GP3: 149.1 cm). A core set of 100 superior shea trees, representing 30% of the original population size and including individuals from all four study districts, was proposed using the "maximum length sub-tree function" in DARwin v. 6.0.21., Conclusion: These findings provide new knowledge of the genetic diversity and population structure of Ivorian shea tree genetic resources for the design of effective collection and conservation strategies for the efficient use of inbreeding., (© 2024. The Author(s).)

Biodiversity loss has reached critical levels partly due to anthropogenic habitat loss and degradation. These landscape changes are damaging as they can fragment species distributions into small, isolated populations, resulting in limited gene flow, population declines and reduced adaptive potential. Genetic rescue, the translocation of individuals to increase genetic diversity and ultimately fitness, has produced promising results for fragmented populations but remains underutilized due to a lack of long-term data and monitoring. To promote a better understanding of genetic rescue and its potential risks and benefits over the short-term, we reviewed and analysed published genetic rescue attempts to identify whether genetic diversity increases following translocation, and if this change is associated with increased fitness. Our review identified 19 studies that provided genetic and fitness data from before and after the translocation; the majority of these were on mammals, and included experimental, natural and conservation-motivated translocations. Using a Bayesian meta-analytical approach, we found that on average, genetic diversity and fitness increased in populations post translocations, although there were some exceptions to this trend. Overall, genetic diversity was a positive predictor of population fitness, and in some cases this relationship extended three generations post-rescue. These data suggest a single translocation can have lasting fitness benefits, and support translocation as another tool to facilitate conservation success. Given the limited number of studies with long-term data, we echo the need for genetic monitoring of populations post-translocation to understand whether genetic rescue can also limit the loss of adaptive potential in the long-term., (© 2024 The Author(s). Molecular Ecology published by John Wiley & Sons Ltd.)

The extremely rich palaeontological record of the horse family, also known as equids, has provided many examples of macroevolutionary change over the last ~55 Mya. This family is also one of the most documented at the palaeogenomic level, with hundreds of ancient genomes sequenced. While these data have advanced understanding of the domestication history of horses and donkeys, the palaeogenomic record of other equids remains limited. In this study, we have generated genome-wide data for 25 ancient equid specimens spanning over 44 Ky and spread across Anatolia, the Caucasus, Central Asia and Mongolia. Our dataset includes the genomes from two extinct species, the European wild ass, Equus hydruntinus, and the sussemione Equus ovodovi. We document, for the first time, the presence of sussemiones in Mongolia and their survival around ~3.9 Kya, a finding that should be considered when discussing the timing of the first arrival of the domestic horse in the region. We also identify strong spatial differentiation within the historical ecological range of Asian wild asses, Equus hemionus, and incomplete reproductive isolation in several groups yet considered as different species. Finally, we find common selection signatures at ANTXR2 gene in European, Asian and African wild asses. This locus, which encodes a receptor for bacterial toxins, shows no selection signal in E. ovodovi, but a 5.4-kb deletion within intron 7. Whether such genetic modifications played any role in the sussemione extinction remains unknown., (© 2024 The Author(s). Molecular Ecology published by John Wiley & Sons Ltd.)

Under allopatric speciation, populations of a species become isolated by a geographic barrier and develop reproductive isolation through genetic differentiation. When populations meet in secondary contact, the strength of evolved reproductive barriers determines the extent of hybridization and whether the populations will continue to diverge or merge together. The yellowhammer (Emberiza citrinella) and pine bunting (E. leucocephalos) are avian sister species that diverged in allopatry on either side of Eurasia during the Pleistocene glaciations. Though they differ greatly in plumage and form distinct genetic clusters in allopatry, these taxa show negligible mitochondrial DNA differentiation and hybridize extensively where they overlap in central Siberia, lending uncertainty to the state of reproductive isolation in the system. To assess the strength of reproductive barriers between taxa, we examined genomic differentiation across the system. We found that extensive admixture has occurred in sympatry, indicating that reproductive barriers between taxa are weak. We also identified a putative Z chromosome inversion region that underlies plumage variation in the system, with the 'pine bunting' haplotype showing dominance over the 'yellowhammer' haplotype. Our results suggest that yellowhammers and pine buntings are currently at a crossroads and that evolutionary forces may push this system towards either continued differentiation or population merging. However, even if these taxa merge, recombination suppression between putative chromosome Z inversion haplotypes may maintain divergent plumage phenotypes within the system. In this way, our findings highlight the important role hybridization plays in increasing the genetic and phenotypic variation as well as the evolvability of a system., (© 2024 The Author(s). Molecular Ecology published by John Wiley & Sons Ltd.)

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., (© 2024 The Author(s). Molecular Ecology published by John Wiley & Sons Ltd.)

Anthropogenic habitat modification and climate change are fundamental drivers of biodiversity declines, reducing the evolutionary potential of species, particularly at their distributional limits. Supportive breeding or reintroductions of individuals are often made to replenish declining populations, sometimes informed by genetic analysis. However, most approaches utilised (i.e. single locus markers) do not have the resolution to account for local adaptation to environmental conditions, a crucial aspect to consider when selecting donor and recipient populations. Here, we incorporate genetic (microsatellite) and genome-wide SNP (ddRAD-seq) markers, accounting for both neutral and putative adaptive genetic diversity, to inform the conservation management of the threatened common midwife toad, Alytes obstetricans at the northern and eastern edges of its range in Europe. We find geographically structured populations (n = 4), weak genetic differentiation and fairly consistent levels of genetic diversity across localities (observed heterozygosity and allelic richness). Categorising individuals based on putatively adaptive regions of the genome showed that the majority of localities are not strongly locally adapted. However, several localities present high numbers of private alleles in tandem with local adaptation to warmer conditions and rough topography. Combining genetic diversity and local adaptations with estimates of migration rates, we develop a decision-making framework for selecting donor and recipient populations which maximises the geographic dispersal of neutral and putatively adaptive genetic diversity. Our framework is generally applicable to any species, but especially to amphibians, so armed with this information, conservationists may avoid the reintroduction of unsuitable/maladapted individuals to new sites and increase the evolutionary potential of populations within species., (© 2024. The Author(s).)

Long-term genetic studies of wild populations are very scarce, but are essential for connecting ecological and population genetics models, and for understanding the dynamics of biodiversity. We present a study of a wild wheat population sampled over a 36-year period at high spatial resolution. We genotyped 832 individuals from regular sampling along transects during the course of the experiment. Genotypes were clustered into ecological microhabitats over scales of tens of metres, and this clustering was remarkably stable over the 36 generations of the study. Simulations show that it is difficult to determine whether this spatial and temporal stability reflects extremely limited dispersal or fine-scale local adaptation to ecological parameters. Using a common-garden experiment, we showed that the genotypes found in distinct microhabitats differ phenotypically. Our results provide a rare insight into the population genetics of a natural population over a long monitoring period., (© 2024 The Author(s). Molecular Ecology published by John Wiley & Sons Ltd.)

This study describes a compact method for determining joint probabilities of identity-by-state (IBS) within and between loci in populations evolving under genetic drift, crossing-over, mutation, and regular inbreeding (partial self-fertilization). Analogues of classical indices of associations among loci arise as functions of these joint identities. This coalescence-based analysis indicates that multi-locus associations reflect simultaneous coalescence events across loci. Measures of association depend on genetic diversity rather than allelic frequencies, as do linkage disequilibrium and its relatives. Scaled indices designed to show monotonic dependence on rates of crossing-over, inbreeding, and mutation may prove useful for interpreting patterns of genome-scale variation., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Neotropical fishes exhibit remarkable karyotype diversity, whose evolution is poorly understood. Here, we studied genetic differences in 60 individuals, from 11 localities of one species, the wolf fish Hoplias malabaricus, from populations that include six different "karyomorphs". These differ in Y-X chromosome differentiation, and, in several cases, by fusions with autosomes that have resulted in multiple sex chromosomes. Other differences are also observed in diploid chromosome numbers and morphologies. In an attempt to start understanding how this diversity was generated, we analyzed within- and between-population differences in a genome-wide sequence data set. We detect clear genotype differences between karyomorphs. Even in sympatry, samples with different karyomorphs differ more in sequence than samples from allopatric populations of the same karyomorph, suggesting that they represent populations that are to some degree reproductively isolated. However, sequence divergence between populations with different karyomorphs is remarkably low, suggesting that chromosome rearrangements may have evolved during a brief evolutionary time. We suggest that the karyotypic differences probably evolved in allopatry, in small populations that would have allowed rapid fixation of rearrangements, and that they became sympatric after their differentiation. Further studies are needed to test whether the karyotype differences contribute to reproductive isolation detected between some H. malabaricus karyomorphs., (© 2024. The Author(s), under exclusive licence to The Genetics Society.)

Speciation can be mediated by a variety of reproductive barriers, and the interaction among different barriers has often been shown to enhance overall reproductive isolation, a process referred to as "coupling." Here, we analyze a population genetics model to study the establishment of linkage disequilibrium (LD) among loci involved in multiple premating barriers, an aspect that has received little theoretical attention to date. We consider a simple genetic framework underlying two distinct premating barriers, each encoded by a preference locus and its associated mating trait locus. We show that their interaction can lead to a decrease in overall reproductive isolation relative to a situation with a single barrier, a process we call "negative coupling." More specifically, in our model, negative coupling results either from sexual selection that reduces divergence at all loci, or from reduced LD that occurs because the presence of many females with "mismatched" preferences causes the mating success of recombinant males to become high. Interestingly, the latter effect may even cause LD among preference loci to become negative when recombination rates among loci are low. We conclude that coincident reproductive barriers may not necessarily reinforce each other, and that the underlying loci may not necessarily develop a positive association., (Copyright © 2024 Cold Spring Harbor Laboratory Press; all rights reserved.)

How frequently hybridisation and gene flow occur in the contact zones of diverging taxa is important for understanding the speciation process. Stigmaeopsis sabelisi and Stigmaeopsis miscanthi high-aggression form (hereafter, S. miscanthi HG) are haplodiploid, social spider mites that infest the Chinese silver grass, Miscanthus sinensis. These two species are closely related and parapatrically distributed in Japan. In mountainous areas, S. sabelisi and S. miscanthi HG are often found in the highlands and lowlands, respectively, suggesting that they are in contact at intermediate altitudes. It is estimated that they diverged from their common ancestors distributed in subtropical regions (south of Japan) during the last glacial period, expanded their distribution into the Japanese Archipelago, and came to have such a parapatric distribution (secondary contact). As their reproductive isolation is strong but incomplete, hybridisation and genetic introgression are expected at their distributional boundaries. In this study, we investigated their spatial distribution patterns along the elevation on Mt. Amagi using male morphological differences, and investigated their hybridisation status using single-nucleotide polymorphisms by MIG-seq. We found their contact zone at altitudes of 150-430 m, suggesting that their contact zone is prevalent in the parapatric area, which is in line with a previous study. Interspecific mating was predicted based on the sex ratio in the contact zone. No obvious hybrids were found, but genetic introgression was detected although it was extremely low., (© 2024. The Author(s), under exclusive licence to The Genetics Society.)

Understanding the evolutionary processes that influence fitness is critical to predicting species' responses to selection. Interactions among evolutionary processes including gene flow, drift and the strength of selection can lead to either local adaptation or maladaptation, especially in heterogenous landscapes. Populations experiencing novel environments or resources are ideal for understanding the mechanisms underlying adaptation or maladaptation, specifically in locally co-evolved interactions. We used the interaction between a native herbivore that oviposits on a patchily distributed introduced plant that in turn causes significant mortality to the larvae to test for signatures of local adaptation in areas where the two co-occurred. We used whole-genome sequencing to explore population structure, patterns of gene flow and signatures of local adaptation. We found signatures of local adaptation in response to the introduced plant in the absence of strong population structure with no genetic differentiation and low genetic variation. Additionally, we found localized allele frequency differences within a single population between habitats with and without the lethal plant, highlighting the effects of strong selection. Finally, we identified that selection was acting on larval ability to feed on the plant rather than on females' ability to avoid oviposition, thus uncovering the specific ontogenetic target of selection. Our work highlights the potential for adaptation to occur in a fine-grained landscape in the presence of gene flow and low genetic variation., (© 2024 John Wiley & Sons Ltd.)

Understanding how life history shapes genetic diversity is a fundamental issue in evolutionary biology, with important consequences for conservation. However, we still have an incomplete picture of the impact of life history on genome-wide patterns of diversity, especially in long-lived semelparous plants. Puya raimondii is a high-altitude semelparous species from the Andes that flowers at 40-100 years of age. We sequenced the whole genome and estimated the nucleotide diversity of 200 individuals sampled from nine populations. Coalescent-based approaches were then used to infer past population dynamics. Finally, these results were compared with results obtained for the iteroparous species, Puya macrura. The nine populations of P. raimondii were highly divergent, highly inbred, and carried an exceptionally high genetic load. They are genetically depauperate, although, locally in the genome, balancing selection contributed to the maintenance of genetic polymorphism. While both P. raimondii and P. macrura went through a severe bottleneck during the Pleistocene, P. raimondii did not recover from it and continuously declined, while P. macrura managed to bounce back. Our results demonstrate the importance of life history, in particular generation time and reproductive strategy, in affecting population dynamics and genomic variation, and illustrate the genetic fragility of long-lived semelparous plants., (© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.)

Insertion or deletion (InDel), a genetic marker with short insertion/deletion fragment length polymorphism, is widely used in the field of forensic biological research. The Guizhou Shui (Shui) ethnic group and Guizhou Dong (Dong) ethnic group are located in the southwestern region of China, with rich historical and cultural background. In this study, a self-developed panel included 56 ancestry informative marker (AIM)-InDel loci on the autosomes, three InDel loci on the Y chromosome, and one sex-determined Amelogenin locus. Firstly, we used the 56 autosomal loci to assess the forensic individual identification and paternity testing abilities in both the Shui and Dong groups. The cumulative probability of match and probability of exclusion for the Shui and Dong groups were 2.228×10 -15 and 0.991518139; 7.604×10 -16 and 0.992253273, respectively. In addition, we also conducted in-depth analyses for the genetic backgrounds and structures of the Shui and Dong groups based on 56 AIM-InDel loci. This research has found that the Shui and Dong groups have close genetic relationships with the East Asian populations. Meanwhile, we also found that the Shui group has a close genetic distance with Chinese Dai in Xishuangbanna (CDX). These insights provide vital information for the genetic structures of the Shui and Dong groups, as well as basic population data and molecular biological evidence support for individual identification and biogeographic ancestry inference in forensic genetic field., Competing Interests: Declaration of Competing Interest The authors declare no conflict of interest., (Copyright © 2024 Elsevier B.V. All rights reserved.)

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 (N e ) 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 N e , low levels of diversity and recent inbreeding on North Atlantic right whale recovery will be important next steps., (© 2023 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

Winter flounder Pseudopleuronectes americanus (Walbaum 1792) are a coastal flatfish species of economic and cultural importance that have dwindled to <15, % of their historic abundance in the southern New England/Mid-Atlantic region of the United States, with evidence indicating near-extirpation of certain local populations. This species exhibits intricate behaviors in spawning and migration that contribute to population complexity and resilience. These behaviors encompass full or partial philopatry to natal estuaries, the generation of multiple pulses of larval delivery, and partial migration. The patterns of genetic diversity within and among estuaries and cohorts presented here carry important implications in understanding the susceptibility to demographic shocks, even if the full extent of genetic diversity within and among winter flounder stocks on the US East Coast remains unresolved. Our findings reveal connectivity between estuaries in Long Island, New York, suggesting the potential for genetic rescue of depleted subpopulations. Family reconstruction and relatedness analysis indicate that split cohorts and migration contingents are not the result of genetically distinct lineages. We found no evidence for genetic structure separating these groups, and in some instances, we were able to detect closely related individuals that belonged to different migratory contingents or cohorts. Characterizing the spatial and behavioral organization of this species at the population level is crucial for comprehending its potential for recovery, not only in terms of biomass but also in reinstating the complex population structure that supports resilience. The search for generality in winter flounder spawning and migration behavior remains elusive, but perhaps the lack of generalities within this species is what has allowed it to persist in the face of decades of environmental and anthropogenic stressors., (© 2024 Fisheries Society of the British Isles.)

Identifying and analysing isolated populations is critical for conservation. Isolation can make populations vulnerable to local extinction due to increased genetic drift and inbreeding, both of which should leave imprints of decreased genome-wide heterozygosity. While decreases in heterozygosity among populations are frequently investigated, fewer studies have analysed how heterozygosity varies among individuals, including whether heterozygosity varies geographically along lines of discrete population structure or with continuous patterns analogous to isolation by distance. Here we explore geographical patterns of differentiation and individual heterozygosity in the threatened eastern barred bandicoot (Perameles gunnii) in Tasmania, Australia, using genomic data from 85 samples collected between 2008 and 2011. Our analyses identified two isolated demes undergoing significant genetic drift, and several areas of fine-scale differentiation across Tasmania. We observed discrete genetic structures across geographical barriers and continuous patterns of isolation by distance, with little evidence of recent or historical migration. Using a recently developed analytical pipeline for estimating autosomal heterozygosity, we found individual heterozygosities varied within demes by up to a factor of two, and demes with low-heterozygosity individuals also still contained those with high heterozygosity. Spatial interpolation of heterozygosity scores clarified these patterns and identified the isolated Tasman Peninsula as a location where low-heterozygosity individuals were more common than elsewhere. Our results provide novel insights into the relationship between isolation-driven genetic structure and local heterozygosity patterns. These may help improve translocation efforts, by identifying populations in need of assistance, and by providing an individualised metric for identifying source animals for translocation., (© 2023 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

Island biotas provide unparalleled opportunities to examine evolutionary processes. Founder effects and bottlenecks, e.g., typically decrease genetic diversity in island populations, while selection for reduced dispersal can increase population structure. Given that support for these generalities mostly comes from single-species analyses, assemblage-level comparisons are needed to clarify how (i) colonization affects the gene pools of interacting insular organisms, and (ii) patterns of genetic differentiation vary within assemblages of organisms. Here, we use genome-wide sequence data from ultraconserved elements (UCEs) to compare the genetic diversity and population structure of mainland and island populations of nine ant species in coastal southern California. As expected, island populations (from Santa Cruz Island) had lower expected heterozygosity and Watterson's theta compared to mainland populations (from the Lompoc Valley). Island populations, however, exhibited smaller genetic distances among samples, indicating less population subdivision. Within the focal assemblage, pairwise Fst values revealed pronounced interspecific variation in mainland-island differentiation, which increases with gyne body size. Our results reveal population differences across an assemblage of interacting species and illuminate general patterns of insularization in ants. Compared to single-species studies, our analysis of nine conspecific population pairs from the same island-mainland system offers a powerful approach to studying fundamental evolutionary processes., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Society for the Study of Evolution (SSE). All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Hunting mortality can affect population abundance, demography, patterns of dispersal and philopatry, breeding, and genetic diversity. We investigated the effects of hunting on the reproduction and genetic diversity in a puma population in western Colorado, USA. We genotyped over 11,000 single nucleotide polymorphisms (SNPs), using double-digest, restriction site-associated DNA sequencing (ddRADseq) in 291 tissue samples collected as part of a study on the effects of hunting on puma population abundance and demography in Colorado from 2004 to 2014. The study was designed with a reference period (years 1-5), during which hunting was suspended, followed by a treatment period (years 6-10), in which hunting was reinstated. Our objectives were to examine the effects of hunting on: (1) paternity and male reproductive success; (2) the relatedness between pumas within the population, and (3) genetic diversity. We found that hunting reduced the average age of male breeders. The number of unique fathers siring litters increased each year without hunting and decreased each year during the hunting period. Mated pairs were generally unrelated during both time periods, and females were more closely related than males. Hunting was also associated with increased relatedness among males and decreased relatedness among females in the population. Finally, genetic diversity increased during the period without hunting and decreased each year when hunting was present. This study demonstrates the utility of merging demographic data with large-scale genomic datasets in order to better understand the consequences of management actions. Specifically, we believe that this study highlights the need for long-term experimental research in which hunting mortality is manipulated, including at least one non-harvested control population, as part of a broader adaptive, zone management scheme., (© 2023 John Wiley & Sons Ltd.)

Genomic-scale datasets, sophisticated analytical techniques, and conceptual advances have disproportionately failed to resolve species boundaries in some groups relative to others. To understand the processes that underlie taxonomic intractability, we dissect the speciation history of an Australian lizard clade that arguably represents a "worst-case" scenario for species delimitation within vertebrates: the Ctenotus inornatus species group, a clade beset with decoupled genetic and phenotypic breaks, uncertain geographic ranges, and parallelism in purportedly diagnostic morphological characters. We sampled hundreds of localities to generate a genomic perspective on population divergence, structure, and admixture. Our results revealed rampant paraphyly of nominate taxa in the group, with lineages that are either morphologically cryptic or polytypic. Isolation-by-distance patterns reflect spatially continuous differentiation among certain pairs of putative species, yet genetic and geographic distances are decoupled in other pairs. Comparisons of mitochondrial and nuclear gene trees, tests of nuclear introgression, and historical demographic modelling identified gene flow between divergent candidate species. Levels of admixture are decoupled from phylogenetic relatedness; gene flow is often higher between sympatric species than between parapatric populations of the same species. Such idiosyncratic patterns of introgression contribute to species boundaries that are fuzzy while also varying in fuzziness. Our results suggest that "taxonomic disaster zones" like the C. inornatus species group result from spatial variation in the porosity of species boundaries and the resulting patterns of genetic and phenotypic variation. This study raises questions about the origin and persistence of hybridizing species and highlights the unique insights provided by taxa that have long eluded straightforward taxonomic categorization., (© 2023 John Wiley & Sons Ltd.)

Syngameons represent networks of otherwise distinct species connected by limited gene exchange. Although most studies have focused on how species maintain their cohesiveness despite gene flow, there are additional relevant questions regarding the evolutionary dynamics of syngameons and their drivers, as well as the success of their members and the network as a whole. Using a ddRADseq approach, we analysed the genetic structure, genomic clines and demographic history of a coastal hybrid zone involving two species of the Armeria (Plumbaginaceae) syngameon in southern Spain. We inferred that a peripheral population of the sand dune-adapted A. pungens diverged from the rest of the conspecific populations and subsequently hybridized with a locally more abundant pinewood congener, A. macrophylla. Both species display extensive plastid DNA haplotype sharing. Genomic cline analysis identified bidirectional introgression, but more outlier loci with excess A. pungens than A. macrophylla ancestry, suggesting the possibility of selection for A. pungens alleles. This is consistent with the finding that the A. pungens phenotype is selected for in open habitats, and with the strong correlation found between ancestry and phenotype. Taken together, our analyses suggest an intriguing scenario in which bidirectional introgression may, on the one hand, help to avoid reduced levels of genetic diversity due to the small size and isolated location of the A. pungens range-edge population, thereby minimizing demographic risks of stochastic extinction. On the other hand, the data also suggest that introgression into A. macrophylla may allow individuals to grow in open, highly irradiated, deep sandy, salt-exposed habitats., (© 2023 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

We introduce a multi-allele Wright-Fisher model with mutation and selection such that allele frequencies at a single locus are traced by the path of a hybrid jump-diffusion process. The state space of the process is given by the vertices and edges of a topological graph, i.e. edges are unit intervals. Vertices represent monomorphic population states and positions on the edges mark the biallelic proportions of ancestral and derived alleles during polymorphic segments. In this setting, mutations can only occur at monomorphic loci. We derive the stationary distribution in mutation-selection-drift equilibrium and obtain the expected allele frequency spectrum under large population size scaling. For the extended model with multiple independent loci we derive rigorous upper bounds for a wide class of associated measures of genetic variation. Within this framework we present mathematically precise arguments to conclude that the presence of directional selection reduces the magnitude of genetic variation, as constrained by the bounds for neutral evolution., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Introduced and invasive species make excellent natural experiments for investigating rapid evolution. Here, we describe the effects of genetic drift and rapid genetic adaptation in pink salmon (Oncorhynchus gorbuscha) that were accidentally introduced to the Great Lakes via a single introduction event 31 generations ago. Using whole-genome resequencing for 134 fish spanning five sample groups across the native and introduced range, we estimate that the source population's effective population size was 146,886 at the time of introduction, whereas the founding population's effective population size was just 72-a 2040-fold decrease. As expected with a severe founder event, we show reductions in genome-wide measures of genetic diversity, specifically a 37.7% reduction in the number of SNPs and an 8.2% reduction in observed heterozygosity. Despite this decline in genetic diversity, we provide evidence for putative selection at 47 loci across multiple chromosomes in the introduced populations, including missense variants in genes associated with circadian rhythm, immunological response and maturation, which match expected or known phenotypic changes in the Great Lakes. For one of these genes, we use a species-specific agent-based model to rule out genetic drift and conclude our results support a strong response to selection occurring in a period gene (per2) that plays a predominant role in determining an organism's daily clock, matching large day length differences experienced by introduced salmon during important phenological periods. Together, these results inform how populations might evolve rapidly to new environments, even with a small pool of standing genetic variation., (© 2023 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

The contributions of divergent selection and spatial isolation to population divergence are among the main focuses of evolutionary biology. Here we employed integrated methods to explore genomic divergence, demographic history and calling-song differentiation in the cicada Subpsaltria yangi, and compared the genotype and calling-song phenotype of different populations occurring in distinct habitats. Our results indicate that this species comprises four main lineages with unique sets of haplotypes and calling-song structure, which are distinctly associated with geographic isolation and habitats. The populations occurring on the Loess Plateau underwent substantial expansion at ∼0.130-0.115 Ma during the Last Interglacial. Geographic distance and host shift between pairs of populations predict genomic divergence, with geographic distance and acoustical signal together explaining > 60% of the divergence among populations. Differences in calling songs could reflect adaptation of populations to novel environments with different host plants, habitats and predators, which may have resulted from neutral divergence at the molecular level followed by natural selection. Geomorphic barriers and climate oscillations associated with Pleistocene glaciation may have been primary factors in shaping the population genetic structure of this species. Ultimately this may couple with a host shift in leading toward allopatric speciation in S. yangi, i.e., isolation by distance. Our findings improve understanding of divergence in allopatry of herbivorous insects, and may inform future studies on the molecular mechanisms underlying the association between genetic/phenotypic changes and adaptation of insects to novel niches and host plants., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

We introduce a modified spatial Λ-Fleming-Viot process to model the ancestry of individuals in a population occupying a continuous spatial habitat divided into two areas by a sharp discontinuity of the dispersal rate and effective population density. We derive an analytical formula for the expected number of shared haplotype segments between two individuals depending on their sampling locations. This formula involves the transition density of a skew diffusion which appears as a scaling limit of the ancestral lineages of individuals in this model. We then show that this formula can be used to infer the dispersal parameters and the effective population density of both regions, using a composite likelihood approach, and we demonstrate the efficiency of this method on a range of simulated data sets., Competing Interests: Declaration of competing interest The authors declare that they have no competing interest relating to the content of this manuscript., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Recent work indicates that feralisation is not a simple reversal of domestication, and therefore raises questions about the predictability of evolution across replicated feral populations. In the present study we compare genes and traits of two independently established feral populations of chickens (Gallus gallus) that inhabit archipelagos within the Pacific and Atlantic regions to test for evolutionary parallelism and/or divergence. We find that feral populations from each region are genetically closer to one another than other domestic breeds, despite their geographical isolation and divergent colonisation histories. Next, we used genome scans to identify genomic regions selected during feralisation (selective sweeps) in two independently feral populations from Bermuda and Hawaii. Three selective sweep regions (each identified by multiple detection methods) were shared between feral populations, and this overlap is inconsistent with a null model in which selection targets are randomly distributed throughout the genome. In the case of the Bermudian population, many of the genes present within the selective sweeps were either not annotated or of unknown function. Of the nine genes that were identifiable, five were related to behaviour, with the remaining genes involved in bone metabolism, eye development and the immune system. Our findings suggest that a subset of feralisation loci (i.e. genomic targets of recent selection in feral populations) are shared across independently established populations, raising the possibility that feralisation involves some degree of parallelism or convergence and the potential for a shared feralisation 'syndrome'., (© 2024 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)