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San Fernando Valley spineflower (Chorizanthe parryi var. fernandina [S. Watson] Jeps.) (Polygonaceae) is an herbaceous annual plant, endemic to California, and until rediscovered in 1999 had been thought to be extinct for almost seven decades. Historically documented at 10 locations, it currently persists at 2, separated by approximately 27 km. State listed as endangered, a description of its genetic diversity and structure is of conservation interest. After determining a lack of variation in ploidy, we examined genetic variation from samples within both populations: a common garden study for potentially adaptive genetic variation in selected growth and phenological traits and analysis of single nucleotide polymorphisms identified through restriction-site associated DNA sequencing. Both measures indicated that this highly restricted taxon nevertheless harbors substantial levels of genetic diversity and has significant between- and within-population genetic structure. Combining approaches from population genomics and common garden studies provided more insight into the patterns and basis of genetic diversity than is typical for studies of non-model species. Although local adaptation was not specifically studied (i.e., via reciprocal transplant studies), the differences determined from these two independent lines of evidence indicate that mixing gene pools between populations is not recommended at this time. Further, with significant differences revealed among subpopulations, we caution against mixing genotypes across subpopulations for the most part, and without much more evidence that this would not pose a risk of outbreeding depression. The importance of supporting pollinator health and diversity is highlighted. With genetic diversity—particularly with an annual species—being dynamic, fluctuating with the usual processes and with contributions from the soil seedbank, we recommend periodic resampling to monitor genetic diversity and structure. Climate change is anticipated to contribute to this variability.

The frigid and droughty climate of Xinjiang in China has given rise to unique indigenous sheep breeds with robust adaptability and resistance. To investigate the genetic mechanism of adaptability of Xinjiang sheep to the local extreme environment, we conducted population genetic structure analyses for three native Xinjiang sheep breeds: Altay sheep (ALT), Bashbay Sheep (BSBC), and Duolang sheep (DLC), as well as two foreign sheep breeds: Suffolk and Dorset, using the Ovine Infinium HD SNP BeadChip(680 K). Our findings revealed distinct genetic and evolutionary histories between Xinjiang and foreign sheep breeds. Principal Component Analysis (PCA) and phylogenetic tree effectively differentiate these five sheep breeds based on their geographical origins, and the domestication level of Xinjiang sheep is comparatively lower than that of foreign sheep breeds. Furthermore, by utilizing three selective signature methods, namely Fixation Index (Fst), Cross Population Extended Haplotype Homozygosity Test (XP-EHH), and Nucleotide Diversity (π), we have successfully identified 22 potential candidate genes. Among these genes, there are TBXT, PDGFD, and VEGFA, which are closely related to tail type and lipid metabolism; VIL1, SLC11A1, and ZBTB46, which are associated with immune function; and candidate genes such as BNC1, HDAC1, and BMP5, which impact sheep reproductive traits. This study establishes a foundation for conserving and utilizing local sheep germplasm resources in Xinjiang and provides molecular insights into the genetic mechanisms governing sheep adaptation to extreme cold and arid environments. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Both natural and anthropogenic forces can play a substantial role in the demographic history and current structure of a wildlife population. Species with strict habitat requirements are especially susceptible to these impacts. Mountain goats (Oreamnos americanus) in Alaska are of particular interest in this regard due to their influence on alpine ecosystems, importance to human cultures, and enigmatic history in some areas. Here, we used genetic tools to examine the population structure and demographic history of mountain goats in Alaska. We genotyped 816 mountain goats at 18 microsatellites, identified the number of genetically distinct subpopulations, and assessed their genetic diversity. We used Bayesian methods to investigate demographic history relative to the known geologic and human history of Alaska, and we simulated human-mediated translocation events onto islands to address the hypothesis that Baranof Island harbored an extant population prior to an early 20th-century introduction. We showed that Alaska has 4 genetically distinct subpopulations of mountain goats. The main demographic split between Southcentral and Southeast Alaska occurred following the retreat of ice after the Last Glacial Maximum. Simulations of translocation events largely aligned with expected genetic diversity patterns of current subpopulations except for Baranof Island which showed greater diversity than the simulation, consistent with the hypothesis of an endemic population prior to the translocation. This study highlights the value of considering both natural and anthropogenic forces when assessing the biogeographic history of a species and provides new insights about the complex demographic history and biogeography of mountain goats in Alaska. [ABSTRACT FROM AUTHOR]

Aim: Human‐induced environmental changes result in habitat loss and fragmentation, impacting wildlife population genetic structure and evolution. Urbanised and geographically peripheral areas often represent unfavourable environments, reducing connectivity among populations and causing higher population genetic differentiation and lower intra‐population genetic diversity. We examined how geographic peripherality and anthropogenic pressures affect genetic diversity and genetic differentiation in the protected southern damselfly (Coenagrion mercuriale, Odonata), which has low dispersal capabilities and specific habitat requirements and whose populations are declining. Location: We studied two areas: one in semi‐natural habitats at the periphery of the species geographic range (northern France) and the other more central to the species' range, in an urbanised area surrounding the city of Strasbourg (Alsace, eastern France). Methods: We genotyped 2743 individuals from 128 populations using 11 microsatellite loci. We analysed the spatial distribution of neutral genetic diversity (allelic richness, heterozygosity, levels of inbreeding and genetic relatedness), the extent of genetic differentiation and population affiliations (sPCAs) within the two areas. We also examined fine‐scale patterns of gene flow in the urbanised area of Alsace by investigating patterns of isolation by distance and estimating effective migration surfaces (EEMS) method. Results: Northern peripheral populations showed lower levels of genetic diversity and higher levels of genetic differentiation than central Alsacian populations. Although located in anthropised habitats, geographically central Alsacian populations showed high levels of gene flow, with dispersal events mainly occurring overland and not restricted to watercourses. However, the highly urbanised city of Strasbourg negatively impacted nearby populations by reducing levels of genetic diversity and increasing population genetic differentiation. Main Conclusions: These results showed the need for management action by restoring breeding sites and creating migratory corridors for peripheral southern damselfly populations. However, our results also highlighted the resilience of southern damselfly in central range populations facing strong urbanisation pressures. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The northern leopard frog (Lithobates pipiens) has undergone dramatic declines in population size and range over recent decades in western Canada and the United States. In British Columbia, only a single population remains at the Creston Valley Wildlife Management Area. Yet, the continuing viability of this population is uncertain. In this paper, the current genetic structure of northern leopard frog populations in western Canada was assessed using microsatellite markers. Historical samples from the extinct population of Fort Steele in British Columbia were compared with the Creston Valley population to understand changes in population genetic parameters over time. Genotypic data from four populations (Creston Valley, Drain K, Prince Spring, and Cypress Hill) sampled in 2004 and 2019 were compared. To evaluate changes in the genetic diversity of the Creston Valley population over time, allelic richness and expected heterozygosity of the population were compared at three time points using genotypes from 2000, 2004, and 2019. Northern leopard frog populations in western Canada showed high genetic differentiation, with genetic diversity decreasing from east to west. Although there weren't notable changes in genetic parameters between 2004 and 2019, there was evidence of a decline in diversity between 2000 and 2019. The extinct population of Fort Steele had private alleles, while the current Creston Valley population did not, suggesting a genetic bottleneck in the Creston Valley population. Therefore, genetic rescue, specifically for the endangered Creston Valley population, can be considered as an action to support recovery. Additionally, continued genetic monitoring will help in the effective management of the species by providing information on the success of conservation actions. [ABSTRACT FROM AUTHOR]

Human activities often induce maladaptive effects in urban wildlife, such as increased inbreeding and decreased gene flow, consequently leading to a loss of biodiversity. Although maladaptive effects are commonly reported in urban wildlife, some wildlife species are not affected. Understanding the conditions and factors that affect the genetic structure of wildlife is crucial for its conservation in urban environments. Eurasian red squirrels Sciurus vulgaris in Obihiro City, Hokkaido, Japan, have settled in large residential lots with a high risk of vehicle collisions for approximately 30 years, raising the possibility that the urban population would be genetically isolated from nearby rural populations and may experience a rapid decrease in genetic diversity. In this study, we analysed the population structure, genetic distance, and nucleotide diversity of squirrels in the Obihiro area using genome-wide single nucleotide polymorphisms (SNPs). Principal component analysis and ADMIXTURE showed that urban and rural squirrel populations formed distinct clusters with intermediate urban and rural boundary populations. Genetic distances between the urban populations were greater than that of other pairs. Nucleotide diversities were lower in urban populations than in other populations, suggesting limited gene flow between urban and other populations, possibly due to urbanisation. The change in the genetic characteristics of urban squirrel populations during this short period demonstrates the strong impact of urbanisation. Our findings suggest that a genome-wide approach to the genetic structure of wildlife contributes to its conservation in urban environments. [ABSTRACT FROM AUTHOR]

Ophiothrix (Ophiothrix) exigua is a common brittle star in the northwestern Pacific. As a dominant species, O. exigua inhabiting the intertidal rocky ecosystem are affected by multiple environmental stressors, but molecular insights into their genetic population structure remain poorly studied. In this study, we investigated the population genetics and evolutionary history of six O. exigua populations from the northern China Sea using mitochondrial (COI, NAD4) and nuclear (ITS2, 18S) gene markers. High haplotype diversity, low nucleotide diversity, and low rates of gene differentiation among the populations of O. exigua were detected. Pairwise genetic differentiation (ΦST) statistics between different localities were negative or low and insignificant, suggesting strong gene flow of this species over the study areas. The phylogenetic analyses showed that the populations exhibited high homogeneity between localities in our study area. Demographic analyses indicated that the populations experienced sustained expansion around 0.2 million years ago. This expansion was likely related to transgressions events in the Yellow Sea during the Pleistocene period. Additional samples of O. exigua from disparate geographical locations, especially the Japan Sea and the Korean Peninsula, will be needed to unravel the population genetic patterns and evolutionary history of this species. [ABSTRACT FROM AUTHOR]

Grassland caterpillars (Lepidoptera: Lymantriinae: Gynaephora) are the most damaging pests to alpine meadows in the Qinghai–Tibetan Plateau (QTP). Here, we conducted extensive sampling from 39 geographic populations covering almost the entire distribution of the eight QTP Gynaephora (Hübner) species to investigate phylogeographic patterns and speciation based on two mitochondrial genes (COI and ND5). A total of 40 haplotypes were detected in the 39 populations, with >70% of all haplotypes not shared between populations. The monophyletic QTP Gynaephora migrated from non‐QTP regions during the Pliocene, corresponding to the uplift of the QTP, suggesting a mode of transport into the QTP. Among the eight QTP Gynaephora species described by morphological characteristics, two species (G. alpherakii and G. menyuanensis) were recovered as monophyletic groups (Clades B and C), while the remaining six formed two monophyletic clades: Clade A (G. qinghaiensis, G. jiuzhiensis, and G. qumalaiensis) and Clade D (G. aureata, G. ruoergensis, and G. minora). These results suggested that the number of the QTP Gynaephora species may be overestimated and further studies based on both morphological and nuclear gene data are needed. Genetic differentiation and speciation of the QTP Gynaephora were likely driven by the QTP uplifts and associated climate fluctuations during the Pleistocene, indicated by divergence time estimation, suggesting that isolation and subsequent divergence was the dominant mode of speciation. The Sanjiangyuan region (i.e., Clade A, characterized by high genetic diversity) may have been a glacial refugium of the QTP Gynaephora, as supported by analyses of gene flow and biogeography. High levels of genetic diversity were found in QTP Gynaephora, without population expansion, which may explain the high‐altitude adaptation and outbreaks of grassland caterpillars in alpine meadows of the QTP. This study provides the largest phylogeographic analysis of QTP Gynaephora and improves our understanding of the diversity and speciation of QTP insects. [ABSTRACT FROM AUTHOR]

Geoffroy's cat (Leopardus geoffroyi) is a small‐sized felid native to South America. Given the species' distribution covering a wide variety of habitats, and the presence of high levels of anthropization in part of its range, it is possible that genetically differentiated groups exist and that they occupy different climatic niches. We assessed patterns of contemporary genetic diversity and structure in the species across most of its range, characterizing each inferred genetic group based on ecological niche models. We genotyped 11 microsatellites for 142 samples covering most of Geoffroy's cat distribution, and investigated patterns of genetic structure and diversity, applying spatial and nonspatial Bayesian clustering methods and a spatial principal component analysis. We created ecological niche models for each genetic cluster, evaluating whether these clusters occupy different climatic spaces and display differences in the suitability of different values of the climatic variables analyzed. We identified two genetic clusters, one in the north‐northeast and the other in the south‐southwest of the species' distribution. These clusters showed moderate FST values between them and differences in dispersal/genetic diversity. We found isolation‐by‐distance patterns globally and within each cluster. We observed lower expected heterozygosity compared with other studies and a north–south gradient in allelic richness. The southern cluster showed lower genetic variability and a more restricted climatic niche suggesting that this group is more vulnerable to the effects of the current context of climate change. Individuals from the southern genetic cluster are under different pressures, likely a product of the particularly dry habitat they occupy. Climatic variables associated with habitat suitability suggest the southern cluster has affinity for the arid and semiarid conditions present in its distribution. Conservation measures should consider the genetic structure observed and differences in climatic spaces to maintain the evolutionary potential of the species. [ABSTRACT FROM AUTHOR]

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

Abstract The frigid and droughty climate of Xinjiang in China has given rise to unique indigenous sheep breeds with robust adaptability and resistance. To investigate the genetic mechanism of adaptability of Xinjiang sheep to the local extreme environment, we conducted population genetic structure analyses for three native Xinjiang sheep breeds: Altay sheep (ALT), Bashbay Sheep (BSBC), and Duolang sheep (DLC), as well as two foreign sheep breeds: Suffolk and Dorset, using the Ovine Infinium HD SNP BeadChip(680 K). Our findings revealed distinct genetic and evolutionary histories between Xinjiang and foreign sheep breeds. Principal Component Analysis (PCA) and phylogenetic tree effectively differentiate these five sheep breeds based on their geographical origins, and the domestication level of Xinjiang sheep is comparatively lower than that of foreign sheep breeds. Furthermore, by utilizing three selective signature methods, namely Fixation Index (Fst), Cross Population Extended Haplotype Homozygosity Test (XP-EHH), and Nucleotide Diversity (π), we have successfully identified 22 potential candidate genes. Among these genes, there are TBXT, PDGFD, and VEGFA, which are closely related to tail type and lipid metabolism; VIL1, SLC11A1, and ZBTB46, which are associated with immune function; and candidate genes such as BNC1, HDAC1, and BMP5, which impact sheep reproductive traits. This study establishes a foundation for conserving and utilizing local sheep germplasm resources in Xinjiang and provides molecular insights into the genetic mechanisms governing sheep adaptation to extreme cold and arid environments.

Abstract Geographic distribution, as well as evolutionary and biogeographic processes and patterns of marine invertebrate benthic species are strongly shaped by dispersal ability during the life cycle. Remote oceanic islands lie at the brink of complex biotic and abiotic interactions which have significantly influenced the biodiversity patterns we see today. The interaction between geological environmental change and taxon-specific dispersal modes can influence species evolutionary patterns, eventually delimiting species-specific biogeographic regions. In this study, we compare the population genetic patterns of the marine bivalve Cardita calyculata in the northeast Atlantic, discussing the role of Macaronesian islands during past climatic cycles. The genetic structure and diversity patterns were outlined based on SSR-GBAS loci of 165 individuals and on the mitochondrial COI marker of 22 individuals from the Canary Islands, Madeira, Azores and the Mediterranean. The highly structured genetic pattern found among regions and within archipelagos suggests the central role of oceanic islands in promoting the divergence of the species in both the NE Atlantic and the Mediterranean. The high degree of divergence in the COI dataset (> 7%) suggests the existence of potential cryptic speciation that needs to be further explored with a more comprehensive sampling. Such patterns are only congruent with a scenario where C. calyculata populations were maintained during glacial/interglacial cycles, supporting the role of the studied archipelagos as drivers of diversity for marine biota. We stress the importance of developing studies for species with various life history and dispersal modes. In such a way, a more profound understanding of the biogeographic and evolutionary significance of oceanic islands can catalyse directed conservation efforts, especially in the context of the ongoing climate crisis.

Abstract 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.

Introduction: Preventing crop yield loss caused by pests is critical for global agricultural production. Agricultural pest control has largely relied on chemical pesticides. The interaction between insecticide resistance and the adaptation of herbivorous pests to host plants may represent an emerging threat to future food security. Objectives: This study aims to unveil genetic evidence for the reduction in the profitability of resistant cultivars derived from insecticide resistance in target pest insects. Methods: An experimental evolution system encompassing resistant rice and its major monophagous pest, the brown planthopper Nilaparvata lugens, was constructed. Whole genome resequencing and selective sweep analysis were utilized to identify the candidate gene loci related to the adaptation. RNA interference and induced expression assay were conducted to validate the function of the candidate loci. Results: We found that the imidacloprid-resistant population of N. lugens rapidly adapted to resistant rice IR36. Gene loci related to imidacloprid resistance may contribute to this phenomenon. Multiple alleles in the nicotinic acetylcholine receptor (nAChR)-7-like and P450 CYP4C61 were significantly correlated with changes in virulence to IR36 rice and insecticide resistance of N. lugens. One avirulent/susceptible genotype and two virulent/resistant genotypes could be inferred from the corresponding alleles. Importantly, we found that the virulent/resistant genotypes already exist in the wild in China, exhibiting increasing frequencies along with insecticide usage. We validated the relevance of these genotypes and the virulence to three more resistant rice cultivars. Knockdown of the above two genes in N. lugens significantly decreased both the resistance to imidacloprid and the virulence towards resistant rice. Conclusion: Our findings provide direct genetic evidence to the eco-evolutionary consequence of insecticide resistance, and suggest an urgent need for the implementation of predictably sustainable pest management.

Invasive species are a growing global economic and ecological problem. However, it is not well understood how environmental factors mediate invasive range expansion. In this study, we investigated the recent and rapid range expansion of common tansy across environmental gradients in Minnesota, USA. We densely sampled individuals across the expanding range and performed reduced representation sequencing to generate a dataset of 3071 polymorphic loci for 176 individuals. We used non‐spatial and spatially explicit analyses to determine the relative influences of geographic distance and environmental variation on patterns of genomic variation. We found no evidence for isolation by distance but strong evidence for isolation by environment, indicating that environmental factors may have modulated patterns of range expansion. Land use classification and soils were particularly important variables related to population structure although they operated on different spatial scales; land use classification was related to broad‐scale patterns and soils were related to fine‐scale patterns. All analyses indicated a distinctive genetic cluster in the most recently invaded portion of the range. Individuals from the far northwestern range margin were separated from the remainder of the range by reduced migration, which was associated with environmental resistance. This portion of the range was invaded primarily in the last 15 years. Ecological niche models also indicated that this cluster was associated with the expansion of the niche. While invasion is often assumed to be primarily influenced by dispersal limitation, our results suggest that ongoing invasion and range shifts with climate change may be strongly affected by environmental heterogeneity. [ABSTRACT FROM AUTHOR]

The present study examined the genetic diversity of two populations of Dotilla myctiroides (Milne-Edwards) from Peninsular Malaysia. Based on 640-bp COX1 (cytochrome c oxidase subunit 1) gene sequences, the D. myctiroides specimens from Peninsular Malaysia, Singapore and India formed a lineage which was distinctly separated from Dotilla wichmanni and D. fenestrata. Sixteen COX1 haplotypes were found in Peninsular Malaysia samples, with 11 haplotypes in the Morib sample, eight in the Tanjung Tuan sample, and three common haplotypes in these samples. The Singapore specimen had the commonest haplotype of Peninsular Malaysia, while the Indian specimen had a distinct haplotype. The proportions of the two most common COX1 haplotypes were not significantly different between the Morib and Tanjung Tuan samples. The difference in the mean haplotype diversity between these samples was statistically significant. However, the nucleotide diversity of the two samples was not significantly different and there was no genetic subdivision/differentiation between the two populations. The high number of closely related haplotypes indicates the possibility of a recent population expansion. The data provide valuable information for future studies on the genetic diversity, population structure and phylogeography of Dotilla species. [ABSTRACT FROM AUTHOR]

Introduction: To enhance the beef cattle industry, Heilongjiang Province has developed a new Crossbred beef cattle variety through crossbreeding with exotic commercial breeds. This new variety exhibits relatively excellent meat quality, and efficient reproductive performance, catering to market demands. Method: This study employed whole genome resequencing technology to analyze the genetic pedigree and diversity of 19 Heilongjiang Crossbred beef cattle, alongside 59 published genomes from East Asian, Eurasian, and European taurine cattle as controls. In addition, genes related to production traits were also searched by identifying Runs of Homozygosity (ROH) islands and important fragments from ancestors. Results: A total of 14,427,729 biallelic SNPs were discovered, with the majority located in intergenic and intron regions and a small percentage in exon regions, impacting protein function. Population genetic analyses including Principal Component Analysis (PCA), Neighbor-Joining (NJ) tree, and ADMIXTURE identified Angus, Holstein, and Mishima as the main ancestors of Crossbred beef cattle. In genetic diversity analysis, nucleotide diversity, linkage disequilibrium, and inbreeding coefficient analysis reveal that the genetic diversity of Crossbred beef cattle is at a moderate level, and a higher inbreeding coefficient indicates the need for careful breeding management. In addition, some genes related to economic traits are identified through the identification of Runs of Homozygosity (ROH) islands and important fragments from ancestors. Conclusion: This comprehensive genomic characterization supports the targeted improvement of economically important traits in Crossbred beef cattle, facilitating advanced breeding strategies. [ABSTRACT FROM AUTHOR]

Despite concerns about overfishing and the potential impact of release programs on wild populations, our study of 3116 individuals from 13 wild populations and 2787 individuals from two cultured populations in Zhejiang and Fujian provinces spanning 2008 to 2023 reveals a relatively stable genetic diversity in Larimichthys crocea. Surprisingly, the genetic diversity of wild large yellow croaker populations has remained consistent over the years, suggesting minimal influence from population declines due to overfishing. With the exception of populations in Sansha Bay and Luoyuan Bay, no significant genetic differences were observed among wild populations, indicating a single panmictic genetic population across the East and South China seas. Notably, significant genetic differentiation exists between cultured and wild populations, suggesting a possible limited genetic adaptation of cultured‐released individuals to the wild environment. The genetic differences observed between the Sansha Bay, with its adjacent Luoyuan Bay populations, and other wild populations underscore the dual effects of habitat environment and farming activities on the genetic structure of large yellow croaker. Our findings suggest that, despite declines in population numbers due to overfishing and expands extensive cultured releases, the genetic diversity of L. crocea populations remains largely unaffected. Moreover, the L. crocea population along the Chinese coast appears to form a single panmictic population with considerable genetic diversity. [ABSTRACT FROM AUTHOR]

Simple Summary: Whole-genome resequencing technology is widely applicated in the genetic breeding research of beef cattle. Pinan cattle are a specialized beef cattle population bred in Henan Province for more than 30 years. It has advantages in traits such as a fast growth rate, good reproductive performance, and high slaughter rate. But the genetic variation at the genome level of Pinan cattle has not been thoroughly explored. The whole-genome resequencing of a Pinan cattle population was conducted, combined with genome resequencing data of other cattle breeds, to detect the variations at the whole-genome level. Furthermore, the population genetic diversity and structure were analyzed, and the genes and loci under positive selection affecting important traits of Pinan cattle were identified using a selective sweep strategy. This study contributes to accelerating further breeding of the economic traits such as growth and reproductive performance in Pinan cattle. The breeding of high-quality beef cattle breeds is crucial for the development of animal husbandry, and whole-genome resequencing is widely applicated in the field of molecular breeding. Advantages in growth and reproductive traits exist in Pinan cattle compared with other cattle breeds, but there is limited research on its genomic mechanism. Using whole-genome resequencing, the genetic structure and genomic selection signatures in Pinan cattle were investigated in this study. Phylogenetic, cluster, and admixture analysis results indicated that Pinan cattle have a closer genetic relationship with Kholmogory cattle and China north cattle breeds. Through a selective sweep strategy, 207 and 54 candidate genes related to growth and reproduction and immunity, respectively, were identified in the Pinan cattle population. Given the crucial role of the glutamate–cysteine ligase catalytic (GCLC) gene in muscle antioxidative defense, the high frequency of allele T of the GCLC c.429 C>T locus in the Pinan cattle population might partially contribute to the advantages of Pinan cattle in growth performance. This study laid the foundation for the genetic improvement in Chinese local beef cattle and provide background for the studies on the growth and development of Pinan cattle. [ABSTRACT FROM AUTHOR]

Tamarix taklamakanensis is an endangered shrub endemic to northwestern China. Single-nucleotide polymorphism (SNP) loci obtained by Genotype-by-sequencing (GBS) method were used to estimate the genetic diversity and population structure of the species for developing conservation strategies. A moderate level of genetic diversity was (mean HE = 0.16) detected for the species, and sampled sites were grouped into two genetically distinct clusters by Bayesian assignment, principal coordinates analyses, and maximum-likelihood (ML) tree. The moderate level of genetic diversity is likely due to its reproductive characteristics and long-lived life-history traits, and the strong genetic differentiation between the two clusters suggests a positive response to habitat fragmentation. Based on the results, we provide useful conservation strategies for this species. [ABSTRACT FROM AUTHOR]

The Yangtze River floodplain is an area with an extremely rich diversity of fish species. Poyang Lake, as an important part of this river–floodplain system, is a crucial habitat for the survival of fish. However, prolonged human activities, such as environmental pollution and hydroelectric development, have degraded the habitat in the Poyang Lake Basin, posing threats to fish populations. Understanding genetic diversity is crucial for maintaining fish populations and understanding their dynamics. The genetic diversity of Hemiculterella wui, an economically endemic species in China of subfamily Cultrinae (Cypriniformes: Cyprinidae), has been understudied. This study investigated the genetic diversity and structure of H. wui populations from the Ganjiang, Xinjiang, Fuhe, and Raohe rivers in the Poyang Lake Basin using mitochondrial Cytb gene analysis. Results showed high haplotype diversity but low nucleotide diversity in H. wui's Cytb sequences. Analysis of molecular variance (AMOVA) showed no significant geographic genetic structure among populations. Haplotype network analysis revealed no clear geographical clustering. Neutrality tests and haplotype nucleotide mismatch distribution indicated that all populations had experienced expansion events. These findings suggest that H. wui in Poyang Lake does not show a distinct geographic structure. However, it is still necessary to monitor the genetic characteristics of H. wui to maintain the genetic diversity of fishes in Poyang Basin, considering the threat of habitat loss and fragmentation to the population. [ABSTRACT FROM AUTHOR]

Amynthas aspergillum (Perrier, 1872), a natural resource used in traditional Chinese medicine (Guang‐dilong) with high economic value, is widely distributed in forests and farmland habitats in the hilly areas of southern China. To investigate the extent of genetic differentiation and diversity in A. aspergillum, a population genetic structure study was performed on 157 samples from 75 locations in southern China using the mitochondrial genes COI, COII, 12S rRNA, 16S rRNA, and NDI. The results indicated that A. aspergillum had a high level of genetic diversity, and variation within populations was the main source of the total variation. Six deeply divergent mitochondrial clades (I–VI) were detected using both phylogenetic tree and haplotype network analyses. This finding was supported by the high Kimura two‐parameter genetic distance and the pairwise fixation index value obtained based on the COI gene. No significant phylogeographic structures were observed. The widespread geographic distribution of clades II, IV, and VI suggested a recent demographic expansion based on multiple analysis results. These results include a high level of Hd and low π, star‐shaped haplotype network structures with a high number of less frequent haplotypes, significantly negative neutrality test values, and a unimodal mismatch distribution pattern. The divergence time estimates and reconstruction of the ancestral area revealed that A. aspergillum originated in Guangxi Province and underwent initial intraspecific diversification in the early Pliocene to generate clade I. Then, it gradually dispersed eastward and rapidly differentiated into clades II–V during the Pleistocene. The Yunnan‐Guizhou Plateau and Nanling and Wuyi Mountains might act as geographical barriers for the spread of A. aspergillum to the west and north. [ABSTRACT FROM AUTHOR]

Anthropogenic activities such as mining pose a putative threat to deep-sea ecosystems and baseline studies of key indicator species are required to assess future loss of biodiversity. We examined population genetic structure, connectivity, cryptic diversity and phylogeography of the deep-sea scavenging amphipod, Abyssorchomene distinctus, using DNA sequence data (mitochondrial COI and nuclear 28S genes) from 373 specimens collected from six abyssal basins. We observed a striking absence of cryptic diversity, suggesting a single, widely distributed species in the Pacific and Indian Ocean. A single event of population expansion across distances up to 24,000 km is further supported by a main ancestral haplotype in the star-like shaped COI haplotype network, a skewed nucleotide mismatch distribution and deviations from evolutionary neutrality tests. In the Pacific, A. distinctus showed weak genetic population structure and low differentiation between the basins of the Clarion-Clipperton Zone and the DISCOL Experimental Area, suggesting a possible higher chance of recovery from deep-sea mining impacts. However, since our data indicate a single recent historic population expansion event, A. distinctus populations will likely be affected to unknown extents, as the exact drivers shaping distribution and dispersion of A. distinctus are still unclear. [ABSTRACT FROM AUTHOR]

Breeding resilient cultivars with increased tolerance to environmental stress and enhanced resistance to pests and diseases demands pre-breeding efforts that include understanding genetic diversity. This study aimed to evaluate the genetic diversity and population structure of 265 pea accessions. The diversity arrays technology (DArT) genotyping method was employed to identify singlenucleotide polymorphisms (SNPs) and silico markers. After stringent filtering, 6966 SNP and 8,454 silico markers were selected for diversity analysis. Genetic diversity was estimated by grouping accessions based on plant material type, geographic origin, growth habit, and seed color. Generally, diversity estimations obtained using SNPs were similar to those estimated using silico markers. The polymorphism information content (PIC) of the SNP markers ranged from 0.0 to 0.5, with a quarter of them displaying PIC values exceeding 0.4, making them highly informative. Analysis based on plant material type revealed narrow observed heterozygosity (Ho = 0.02-0.03) and expected heterozygosity (He = 0.26-0.31), with landrace accessions exhibiting the highest diversity. Geographic origin-based diversity analysis revealed Ho = 0.02-0.03 and He = 0.22 to 0.30, with European accessions showing the greatest diversity. Moreover, private alleles unique to landrace (4) and European (22) accessions were also identified, which merit further investigation for their potential association with desirable traits. The analysis of molecular variance revealed a highly significant genetic differentiation among accession groups classified by seed color, growth habit, plant material types, and geographic origin (p < 0.01). Principal coordinate analysis and neighbor-joining cluster analysis revealed weak clustering of accessions at different grouping levels. This study underscores the significance of genetic diversity in pea collections, offering valuable insights for targeted breeding and conservation efforts. By leveraging genomic data and exploring untapped genetic resources, pea breeding programs can be fortified to ensure sustainable plant protein production and address future challenges in agriculture. [ABSTRACT FROM AUTHOR]

The Sichuan-Yunnan region is the main production area of yaks in southwestern China, with rich genetic resources of Yaks. Nevertheless, there have been limited study on the genetic characteristics of the entire yak populations in Tibet and southwestern China. In this study, we performed whole-genome resequencing to identify genetic variation information in a total of 198 individuals fromsix yak breeds (populations) in Sichuan (Muli yak, Jinchuan yak, Changtai yak, Maiwa yak), Yunnan (Zhongdian yak), and Tibet (Tibetan yak). The aim was to investigate the wholegenome genetic diversity, population genetic structure, and genome selection signatures. We observed that all six populations exhibit abundant genetic diversity. Except for Tibetan yaks, which showed low nucleotide diversity (0.00104), the remaining yak populations generally displayed high nucleotide diversity (0.00129-0.00153). Population genetic structure analysis revealed that, among the six yak populations, Muli yak exhibited greater differentiation from other yak populations and formed a distinct cluster independently. TheMaiwa yak population displayed a complex genetic structure and exhibited gene exchangewith Jinchuan and Changtai yaks. Positive selection signals were detected in candidate genes associated with growth (GNB4, HMGA2, TRPS1, and LTBP1), reproduction (PI4KB, DYNC1I1, and GRIP1), immunity (CD200 and IL1RAP), lactation (SNX13 and CPM), hypoxia adaptation (NDUFB6, PRKN, and MRPS9), hair (KRT24, KRT25, and KRT26), meat quality (SUCLG2), digestion and absorption (CLDN1), and pigment deposition (OCA2) using the integrated Pi and FST methods. This study provides significant insights into understanding the whole-genome genetic characteristics of yak populations in Tibet and southwestern China. [ABSTRACT FROM AUTHOR]

The Baise horse, an indigenous horse breed mainly distributed in the Baise region of Guangxi province in southwest China, has a long history as draft animal. However, there is a lack of research regarding the origin and ancestral composition of the Baise horse. In this study, whole‐genome resequencing data from 236 horses of seven Chinese indigenous horse breeds, five foreign horse breeds, and four Przewalski's horses were used to investigate the relationships between the Baise horse and other horse breeds. The results showed that foreign horse breeds had no significant impact on the formation of the Baise horse. The two southwestern horse populations, the Debao pony and the Jinjiang horse, exhibit the closest genetic affinity with the Baise horse. This is consistent with their adjacent geographical distribution. Analysis of the migration route revealed a gene flow from the Chakouyi horse into the Baise horse. In summary, our results confirm that the formation of the Baise horse did not involve participation from foreign breeds. Geographical distance emerges as a crucial factor in determining the genetic relationships with the Baise horse. Gene flows of indigenous horse breeds along ancient routes of trade activities had played a role in the formation of the Baise horse. [ABSTRACT FROM AUTHOR]

Qaidam cattle are a typical Chinese native breed inhabiting northwest China. They bear the characteristics of high cold and roughage tolerance, low‐oxygen adaptability and good meat quality. To analyze the genetic diversity of Qaidam cattle, 60 samples were sequenced using whole‐genome resequencing technology, along with 192 published sets of whole‐genome sequencing data of Indian indicine cattle, Chinese indicine cattle, North Chinese cattle breeds, East Asian taurine cattle, Eurasian taurine cattle and European taurine cattle as controls. It was found that Qaidam cattle have rich genetic diversity in Bos taurus, but the degree of inbreeding is also high, which needs further protection. The phylogenetic analysis, principal component analysis and ancestral component analysis showed that Qaidam cattle mainly originated from East Asian taurine cattle. Qaidam cattle had a closer genetic relationship with the North Chinese cattle breeds and the least differentiation from Mongolian cattle. Annotating the selection signals obtained by composite likelihood ratio, nucleotide diversity analysis, integrated haplotype score, genetic differentiation index, genetic diversity ratio and cross‐population extended haplotype homozygosity methods, several genes associated with immunity, reproduction, meat, milk, growth and adaptation showed strong selection signals. In general, this study provides genetic evidence for understanding the germplasm characteristics of Qaidam cattle. At the same time, it lays a foundation for the scientific and reasonable protection and utilization of genetic resources of Chinese local cattle breeds, which has great theoretical and practical significance. [ABSTRACT FROM AUTHOR]

The Bagrid catfish, Bagrus orientalis, historically sustained communities in the Rufiji River basin (RRB), Tanzania, but has rapidly declined due to high consumer demand and unsustainable fishing. Consequently, a Ramsar site was designated within the RRB, although its potential to revitalize overexploited populations beyond its boundaries is uncertain because of limited information on genetic connectivity. To address this uncertainty, 158 partial cytochrome oxidase subunit I sequences of B. orientalis were analyzed to quantify genetic connectivity in the RRB. We observed significant genetic differentiation, indicating limited connectivity among populations. Populations in the Ramsar site were genetically connected to those in the Kilombero Valley Floodplain (KVFP), but were distinct from those in Ruaha and Rufiji, which clustered separately. Our findings suggested the Ramsar site could revitalize overexploited KVFP populations, and emphasized the need for sustained efforts against its encroachment. However, limited genetic connectivity with Ruaha and Rufiji implied that conservation measures in the site might have restricted effect in these areas. Conservation efforts should extend beyond the Ramsar site, by promoting sustainable fishing and enhancing habitat connectivity in Ruaha and Rufiji. [ABSTRACT FROM AUTHOR]

[Display omitted] • Imidacloprid-resistant N. lugens population rapidly adapted to resistant rice IR36. • Insecticide resistance-related genes nAChR - 7 - like and CYP4C61 contributed to the adaptation to resistant rice in N. lugens. • One avirulent/susceptible genotype and two virulent/resistant genotypes could be inferred from the corresponding alleles of genes nAChR - 7 - like and CYP4C61. • The virulent/resistant genotypes of N. lugens already existed in the wild in China with increasing frequencies along with insecticide usage. Preventing crop yield loss caused by pests is critical for global agricultural production. Agricultural pest control has largely relied on chemical pesticides. The interaction between insecticide resistance and the adaptation of herbivorous pests to host plants may represent an emerging threat to future food security. This study aims to unveil genetic evidence for the reduction in the profitability of resistant cultivars derived from insecticide resistance in target pest insects. An experimental evolution system encompassing resistant rice and its major monophagous pest, the brown planthopper Nilaparvata lugens , was constructed. Whole genome resequencing and selective sweep analysis were utilized to identify the candidate gene loci related to the adaptation. RNA interference and induced expression assay were conducted to validate the function of the candidate loci. We found that the imidacloprid-resistant population of N. lugens rapidly adapted to resistant rice IR36. Gene loci related to imidacloprid resistance may contribute to this phenomenon. Multiple alleles in the nicotinic acetylcholine receptor (nAChR)- 7 - like and P450 CYP4C61 were significantly correlated with changes in virulence to IR36 rice and insecticide resistance of N. lugens. One avirulent/susceptible genotype and two virulent/resistant genotypes could be inferred from the corresponding alleles. Importantly, we found that the virulent/resistant genotypes already exist in the wild in China, exhibiting increasing frequencies along with insecticide usage. We validated the relevance of these genotypes and the virulence to three more resistant rice cultivars. Knockdown of the above two genes in N. lugens significantly decreased both the resistance to imidacloprid and the virulence towards resistant rice. Our findings provide direct genetic evidence to the eco-evolutionary consequence of insecticide resistance, and suggest an urgent need for the implementation of predictably sustainable pest management. [ABSTRACT FROM AUTHOR]

Abstract Geoffroy's cat (Leopardus geoffroyi) is a small‐sized felid native to South America. Given the species' distribution covering a wide variety of habitats, and the presence of high levels of anthropization in part of its range, it is possible that genetically differentiated groups exist and that they occupy different climatic niches. We assessed patterns of contemporary genetic diversity and structure in the species across most of its range, characterizing each inferred genetic group based on ecological niche models. We genotyped 11 microsatellites for 142 samples covering most of Geoffroy's cat distribution, and investigated patterns of genetic structure and diversity, applying spatial and nonspatial Bayesian clustering methods and a spatial principal component analysis. We created ecological niche models for each genetic cluster, evaluating whether these clusters occupy different climatic spaces and display differences in the suitability of different values of the climatic variables analyzed. We identified two genetic clusters, one in the north‐northeast and the other in the south‐southwest of the species' distribution. These clusters showed moderate FST values between them and differences in dispersal/genetic diversity. We found isolation‐by‐distance patterns globally and within each cluster. We observed lower expected heterozygosity compared with other studies and a north–south gradient in allelic richness. The southern cluster showed lower genetic variability and a more restricted climatic niche suggesting that this group is more vulnerable to the effects of the current context of climate change. Individuals from the southern genetic cluster are under different pressures, likely a product of the particularly dry habitat they occupy. Climatic variables associated with habitat suitability suggest the southern cluster has affinity for the arid and semiarid conditions present in its distribution. Conservation measures should consider the genetic structure observed and differences in climatic spaces to maintain the evolutionary potential of the species.

Abstract Ophiothrix (Ophiothrix) exigua is a common brittle star in the northwestern Pacific. As a dominant species, O. exigua inhabiting the intertidal rocky ecosystem are affected by multiple environmental stressors, but molecular insights into their genetic population structure remain poorly studied. In this study, we investigated the population genetics and evolutionary history of six O. exigua populations from the northern China Sea using mitochondrial (COI, NAD4) and nuclear (ITS2, 18S) gene markers. High haplotype diversity, low nucleotide diversity, and low rates of gene differentiation among the populations of O. exigua were detected. Pairwise genetic differentiation (ΦST) statistics between different localities were negative or low and insignificant, suggesting strong gene flow of this species over the study areas. The phylogenetic analyses showed that the populations exhibited high homogeneity between localities in our study area. Demographic analyses indicated that the populations experienced sustained expansion around 0.2 million years ago. This expansion was likely related to transgressions events in the Yellow Sea during the Pleistocene period. Additional samples of O. exigua from disparate geographical locations, especially the Japan Sea and the Korean Peninsula, will be needed to unravel the population genetic patterns and evolutionary history of this species.

Abstract Grassland caterpillars (Lepidoptera: Lymantriinae: Gynaephora) are the most damaging pests to alpine meadows in the Qinghai–Tibetan Plateau (QTP). Here, we conducted extensive sampling from 39 geographic populations covering almost the entire distribution of the eight QTP Gynaephora (Hübner) species to investigate phylogeographic patterns and speciation based on two mitochondrial genes (COI and ND5). A total of 40 haplotypes were detected in the 39 populations, with >70% of all haplotypes not shared between populations. The monophyletic QTP Gynaephora migrated from non‐QTP regions during the Pliocene, corresponding to the uplift of the QTP, suggesting a mode of transport into the QTP. Among the eight QTP Gynaephora species described by morphological characteristics, two species (G. alpherakii and G. menyuanensis) were recovered as monophyletic groups (Clades B and C), while the remaining six formed two monophyletic clades: Clade A (G. qinghaiensis, G. jiuzhiensis, and G. qumalaiensis) and Clade D (G. aureata, G. ruoergensis, and G. minora). These results suggested that the number of the QTP Gynaephora species may be overestimated and further studies based on both morphological and nuclear gene data are needed. Genetic differentiation and speciation of the QTP Gynaephora were likely driven by the QTP uplifts and associated climate fluctuations during the Pleistocene, indicated by divergence time estimation, suggesting that isolation and subsequent divergence was the dominant mode of speciation. The Sanjiangyuan region (i.e., Clade A, characterized by high genetic diversity) may have been a glacial refugium of the QTP Gynaephora, as supported by analyses of gene flow and biogeography. High levels of genetic diversity were found in QTP Gynaephora, without population expansion, which may explain the high‐altitude adaptation and outbreaks of grassland caterpillars in alpine meadows of the QTP. This study provides the largest phylogeographic analysis of QTP Gynaephora and improves our understanding of the diversity and speciation of QTP insects.

Island endemic bats are a considerable cause of conservation concerns, as islands are vulnerable ecosystems facing natural and anthropogenic threats such as growing urbanization. Here, we studied the Reunion free-tailed bat (Mormopterus francoismoutoui), an endemic species to Reunion Island that has adapted to urban settings. We investigated the evolutionary history of Mormopterus at a regional scale, as well as on Reunion Island sex-specific and seasonal patterns of genetic structure. We used an extensive spatio-temporal sampling including 1136 individuals from 18 roosts and three biological seasons (non-reproductive/winter, pregnancy/summer, and mating), with additional samples of Mormopterus species from neighbouring islands (M. jugularis from Madagascar and M. acetabulosus from Mauritius). Complementary information gathered from both microsatellite and mitochondrial markers revealed high genetic diversity but no signal of spatial genetic structure and weak evidence of female philopatry. Regional analysis suggests a single colonization event for M. francoismoutoui, dated around 175,000 years ago, and followed by in-situ diversification and the evolution of divergent ancestral lineages, which today form a large metapopulation. Population expansion was relatively ancient (55,000 years ago) and thus not linked to human colonization and the availability of human-constructed day-roost sites. Discordant structure between mitochondrial and microsatellite markers suggests the presence of yet-unknown mating sites, or the recent evolution of putative ecological adaptations. Our study illustrates the challenge of detailed genetic studies to provide critical insights to insular ecology and evolutionary history, and the importance of both mitochondrial and nuclear DNA in exploring in-situ diversification of an urban-dwelling bat, endemic to a small island.

Hippophae rhamnoides subsp. sinensis Rousi is a cold- and drought-tolerant pioneer specieswith significant economic and ecological value. Evaluating its genetic diversity and population structure is of great importance for guiding the development and utilization of resources. In this study, a total of 41,804 SSRs were generated by transcriptome sequencing of Hippophae rhamnoides subsp. sinensis Rousi. Among the different SSR motif types, mononucleotide repeats (26,972) were the most abundant, followed by trinucleotides, tetranucleotides, and pentanucleotides. 200 pairs of SSR primers were selected to detect polymorphisms, of which 15 pairs primers were selected as validated polymorphic SSRs used for genetic diversity and population structure analysis. A total of 63 alleles were identified with 15 pairs primers, with Nei's genetic diversity index ranged from 0.27 to 0.83 (average: 0.54), and the expected heterozygosity ranged from0.16 to 0.73 (average: 0.46). The polymorphisminformation content ranged from0.23 to 0.81 (average: 0.48). Genetic structure analyses showed that the 10 populations could be broadly categorized into two groups. AMOVA denoted that genetic variations primarily originated from within the populations, withminimal differences observed between the groups, accounting for only 7% of the total genetic variation. This implies that mutation in H. rhamnoides subsp. sinensis Rousimainly occurredwithin the populations. The results showed that the 10 populations of H. rhamnoides subsp. sinensis Rousi are rich in genetic diversity, with low levels of population differentiation and a high degree of gene exchange, which should be taken into consideration for the future work of germplasm resource preservation and seedling breeding. [ABSTRACT FROM AUTHOR]

Adaptive evolution following colonization can affect the impact of invasive species. The fall webworm (FWW) invaded China 40 years ago through a single introduction event involving a severe bottleneck and subsequently diverged into two genetic groups. The well‐recorded invasion history of FWW, coupled with a clear pattern of genetic divergence, provides an opportunity to investigate whether there is any sign of adaptive evolution following the invasion. Based on genome‐wide SNPs, we identified genetically separated western and eastern groups of FWW and correlated spatial variation in SNPs with geographical and climatic factors. Geographical factors explained a similar proportion of the genetic variation across all populations compared with climatic factors. However, when the two population groups were analysed separately, environmental factors explained more variation than geographical factors. SNP outliers in populations of the western group had relatively stronger response to precipitation than temperature‐related variables. Functional annotation of SNP outliers identified genes associated with insect cuticle protein potentially related to desiccation adaptation in the western group and genes associated with lipase biosynthesis potentially related to temperature adaptation in the eastern group. Our study suggests that invasive species may maintain the evolutionary potential to adapt to heterogeneous environments despite a single invasion event. The molecular data suggest that quantitative trait comparisons across environments would be worthwhile. [ABSTRACT FROM AUTHOR]

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The Black Skimmer (Rynchops niger) is a charismatic representative of coastal-nesting waterbird communities in North America and freshwater riverine and coastal systems in South America. Skimmers are at high risk of decline due to threats including habitat loss, human activity, and climate change throughout the annual cycle. To understand range-wide population connectivity, eight microsatellite loci were used to reveal genetic differentiation between North American Pacific and Atlantic Coasts, including the Gulf of Mexico, and very strong differentiation between the North American sites and a site in Peru, South America. A reduced dataset, incorporating previously published data from South America, documented strong inter-continental differentiation and moderate differentiation among sites within South America in a pattern inconsistent with current subspecies designations, and suggesting a more complex pattern of dispersal. We recommend combined use of telemetry and genomic tools to assist in future delineation of skimmer subspecies ranges and non-breeding habitat use in South America. Because genetic diversity was relatively low in North America and higher in South America, genetics could determine whether skimmers in South America represent the ancestral population now expanding along the Atlantic and Pacific Coasts of North America. Detailed knowledge of seasonal movement and non-breeding habitat use that can be obtained by telemetry and population-wide molecular analyses will be essential to informing effective management across the Americas. [ABSTRACT FROM AUTHOR]

Background: The Ganga River System (GRS) is a biodiversity hotspot, its ecological richness is shaped by a complex geological history. In this study, we examined the genetic diversity, spatial connectivity, and population structure of the Asian Silurid catfish, Wallago attu, across seven tributaries of the GRS. Methods and results: We employed three mitochondrial DNA (mtDNA) regions: cytochrome c oxidase subunit I (COXI), cytochrome b (Cyt b), and control region (CR). Our comprehensive dataset encompassed 2420 bp of mtDNA, derived from 176 W. attu individuals across 19 sampling sites within the seven rivers of GRS. Our findings revealed high gene diversity (Hd:0.99) within W. attu populations. Analysis of Molecular Variance (AMOVA) highlighted that maximum genetic variations were attributed within the populations, and the observed genetic differentiation among the seven populations of W. attu ranged from low to moderate. Network analysis uncovered the presence of three distinct genetic clades, showing no specific association with seven studied rivers. Bayesian skyline plots provided insights into the demographic history of W. attu, suggesting a recent population expansion estimated to have occurred approximately 0.04 million years ago (mya) during the Pleistocene epoch. Conclusions: These results significantly enhance our understanding of the genetic diversity and spatial connectivity of W. attu, serving as a vital foundation for developing informed conservation strategies and the sustainable management of this economically valuable resource within the Ganga River System. [ABSTRACT FROM AUTHOR]

Abstract Despite concerns about overfishing and the potential impact of release programs on wild populations, our study of 3116 individuals from 13 wild populations and 2787 individuals from two cultured populations in Zhejiang and Fujian provinces spanning 2008 to 2023 reveals a relatively stable genetic diversity in Larimichthys crocea. Surprisingly, the genetic diversity of wild large yellow croaker populations has remained consistent over the years, suggesting minimal influence from population declines due to overfishing. With the exception of populations in Sansha Bay and Luoyuan Bay, no significant genetic differences were observed among wild populations, indicating a single panmictic genetic population across the East and South China seas. Notably, significant genetic differentiation exists between cultured and wild populations, suggesting a possible limited genetic adaptation of cultured‐released individuals to the wild environment. The genetic differences observed between the Sansha Bay, with its adjacent Luoyuan Bay populations, and other wild populations underscore the dual effects of habitat environment and farming activities on the genetic structure of large yellow croaker. Our findings suggest that, despite declines in population numbers due to overfishing and expands extensive cultured releases, the genetic diversity of L. crocea populations remains largely unaffected. Moreover, the L. crocea population along the Chinese coast appears to form a single panmictic population with considerable genetic diversity.

Abstract Amynthas aspergillum (Perrier, 1872), a natural resource used in traditional Chinese medicine (Guang‐dilong) with high economic value, is widely distributed in forests and farmland habitats in the hilly areas of southern China. To investigate the extent of genetic differentiation and diversity in A. aspergillum, a population genetic structure study was performed on 157 samples from 75 locations in southern China using the mitochondrial genes COI, COII, 12S rRNA, 16S rRNA, and NDI. The results indicated that A. aspergillum had a high level of genetic diversity, and variation within populations was the main source of the total variation. Six deeply divergent mitochondrial clades (I–VI) were detected using both phylogenetic tree and haplotype network analyses. This finding was supported by the high Kimura two‐parameter genetic distance and the pairwise fixation index value obtained based on the COI gene. No significant phylogeographic structures were observed. The widespread geographic distribution of clades II, IV, and VI suggested a recent demographic expansion based on multiple analysis results. These results include a high level of Hd and low π, star‐shaped haplotype network structures with a high number of less frequent haplotypes, significantly negative neutrality test values, and a unimodal mismatch distribution pattern. The divergence time estimates and reconstruction of the ancestral area revealed that A. aspergillum originated in Guangxi Province and underwent initial intraspecific diversification in the early Pliocene to generate clade I. Then, it gradually dispersed eastward and rapidly differentiated into clades II–V during the Pleistocene. The Yunnan‐Guizhou Plateau and Nanling and Wuyi Mountains might act as geographical barriers for the spread of A. aspergillum to the west and north.

Arnebiae Radix is an important medicinal and perennial herb found in Western China, particularly in the Xinjiang region. However, the assessment, utilization and conservation of Arnebiae Radix resources are still unexplored. In this study, we evaluated the genetic diversity of three Arnebiae Radix populations across 47 regions (Ae = 16, Ag = 16, Ad = 15) in Xinjiang, China, using inter-simple sequence repeat (ISSR) molecular markers. In total, 48 alleles were amplified by six pairs of primers screened with ISSR markers. The average number of effective alleles (Ne) was 1.5770. The percentage of interspecific genetic polymorphisms in A. guttata (Ag = 89.58 %) was greater than that in A. euchroma. and A. decumbens (Ae = Ad = 87.50 %). Intraspecific genetic polymorphisms, Bo Le (BL) population of A. euchroma exhibited the highest percentage of polymorphic bands (PPB% = 58.33 %, Na = 1.313, Ne = 1.467, I = 0.0.366, H = 0.255), which indicated high genetic diversity. In contrast, the Tuo Li (TL) population of A. guttata had the lowest values for these parameters (PPB% = 0.00 %, Na = 0.313, Ne = 1,000, I = 0.000, H = 0.000). The Arnebiae Radix germplasms were classified into two major groups (I and II) based on UPGMA cluster analysis (Fig. 8a) and principal coordinate analysis (PCOA). In addition, A. decumbens is placed in a separate category due to its high differentiation coefficient. The AMOVA and genetic differentiation coefficient results indicated that the genetic variation in Arnebiae Radix was predominantly due to intrapopulation differences (78 %). Additionally, the gene flow index (Nm) between populations was 2.4128, which further indicated that the genetic diversity of Arnebiae Radix was greater at the intrapopulation level. The destruction of the ecological environment leads to the continuous reduction and degradation of the genetic diversity of Arnebiae Radix germplasm resources. In this study, we used ISSR molecular markers to analyze the genetic diversity and relatedness of Arnebiae Radix, which revealed the genetic relationship of Arnebiae Radix germplasm resources at the molecular level and provided a scientific basis for future research on selecting and breeding good varieties, evaluating the quality of Arnebiae Radix, and conserving and utilizing its resources.

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

Recently emerged S. Infantis strains carrying resistance to several commonly used antimicrobials have been reported from different parts of the globe, causing human cases of salmonellosis and with occurrence reported predominantly in broiler chickens. Here, we performed phylogenetic and genetic clustering analyses to describe the population structure of 417 S. Infantis originating from multiple European countries and the Americas collected between 1985 and 2019. Of these, 171 were collected from 56 distinct premises located in England and Wales (E/W) between 2009 and 2019, including isolates linked to incursions of multidrug-resistant (MDR) strains from Europe associated with imported poultry meat. The analysis facilitated the comparison of isolates from different E/W sources with isolates originating from other countries. There was a high degree of congruency between the outputs of different types of population structure analyses revealing that the E/W and central European (Germany, Hungary, and Poland) isolates formed several disparate groups, which were distinct from the cluster relating to the United States (USA) and Ecuador/Peru, but that isolates from Brazil were closely related to the E/W and the central European isolates. Nearly half of the analysed strains/genomes (194/417) harboured the IncFIB(pN55391) replicon typical of the "parasitic" pESI-like megaplasmid found in diverse strains of S. Infantis. The isolates that contained the IncFIB(pN55391) replicon clustered together, despite originating from different parts of the globe. This outcome was corroborated by the time-measured phylogeny, which indicated that the initial acquisition of IncFIB(pN55391) likely occurred in Europe in the late 1980s, with a single introduction of IncFIB(pN55391)-carrying S. Infantis to the Americas several years later. Most of the antimicrobial resistance (AMR) genes were identified in isolates that harboured one or more different plasmids, but based on the short-read assemblies, only a minority of the resistance genes found in these isolates were identified as being associated with the detected plasmids, whereas the hybrid assemblies comprising the short and long reads demonstrated that the majority of the identified AMR genes were associated with IncFIB(pN55391) and other detected plasmid replicon types. This finding underlies the importance of applying appropriate methodologies to investigate associations of AMR genes with bacterial plasmids. [ABSTRACT FROM AUTHOR]

Through whole-genome re-sequencing of 18 Hymenopellis radicata germplasm resources collected from diverse regions in China, we identified significant variations in the form of Single Nucleotide Polymorphisms (SNPs) and Insertions and Deletions (InDels). These variations were comprehensively annotated, shedding light on the mutation types present in the entire genome of the H. radicata germplasm. This analysis revealed the number and position information of each mutation and provided insights into the overall genomic landscape of H. radicata germplasm. Utilizing SNP data, we delved into the population structure of the 18 H. radicata germplasm resources. The results indicated the presence of 2,335,179 Indel sites and 12,050,448 SNP sites. The population structure analysis unveiled two distinct subgroups among the H. radicata germplasm resources. Phenotypic statistics, principal component analysis, and phylogenetic tree results echoed the findings of the population structure analysis. Different strains of H. radicata from various regions in China exhibited notable differences in genetic diversity, mycelial growth rate, yield, and fruiting body characteristics. Significant disparities were observed between the two subgroups, while strains within each subgroup shared common characteristics. This research establishes a solid foundation for integrating H. radicata into diverse breeding programs. The data underscore the potential of H. radicata for genetic improvement and exploitation in breeding initiatives, paving the way for future advancements in this field. [ABSTRACT FROM AUTHOR]

The Andaman Sea-Malacca Strait is an area with high maritime complexity and rich seaweed biodiversity. The brown seaweed Sargassum plagiophyllum C.Agardh occurs abundantly in the intertidal in the area. However, its population genetics has not been studied. Here, we used the nuclear Internal Transcribed Spacer 2 of the ribosomal cistron ITS2 and the mitochondrial cytochrome c oxidase subunit 1 gene cox1 as genetic markers to determine the population genetic structure along the entire west coast of Thailand. A total of 351 individuals from the ten populations were genotyped. Nine different cox1 haplotypes and 17 different ITS2 ribotypes were found. Generally, S. plagiophyllum populations were found to have low genetic diversity. Two lineages were found based on ITS2 and two cryptic diversities were inferred from cox1 data. Most individuals belonged to the one single ribotype and haplotype. Ocean currents are believed to influence the S. plagiophyllum distributions and connectivity between populations. Higher phosphate concentrations during the northeast monsoon season could promote its growth and propagation. Our study suggested that the temporal and spatial transformation of the marine environment in the Andaman Sea influences the distribution, biomass, and population genetic structure of S. plagiophyllum, our results are beneficial for the management of seaweed resources. [ABSTRACT FROM AUTHOR]

The western Terai Arc Landscape (wTAL) in Uttarakhand, India, marks the range limit for the Asian elephant in north‐western India. This region has been impacted by land‐use changes and infrastructure expansion for the last seven decades. To evaluate the impact of habitat deterioration on the population structure of elephants in the region, we characterized their genetic diversity and local genetic structure using mitochondrial (D loop) and nuclear DNA (microsatellites; n = 15) markers. We used tissue samples of 114 elephants from five different sub‐populations, collected between 2005 and 2014. The genetic variation was moderate (HO = 0.49–0.55) compared with other Indian elephant populations. Two mtDNA haplotypes were identified without strong spatial patterns across wTAL. Bayesian individual‐based clustering algorithm identified two genetic clusters (K = 2) with high admixture (50% at Q < 0.7) and no spatial adherence. Though K = 1 was not supported by the Bayesian algorithm, multivariate analysis and sibship patterns did not indicate genetic differentiation. The lack of spatial genetic structuring suggests high levels of gene flow, indicating that this population is still panmictic. This suggests that the life history traits of elephants as well as the ecological features of this landscape influence genetic connectivity. However, ongoing land use changes necessitate regular genetic monitoring in wTAL to identify incipient structuring caused by anthropogenic barriers to movement. [ABSTRACT FROM AUTHOR]

The genetic structure of Karachay population has been studied on the basis of analysis of ten autosomal DNA markers (diallelic and multiallelic) of the nuclear genome: CCR5∆32, ID/АСЕ, D7S23(KM19), STR/THOI, STR/FABP2, STR/IVS6aGATT(CFTR), VNTR/PAH, VNTR/DAT1, VNTR/NOS3, VNTR/APOB. The total number of the sample comprises 485 individuals who are residents of four Karachay regions: Karachaevsky, Prikubansky, Malokarachayevsky, Ust-Dzhegutinsky, and the city of Cherkessk, the capital of the Karachay-Cherkess Republic. Analysis of allele's frequency of autosomal DNA markers in Karachay geographic subgroups shows considerable genetic differentiation between them. The highest level of genetic diversity for Karachay people on the diallelic system is set at the locus ID/АСЕ, Hobs = 0.513, and on the multiallelic system is at the locus STR/THOI, Hobs = 0.792. The average value of the observed heterozygosity per locus is 0.466, varying from 0.441 in Ust-Dzhegutinsky region to 0.503 in Cherkessk. The level of genetic differences between Karachay groups (FST = 0.007) is inside the variance defined in the previously studied peoples: Mari (FST = 0.0024), Udmurt (FST = 0.0048), Chuvash (FST = 0.006), Tatars (FST = 0.0075), and Bashkir (FST = 0.008). [ABSTRACT FROM AUTHOR]