Neighbor-joining Tree Research Articles

Phylogenetic and population genetic analysis of Arunachali Yak (Bos grunniens) using mitochondrial DNA D-loop region.

The Arunachali yak (Bos grunniens) is an important breed native to the northeastern Himalayas of India. Understanding its genetic diversity and evolutionary relationships with other bovine species is crucial for effective conservation and breeding strategies. This study investigates the mitochondrial DNA (mtDNA) D-loop region of Arunachali yak and compares it with other bovines to elucidate these relationships. We collected blood samples from 18 Arunachali yak individuals and isolated genomic DNA. The partial mtDNA D-loop region was amplified using PCR and sequenced. Sequences were compared with those from Bos frontalis, Bos gaurus, Bos indicus, Bubalus bubalis, and Capra hircus available in GenBank. Phylogenetic relationships were assessed through Neighbor-Joining trees and median-joining networks. Genetic diversity indices and neutrality tests were applied to evaluate population genetic characteristics. Phylogenetic analysis identified three distinct clades, with Arunachali yak clustering closely with Bos indicus, and forming a separate branch from other bovine species. Median-joining networks revealed six haplogroups, with Arunachali yak uniquely representing Hap_3. Genetic diversity analysis showed no polymorphism within Arunachali yak, indicating very low genetic variation in the selected animal samples. AMOVA demonstrated significant genetic differentiation among populations (Fst = 0.30053, P < 0.001), with a substantial portion of variation occurring within populations. The Arunachali yak exhibits a close genetic relationship with Bos indicus, reflecting recent divergence. The study underscores the distinct genetic profile of Arunachali yak and highlights its limited genetic variability. These findings enhance our understanding of bovine evolutionary relationships and emphasize the need for targeted conservation measures to preserve the genetic integrity of Arunachali yak.

Harnessing genetic diversity in Sudanese sorghum wild relatives for stay-green drought tolerance via microsatellite (SSR) marker assessment

AbstractSudan is the birthplace of sorghum, and vast genetic diversity exists among its wild relatives. To assess the genetic potential of Sudan wild sorghum accessions, we used 41 stay-green-specific microsatellite (SSR) markers to analyze the genetic variability and population structure of 256 accessions. Overall, 17 SSR markers were polymorphic, with 55 alleles on average 3.3 per locus. The polymorphic information content (PIC) ranged from 0.49 to 0.57, with an overall mean of 0.53, indicating the potential of these markers for capturing the genetic construction of wild sorghum. Linkage disequilibrium analysis identified the two most informative markers, Xcup05 and Xtxp212. Accordingly, the Nei gene diversity of the populations varied from 0.032 to 0.127, with an overall mean of 0.083. Molecular variance analysis (AMOVA) demonstrated that 99% and 1% of the genetic variations were within and among populations (Fst = 0.066; P 0.001), respectively. However, gene flow (Nm) values varied from 0.058 in populations 1 and 2 to 1.018 in populations 2 and 3. Neighbor-joining trees identified from 21 Sudanese wild sorghum accessions clustered closely to the universally drought-tolerant landrace B35. Structural analysis generated the highest Delta K value (58.2) at K = 2, revealing two distinct subpopulations. While this work provides valuable information about the potential of sorghum wild relatives from Sudan as sources for stay-green drought tolerance, further research should be directed toward identifying the exact mechanisms and genes underlying this stay-green trait using advanced molecular omics techniques. In conclusion, this study highlights the potential role of Sudanese sorghum accessions as reservoirs of ready-to-use stay-green genes for the design of climate-resilient sorghum cultivars in drought-prone areas of Sudan and beyond. However, these wild relatives would require extensive pre-breeding and validation efforts before their genes can be effectively incorporated into elite cultivars.

Contrasting the role of historic factors in phylogeograpic patterns in the native Johnny darter (Etheostoma nigrum) and invasive round goby (Neogobius melanostomus) in lower michigan.

Round goby (Neogobius melanostomus) is an invasive fish present in all five Great Lakes and is becoming increasingly common in their tributaries. Johnny darter (Etheostoma nigrum) is a native species that often coexists with N. melanostomus. In this work, historic factors are addressed as a source of genomic variation in study populations of these species. To do this, patterns of variation in the mitochondrial gene NADH dehydrogenase subunit 2 (ND2) were characterized for both species throughout Lower Michigan. Populations of N. melanostomus and E. nigrum were sampled from 17 localities representing both eastern and western basins of Lower Michigan to test the hypothesis that populations differ between the eastern and western basins of the Great Lakes. Neogobius melanostomus populations were largely homogenous with no significant differences detected among populations or between the eastern and western basins. Additionally, N. melanostomus exhibited no evidence of overarching historical genetic structure, consistent with the recent invasion and rapid expansion of this species. Etheostoma nigrum exhibited significant differentiation among local populations; however, similarity among mtDNA haplotypes indicated that differences among populations are recent, suggesting that local forces are a more important factor in shaping patterns of variation than historical factors. Contrary to predictions, there were no significant differences detected between the eastern and western basins of the Great Lakes; however, construction of a neighbor-joining tree with F ST estimates revealed clustering of populations by basin with some anomalies. These anomalies may be the result of recent stream capture events facilitating gene flow between the two basins.

Population genetic differentiation and structure of rare plant Anemone shikokiana based on genotyping-by-sequencing (GBS)

BackgroundAnemone 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.ResultsIn 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.ConclusionsHere, 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.

A new leaf spot caused by Alternaria alternata on Atractylodes lancea in Jiangsu, China.

Atractylodes lancea is an important Chinese herbal medicine, which is mainly produced in Jiangsu province, China. In June 2022, leaf spots symptom were observed on some A. lancea seedlingsgrowing in a Chinese herbal medicine resource garden of NanjingBotanical Garden, Jiangsu. Approximately 75% of 100 A. lancea seedlings suffered from the disease. Initially, gray to black spots appeared at the tip of the blade, then spread deep into the petiole, finally causing the blade to wither and fall. To isolate the pathogen, five diseased leaves were collected from five different seedlings. Leaf sections (3 to 4 mm) were excised from the margins between healthy and diseased tissues, surface sterilized in 75% alcohol for 30 s, then in 1.5% NaClO for 90 s, rinsed three times in sterilized distilled water, plated on potato dextrose agar (PDA) and incubated at 25℃in darkness. Pure cultures were obtained by monosporic isolation. Eighteen isolates were obtained, and 77.8% of isolates was identified as Alternaria spp. A representative isolate, CS4-1 was used for further investigation. The colony of CS4-1, growing on PDA was cotton-like and black to brown with gray-white aerial hyphae on their surfaces, and dark gray on the back. The conidia were solitary on conidiophores and were oval to pear-shaped, brown in color, with 1 to 4 transverse septa and 0 to 1 oblique septa, parietal cells extending into the beak, and measured 8.9 to 39.5×6.0 to 13.5 µm (n=35). These characteristics were consistent with the description of Alternaria spp. (Simmons 2007). Six DNA regions, i.e.,internal transcribed spacer (ITS),large subunit ribosomal RNA (LSU), small subunit ribosomal RNA (SSU), anonymous region OPA10-2, Alt a 1 major allergen (Alta1), glyceraldehyde 3-phosphate dehydrogenase (GAPDH)and translation elongation factor 1-alpha (TEF1)with the respective GenBank Accession No. OP836052, OP836054, OP836051, OP851487, OP851488, OP851489, and OP851490, were amplified and sequenced with the primer pairs described by White et al. (1990) and Woudenberg et al. (2015). A neighbor-joining phylogenetic tree was generated by combining all sequenced loci in MEGA7, and CS4-1 clustered in the A. alternata clade. To test pathogenicity, 12 leaves, on three one-month-old A. lancea seedlings (four leaves from each seedling) were wounded with a sterile needle and inoculated with 20 μL of conidial suspension (1×106 spores/mL) on the left sides of leaves. The right sides of the leaves were inoculated with 20 µL sterile water and used as the control. All inoculated detached leaves and seedlings were covered with clear polyethylene bags to keep moisture and were incubated in a greenhouse at 25℃, 80% relative humidity, and a 12-h light/dark cycle. The experiment was repeated three times. After 4 days, typical gray to black spots were visible on the left sides of all inoculated leaves and the inoculated seedlings, and the right sides remained asymptomatic. Subsequently, the same fungus was reisolated and identified based on morphological and molecular traits. A. alternata has a very wide host range but has never been reported on A. lancea worldwide (nt.ars-grin.gov). Because of the medicinal value of A. lancea, further studies should be directed toward control of this disease.

Mitochondrial Genomes of Korean Native Black Goats Reveal Shared Phylogeographic Patterns and Demographic History.

This study explores the phylogeny of Korean native black goats through analysis of their complete mitochondrial DNA. The National Institute of Animal Science has gathered genetic material on purebred goats from isolated regions such as Tongyeong, Dangjin, and Jangsu, and is actively breeding them on a national level. These populations, however, are small and exhibit high inbreeding rates, highlighting the urgent need to preserve genetic diversity. The haplotype diversity within this native group is 0.659, with 39 haplotypes identified. By contrast, including international breeds in the analysis increases the overall haplotype diversity to 0.925 with 203 haplotypes identified, highlighting the limited genetic diversity among native black goats. For phylogenetic assessment, a neighbor-joining tree and median-joining network were constructed using identified haplogroups (A, B, C, D, G, and F) from prior studies. The results pinpoint the native black goats as closely related to, but distinct from, Haplogroup A with a bootstrap value of 98, establishing them as a separate clade (A'). This supports the notion of a shared ancestry with various global populations. This research provides essential data on the origins and evolutionary history of Korean native black goats, supporting conservation and breeding efforts aimed at enhancing genetic diversity.

Genetic diversity and origin of Kazakh Tobet Dogs

The Kazakh Tobet is an indigenous Kazakh dog breed that has been used to guard livestock since ancient times. To understand the genetic structure and phylogenetic relationship of the Kazakh Tobet breed with other herding and livestock guarding dog breeds, we analysed short tandem repeat data of 107 Kazakh Tobet dogs from different regions of Kazakhstan and Mongolia, as well as whole genome sequencing data from two Kazakh Tobet dogs and 43 dogs from 24 working breeds. Our results indicate a high genetic diversity of the Kazakh Tobet, with the average number of alleles per locus ranging from 6.00 to 10.22 and observed heterozygosity ranging from 76 to 78%. The breed has a complex genetic structure characterised by seven different clusters. The neighbour-joining tree constructed based on 14,668,406 autosomal and the maximum likelihood tree based on mitochondrial D-loop sequences indicate a common genetic heritage between the Kazakh Tobet, the Central Asian Shepherd Dog and the Turkish Akbash. The presence of haplotype A18 in the Kazakh Tobets supports the hypothesis of the ancient origin of the breed, which was previously suggested by archaeological finds and written sources. These results provide an important genetic basis for the ongoing efforts to improve the Kazakh Tobet breed, to ensure its preservation as an independent genetic lineage and to recognise a breed on an international level.

DNA barcoding and cryptic diversity in fishes from the Ili River Valley in China, Xinjiang.

The Ili River Valley, located in the northwest of China, serves as a vital repository for fish genetic resources. Its extensive water network and diverse climate have given rise to a unique fish composition and endemic species. In this study, we collected the cytochrome c oxidase subunit I (COI) sequences from 660 fish specimens in the Ili River Valley. The effectiveness of DNA barcoding in identifying fish species in the area was assessed by examining genetic distances, constructing phylogenetic trees, and performing ABGD (Automatic Barcode Gap Discovery) analyses, among other methods. In total, 20 species were identified, including one unidentified species (Silurus sp.). Except for Silurus asotus and Hypophthalmichthys molitrix (only one sample), the maximum intraspecific genetic distance among the remaining species was smaller than the minimum interspecific distance, which proves that the species exhibit obvious barcode gaps. In the Neighbor-Joining trees, 20 species formed separate monophyletic branches. According to ABGD analysis, 660 sequences were categorized into 19 Operational Taxonomic Units, with Silurus sp. and S. asotus grouped into a single OTU. The Silurus in this study exhibits shared haplotypes and significant genetic divergence, suggesting the potential presence of cryptic species. Furthermore, the nucleotide diversity across all species fell below the threshold level, indicating that the local fish population is gradually declining. In conclusion, this study has demonstrated the effectiveness of DNA barcoding in identifying fish species in the Ili River Valley, providing valuable data to support the conservation of local fish resources.

Combating Illegal Trade of Monitor Lizards (Varanus spp) in Malaysia through DNA Barcoding Applications

Abstract Varanids, known as monitor lizards are traded as pet animal commodities and demand for skin trade especially in Southeast Asian countries. Given the significant demand in the international trade, accurate species identification is imperative for Varanids particularly endangered species to prevent misidentification and fraud in marketplaces as Varanids species exhibit morphological similarities. Therefore, advanced molecular technique is vital to facilitate accurate species identification especially for closely related species. Besides, few research have used cytochrome oxidase subunit I (COI) to track the genetic and phylogenetic analysis of Varanids. In this study, the COI mitochondrial DNA region was tested as a molecular marker for species identification of Malaysia monitor lizards using the DNA barcode. Two species were successfully identified from eight samples from Pantai Penyabong, Mersing, Johor which are V. salvator and V. nebulosus based on phylogenetic analysis (Neighbor-Joining, Maximum Parsimony and Bayesian Tree). This study showed that by using their relative genetic divergence and evolutionary links, DNA barcodes can aid in the species identification through molecular technique. Short sequences can be used to identify closely related species, and the possibility of species misidentification among the study’s samples should be taken into account. DNA barcoding techniques should be widely practised especially in wildlife forensics to facilitate precise wildlife identification and improve the efficiencies in combatting illegal wildlife trade in Malaysia.

DNA barcoding of southern African mammal species and construction of a reference library for forensic application.

Combating wildlife crimes in South Africa requires accurate identification of traded species and their products. Diagnostic morphological characteristics needed to identify species are often lost when specimens are processed and customs officials lack the expertise to identify species. As a potential solution, DNA barcoding can be used to identify morphologically indistinguishable specimens in forensic cases. However, barcoding is hindered by the reliance on comprehensive, validated DNA barcode reference databases, which are currently limited. To overcome this limitation, we constructed a barcode library of cytochrome c oxidase subunit 1 and cytochrome b sequences for threatened and protected mammals exploited in southern Africa. Additionally, we included closely related or morphologically similar species and assessed the database's ability to identify species accurately. Published southern African sequences were incorporated to estimate intraspecific and interspecific variation. Neighbor-joining trees successfully discriminated 94%-95% of the taxa. However, some widespread species exhibited high intraspecific distances (>2%), suggesting geographic sub-structuring or cryptic speciation. Lack of reliable published data prevented the unambiguous discrimination of certain species. This study highlights the efficacy of DNA barcoding in species identification, particularly for forensic applications. It also highlights the need for a taxonomic re-evaluation of certain widespread species and challenging genera.

A DNA barcode reference library for the Tipulidae (Insecta, Diptera) of Germany.

Tipulidae, commonly known as true crane flies, represent one of the most species-rich dipteran families, boasting approximately 4,500 known species globally. Their larvae serve as vital decomposers across diverse ecosystems, prompting their frequent and close observation in biomonitoring programs. However, traditional morphological identification methods are laborious and time-consuming, underscoring the need for a comprehensive DNA barcode reference library to speed up species determination. In this study, we present the outcomes of the German Barcode of Life initiative focused on Tipulidae. Our DNA barcode library comprises 824 high-quality cytochrome c oxidase I (COI) barcodes encompassing 76 crane fly species, counting for ca. 54% of the German tipulid fauna. Our results significantly increased the number of European tipulid species available in the Barcode of Life Data System (BOLD) by 14%. Additionally, the number of barcodes from European tipulid specimens more than doubled, with an increase of 118%, bolstering the DNA resource for future identification inquiries. Employing diverse species delimitation algorithms - including the multi-rate Poisson tree processes model (mPTP), Barcode Index Number assignments (BIN), Assemble Species by Automatic Partitioning (ASAP), and the TaxCI R-script - we successfully match 76-86% of the morphologically identified species. Further validation through neighbor-joining tree topology analysis and comparison with 712 additional European tipulid barcodes yield a remarkable 89% success rate for the species identification of German tipulids based on COI barcodes. This comprehensive DNA barcode dataset not only enhances species identification accuracy but also serves as a pivotal resource for ecological and biomonitoring studies, fostering a deeper understanding of crane fly diversity and distribution across terrestrial landscapes.

Whole genome re-sequencing reveals high altitude adaptation signatures and admixture in Ladakhi cattle

Ladakhi cattle, native to the high-altitude region of Ladakh in northern India (ranging from 3,000 to 5,000 m above sea level), have evolved unique genetic adaptations to thrive in harsh environmental conditions, such as hypoxia, extreme cold, and low humidity. This study explored the genome of Ladakhi cattle to investigate genetic structure, selection signatures, and adaptive mechanisms. Whole genome sequencing reads, generated on Illumina NovaSeq 6000 platform, were aligned to the Bos taurus reference genome with BWA-MEM. SNPs were identified and filtered using GATK and bcftools, and functionally annotated with SnpEff. For population genomic analysis, PCA and admixture modeling assessed genetic structure, while Neighbor-Joining trees, LD decay, nucleotide diversity (π), and FST evaluated phylogenetic relationships and genetic variation. Selective sweeps were detected using RAiSD, and gene-set enrichment and protein–protein interaction analyses were conducted to explore functional pathways related to adaptation. The study revealed 3,759,279 unique SNPs and demonstrated that Ladakhi cattle form a distinct genetic cluster with an estimated admixture of 68 % Bos indicus and 32 % Bos taurus ancestry. Key findings include rapid linkage disequilibrium decay, low inbreeding level, and the identification of selection signatures and genes associated with hypoxia response, energy metabolism, and cold adaptation. Mean nucleotide diversity (π, 0.0037) and FST values indicated moderate genetic differentiation from other breeds. The analysis highlighted selection signatures for genes like HIF1A, ENO4, ANGPT1, EPO, NOS3, MAPK3, HMOX1, BCL2,CAMK2D, MTOR, AKT2,PIK3CB, and MAP2K1, among others, including various keratin and heat shock proteins. The interaction between genes associated with hypoxia signaling (HIF-1) and other enriched pathways such as PI3K, mTOR, NFκB, ERK, and ER stress, reveals a complex mechanism for managing hypoxic stress in Ladakhi cattle. These findings offer valuable insights for breeding programs aimed at enhancing livestock resilience in extreme environments and enhance understanding of mammalian adaptation to high-altitude conditions.

Population data for 12 X-STRs loci in Malaysian Malay and Chinese populations

The utilization of X-chromosome short tandem repeats (X-STRs) for human identification particularly in resolving complex kinship cases has been advocated. Since, forensic statistical parameters vary among different populations, and because the X-STRs population data representing the diverse population of Peninsular Malaysia remain unavailable, the specific attempt reported here for the Malays (n = 224) and Chinese (n = 201) populations appears forensically relevant to support the evidential value of the 12 X-STRs markers for human identification in Malaysia. Results derived from the Qiagen Investigator® Argus X-12 kit revealed that DXS10135 as the most polymorphic locus with high genetic diversity, polymorphic information content, heterozygosity as well as power of exclusion. Based on allele frequencies, the combined power of discrimination as well as the mean exclusion chance (MECKrüger, MECKishida, MECDesmarais and MECDesmaraisDuo) values for the Malays and Chinese were individually ≥0.999995532964908. As for the combined power of discrimination as well as the mean exclusion chance (MECKrüger, MECKishida, MECDesmarais and MECDesmaraisDuo) calculated based on haplotype frequencies, the values were ≥0.9999986410567 for the Malays and Chinese populations. In addition, results from the genetic distance, neighbor-joining phylogenetic tree and principal component analysis revealed close biogeographical distributions of the studied populations with other South East Asian populations. Hence, the utilization of the X-STRs data for identifying individuals among the Malays and Chinese populations in Peninsular Malaysia for forensic application appears as highly supported.

Analyzing Molecular Traits of H9N2 Avian Influenza Virus Isolated from a Same Poultry Farm in West Java Province, Indonesia, in 2017 and 2023

Background Indonesia is one of the countries that is endemic to avian influenza virus subtype H9N2. This study aims to compare the molecular characteristics of avian influenza virus (AIV) subtype H9N2 from West Java. Methods Specific pathogen-free (SPF) embryonated chicken eggs were used to inoculate samples. RNA extraction and RT–qPCR confirmed the presence of H9 and N2 genes in the samples. RT–PCR was employed to amplify the H9N2-positive sample. Nucleotide sequences were obtained through Sanger sequencing and analyzed using MEGA 7. Homology comparison and phylogenetic tree analysis, utilizing the neighbor-joining tree method, assessed the recent isolate’s similarity to reference isolates from GenBank. Molecular docking analysis was performed on the HA1 protein of the recent isolate and the A/Layer/Indonesia/WestJava-04/2017 isolate, comparing their interactions with the sialic acids Neu5Ac2-3Gal and Neu5Ac2-6Gal. Results RT–qPCR confirmed the isolate samples as AIV subtype H9N2. The recent virus exhibited 11 amino acid residue differences compared to the A/Layer/Indonesia/WestJava-04/2017 isolate. Phylogenetically, the recent virus remains within the h9.4.2.5 subclade. Notably, at antigenic site II, the recent isolate featured an amino acid N at position 183, unlike A/Layer/Indonesia/WestJava-04/2017. Molecular docking analysis revealed a preference of HA1 from the 2017 virus for Neu5Ac2-3Gal, while the 2023 virus displayed a tendency to predominantly bind with Neu5Ac2-6Gal. Conclusion In summary, the recent isolate displayed multiple mutations and a strong affinity for Neu5Ac2-6Gal, commonly found in mammals.

Niabella digestorum sp. nov., a High Cell-Surface Hydrophobic Bacterium Isolated from Waste Digestion System.

A high cell-surface hydrophobic bacterium, strain A18T, was isolated from a waste digestion system in Chaozhou, China. Cells of strain A18T were Gram-stain-positive, aerobic, non-spore-forming, non-motile, and rod-shaped. Phylogenetic analyses based on the 16S rRNA gene showed that strain A18T shared less than 94.2% sequence similarity to all validated species in the family Chitinophagaceae, and formed a distinct lineage close to genera Niabella and Terrimonas in the neighbor-joining tree, indicating that strain A18T is a novel species. Genome-based phylogenetic analyses revealed that strain A18T is affiliated to the genus Niabella. The cellular components, including iso-C15:0 and iso-C15:1 G as the major fatty acids, menaquinone-7 as the respiratory quinone and a DNA G + C content of 40.54% supported strain A18T as a member of the genus Niabella. However, the physiological and biochemical properties, such as enzyme activities, carbon source utilization and C18:0 3-OH as another major fatty acids, distinguished strain A18T from its close related species. Therefore, the name Niabella digestorum sp. nov. is proposed for this novel species. The type strain is A18T (= GDMCC 1.3242T = KCTC 92386T).

Genomic diversity and population structure of Carniolan honey bee in its native habitat

BackgroundResearch into the genetic diversity of honey bee (Apis melliferaL.) populations has become increasingly significant in recent decades, primarily due to population declines attributed to human activities and climate change. As a species of great importance, breeding programs that leverage understanding of genomic diversity could offer solutions to mitigate these challenges. The objective of this study was to examine the genomic diversity and population structure of Carniolan honey bees (Apis mellifera carnica) using the Illumina SNP chip on a large honey bee sample collected from Central and South-Eastern European countries. The study also aims to offer recommendations for future breeding programs.ResultsOur analysis involved Discriminant Analysis of Principal Components (DAPC), heterozygosity, admixture analysis, fixation indices (FST), Neighbour-Joining tree, gene flow and Isolation-by-distance analysis. DAPC indicated distinct separation between the Carniolan and Italian honey bee (Apis mellifera ligustica) populations, whereas the admixture analysis revealed varying levels of gene flow and genetic admixture within the Carniolan honey bee populations, demonstrating closer relationships between specific geographic regions (confirmed by Isolation-by-distance analysis). Furthermore, the research of heterozygosity, genomic inbreeding, pairwise FST values, and Neighbour-Joining tree provided insights into the patterns of genetic differentiation and similarity among the populations of Carniolan honey bee within its natural habitat. We have observed genetic homogeneity of the Carniolan honey bee population when considered in a broader genetic/geographical context. However, the Carniolan honey bee has sufficient genetic diversity in its geographical home range that needs to be carefully monitored and maintained.ConclusionsThis study provides important insights into the genetic composition, differentiation, and relationships among Carniolan honey bee populations in Central and South-Eastern European countries. The findings are crucial for conservation efforts, breeding programs, and sustainable beekeeping practices. They emphasise the importance of considering genetic factors and population structure in the breeding and management of honey bees. By understanding these genetic relationships, we can develop strategies to preserve genetic diversity, improve breeding outcomes, and ensure the resilience of honey bee populations in the face of environmental changes and challenges. This knowledge can also inform policy makers and stakeholders on best practices to maintain healthy bee populations, which are vital for ecosystem services and agricultural productivity.

Mining expressed sequence tag (EST) microsatellite markers to assess the genetic differentiation of five Hynobius species endemic to Taiwan

Taiwan harbors five endemic species of salamanders (Hynobius spp.) that inhabit distinct alpine regions, contributing to population fragmentation across isolated “sky islands”. With an evolutionary history spanning multiple glacial-interglacial cycles, these species represent an exceptional paradigm for exploring biogeography and speciation. However, a lack of suitable genetic markers applicable across species has limited research efforts. Thus, developing cross-amplifying markers is imperative. Expressed sequence-tag simple-sequence repeats (EST-SSRs) that amplify across divergent lineages are ideal for species identification in instances where phenotypic differentiation is challenging. Here, we report a suite of cross-amplifying EST-SSRs from the transcriptomes of the five Hynobius species that exhibit an interspecies transferability rate of 67.67%. To identify individual markers exhibiting cross-species polymorphism and to assess interspecies genetic diversity, we assayed 140 individuals from the five species across 84 sampling sites. A set of EST-SSRs with a high interspecies polymorphic information content (PIC = 0.63) effectively classified these individuals into five distinct clusters, as supported by discriminant analysis of principal components (DAPC), STRUCTURE assignment tests, and Neighbor-joining trees. Moreover, pair-wise FST values > 0.15 indicate notable between-cluster genetic divergence. Our set of 20 polymorphic EST-SSRs is suitable for assessing population structure within and among Hynobius species, as well as for long-term monitoring of their genetic composition.

Molecular epidemiology of brucellosis in Asia: insights from genotyping analyses.

Brucellosis infects humans and animals worldwide but is particularly prevalent in Asia. In many Asian countries, molecular diagnostic tools for accurate molecular diagnostics and molecular epidemiology are lacking. Nonetheless, some countries have conducted in-depth molecular epidemiological studies. The objective of this study was to reveal the genetic relationships, geographic origins, and distributions of Brucella strains across Asia for two primary species, B. abortus and B. melitensis. For this, we systematically searched genotyping data from published studies on the molecular epidemiology of Brucella species for both humans and livestock in Asia. We used data from multilocus sequence typing (MLST), multiple-locus variable-number tandem repeat analysis (MLVA), and whole genome sequencing analysis of Brucella strains. We also analyzed the MLVA genotypes of 129 B. abortus isolates and 242 B. melitensis isolates with known origins in Asia from an online MLVA database using MLVA-11 data in minimum spanning trees and MLVA-16 data in neighbor-joining trees. We found that the B. melitensis East Mediterranean lineage is predominant across the continent, with only a small number of samples from the Africa and Americas lineages, and none from the West Mediterranean lineage. The "abortus C" genotype was the most common group of B. abortus in Asia, with limited genetic variation for this species. Several studies also reported that Near Eastern countries frequently encounter human brucellosis cases of B. abortus from genotypes 42 and 43. Our study highlights the inconsistent collection of genetic data for Brucella species across Asia and a need for more extensive sampling in most countries. Finally, a consistent nomenclature is necessary to define various groupings of strains within a lineage (i.e., clade) so uniform terminology should denote particular genetic groups that are understood by all researchers.

Conservation genomic study of Hopea hainanensis (Dipterocarpaceae), an endangered tree with extremely small populations on Hainan Island, China.

Hopea hainanensis Merrill & Chun is considered a keystone and indicator species in the tropical lowland rainforests of Hainan Island. Owing to its high-quality timber, H. hainanensis has been heavily exploited, leading to its classification as a first-class national protected plant in China and a plant species with extremely small populations (PSESPs). This study analyzed genome-wide single nucleotide polymorphisms obtained through restriction site-associated DNA sequencing from 78 adult trees across 10 H. hainanensis populations on Hainan Island. The nucleotide diversity of the sampled populations ranged from 0.00096 to 0.00138, which is lower than that observed in several other PSESPs and endangered tree species. Bayesian unsupervised clustering, principal component analysis, and neighbor-joining tree reconstruction identified three to five genetic clusters in H. hainanensis, most of which were geographically widespread and shared by multiple populations. Demographic history analysis based on pooled samples indicated that the decline in the H. hainanensis population began approximately 20,000 years ago, starting from an ancestral population size of approximately 10,000 individuals. The reduction in population size accelerated approximately 4,000 years ago and has continued to the present, resulting in a severely reduced population on Hainan Island. Intensified genetic drift in small and isolated H. hainanensis populations may contribute to moderate differentiation between some of them, as revealed by pairwise F st. In conclusion, our conservation genomic study confirms a severe population decline and an extremely low level of nucleotide variation in H. hainanensis on Hainan Island. These findings provide critical insights for the sustainable management and genetic restoration of H. hainanensis on Hainan Island.

SSR-BASED ASSESSMENT OF GENETIC DIVERSITY IN BARLEY COLLECTION FROM THE STATE COMMISSION FOR VARIETY TESTING OF AGRICULTURAL CROPS OF KAZAKHSTAN

Barley (Hordeum vulgare L.) is a globally significant cereal crop with a substantial production footprint. As a versatile commodity, it serves as a primary resource for animal feed, malting, and human consumption. Genetic diversity among 49 barley accessions procured from the State Commission for Variety Testing of Agricultural Crops in Kazakhstan was assessed using a set of 21 SSR markers associated with various agronomic traits. The collection exhibited moderate genetic diversity, as indicated by a mean polymorphic information content (PIC) of 0.548 ± 0.153 and a mean Shannon's information index (I) of 0.980 ± 0.317, aligning with previously reported estimates of barley genetic variation in the World. STRUCTURE analysis identified three distinct population clusters (K = 3) using Bayesian clustering and DeltaK, which was confirmed by PCoA results. However, neighbor-joining tree analysis revealed a more detailed population structure with six distinct clusters, indicating substantial genetic diversity within the barley collection. Distinct phenotypic variations were observed among identified genetic clusters, implying a strong association between genetic diversity and agronomic traits, including plant height, kernel number per spike, and grain yield. Seven barley accessions (GSI_B_60, GSI_B_82, GSI_B_216, GSI_B_85, GSI_B_96, GSI_B_141, and GSI_B_208) forming a cluster NJ_tree_2 demonstrated the highest mean grain yield of 50.99 ± 2.95 g/ m2. This specific cluster and its constituent accessions exhibit promising potential for development into high-yielding cultivars or as a valuable source of beneficial alleles for barley breeding initiatives.