Patterns Of Population Structure Research Articles

Genetic Diversity, Linkage Disequilibrium, and Population Structure in a Common Bean Reference Collection

An in-depth understanding of the extent and pattern of genetic diversity and population structure in crop populations is of paramount importance for any crop improvement program to efficiently promote the translation of genetic diversity into genetic gain. A reference collection of 150 common bean genotypes selected from the International Center for Tropical Agriculture’s global core collection was evaluated using single-nucleotide polymorphism (SNP) markers to quantify the amount of genetic diversity, linkage disequilibrium, and population structure. The cultivars and landraces of the collection were diverse and originated from 14 countries, and wild accessions were used as controls for each gene pool. The collection was genotyped using an SNP array, generating a total of 5398 locus calls distributed across the entire bean genome. The SNP data quality was checked, and two datasets were generated. The first dataset (Dataset_1) comprised a set of 5108 SNPs and 150 genotypes after filtering for 10% missing alleles and an MAF < 0.05. The second dataset (Dataset_2) comprised a set of 2300 SNPs that remained after removing any null-allele SNPs and LD pruning for a criterion of r2 < 0.2. Dataset_1 was used for a principal coordinate analysis (PCoA), phylogenetic relationship determination, an analysis of molecular variance (AMOVA), and a discriminant analysis of principal components. Dataset_2 was used for a population structure analysis using STRUCTURE software and is proposed for a genome-wide association study (GWAS). The population structure analysis split the reference collection into two subpopulations according to an Andean or Mesoamerican gene pool. The Mesoamerican populations displayed higher genetic differentiation and tended to split into more groups that were somewhat aligned with common bean races. Andean beans were characterized by a larger average LD but lower LD percentage, a small average genetic distance between members of the population, and a higher major allele frequency, which suggested narrower genetic diversity compared to the Mesoamerican gene pool. In conclusion, the results indicated the presence of high genetic diversity, which is useful for a GWAS. However, the presence of significant linkage disequilibrium requires that genetic distance be considered as a co-factor for any further genetic studies. Overall, the molecular variation observed in the genotypes shows that this reference collection is valuable as a genebank-derived diversity panel which is useful for marker trait association studies.

The pattern of genetic variability in a core collection of 2,021 cowpea accessions.

Cowpea is a highly drought-adapted leguminous crop with great promise for improving agricultural sustainability and food security. Here, we report analyses derived from array-based genotyping of 2,021 accessions constituting a core subset of the world's largest cowpea collection, held at the International Institute of Tropical Agriculture (IITA) in Ibadan, Nigeria. We used this dataset to examine genetic variation and population structure in worldwide cowpea. We confirm that the primary pattern of population structure is two geographically defined subpopulations originating in West and East Africa, respectively, and that population structure is associated with shifts in phenotypic distribution. Furthermore, we establish the cowpea core collection as a resource for genome-wide association studies by mapping the genetic basis of several phenotypes, with a focus on seed coat pigmentation patterning and color. We anticipate that the genotyped IITA Cowpea Core Collection will serve as a powerful tool for mapping complex traits, facilitating the acceleration of breeding programs to enhance the resilience of this crop in the face of rapid global climate change.

Resequencing Analyses Revealed Genetic Diversity and Selection Signatures during Rabbit Breeding and Improvement.

Domestication has shaped the diverse characteristics of rabbits, including coat color, fur structure, body size, and various physiological traits. Utilizing whole-genome resequencing (DNBSEQ-T7), we analyzed the genetic diversity, population structure, and genomic selection across 180 rabbits from 17 distinct breeds to uncover the genetic basis of these traits. We conducted whole-genome sequencing on 17 rabbit breeds, identifying 17,430,184 high-quality SNPs and analyzing genomic diversity, patterns of genomic variation, population structure, and selection signatures related to coat color, coat structure, long hair, body size, reproductive capacity, and disease resistance. Through PCA and NJ tree analyses, distinct clusters emerged among Chinese indigenous rabbits, suggesting varied origins and domestication histories. Selective sweep testing pinpointed regions and genes linked to domestication and key morphological and economic traits, including those affecting coat color (TYR, ASIP), structure (LIPH), body size (INSIG2, GLI3), fertility (EDNRA, SRD5A2), heat stress adaptation (PLCB1), and immune response (SEC31A, CD86, LAP3). Our study identified key genomic signatures of selection related to traits such as coat color, fur structure, body size, and fertility; these findings highlight the genetic basis underlying phenotypic diversification in rabbits and have implications for breeding programs aiming to improve productive, reproductive, and adaptive traits. The detected genomic signatures of selection also provide insights into rabbit domestication and can aid conservation efforts for indigenous breeds.

Stock Assessment of the Commercial Small Pelagic Fishes in the Beibu Gulf, the South China Sea, 2006-2020.

Long-term variations in population structure, growth, mortality, exploitation rate, and recruitment pattern of two major commercial small pelagic fishes (CSPFs) (Decapterus maruadsi and Trachurus japonicus) are reported based on bottom trawl survey data collected during 2006-2020 in the Beibu Gulf, South China Sea. All individuals collected during each sampling quarter over a period of 15 years were subjected to laboratory-based analysis. In this study, the stock of D. maruadsi and T. japonicus inhabiting the Beibu Gulf was assessed using length-based methods (bootstrapped electronic length frequency analysis (ELEFAN)) to complete stock assessment in different fishery management periods (the division of fisheries management periods was based on China's input and output in the South China Sea offshore fisheries over 15 years, specifically divided into period I (2006-2010), period II (2011-2015), and period III (2016-2020)). The results showed that the mean body length, dominant body size, and estimated asymptotic length of two CSPFs decreased, whereas their growth coefficient decreased, indicating miniaturization and slower growth, respectively. Estimated exploitation rates and catching body length for two CSPFs indicated that both stocks in the Beibu Gulf were overexploited in period I and moderately exploited after 2011. These stocks were taking a good turn in status in period III, with the exploitation rate much lower than the initial period and reversing the downward trend in catching body length. Furthermore, the variations in the spawning season of the two CSPF stocks and their barely satisfactory expected yield indicated the complexity of the current fishery management in the Beibu Gulf. These results suggest that management measures to reduce fishing pressure may have a positive influence on the biological characteristics of those CSPFs in the Beibu Gulf; however, the stock structure already affected by overfishing will be a huge challenge for the conservation and restoration of fisheries resources in the future. Given that the current stocks of D. maruadsi and T. japonicus in the Beibu Gulf still have low first-capture body length (Lc) and high fishing mortality (F) (compared to F0.1), we identify a need to refine population structure by controlling fishing efforts and increasing catchable size, and more consideration should be given to the local fishery resource status in fisheries management.

Population genetics of the critically endangered three-striped turtle, Batagur dhongoka, from the Ganga river system using mitochondrial DNA and microsatellite analysis

The three-striped roofed (Batagur dhongoka) is a semi-aquatic turtle that belongs to family Geoemydidae. Due to anthropogenic pressure, it has been facing an intense decline of over 80% in its distribution range in the past 50 years. It is considered as 'Critically Endangered' so effective conservation strategies are needed to protect the species by determining their genetic diversity and population genetic structure. This study investigates the genetic diversity, population structure and demographic pattern of B. dhongoka from two Turtle Rescue and Rehabilitation Centre established near Ganga river using mitochondrial cytochrome b (Cyt b: 1140 bp) ; control region (CR: 451 bp) and ten nuclear microsatellite loci. mtDNA results show low levels of nucleotide diversity (π = 0.0022) in B. dhongoka haplotypes and provide evidence for a low substitution rate. The demographic pattern estimated by the Bayesian skyline plot (BSP) analysis indicates historical stability followed by growth in the effective population size, with a recent reduction in population size from ~ 2 thousand years ago. The microsatellite findings show a moderate level of observed heterozygosity (Ho: 0.49). Bayesian-based clustering analysis revealed weak genetic structures in B. dhongoka and presence of admixed assignations suggesting close genetic relationships. These findings shed light on B. dhongoka's genetic status and underline the necessity of comprehensive rehabilitation and relocation programs and conservation and management techniques to ensure the species' long-term survival. In order to ensure the effective protection and conservation of B. dhongoka, the Government of India has taken a proactive measure by incorporating it into Schedule I of the Wildlife (Protection) Act, 1972, as amended in 2022.

Long‐term differences in population structure, body size and distribution patterns of amphipods and isopods in wetlands with declining hydroperiods

Abstract In many regions, climatic drying is shortening hydroperiods and freshwater biodiversity is declining. Aquatic species that lack a desiccation‐resistant life stage are predicted to have the least ability to persist in drying climates, yet such species may occur in intermittent waterbodies. We examined the distribution of two crustacean species that lack desiccation‐resistant life stages: the isopod Paramphisopus palustris and amphipod Chiltoniidae sp.nov., before and after the commencement of severe climatic drying in Swan Coastal Plain wetlands, south‐western Australia. Historical distribution data for these species were obtained from studies of the same set of wetlands in 1989–1990. We determined whether population or body size differed between hydrological regimes (perennial, semi‐perennial, seasonal) between 1989–1990 and 2018–2019 for both species. Amphipods, isopods and environmental variables were sampled from 42 wetlands in 2018–2019. Thirty‐three wetlands (22 perennial, 11 seasonal) persisted with the same hydrological regime in both time periods and eight wetlands that were perennial in 1989–1990 had shifted to a drier hydrological regime (four became semi‐perennial, four became seasonal) by 2018–2019. Drying wetland hydrological regimes did not correspond to more limited spatial distributions for either species. Hydrological regime had no effect on amphipod counts, although abundances were lower in 2018–2019 than 1989–1990. In 2018–2019, male amphipods were larger than females in seasonal wetlands, but sexes were the same size in perennial wetlands and females were larger than males in semi‐perennial wetlands. Furthermore, amphipods of both sexes were considerably smaller in semi‐perennial than seasonal or perennial wetlands. Isopod distributions differed between the two sampling periods, with populations primarily lost from wetlands that remained perennial. This unexpected result was likely caused by prolonged periods of high summer–autumn water temperatures and stratification in shallow perennial wetlands that caused anoxia in bottom waters and made surface waters excessively hot for isopods. By contrast, drying seasonal wetlands seemingly offered suitable habitat in summer–autumn. Mean isopod head and body length did not differ between hydrological regimes or sexes, but became smaller between 1989–1990 and 2018–2019 (15 mm average body length in 1989 vs. 8.3 mm in 2018–2019; 17 mm maximum size in 1989–1990 vs. 13.2 mm in 2018–2019). The absence of population losses associated with drying hydrological regimes indicates that the current level of drying is within the tolerance range of both species. However, increased temperatures may be causing body size (and possibly fecundity) to decline for isopods. As global warming continues to shorten wetland hydroperiods in many regions, numerous species will struggle to complete their life cycles, leading to extirpation. Our findings suggest that climate change may also cause conditions in perennial wetlands to exceed the tolerances of species that lack desiccation resistance traits. This emphasises the need to better understand both environmental and habitat changes along the drying trajectory in wetlands and the fundamental life‐history and physiological traits that enable the survival of aquatic invertebrates that lack desiccation resistance. This includes not only species responses to drying, but also responses to other stressors (e.g., prolonged stratification) caused by global warming.

Elevation gradients alter vegetation attributes in mountain ecosystems of eastern Himalaya, India

The present study describes how vegetation (the tree layer) is shaped along the elevation gradients in the eastern part of the Indian Himalayan Region. Various vegetation attributes, distribution, population structure, and regeneration patterns of 75 tree species belonging to 31 families were studied. Tree species richness shows a low plateau (peaked between 1,300–1,500 m) with a linearly decreasing pattern above 1,500 m asl. Ericaceae was found as the dominant family, followed by Lauraceae and Rosaceae. The distributional pattern of species-to-genera ratio (S/G) did not follow any particular trends, while β-diversity increased along the elevation gradient. The Margalef index of species richness, the Menheink index of species richness, and the Fisher alpha were found to be highest at lower altitudes (1,000–1,500 m), while the Simpson index was highest at middle altitudes (2,600–3,000 m). Random distribution was shown by maximum tree species (47.3%), followed by a contagious distribution (42.9%), and regular distribution (10.8%). The regeneration of tree species was found to be good with a healthier number of seedlings (10.2%), fair (43.5%), poor (30.3%), while 16% were observed not regenerating. Acer laevigatum (1,500 m), Prunus nepalensis (3,300 m), Viburnum sympodiale (3,400 m) were among the new regenerating species at the respective altitudes. The population structure of tree species in terms of proportion of individuals in seedlings, saplings, and the adult class varied in all the elevation transects. Species with better regeneration on upper distribution limits have been recognized as probable for upward movement.

Population structure and distribution pattern of endangered species, Dillenia pentagyna, in Indonesian natural reserve forest

Regeneration strategy of endangered species is crucial for maintaining ecosystem sustainability in its endemic habitat. Dillenia pentagyna is a deciduous tree species with many potential benefits for medical use, silkworms’ fodder, and furniture, and is considered as an endangered tree species in Indonesia due to over exploitation in 1980s. The species is an important asset for Gunung Abang Natural Reserve Forest (GANRF) due to essential historical functions for flora, fauna, and local communities. We conducted an initial research to observe the population structure and distribution pattern of D.pentagyna in its native habitat to understand the growth- and population behavior. Using a random sampling method, we built 157 plots to identify the number of seedlings, saplings, poles, and trees followed by measurement of height and diameter-breast-height. We only found fifteen poles, six saplings, five trees, and no seedlings in the plots with dominant distribution in the center of GANRF area. The distribution pattern was random according to Morisita index (Iδ= 0.011 equal to 0), which explains that D.pentagyna grows randomly in nature independent to canopy gaps and slopes. Findings suggested that low population needs to be recovered by seedling initiation growth in the nursery before sowing in the field to avoid high mortality.

Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations.

Genomic structural variants (SVs) are now recognized as an integral component of intraspecific polymorphism and are known to contribute to evolutionary processes in various organisms. However, they are inherently difficult to detect and genotype from readily available short-read sequencing data, and therefore remain poorly documented in wild populations. Salmonid species displaying strong interpopulation variability in both life history traits and habitat characteristics, such as Atlantic salmon (Salmo salar), offer a prime context for studying adaptive polymorphism, but the contribution of SVs to fine-scale local adaptation has yet to be explored. Here, we performed a comparative analysis of SVs, single nucleotide polymorphisms (SNPs) and small indels (<50 bp) segregating in the Romaine and Puyjalon salmon, two putatively locally adapted populations inhabiting neighboring rivers (Québec, Canada) and showing pronounced variation in life history traits, namely growth, fecundity, and age at maturity and smoltification. We first catalogued polymorphism using a hybrid SV characterization approach pairing both short- (16X) and long-read sequencing (20X) for variant discovery with graph-based genotyping of SVs across 60 salmon genomes, along with characterization of SNPs and small indels from short reads. We thus identified 115,907 SVs, 8,777,832 SNPs and 1,089,321 short indels, with SVs covering 4.8 times more base pairs than SNPs. All three variant types revealed a highly congruent population structure and similar patterns of F ST and density variation along the genome. Finally, we performed outlier detection and redundancy analysis (RDA) to identify variants of interest in the putative local adaptation of Romaine and Puyjalon salmon. Genes located near these variants were enriched for biological processes related to nervous system function, suggesting that observed variation in traits such as age at smoltification could arise from differences in neural development. This study therefore demonstrates the feasibility of large-scale SV characterization and highlights its relevance for salmonid population genomics.

Population genetic structure in the critically endangered Crocodylus intermedius (Crocodilia: Crocodylidae): a shift in perspective for conservation actions in Colombia

Abstract Conservation actions for threatened species and populations aim to preserve their genetic diversity and prevent issues such as inbreeding or outbreeding depressions. This perspective has been incorporated into the management plans proposed for the critically endangered Orinoco crocodile (Crocodylus intermedius) in Colombia. A previous study, which used mitochondrial cytochrome b and cytochrome c oxidase subunit I, suggested that the in situ population management of the Orinoco crocodile in Colombia does not face genetic restrictions. In this research, we re-evaluated this proposal by using an expanded sampling and additional molecular markers (microsatellite nuclear DNA and the mitochondrial D-loop) that have successfully identified crucial information at the population level in other crocodilians. Our findings reveal, for the first time, a pattern of population structure consisting of three genetic clusters with geographical correspondence, matching three ecoregions in the Colombian Orinoco basin. This pattern might be a historical and current consequence of the ecological, bioclimatic, and/or geographical features of the ecoregion. Additionally, we examined the correspondence with the genetic clusters of the confiscated individuals that formed part of the initial population (F0) of the Colombian ex situ species population and successfully assigned most of them to one of these clusters. The genetically distinct clusters should be regarded as independent management units for conserving and managing the species in Colombia.

The weak genetic structure of Melolontha melolontha (L.) and Melolontha hippocastani (Fabr.), two important forest pests, indicates their large population sizes and effective gene flow

Abstract Cockchafers Melolontha spp. are polyphagous root pests and outbreak species of considerable economic importance to forestry in Europe. Knowledge of genetic diversity within and between cockchafer populations is largely unexplored but could lead to more effective monitoring and management strategies of these pests. In this study, we fill several gaps in the knowledge of the genetic population structure of Melolontha melolontha and Melolontha hippocastani. Using microsatellite loci and over 200 individuals per species, we examined the genetic structure of Melolontha spp. populations collected from three primary outbreak areas in central and southeastern Poland. We demonstrated that our focal species share some common genetic patterns, such as considerable genetic diversity within subpopulations (within sampling sites) with minor effects of past bottlenecks possibly masked by current population sizes. The estimates of effective population sizes, although subject to wide credibility intervals, indicated a large number of individuals contributing to further generations of the population. The migration rates exceed the threshold of one per generation required for gene flow and maintenance of population equilibrium, indicating limited impact from forest management practices on either cockchafer species. While genetic differentiation was observed in M. melolontha populations, supported by various indices (fixation index, principal coordinate analysis, assignment tests), the M. hippocastani populations were genetically similar. This disparity may hint at the potential historical divergence between these species. In this aspect, more detailed phylogeographic and population genetic studies covering a large area of the Palaearctic distributions of both species are required. Our findings constitute one of the initial efforts aimed at delineating the genetic diversity, differentiation, population structure, gene flow, and migration patterns within Melolontha spp. This exploration is especially significant for M. hippocastani, given its completely unexplored genetic population structure.

Genetic structure of the commercially important Asian monsoon scallop, Amusium pleuronectes (Linnaeus 1758), across the Indonesian Archipelago

AbstractThe Asian monsoon scallop, Amusium pleuronectes, is a key member of the most commercially harvested shellfish community in Asia. Patterns of genetic diversity and natural population structure in the target species were investigated to gain a better understanding of its evolutionary history. Samples were collected from five sites across the Indonesian Archipelago. We characterized sequence variation in an mtDNA control region fragment in 249 individuals. The genetic diversity (h = ranging from 0.83 to 0.92) and nucleotide diversity (π = ranging from 0.24 to 0.32) were low compared to the estimates reported for many other similar shellfish taxa. Nonetheless, analysis of molecular variance revealed significant genetic differentiation, FST = 0.0203 (p &lt; .005 after Bonferroni corrections). Furthermore, both Pairwise fixation index values showed significance among majority population sites, indicating that dispersal potential and gene flow were low in the past. This pattern likely reflects a low dispersal potential, potentially allowing local adaptation to sites that augment any oceanographic and geographic contribution to genetic structure. The results described herein provide a foundation for developing better conservation strategies for the target species in the future.

Differentiated genomic footprints suggest isolation and long-distance migration of Hmong-Mien populations

BackgroundThe underrepresentation of Hmong-Mien (HM) people in Asian genomic studies has hindered our comprehensive understanding of the full landscape of their evolutionary history and complex trait architecture. South China is a multi-ethnic region and indigenously settled by ethnolinguistically diverse HM, Austroasiatic (AA), Tai-Kadai (TK), Austronesian (AN), and Sino-Tibetan (ST) people, which is regarded as East Asia’s initial cradle of biodiversity. However, previous fragmented genetic studies have only presented a fraction of the landscape of genetic diversity in this region, especially the lack of haplotype-based genomic resources. The deep characterization of demographic history and natural-selection-relevant genetic architecture of HM people was necessary.ResultsWe reported one HM-specific genomic resource and comprehensively explored the fine-scale genetic structure and adaptative features inferred from the genome-wide SNP data of 440 HM individuals from 33 ethnolinguistic populations, including previously unreported She. We identified solid genetic differentiation between HM people and Han Chinese at 7.64‒15.86 years ago (kya) and split events between southern Chinese inland (Miao/Yao) and coastal (She) HM people in the middle Bronze Age period and the latter obtained more gene flow from Ancient Northern East Asians. Multiple admixture models further confirmed that extensive gene flow from surrounding ST, TK, and AN people entangled in forming the gene pool of Chinese coastal HM people. Genetic findings of isolated shared unique ancestral components based on the sharing alleles and haplotypes deconstructed that HM people from the Yungui Plateau carried the breadth of previously unknown genomic diversity. We identified a direct and recent genetic connection between Chinese inland and Southeast Asian HM people as they shared the most extended identity-by-descent fragments, supporting the long-distance migration hypothesis. Uniparental phylogenetic topology and network-based phylogenetic relationship reconstruction found ancient uniparental founding lineages in southwestern HM people. Finally, the population-specific biological adaptation study identified the shared and differentiated natural selection signatures among inland and coastal HM people associated with physical features and immune functions. The allele frequency spectrum of cancer susceptibility alleles and pharmacogenomic genes showed significant differences between HM and northern Chinese people.ConclusionsOur extensive genetic evidence combined with the historical documents supported the view that ancient HM people originated from the Yungui regions associated with ancient “Three-Miao tribes” descended from the ancient Daxi-Qujialing-Shijiahe people. Then, some have recently migrated rapidly to Southeast Asia, and some have migrated eastward and mixed respectively with Southeast Asian indigenes, Liangzhu-related coastal ancient populations, and incoming southward ST people. Generally, complex population migration, admixture, and adaptation history contributed to the complicated patterns of population structure of geographically diverse HM people.

Population structure and history of North Atlantic Blue whales (Balaenoptera musculus musculus) inferred from whole genome sequence analysis

Knowledge of genetic diversity and structure is essential for developing conservation strategies for endangered species. Blue whales were hunted to near extinction in the mid-twentieth century. Not-withstanding almost 380,000 animals killed globally, much remains unknown about their population structure and migration patterns. Herein, we use whole genome sequencing to elucidate the poorly understood population genetics of North Atlantic (NA) blue whales. We generated a de novo genome assembly for a NA blue whale to analyze 19 other whole genomic sequences and 31 complete mitochondrial genomes. Present-day and historical samples (earliest from 1876) from the Atlantic and Antarctic Oceans were included to understand the impact of whaling on the genetic diversity of this species. We found low but statistically significant population structuring and high genetic diversity. Demographic modeling using fastsimcoal2 rejected an absence of gene flow between eastern and western NA blue whales and suggested an asymmetric west to east gene flow. Introgression estimated using D-statistics between blue and fin whales (Balaenoptera physalus), was observed in all present-day samples. This gene flow was found to be unidirectional from fin whales to blue whales and accounts for ~ 3.5% of the NA blue whale’s genome. Our sequencing and population structure analyses provide a genomic baseline to inform ongoing conservation strategies for this iconic species.

Impacts of bamboo dominance and die‐off on seedling dynamics in a tropical secondary forest (Brazil)

AbstractAulonemia aristulata is a tropical bamboo species of mixed rhizome type and monocarpic flowering that can become super‐dominant after anthropogenic disturbances in tropical forests. The synchronized reproductive events of flowering and die‐off of monocarpic bamboo systems provide a rare opportunity to evaluate the temporal effects of bamboo dominance on forest regeneration. To evaluate the effects of bamboo dominance on forest regeneration, we compared the structure (abundance, richness, composition) and dynamics (mortality, recruitment, survival and growth) of tree and shrub seedling communities from two non‐contiguous forests stands (bamboo‐dominated vs. non‐dominated sites) for 2 years, before and after a synchronized reproductive event. Bamboo dominated plots had higher abundance, floristic richness and recruitment of tree and shrub seedlings when compared with bamboo non‐dominated plots. Bamboo die‐off did not represent an opportunity to improve establishment and investment in the vertical growth (height) of seedlings in bamboo‐dominated plots. We postulate that the mode of rhizome extension seen in bamboos might be a consistent trait determining the spatial pattern of occupation and population structure and thereby playing a fundamental role in the pattern of native tree community establishment after bamboo die‐off. The formulation of a management approach is necessary in order to better understand the biological traits of bamboo species and their influence on the spatial pattern of occupation and population structure. Additionally, this influence may differently impact restoration and definition of management practices, including the need for direct intervention by manually controlling bamboo cover following die‐off to promote and maintain seedling establishment and diversity.

Genetic variation and geographic distribution of Leishmania orientalis and Leishmania martiniquensis among Leishmania/HIV co-infection in Thailand

Since 1999, the number of asymptomatic leishmaniasis cases has increased continuously in Thailand, particularly among patients with HIV who are prone to develop symptoms of cutaneous and visceral leishmaniasis further. The asymptomatic infection could play a key role in Leishmania transmission and distribution. Understanding population structure and phylogeographic patterns could be crucially needed to develop effective diagnoses and appropriate guidelines for therapy. In this study, genetic variation and geographic distribution of the Leishmania/HIV co-infected population were investigated in endemic northern and southern Thailand. Interestingly, Leishmania orientalis was common and predominant in these two regions with common regional haplotype distribution but not for the others. Recent population expansion was estimated, probably due to the movement and migration of asymptomatic individuals; therefore, the transmission and prevalence of Leishmania infection could be underestimated. These findings of imbalanced population structure and phylogeographic distribution patterns provide valuable, insightful population structure and geographic distribution of Leishmania/HIV co-infection to empower prevention and control of transmission and expansion of asymptomatic leishmaniasis.

Reference genome of Townsend's big-eared bat, Corynorhinus townsendii.

Townsend's big-eared bat, Corynorhinus townsendii, is a cave- and mine-roosting species found largely in western North America. Considered a species of conservation concern throughout much of its range, protection efforts would greatly benefit from understanding patterns of population structure, genetic diversity, and local adaptation. To facilitate such research, we present the first de novo genome assembly of C. townsendii as part of the California Conservation Genomics Project (CCGP). Pacific Biosciences HiFi long reads and Omni-C chromatin-proximity sequencing technologies were used to produce a de novo genome assembly, consistent with the standard CCGP reference genome protocol. This assembly comprises 391 scaffolds spanning 2.1 Gb, represented by a scaffold N50 of 174.6 Mb, a contig N50 of 23.4 Mb, and a benchmarking universal single-copy ortholog (BUSCO) completeness score of 96.6%. This high-quality genome will be a key tool for informed conservation and management of this vulnerable species in California and across its range.

Population structure, runs of homozygosity analysis and construction of single nucleotide polymorphism fingerprinting database of Longnan goat population

AbstractThe Longnan goat (LN) is a local breed discovered during the third census of China's livestock and poultry genetic resources. In order to thoroughly comprehend the population traits, this research examined a total of 70 animals from three different goat populations, namely the LN goat, Nanjiang Brown goat (NJ), and Boer goat (Boer). Specific‐Locus Amplified Fragment Sequencing was employed to analyze genetic diversity, population structure, and selective sweep patterns. Additionally, individual DNA fingerprints were generated to provide detailed genetic profiles for each subject. A total of 643,868 single nucleotide polymorphisms (SNPs) were detected, with a majority located in intergenic and intronic regions. Genetic diversity analysis uncovered lower diversity within the LN population compared to the other two populations. The analysis of population structure unveiled significant genetic distance between LN and both NJ and Boer populations, with distinct clustering patterns observed. Moreover, genetic differentiation coefficients (FST) of 0.1019 and 0.0854 were determined between LN and Boer, as well as LN and NJ, respectively, indicating substantial genetic differentiation. Selective sweep analysis, combining FST and π ratio, identified several genes associated with growth and development, reproduction, hair color, and immunity that may serve as valuable candidates for marker‐assisted breeding. Furthermore, identification of 47,541 runs of homozygosity (ROHs) revealed non‐uniform distribution across chromosomes, with the highest frequency on chromosome 1 and the lowest on chromosome 27. Correlations between different inbreeding coefficients varied, with the highest observed between FHOM and FGRM, and the lowest between FROH &gt;1.5Mb and FROH &lt;500kb. A total of 46 candidate genes were annotated within high‐frequency ROH islands, primarily associated with biological processes such as reproduction, growth and development, and immunity. Finally, a DNA fingerprint, consisting of 371 highly polymorphic SNPs, was generated and presented in the form of a two‐dimensional code for convenient access. Based on the population structure analysis, LN goats have been found to have a distant genetic distance and a higher degree of differentiation from both the Boer and NJ populations. Evaluation of genetic diversity parameters and ROH analysis indicates that the LN population exhibits lower genetic diversity and shows signs of inbreeding. Our findings offer theoretical support for the identification of genetic resources within this population.

Population Structure, Distribution, and Spatial Characteristics of Alsophila spinulosa in Chishui, China

Endangered plants are essential components of most forest ecosystems and reflect the ecological integrity of forests. The study of the population structure and spatial pattern of Alsophila spinulosa is of great significance for its conservation. In the subtropical Chishui Tree fern valley in China, we studied the best structure of A. spinulosa to reflect the environmental change, the range of the most intense spatial aggregation change, and the spatial relationship with the community structure, and explored the survival characteristics of A. spinulosa. Our results showed that the variation in tree height structure was the most obvious response to the change in community type. The spatial aggregation degree of A. spinulosa had the most obvious change in the range of 1–5 m. There was an obvious spatial correlation between the dominant plants, the vertical structure of the community, and the distribution of A. spinulosa. These findings provided a reference for exploring the population structure, distribution pattern, and the influence of community types on A. spinulosa populations.

Assessing population structure and migration patterns of wild boar (Sus scrofa) in Japan

Geographical wildlife patterns reflect historical range expansion and connectivity and provide insights into wildlife population management. In our large-scale phylogeographic population analysis of wild boars (Sus scrofa leucomystax) in Japan, we identified 15 clusters using 29 microsatellite markers, each structured within a range of approximately 200 km. This suggests that evolution was essentially driven by isolation by distance, and that the range of gene flow was limited. One cluster contained subpopulations located approximately 900 km apart, indicating the occurrence of past anthropogenic introductions. Moreover, we estimated effective migration to visualize the geographic genetic population diversity. This analysis identified six potential barriers, one of which involved large plains and mountainous areas in the Kanto region of eastern Japan. This barrier likely persisted in the two eastern clusters for an extended period, restricting migration to the neighboring areas. Overall, our study sheds light on the demographic history of wild boar in Japan, provides evidence of past anthropogenic introductions from distant areas, and highlights the importance of geographic barriers in shaping genetic diversity and population dynamics. This knowledge will be beneficial for forming informed wildlife management strategies toward the conservation of genetic integrity and ecological balance of wild boar populations in Japan.