Population Genetic Structure Research Articles

Comparative Population Genomic Diversity and Differentiation in Trapdoor Spiders and Relatives (Araneae, Mygalomorphae).

Although patterns of population genomic variation are well-studied in animals, there remains room for studies that focus on non-model taxa with unique biologies. Here we characterise and attempt to explain such patterns in mygalomorph spiders, which are generally sedentary, often occur as spatially clustered demes and show remarkable longevity. Genome-wide single nucleotide polymorphism (SNP) data were collected for 500 individuals across a phylogenetically representative sample of taxa. We inferred genetic populations within focal taxa using a phylogenetically informed clustering approach, and characterised patterns of diversity and differentiation within- and among these genetic populations, respectively. Using phylogenetic comparative methods we asked whether geographical range sizes and ecomorphological variables (behavioural niche and body size) significantly explain patterns of diversity and differentiation. Specifically, we predicted higher genetic diversity in genetic populations with larger geographical ranges, and in small-bodied taxa. We also predicted greater genetic differentiation in small-bodied taxa, and in burrowing taxa. We recovered several significant predictors of genetic diversity, but not genetic differentiation. However, we found generally high differentiation across genetic populations for all focal taxa, and a consistent signal for isolation-by-distance irrespective of behavioural niche or body size. We hypothesise that high population genetic structuring, likely reflecting combined dispersal limitation and microhabitat specificity, is a shared trait for all mygalomorphs. Few studies have found ubiquitous genetic structuring for an entire ancient and species-rich animal clade.

Genetic diversity, population structure, and a genome-wide association study of sorghum lines assembled for breeding in Uganda.

Sorghum is an important source of food and feed worldwide. Developing sorghum core germplasm collections improves our understanding of the evolution and exploitation of genetic diversity in breeding programs. Despite its significance, the characterization of the genetic diversity of local germplasm pools and the identification of genomic loci underlying the variation of critical agronomic traits in sorghum remains limited in most African countries, including Uganda. In this study, we evaluated a collection of 543 sorghum accessions actively used in Ugandan breeding program across two cropping seasons at NaSARRI, Uganda, under natural field conditions. Phenotypic data analysis revealed significant (p<0.01) variation among accessions for days to 50% flowering, plant height, panicle exsertion, and grain yield, with broad-sense heritability (H²) estimates of 0.54, 0.9, 0.81, and 0.48, respectively, indicating a high genetic variability for these traits. We used a newly developed genomic resource of 7,156 single nucleotide polymorphism (SNP) markers to characterize the genetic diversity and population structure of this collection. On average, the SNP markers exhibited moderately high polymorphic information content (PIC = 0.3) and gene diversity (He = 0.3), while observed heterozygosity (Ho = 0.07) was low, typical for self-pollinating crops like sorghum. Admixture-based models, PCA, and cluster analysis all grouped the accessions into two subpopulations with relatively low genetic differentiation. Genome-wide association study (GWAS) identified candidate genes linked to key agronomic traits using a breeding diversity panel from Uganda. GWAS analysis using three different mixed models identified 12 genomic regions associated with days to flowering, plant height, panicle exsertion, grain yield, and glume coverage. Five core candidate genes were co-localized with these significant SNPs. The SNP markers and candidate genes discovered provide valuable insights into the genetic regulation of key agronomic traits and, upon validation, hold promise for genomics-driven breeding strategies in Uganda.

Analysis of genetic diversity and genetic structure of indigenous chicken populations in Guizhou province based on genome-wide single nucleotide polymorphism markers

Guizhou province in China is rich in indigenous chicken breeds, playing an essential role in the genetic improvement of modern chickens. Genetic diversity has decreased in recent decades due to accelerated breeding processes and changing conservation priorities. To determine the genetic diversity and population structure of Guizhou indigenous chicken breeds, we used 55K genotyping arrays to conduct population genetic analysis on 233 individuals from 8 Guizhou indigenous breeds and 263 individuals from 9 Guizhou indigenous chicken populations. We evaluated the genetic diversity parameter (heterozygosity, proportion of polymorphic markers, and nucleotide diversity), linkage disequilibrium (LD), population structure, and genetic differentiation (FST and genetics distance). Genetic diversity results indicated that the genetic diversity of chicken breeds in Guizhou province is relatively affluent. Among Guizhou breeds, Baiyi black-bone and Guizhou yellow chicken displayed the lowest genetic diversity, as the 2 breeds exhibit lower PN and heterozygosity, the extent of linkage disequilibrium is higher. According to the LD pattern, Guizhou indigenous breeds can be divided into 3 categories. Population structure analysis showed a certain degree of genetic differentiation among local chickens in Guizhou. We argue that Chishui black-bone and Puan black-bone chickens are 2 different geographical regional groups of the same breed. In principal component analysis, individuals from the 2 groups clustered together, and the phylogenetic tree results showed that the 2 groups clustered together to form a branch independent of other breeds, and they displayed an identical pattern of ancestral lineage composition. The research results will provide a reference for protecting local chicken genetic resources in Guizhou Province and promote the protection and utilization of genetic resources.

Genome-Wide Characterization and Development of Simple Sequence Repeat Markers for Molecular Diversity Analyses in Yellowhorn (Xanthoceras sorbifolium Bunge).

Yellowhorn (Xanthoceras sorbifolium Bunge) is a valuable ornamental, medicinal, and woody oilseed species that is indigenous to China. The breeding improvement of yellowhorn has been hindered by a lack of suitable markers and sufficient information regarding the molecular diversity of this species. In this study, we conducted a comprehensive analysis of the yellowhorn genome to characterize the simple sequence repeat (SSR) loci. A total of 4,007,201 SSRs were successfully identified. Among these markers, mono-nucleotide SSRs were most abundant in the genome, while the tri-nucleotide SSRs accounted for the highest proportion in coding sequences. The GO and KEGG function enrichment analysis revealed that most SSR loci in coding sequences were associated with potential biological functions. Additionally, we used 30 pairs of primers to amplify SSR markers to gain a better understanding of the genetic variation in yellowhorn germplasms. The average values of observed heterozygosity and polymorphism information content were 0.625 and 0.517, respectively. Population structure, phylogeny and principal component analyses identified two distinct subclusters. Furthermore, yellowhorn germplasms with the same geographical distribution tended to group together. Moreover, a total of 26 yellowhorn core collections, which accounted for approximately 14.94% of the total yellowhorn germplasms, effectively represented the genetic diversity of all original germplasms. Our findings not only unveiled the genetic diversity and population structure of yellowhorn germplasms but also investigated the yellowhorn core collection, which will serve as a strong basis for yellowhorn management and genetic improvement.

Towards the understanding of genetic and morphological variations of a highly abundant seaweed-associated marine invertebrate

Unraveling the patterns of genetic structure and demographic history of marine species, as well as the factors that shape their genetic variations, is fundamental for informing conservation strategies for species and their environments. In this work, we investigate the current population structure and historical demographic patterns of the conspicuous seaweed-associated amphipod Hyale niger at a fine spatial scale in the subtropical SW Atlantic coast, in Brazil, by using both genome-wide and mitochondrial DNA markers. We also investigate how geographic distance, current oceanographic conditions, and variations in a key morphological trait contribute to the genetic variability of the amphipod. We observed an evident population genetic structure, even at a fine spatial scale, although genetic differentiation was lower than our expectations for a benthic direct brooder. Demographic history inferences were consistent across populations and showed two major demographic expansions on interglacial periods during the late Pleiostocene, before and after the last glacial maximum. We also demonstrated that isolation-by-environment (IBE) was the main driver of genetic differentiation, although we could not separate it from the effects of isolation-by-distance (IBD). Among environmental factors, nutrient concentrations in seawater were most relevant for explaining genetic structure. In addition, our data suggest that morphological variation in gnathopod 2 structure of males were not genetic-related and were probably plastic as a response to variations in macroalgae frond size. Our study reinforces the importance of using multiple molecular markers and analytical approaches to unveil patterns and processes generating genetic variation in natural populations.

Landscape Heterogeneity Drives Genetic Diversity in the Highly Dispersive Moss Funaria hygrometrica Hedw.

Funaria hygrometrica, a cosmopolitan moss species known for its remarkable dispersal capacity, was selected as the focal organism to investigate the relationship between landscape features and genetic diversity. Our study encompassed samples collected from two distinct regions: the Spanish Sierra Nevada Mountains (SN), characterized by a diverse landscape with an altitudinal difference of nearly 3500 m within a short distance, and the Murcia Region (MU) in Southeast Spain, characterized by a uniform landscape akin to the lowlands of Sierra Nevada. Genotyping analysis targeted three genetic regions: the nuclear ribosomal internal transcribed spacer (nrITS), the chloroplast rps3-rpl16 region, and the mitochondrial rpl5-rpl16 spacer. Through this analysis, we aimed to assess genetic variability and population structure across these environmentally contrasting regions. The Sierra Nevada populations exhibited significantly higher haplotype diversity (Hd = 0.78 in the highlands and 0.67 overall) and nucleotide diversity (π% = 0.51 for ITS1) compared to the Murcia populations (Hd = 0.35, π% = 0.14). Further investigation unveiled that samples from the lowlands of Sierra Nevada showed a closer genetic affinity to Murcia than to the highlands of Sierra Nevada. Furthermore, the genetic differentiation between highland and lowland populations was significant (ΦST = 0.55), with partial Mantel tests and ResistanceGA analysis revealing a strong correlation between ITS1-based genetic diversity and landscape features, including altitude and bioclimatic variables. Our study elucidated potential explanations for the observed genetic structuring within F. hygrometrica samples' populations. These included factors such as a high selfing rate within restricted habitats, a limited average dispersal distance of spores, hybrid depression affecting partially incompatible genetic lineages, and recent migration facilitated via human activities into formerly unoccupied areas of the dry zones of Southeast Spain.

Population structure analysis of Phlebotomus papatasi populations using transcriptome microsatellites: possible implications for leishmaniasis control and vaccine development

BackgroundPhlebotomus papatasi is considered the primary vector of Leishmania major parasites that cause zoonotic cutaneous leishmaniasis (ZCL) in the Middle East and North Africa. Phlebotomus papatasi populations have been studied extensively, revealing the existence of different genetic populations and subpopulations over its large distribution range. Genetic diversity and population structure analysis using transcriptome microsatellite markers is important to uncover the vector distribution dynamics, essential for controlling ZCL in endemic areas.MethodsIn this study, we investigated the level of genetic variation using expressed sequence tag-derived simple sequence repeats (EST-SSRs) among field and colony P. papatasi samples collected from 25 different locations in 11 countries. A total of 302 P. papatasi sand fly individuals were analyzed, including at least 10 flies from each region.ResultsThe analysis revealed a high-level population structure expressed by five distinct populations A through E, with moderate genetic differentiation among all populations. These genetic differences in expressed genes may enable P. papatasi to adapt to different environmental conditions along its distribution range and likely affect dispersal.ConclusionsElucidating the population structuring of P. papatasi is essential to L. major containment efforts in endemic countries. Moreover, the level of genetic variation among these populations may improve our understanding of Leishmania–sand fly interactions and contribute to the efforts of vaccine development based on P. papatasi salivary proteins.Graphical

Genetic diversity and population structure of superior shea trees (Vitellaria paradoxa subsp. paradoxa) using SNP markers for the establishment of a core collection in Côte d'Ivoire.

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

Genetic Stock Identification Reveals Mismatches Between Management Areas and Population Genetic Structure in a Migratory Pelagic Fish.

Sustainable fisheries management is important for the continued harvest of the world's marine resources, especially as they are increasingly challenged by a range of climatic and anthropogenic factors. One of the pillars of sustainable fisheries management is the accurate identification of the biological units, i.e., populations. Here, we developed and implemented a genetic baseline for Atlantic herring harvested in the Norwegian offshore fisheries to investigate the validity of the current management boundaries. This was achieved by genotyping > 15,000 herring from the northern European seas, including samples of all the known populations in the region, with a panel of population-informative SNPs mined from existing genomic resources. The final genetic baseline consisted of ~1000 herring from 12 genetically distinct populations. We thereafter used the baseline to investigate mixed catches from the North and Norwegian Seas, revealing that each management area consisted of multiple populations, as previously suspected. However, substantial numbers (up to 50% or more within a sample) of herring were found outside of their expected management areas, e.g., North Sea autumn-spawning herring north of 62° N (average = 19.2%), Norwegian spring-spawning herring south of 62° N (average = 13.5%), and western Baltic spring-spawning herring outside their assumed distribution area in the North Sea (average = 20.0%). Based upon these extensive observations, we conclude that the assessment and management areas currently in place for herring in this region need adjustments to reflect the populations present. Furthermore, we suggest that for migratory species, such as herring, a paradigm shift from using static geographic stock boundaries towards spatial dynamic boundaries is needed to meet the requirements of future sustainable management regimes.

Relationship Between Genetic and Phenotypic Variations in Natural Populations of Perennial and Biennial Sagebrush.

Plant responses to environmental heterogeneity depend on life-history traits, which could relate to phenotypical and genetic characteristics. To elucidate this relationship, we examined the variation in population genetics and functional traits of short- and long-lived Artemisia species that are co-occurring in the steppes of Mongolia. Mongolian steppes represent stressful and water-limited habitats, demanding phenotypic modifications in the short term and/or genetic adaptation in the long term. However, detailed knowledge is missing about both plant phenotypic and genetic differentiation, and their interrelationships in temperate grasslands. Here, we investigated 21 populations of the widely distributed subshrub Artemisia frigida and the herbaceous biennial Artemisia scoparia. Genetic variation was assessed with newly developed simple sequence repeats (SSRs) markers. Functional trait data were collected from each individual, and data on environmental variables was collected for each population. We detected significantly higher genetic diversity in the biennial species (H E = 0.86) compared with the perennial (H E = 0.79). For both species, the largest share of genetic variation was partitioned within populations (96%). Population genetic structure in the biennial A. scoparia was weak, while the perennial A. frigida showed some spatial genetic structure, which was impacted by geographical factors, soil nutrients, and precipitation amount. Morphology-related functional traits (i.e., plant height) were predominantly associated with environmental variables rather than with genetic variation, whereas physiology-related trait (i.e., specific leaf area [SLA]) was partly genetically determined.

Population genetic structure and ecological differentiation in the bryozoan genus Reteporella across the Azores Archipelago (central North Atlantic)

The processes shaping population dynamics of benthic marine invertebrates with non-planktotrophic larvae are still poorly understood but have seen a renewed interest in applying integrative taxonomic approaches. We used mitochondrial and microsatellite (SSR-GBAS) data to estimate connectivity across islands and seamounts in the central North Atlantic Azores Archipelago in five species of the bryozoan genus Reteporella Busk, 1884. Discordant patterns were inferred between datasets, which might be due to methodological constraints related to the application of multilocus approaches based on amplification to multiple species or due to interspecific introgression in deep waters. A divergent cryptic ecotype of Reteporella atlantica (Busk, 1884) was found in shallow waters, likely resulting from ecologically-driven incipient speciation, posing new questions regarding the role of bathymetrical zonation as a promoter of differentiation. The occurrence of ecologically-driven differentiation and potential interspecific introgression in other bryozoans should be considered, both with potentially important evolutionary and biogeographical consequences. The discovery of incipient species, prompted by ecological factors, calls for the need to consider marine invertebrates when developing conservation strategies in oceanic insular ecosystems.

Генетические портреты хантов и манси по гаплогруппам Y-хромосомы в контексте генофондов России

Khanty and Mansi are small indigenous peoples of Western Siberia with the unique cultural, anthropological, and linguistic characteristics. The study of their gene pool will make it possible to reconstruct the genetic structure of the Ugric-speaking population, of which in modern times only Khanty and Mansi remain, along with Hungarians, in whose gene pool there are traces of medieval migration of the Ugric-speaking Magyars. The detailed characterization of the gene pool of Khanty and Mansi is important for reconstruction of Ugric populations and genetic history of the region. The study was aimed to assess representative samples of Khants (n = 83) and Mansi (n = 74) based on the standard panel of 60 SNP markers and the extended panel of 74 Y-chromosomal SNP markers by statistical and cartographic methods in the context of indigenous population of Urals and Western Siberia. The differences between the gene pools of Khanty and Mansi have been revealed based on both standard panel of Y chromosome haplogroups and branches of haplogroups N2 and N3a4. Most of the Khanty gene pool is evenly distributed between N2-Y3195 (26%), N2-VL67 (23%), and N3a4-Z1936 (23%). The “Western” branch N2-Y3195 predominates in the Mansi gene pool (69%). Mansi gravitate towards populations of the Urals-Volga region in the multidimensional genetic space. Based on the standard panel of Y haplogroups, Khanty are close to the populations of Western and South Siberia. However, the analysis of branches N3a4 has shown that Khanty are intermediate between the “Uralic” and “Siberian” clusters: when the ancestors of Khanty moved from the Ural region to the northeast, these acquired both genetic components. The gene geographic maps of 10 haplogroup N3a4 branches in the populations of Urals and Western Siberia reflect the dynamic changes of the gene pool that took place 4–2 kya.

Deep genetic substructure within bonobos.

Establishing the genetic and geographic structure of populations is fundamental, both to understand their evolutionary past and preserve their future. Nevertheless, the patterns of genetic population structure are unknown for most endangered species. This is the case for bonobos (Pan paniscus), which, together with chimpanzees (Pan troglodytes), are humans' closest living relatives. Chimpanzees live across equatorial Africa and are classified into four subspecies,1 with some genetic population substructure even within subspecies. Conversely, bonobos live exclusively in the Democratic Republic of Congo and are considered a homogeneous group with low genetic diversity,2 despite some population structure inferred from mtDNA. Nevertheless, mtDNA aside, their genetic structure remains unknown, hampering our understanding of the species and conservation efforts. Mapping bonobo genetic diversity in space is, however, challenging because, being endangered, only non-invasive sampling is possible for wild individuals. Here, we jointly analyze the exomes and mtDNA from 20 wild-born bonobos, the whole genomes of 10 captive bonobos, and the mtDNA of 136 wild individuals. We identify three genetically distinct bonobo groups of inferred Central, Western, and Far-Western geographic origin within the bonobo range. We estimate the split time between the central and western populations to be ∼145,000 years ago and genetic differentiation to be in the order of that of the closest chimpanzee subspecies. Furthermore, our estimated long-term Ne for Far-West (∼3,000) is among the lowest estimated for any great ape lineage. Our results highlight the need to attend to the bonobo substructure, both in terms of research and conservation.

Leading report regarding the molecular epidemiology of Taenia hydatigena from Pakistan and global overview of the genetic diversity and population structure of the parasite: Correspondence

Leading report regarding the molecular epidemiology of Taenia hydatigena from Pakistan and global overview of the genetic diversity and population structure of the parasite: Correspondence

Of Clams and Clades: Genetic Diversity and Connectivity of Small Giant Clams (Tridacna maxima) in the Southern Pacific Ocean.

Giant clams (Tridacna and Hippopus) are large marine bivalves occupying tropical and subtropical reefs in the Indo-Pacific. Giant clam populations have declined in many areas of the Indo-Pacific and continue to be threatened by harvesting and environmental change. The small giant clam (Tridacna maxima) occurs throughout the Indo-Pacific and has been subject to several phylogeographic studies across its range. However, given its broad range, there are several areas where the genetic diversity and connectivity of T. maxima populations has not been characterised. Here, we analyse the mitochondrial marker cytochrome oxidase 1 (CO1) to examine the genetic diversity and connectivity of T. maxima in two regions: Australia's Coral Sea Marine Park and the Cook Islands. Samples were collected from 13 reefs within the Coral Sea Marine Park and ten islands within the Cook Islands archipelago. Tridacna maxima across the sampled region of the Coral Sea did not display any population structure, whereas significant population structure was detected for T. maxima within the Cook Islands. For the Cook Islands, most pairwise comparisons involving an island in the northern group (Manihiki) were significant, as were comparisons for Palmerston (a more centrally located island) and the southern islands, Rarotonga and Mangaia. Both regions displayed high haplotype diversities (> 0.90), indicating that they are important repositories of genetic diversity. Additional CO1 data from throughout T. maxima's distribution showed that the Coral Sea clams belonged to the clade occurring in the South-Western Pacific Ocean, whilst those from the Cook Islands belonged to a unique clade found in the Central Pacific Ocean. This clade extended from Fiji in the west to French Polynesia in the east and the atolls of Palmyra and Tarawa (Kiribati) in the north. Our assessment of genetic diversity and population structure in these regions will assist with management decisions for the species.

Genetic Structure and Phylogeographic Divergence of Thymallus brevicephalus in the Ob‐Irtysh River Headwaters

ABSTRACTClarifying the genetic structure and population history of a species can reveal the impacts of historical climate and geological changes, providing critical insights for developing effective conservation strategies for ecologically significant fish. The Markakol grayling (Thymallus brevicephalus), an endangered species found in the Altai‐Sayan Mountain region of Central Asia, serves as an ideal model for studying these factors. In this study, populations of a grayling (Thymallus) species discovered in the upper Irtysh River headwaters in Xinjiang, China, were analyzed to assess genetic diversity and population structure. Mitochondrial DNA sequences (cytochrome b and control region), along with 10 microsatellite markers, were used to examine genetic variation. Phylogenetic and genetic distance analyses confirmed the species, long misidentified as Arctic grayling (T. arcticus), as T. brevicephalus. This species can be divided into two distinct geographic groups: eastern and western, with the Crane River acting as the boundary. The divergence between these groups likely corresponds to refugia formed during the Pleistocene glaciation of the Altai Mountains, approximately 0.48 MA (million years ago) (range: 0.30 to 0.71 Ma). High haplotype diversity (Hd &gt; 0.5) and low nucleotide diversity (π &lt; 0.005) suggest that, despite the species' genetic richness, T. brevicephalus remains vulnerable to genetic drift, which could threaten its long‐term survival. This vulnerability may stem from inbreeding within small refugial populations during the glacial period, followed by gradual population expansion. Our study offers novel insights into grayling populations, with results that have direct implications for management by serving as a tool for the identification of conservation units.

Unique among high passes: Insights into the genetic uniqueness among butterflies of Ladakh Trans-Himalaya through DNA barcoding.

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

Seasonal distribution and population genetic structure of Psenopsis anomala (Japanese butterfish) inferred from otolith oxygen isotope ratios and mitochondrial DNA

Psenopsis anomala (Japanese butterfish) is a commercially important fish species with a wide distribution in the Northwest Pacific Ocean, but its catch in Taiwanese waters has been declining for decades. This study aims to elucidate the migration pattern and population structure of P. anomala by analyzing otolith δ18O values, mitochondrial COI and cyt b sequences, respectively. The results reveal a seasonal migration pattern between the northern South China Sea and the Yellow Sea. Analysis of the haplotype network reveals that most P. anomala collected from each location share the haplotypes Hap1 and Hap5, while each population also has its own unique haplotypes. Analysis of molecular variance reveals that the primary variation (92.98%) is observed among individuals within the populations. Fu's FS test conducted for all populations showed no significant differences, and the mismatch distribution aligns with recent population expansion. Both the maximum likelihood tree and the median-joining network show no geographic population structuring in P. anomala samples from Japan and Taiwan. The combined findings from otolith microchemistry and genetic analysis suggests that P. anomala distributed in east Asia shall be managed as a single stock.

Phylogeography and population genomics of the critically endangered aquatic plant Caldesia grandis in China

Caldesia grandis, a critically endangered aquatic species, is predominantly found in the mid-low mountainous swamps of subtropical China. This study assessed the genetic diversity and population structure of the species using RAD-seq data, explored its phylogeography across the extant nine populations based on five plastid DNA (ptDNA) regions, and conducted niche modeling analysis. We found low genetic diversity (HE = 0.180, Ho = 0.222, and π = 0.197) and genetic differentiation among populations (Fst = 0.089), which was likely due to genetic drift in small populations and frequent inter-population contact during the Quaternary period. Although RAD-seq analysis did not reveal a clear population structure, two distinct clades, comprising western and eastern populations, were identified using five ptDNA haplotypes. Molecular dating and niche modeling suggested that the uplift of the Luoxiao Mts may have contributed to the divergence of the eastern and western clades (ca. 1.51 Ma)during the Pleistocene, which also supports the hypothesis that the Nanling Mts acted as a refugium for C. grandis. Additionally, the repeated glacial periods of the Quaternary, accompanied by contraction and expansion of suitable habitats, likely facilitated gene exchange among populations, influencing the current distribution pattern in subtropical China. Our results suggested that each ptDNA haplotype should be treated as an independent unit for conservation purposes, and ex-situ efforts should be prioritized to conserve C. grandis in China.

Genetic Attributes and Conservation of an Endangered Giant Water Bug Species, Diplonychus esakii Miyamoto and Lee, 1966 (Hemiptera: Belostomatidae).

Diplonychus esakii, a water bug from the family Belostomatidae, plays an important role in freshwater ecosystems as one of the top predators. In this study, we investigated the genetic diversity and population structure of D. esakii by analyzing 318 specimens across 27 sites in South Korea. We found that the populations of D. esakii possess 11 haplotypes with a haplotype diversity of 0.623. This represents a relatively low level of genetic diversity compared to other known belostomatids and endangered species. AMOVA and FST analyses revealed significant genetic differentiation among populations, with most populations harboring only 1-2 haplotypes, suggesting restricted gene flow between populations and a low level of genetic diversity. This low genetic diversity and limited gene flow suggest a potential vulnerability to environmental changes and an increased risk of extinction, indicating that D. esakii should be designated as a protected species in South Korea as part of future conservation efforts. Based on the results of this study, Upo Wetland, which maintains relatively high levels of genetic diversity and Jeju Island, which, despite its lower genetic diversity compared to the mainland, does not share haplotypes with other regions, should be considered key conservation units for this species. This study highlights the importance of incorporating genetic information into conservation status assessments under the Red List Categories and Criteria and also emphasizes the need to evaluate this species on the Korean Red List. The data provided here will serve as essential baseline information and valuable resources for the development of effective conservation strategies.