Haplotype Diversity Research Articles

Genetic diversity of Dalbergia melanoxylon Guill. & Perr. populations in the Ferlo zone (Senegal) using nuclear and chloroplast microsatellite markers

AbstractDalbergia melanoxylon Guill. & Perr. is a highly valued species in the Ferlo region, and its wood is used for various purposes by local populations, including firewood, service wood, and timber. This multifunctionality has weakened its populations, and it has been identified as threatened in previous research. The aim of this study was to investigate the genetic variability of three populations (LC, VC, and YC) along a north–south rainfall gradient, to support the species’ sustainable management and conservation. Eighteen microsatellite markers were used, including eight nuclear (nSSR) and 10 chloroplast (cpSSR) markers, to test their transferability to D. melanoxylon and study the genetic variability. The results showed that all nSSRs and cpSSRs were transferable, however, only five nSSRs and one cpSSR were polymorphic and used in the downstream analysis. Based on the nSSRs, comparatively high, but non-significantly different, genetic variation was found in all populations (LC: He = 0.650, VC: He = 0.674, YC: He = 0.706), however, indications of inbreeding were detected. For the single polymorphic cpSSR, three haplotypes were identified. Haplotype diversity (Hd) varied in LC (Hd = 0.536), VC (Hd = 0.577), and YC (Hd = 0.674). Low to moderate genetic differentiation was observed between populations (Fst nSSR = 0.019 and Fst cpSSR = 0.133) suggesting recent fragmentation of populations that has not yet impacted genetic variation but could become more pronounced in future generations. This finding underscores the need for further research on effective management and conservation strategies for D. melanoxylon populations in the Ferlo region.

Global Invasion of Thrips parvispinus (Karny) (Thysanoptera: Thripidae) Across Three Continents Associated With Its One Haplotype

ABSTRACTThrips parvispinus (Karny) is an exotic pest that has invaded many regions around the world in the last three decades. It was first detected in Florida in 2020 on ornamental plants (Hoya and Anthurium) in greenhouses and subsequently on ornamental plants in residential landscapes (Gardenia) in 2021. However, its first report on open vegetable field crops (Capsicum) in Florida was in 2022. We conducted field surveys and genetic analysis to answer three questions: (1) Is the population of T. parvispinus that invaded Florida the same as the one that has spread globally in the last few decades? (2) Is the host expansion to Capsicum in Florida a new population or the extension of the existing population reported on ornamental plants? and (3) What are the native and invaded distribution ranges of T. parvispinus? We analysed the genetic variation in the mitochondrial gene cytochrome oxidase I (COI) to address these questions. The global genetic diversity analysis of T. parvispinus revealed 18 haplotypes (populations) worldwide based on available data, but only one population (Hap1) invaded three continents: Africa, Europe, and North America. Based on available data, the highest haplotype diversity was observed in India, suggesting India may be part of the presumed native range (South and Southeast Asian countries) of T. parvispinus. Our survey of retail plant stores across 10 Florida counties indicated that plant trade is the source of T. parvispinus in open vegetable field crops and ornamental landscape plants. The outcome of this study will assist with regulatory and management decisions of T. parvispinus in Florida and elsewhere.

Genetic Variation and Population Structure of Clonorchis sinensis: An In Silico Analysis

Clonorchis sinensis is an important zoonotic parasite that is mainly prevalent in China, Korea, Vietnam and the Russian Far East. To explore the genetic variation and population structure of C. sinensis, an in silico analysis was conducted based on mitochondrial cytochrome c oxidase subunit 1 (COX1), ribosomal internal transcribed spacer 1 (ITS1) and ribosomal internal transcribed spacer 2 (ITS2) sequences. The sequences obtained from NCBI were truncated for further analyses, including haplotype network, phylogenetic, gene flow, diversity and neutrality analyses. The results showed that there were 20, 11 and 4 haplotypes for COX1, ITS1 and ITS2, respectively. The results of both the haplotype network and phylogenetic analyses indicated that the haplotypes for each type of sequence from the same country were not all clustered together. Haplotype diversity values were all lower than 0.5. Values of nucleotide diversity were higher than 0.005, except for ITS2. Tajima’s D and Fu’s Fs values were all negative, and p-values showed significant differences, indicating that the population of C. sinensis is growing. Fst values were all lower than 0.05. In conclusion, this study found that there are specific variations of C. sinensis in different countries, and the population of this parasite is growing with less genetic variation. The findings provide a crucial foundation for understanding the molecular epidemiology and population dynamics of C. sinensis.

Declining genetic polymorphism of the C-terminus Merozoite Surface Protein-1 amidst increased Plasmodium knowlesi transmission in Thailand.

Recent reports from Thailand reveal a substantial surge in Plasmodium knowlesi cases over the past decades, with a more than eightfold increase in incidence by 2023 compared to 2018. This study investigates temporal changes in genetic polymorphism associated with the escalating transmission of P. knowlesi malaria in Thailand over time using the prominent vaccine candidate, pkmsp1 as a marker. Twenty-five P. knowlesi samples collected in 2018-2023 were sequenced for the 42-kDa region of pkmsp1 and compared with 24 retrieved sequences in 2000-2009, focusing on nucleotide diversity, natural selection, recombination rate, and population differentiation. Seven unique haplotypes were identified in recent samples, compared to 15 in earlier samples. Nucleotide and haplotype diversity were lower in recent samples (π = 0.016, Hd = 0.817) than in earlier samples (π = 0.018, Hd = 0.942). Significantly higher synonymous substitution rates were observed in both sample sets (dS-dN = 2.77 and 2.43, p < 0.05), indicating purifying selection and reduced genetic diversity over time. Additionally, 8 out of 17 mutation points were located on predicted B-cell epitopes, suggesting an adaptive response by the parasites to evade immune recognition. Population differentiation analysis using the fixation index (Fst) revealed high genetic differentiation between parasite populations in central and southern Thailand or Malaysia. Conversely, the relatively lower Fst value between southern Thailand and Malaysia suggests a closer genetic relationship, possibly reflecting historical gene flow. This study highlights a decline in genetic diversity and evidence of purifying selection associated with the recently increased incidence of P. knowlesi malaria in Thailand. The minor genetic differentiation between P. knowlesi populations from southern Thailand and Malaysia suggests a shared recent ancestry of these parasites and underscores the need for coordinated efforts between the two countries for the elimination of P. knowlesi.

Population genetic structure of the bottlenose dolphin in the Turkish waters based on mtDNA sequences with implications for the Black Sea subspecies Tursiops truncatus ponticus

The bottlenose dolphin is a widely distributed species found in temperate waters, including the Mediterranean and Black Seas. The Black Sea population is recognized as a distinct subspecies, Tursiops truncatus ponticus, due to genetic and morphological differences. This study analyzed mitochondrial DNA (mtDNA) sequences of 73 bottlenose dolphin samples collected between 1999 and 2016 along the Turkish Black Sea coast, Turkish Straits System (TSS), Aegean, and Mediterranean Seas revealing 14 haplotypes, eight of which are reported here for the first time. The haplotype network shows two main nodes with star-like sub-networks, but no apparent geographic pattern. The lack of geographical groupings of haplotypes indicates the high mobility of the species within the sampled area. The northern Black Sea bottlenose dolphins (NBS) appear to be genetically differentiated from those in the southwestern Black Sea (SBS), Mediterranean, and Atlantic Ocean, but not from the TSS and Aegean Sea populations. Besides, SBS bottlenose dolphins were differentiated only from those in the western Mediterranean (WM) and the Atlantic. Therefore, NBS and SBS bottlenose dolphins should at least be categorized as different populations. However, contrary to some previous studies there was no evidence supporting the classification of Black Sea bottlenose dolphins as a separate subspecies. The TSS differs only from the Atlantic and the Aegean, and functions like a migratory ‘melting pot’ for surrounding populations. Despite the largest sample size, NBS bottlenose dolphins exhibited the lowest haplotype and nucleotide diversity. This low genetic diversity and potential isolation from adjacent populations highlight the need for prioritizing the conservation of NBS bottlenose dolphins.

Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean.

The timing of flowering in soybean [Glycine max(L.) Merr.], a key legume crop, is influenced by many factors, including daylight length or photoperiodic sensitivity, that affect crop yield, productivity, and geographical adaptation. Despite its importance, a comprehensive understanding of the local linkage landscape and allelic diversity within regions of the genome influencing flowering and contributing to phenotypic variation in subpopulations has been limited. This study addresses these gaps by conducting an in-depth trait association and linkage analysis coupled with local haplotyping using advanced bioinformatics tools, including crosshap, to characterize genomic variation using a pangenome dataset representing 915 domesticated and wild-type individuals. The association analysis identified eight significant loci on seven chromosomes. Moving beyond traditional association analysis, local haplotyping of targeted regions on chromosomes 6 and 20 identified distinct haplotype structures, variation patterns, and genomic candidates influencing flowering in subpopulations. These results suggest the action of a network of genomic candidates influencing flowering time and an untapped reservoir of genomic variation for this trait in wild germplasm. Notably, GlymaLee.20G147200 on chromosome 20 was identified as a candidate gene that may cause delayed flowering in soybean, potentially through histone modifications of floral repressor loci as seen in Arabidopsis thaliana (L.) Heynh. These findings support future functional validation of haplotype-based alleles for marker-assisted breeding and genomic selection to enhance latitude adaptability of soybean without compromising yield.

Integrated Genetic and Statolith Shape Analysis Reveals the Population Structure of Loliolus (Nipponololigo) uyii (Cephalopoda: Loliginidae) in the Coastal Waters of China

Understanding population structure is a priority for evaluating population dynamics of commercially fished cephalopods under fishing pressure and environmental changes. This study employed a multidisciplinary approach to clarify the population structure of Loliolus (Nipponololigo) uyii, a common squid in inshore fisheries. Sampling was conducted multiple times to cover the distribution range across the East China Sea and South China Sea. High haplotype diversity was revealed by three gene markers (COI, 16S and ODH). Two geographical clades with significant genetic differentiation were divided through phylogenetic trees and haplotype networks. The boundary between the two clades is delineated by the Dongshan population in the southern East China Sea. Furthermore, the neutrality tests and mismatch analysis suggested that L. (N.) uyii populations may have undergone population expansion. Correspondingly, statolith differences in lateral dome and posterior indentation, along with high classification success, further supported the genetic division. The overall difference in statolith shape also efficiently identified seasonal groups in the Beibu Gulf lacking genetic differentiation. This result offers new insights into the influence of genetic and environmental factors on statolith shape. The integrated results provide a comprehensive understanding of the population structure of L. (N.) uyii, laying the foundation for resource development and the conservation of the species.

Mitogenome diversity and evolution of Bos indicus cattle in India.

Mitochondrial DNA has been widely utilized as a valuable tool for studying the evolutionary and demographic history both within and between different livestock speciesover the past three decades. Evaluation of the evolutionary history, population structure and genetic diversity is imperative for their productivity, ecosystem services, and breeding and conservation strategies for effective management. The present study included complete mitogenome of 78 cattle, out of which 33 samples belonged to 6 Bos indicus breeds of India. Mitogenome diversity of zebu cattle within population (π- nucleotide, haplotype diversity) was estimated using DnaSP v6 software and between populations (FST ratio, AMOVA analysis) was estimated using Arlequin 3.5.2.2. Ladakhi breed showed maximum (π = 0.00645) while Gir (π = 0.00042) and Tharparkar (π = 0.00053) showed minimum diversity. The diversity between the breeds of Indian cattle was 16.34 %. There were 13 and 14 haplotypes in each of I1 and I2 halogroups respectively suggesting that the divergence of Bos indicus haplotypes likely occurred within the Indian subcontinent. The Bos indicus and Bos taurus cattle lineages separated approximately 0.75 million years ago. The divergence pattern observed in zebu cattle highlighted the probability of a distinct ancestor and supported notion of independent divergence of Bos indicus.

Microsatellite Markers & Mitochondrial D-Loop Based Phylogenetic And Diversity Analysis In Gabrali Cattle.

The Gabrali cattle is a multipurpose breed, native to Khyber Pakhtunkhwa, Pakistan. Despite its economic importance, scientific data about its phylogeny and genetic diversity is scarce. To address this issue, the present study was conducted on thirty (30) unrelated Gabrali male and female animals, from which blood samples were collected and DNA was extracted. Twelve (12) microsatellite loci and 1159bp of D-loop region were amplified via PCR and visualized on a 2% agarose gel. Sanger sequencing technique was used to sequence the D-loop amplicons. The microsatellite loci revealed 83 alleles with MNA (mean no of alleles per locus) = 8.8, the Ho (observed heterozygosity) and He (expected heterozygosity) of all loci were 0.58 and 0.50 respectively, mean PIC (Polymorphic Information content) = 0.59 and FIS (Inbreeding coefficient) = 0.056 using GeneAlEx® software. Microsatellite analysis revealed a normal allelic distribution across the breed, consistent with Hardy-Weinberg equilibrium. D-loop sequencing revealed eight haplotypes with 30 SNPs using DNA SP 6.0 software. High AT content was observed than GC content i.e. 55.9% and 44.1% respectively, while the transition to transversion ratio was R = 10:1. The value of Haplotype and Nucleotides diversity was Hd = 0.8601 ± SD = 0.0895 and Π = 0.0136 ± SD = 0.00197 respectively. Phylogenetic analysis done using Neighbor-joining method with bootstraps value of 1000, revealed the monophyletic clade of both Gabrali and Bos indicus haplotypes. Furthermore, the introgression of genes from national cattle breeds into Gabrali cattle was observed. It is concluded that Gabrali cattle have common ancestry with Bos indicus having no threats of genetic bottleneck having substantial genetic diversity.

Genetic diversity of Plasmodium vivax population in northeast Myanmar assessed by amplicon sequencing of PvMSP1 and PvMSP3α

This study aimed to assess the baseline genetic diversity of the Plasmodium vivax population in an endemic area of northeast Myanmar at the onset of the malaria elimination campaign in the Greater Mekong Subregion. We genotyped 125 P. vivax clinical samples at two merozoite surface protein loci, PvMSP1 and PvMSP3α, by amplicon deep sequencing. Our study revealed that the parasite population in this region was highly diverse, identifying 60 PvMSP1 and 98 PvMSP3α haplotypes, with haplotype diversity of 0.929 and 0.944, respectively. Remarkably, 97.6% (122/125) of the patients harbored multiclonal infections with a mean multiplicity of infection of 4.18, indicating a relatively high transmission intensity. Neutrality tests and network analysis suggested a recent parasite population expansion, consistent with the concurrent malaria outbreak in the region. These findings underscore the existence of a highly diverse P. vivax population at the China-Myanmar border, highlighting the need for effective malaria control strategies to achieve the goal of regional malaria elimination.

Combining Morphological and Molecular Tools Can Enhance Tick Species Identification for Improved Tick-Borne Disease Surveillance Among Pastoral Communities in Kenya.

Background: Ticks are ecto-parasites of domestic animals, rodents, and wildlife living for periods at a time on one or more vertebrate hosts. They are important vectors of viral, bacterial, or parasitic diseases in livestock and humans. Crimean-Congo haemorrhagic fever virus and the spotted fever rickettsiae are some of the tick-borne diseases of public health importance reported in Kenya. Their distribution and public health risks among communities, especially pastoralists, remain poorly characterized due to limited surveillance, affected partly by inadequate capacity for tick identification arising from a limited number of skilled taxonomists. Materials and Methods: The aim of this survey was to identify tick species currently circulating in different livestock hosts in northern Kenya. Ticks were sampled from cattle, sheep, goats, and camels in Turkana, Isiolo, Baringo, and West Pokot counties, and differential identification was carried out using morphological identification keys followed by molecular characterization based on the cytochrome c oxidase I gene (cox1). Haplotypes were determined using the DnaSP v6 software and phylogenetic relationships inferred using the maximum likelihood algorithm. Results: A total of 12,206 ticks were collected, from Turkana (45.4%), Isiolo (23.1%), Baringo (22.7%), and West Pokot (8.8%) counties in Kenya. Ten species were confirmed by molecular analysis; H. rufipes, H. impeltatum, H. dromedarii, R. pravus, R. camicasi, R. pulchellus, R. evertsi evertsi, A. variegatum, A. gemma, and A. lepidum. There was no disparity in the morphological and molecular identification of Amblyomma species. However, molecular analysis provided insight into the complexity of morphological identification especially among Hyalomma and Rhipicephalus species. High haplotype diversities (0.857-1.000) and low nucleotide diversities (0.00719-0.06319) were observed in all the tick samples tested. Conclusion: The findings highlight the diversity of tick species in dry pastoral ecologies in Kenya and the importance of confirming morphological identification by molecular analysis thus contributing to accurate mapping of tick-borne disease distribution and risk.

Genetic analyses of Anisakis pegreffii (Nematoda: Anisakidae) from the East Asian finless porpoise Neophocaena asiaeorientalis sunameri (Cetacea: Phocoenidae) in Korean waters

The East Asian finless porpoise, Neophocaena asiaeorientalis sunameri, is an endangered species that inhabits the coastal marine environments of East Asia. In the present study, we investigated the overall infection status of anisakid nematodes in East Asian finless porpoises from three sea sectors off the Korean Peninsula. The genetic diversity and population genetic structure of the identified nematode species were evaluated. The prevalence of all stages of anisakid nematodes collected from the stomach was 57.55% (61 among the 106 porpoises examined), and 16 of the hosts were found to have adult worms. The mean number of infected adults was 211 (± 419.54, 5–1455 per host). Only one species of anisakids, Anisakis pegreffii, was identified from randomly selected worms by molecular approaches. Analysis of the mitochondrial (mt) cox2 partial gene in 50 newly generated sequences of A. pegreffii revealed 24 haplotypes, including 14 new haplotypes. We observed below-average levels of nucleotide diversity and haplotype diversity compared to other seas around the world. The mtDNA cox2 haplotypes of the species in the three Korean sea areas showed no genetic structure, suggesting well-connected gene flow within these areas. This study represents the first record of a definitive host of A. pegreffii in Korean waters, providing important information regarding anisakids genetic diversity in the cetacean species inhabiting limited regions.

Genetic and Haplotype Diversity of Clarias gariepinus (Burchell 1822) Based on Cytochrome c Oxidase I (COI) Gene

The evaluation of mitochondrial DNA and genetic analysis is helpful for economically significant species. Clarias gariepinus is a critical species in aquaculture. This study investigates the genetic diversity and population differentiation of C. gariepinus from 19 countries using 164 sequences of the mitochondrial DNA’s Cytochrome c oxidase I (COI) gene. The haplotype analysis revealed a total of 17 haplotypes, with a nucleotide diversity (π) of 0.012 and a haplotype diversity (Hd) of 0.87. The results of an AMOVA and fixation index indicated significant genetic variation and structure among the populations. Additionally, neutrality tests and mismatch distribution analysis supported the hypothesis of under-purifying selection in C. gariepinus. The findings suggested that the population did not experience expansion. In conclusion, the genetic analysis highlighted substantial variation among C. gariepinus populations from different locations, providing valuable insights for the global management of this species.

Genetic diversity and molecular evolution of the internal transcribed spacer regions (ITS1–5.8S–ITS2) of Babesia vogeli

Canine babesiosis, a severe haemoparasitic disease caused by Babesia species, has a significant global presence and can be fatal if left untreated. The current study was aimed to perform the population genetic characterization of B. vogeli on the basis of the internal transcribed spacer regions (ITS1–5.8S–ITS2). A maximum likelihood tree constructed with the Hasegawa-Kishino-Yano model grouped all sequences into a single major clade (BvG1), with the exception of a Taiwanese isolate (EF186914), which branched separately. This Taiwanese isolate represented a novel genotype (BvG2) identified in the present study. Nucleotide sequences (n = 62) exhibited 92.5–100 % nucleotide identity among themselves. However, the BvG1 and BvG2 genotypes shared a lower identity of 92.5–93.8 % between them. Notably, the newly generated Indian sequences (n = 21) demonstrated a high degree of homology, with 98.3–100 % identity. Alignment of the nucleotide sequences revealed 58 variations across the dataset. Additionally, 32 sites exhibited variation within the BvG1 genotype, while 56 sites differed between BvG1 and BvG2 genotypes. Within different B. vogeli populations, the nucleotide diversity (π) was low, but the haplotype diversity (Hd) was high. The haplotype diversity of the Indian population, BvG1 genotype, and the combined dataset was ∼0.8 suggesting a high haplotype diversity. The median-joining haplotype network displayed a total of 21 haplotypes, out of which six haplotypes consisted of more than one sequence (2–25 sequences). Haplotype distribution showed significant geographical structuring, with most haplotypes confined to a single country. Only two haplotypes (9.52 %; Hap_1 and Hap_4) were shared between countries, whereas 19 haplotypes (90.48 %) were country-specific. Hap_1, Hap_6, and Hap_4 were the most representative haplotypes, comprising 25, 10, and four sequences, respectively. India exhibited the highest number of haplotypes (h = 13) followed by China (h = 4), the United States of America (h = 3), Taiwan and Tunisia (h = 2), and Thailand (h = 1). Both location-wise and genotype-wise median joining haplotype networks clustered the haplotypes in two groups, representing two distinct genotypes (BvG1 and BvG2). The B. vogeli populations between Thailand and Tunisia exhibited the highest genetic differentiation (FST = 0.80) with a low gene flow (Nm = 0.125) between them. Results of AMOVA revealed a higher genetic variation within populations (69.43 %) as compared to the variation between them (30.57 %). Neutrality indices and the mismatch distributions of the Indian population and the overall dataset of B. vogeli indicated a constant population size to population expansion and population expansion, respectively, with the presence of two distinct genotypes. These data provide information about parasite population genetics and highlight the importance of starting a long-term molecular surveillance program. In conclusion, a high genetic diversity along with the presence of two distinct genotypes of B. vogeli were observed on the basis of internal transcribed spacer regions (ITS1–5.8S–ITS2).

Multiple Maternal Lineages of &lt;i&gt;Strauchbufo raddei&lt;/i&gt; (Strauch, 1876) in Mongolia Revealed by Mitochondrial DNA

The Mongolian toad Strauchbufo raddei (Strauch, 1876) is one of widely distributed and dominated amphibian species in eastern Asian, including Mongolia. In this study, we amplified and sequenced a total of 50 samples of S. raddei, from three main regions in its Mongolian distribution range namely, Northern, Eastern, and Gobi regions. Our phylogenetic trees (Bayesian inference; BI and time-calibrated) and network analysis clearly support presence of multiple maternal mitochondrial DNA lineages for S. raddei in Mongolia. As expected, samples from these three regions were clustered separately in BI tree (Bayesian posterior probability (BPP 0.52). In addition, the population specific haplotypes, estimated genetic distances (e.g. uncorrelated p distance; ranged from 1% to 25%) and hierarchical AMOVA suggested relatively strong population genetic structure of S. raddei across Mongolia. Time-calibrated tree and ancestral range analysis showed that the first colonization of S. raddei may have occurred in Northern part of Mongolia approximately 9.63 mya, then dispersed over other parts of the country. Estimated approximate time for crossing event of S. raddei over dry steppe and semi-desert regions in Mongolia was 5.02 – 2.50 mya. Finally, high level of genetic diversity (overall; haplotype diversity, Hd = 0.93; nucleotide diversity, π = 0.011) of S. raddei were observed in Mongolia. Importantly, through this study, we contributed to closing sampling gaps in distribution range of S. raddei in Eastern Asia, which is key to better understanding species history, as well as describing cryptic lineages.

Genetic variability and discriminatory power of RM Y-STRs in gilgit men: a population study

AbstractShort Tandem Repeats (STRs) found on the Y chromosome have multiple applications, such as in forensic investigations, male identification for legal reasons, as well as population genetics. However, commercially accessible Y-STR tests are limited in their capability to distinguish closely linked male individuals in forensic genetics. Recent studies have revealed that Rapidly Mutating Y-STRs (RM Y-STRs) offer significantly greater haplotype diversity around the worldwide populations associated to conventional Y-STRs, though some RM Y-STR loci are not contained, current commercial kits. The objective of this research is to create a database of RM Y-STR haplotype frequencies for the Gilgit population in Pakistan and evaluate the effectiveness of these genetic markers in distinguishing individuals with genetic variations. The research involved examining several RM Y-STRs in 56 unrelated Gilgit men. The statistical analysis determined that the majority of the loci-maintained haplotype values, as specific varied in certain cases. The results presented that the RM Y-STRs were very effective in distinguishing genetic changes among the Gilgit population, through a GD value of 0 for DYD403S1 and GD values greater than 0.7 for all other loci, with maximum value of 0.9920 for the RM Y-STR DYS612.

To be, or not tu-be? Population structure and connectivity in three Arctic kinorhynch species: Echinoderes aquilonius, Echinoderes eximus and Echinoderes remanei

The Arctic, despite being profoundly affected by global climate change, remains largely understudied. Its local ecosystems and fauna are undergoing significant changes, including marine meiobenthic invertebrates, such as kinorhynchs. However, although they are an important component of the benthic meiofauna, our understanding of their communities remains relatively limited. The present study focuses on the structure and connectivity of the populations of three Echinoderes species: Echinoderes aquilonius, Echinoderes eximus and Echinoderes remanei, inhabiting the coastal area of Disko Island (Western Greenland). A hypothesis of low population diversity was tested through analyses based on both morphology and the molecular cox1 marker. For the first time the distribution and relationships between and within species were described. Phylogenetic analysis and haplotype networks reflected the results of population statistics (nucleotide and haplotype diversity, Tajima's D and Fu's Fs), revealing expected homogeneity and low diversity, without any noticeable patterns of geographical distribution. The results indicate that Arctic kinorhynchs form progressively developing and expanding communities. Additionally, the analyses revealed a taxonomically important example of intraspecific polymorphism. Presence or absence of tubes are usually considered to be species diagnostic characters, and the finding an isolated population of E. eximus-like specimens with sublateral tubes on segment 9, suggested that this could be a new, yet undescribed species. However, the genetic divergence between these specimens and other populations of E. eximus without tubes on segment 9 was so low that they all have to be considered conspecific. This is the first time molecular sequence data has provided evidence for intraspecific tube polymorphism among kinorhynchs.

Polymorphic Loci of Adaptively Significant Genes Selection for Determining Nucleotide Polymorphism of Pinus sylvestris L. Populations in the Urals

Background: Scots Pine is one of the main forest-forming species in boreal forests; it has great economic and ecological significance. This study aimed to develop and test primers for detecting nucleotide polymorphisms in genes that are promising for detecting adaptive genetic variability in populations of Pinus sylvestris in the Urals and adjacent territories. Objectives: The objects of the study were 13 populations of Scots Pine located in the Perm Territory, Chelyabinsk Region, and the Republic of Bashkortostan. Results: Sixteen pairs of primers to loci of potentially adaptively significant genes were developed, from which three pairs of primers were selected to detect the nucleotide diversity of the studied populations. The indicator of total haplotype diversity determined in the three studied loci varied from 0.620 (Pinus-12 locus) to 0.737 (Pinus-11 locus) and, on average, amounted to 0.662. The nucleotide diversity indicators in P. sylvestris in the study region were, on average, low (π = 0.004, θW = 0.013). Their highest values were found at the Pinus-12 locus (π = 0.005; θW = 0.032), and the lowest were found at the Pinus-15 locus (π = 0.003; θW = 0.002). This indicates that Pinus-15 is the most conserved of the three studied loci. In the three studied P. sylvestris loci associated with adaptation to environmental factors, 97 polymorphic positions were identified. The 13 populations of P. sylvestris are characterized by an average level of genetic diversity (Hd = 0.662; π = 0.004; θ = 0.013). Conclusions: The polymorphic loci of adaptively significant genes of P. sylvestris can help identify the adaptive potential of pine forests in conditions of increasing ambient temperatures.

Persistence Over Millennia Through Extreme Clonal Longevity: Phylogenomic Insight Into History of One of the World's Rarest Plant Species

ABSTRACTAimThe evolutionary history of European alpine plant species with medium to large geographical ranges is relatively well explored. Here, we investigate the genetic structure and diversity of an extremely narrow endemic and one of the world's rarest plants.LocationEastern Carpathians, Romania.TaxonAndryala laevitomentosa (Asteraceae), an evolutionarily isolated herb species with a worldwide range limited to five micropopulations distributed along a 1.8 km long mountain ridge.MethodsWe used three plastid loci, nuclear ribosomal ITS and genome‐wide, mostly nuclear 26,272 Single‐Nucleotide Polymorphism (SNPs) obtained from RAD‐seq data. We assessed haplotype and genotype diversity, dated the resulting phylogeographic structure, quantified seed production and inferred vegetative propagation.ResultsMaternally inherited plastid markers and nuclear genomic data revealed a concordant pattern: (i) limited genetic diversity, with seven cpDNA haplotypes and 11 RAD‐seq multilocus genotypes; (ii) a strong geographic structure corresponding to spatially isolated genets (clones). The species is likely of early Pleistocene origin (c. 2 Mya), and the estimated age of individual clones varied from c. 24 to 64 Kya. The average seed set assessed over 3 years was only 0.4%. However, the species reproduces veg by axillary and adventitious rosettes formed on rhizomes and roots, respectively.Main ConclusionsThe strong trade‐off between sexual and vegetative reproduction explains not only a deep and ancient phylogeographic structure but also the rarity of the species. Its survival depends almost entirely on vegetative reproduction. The genets of A. laevitomentosa are amongst the oldest clones ever documented in angiosperms. The persistence of these clones in situ for tens of thousands of years suggests an exceptional ability of this species to adapt to major climatic oscillations throughout the Pleistocene and Holocene and challenge our perception of the extent of resilience in plants.

Reconstruction of the human amylase locus reveals ancient duplications seeding modern-day variation.

Previous studies suggested that the copy number of the human salivary amylase gene, AMY1, correlates with starch-rich diets. However, evolutionary analyses are hampered by the absence of accurate, sequence-resolved haplotype variation maps. We identified 30 structurally distinct haplotypes at nucleotide resolution among 98 present-day humans, revealing that the coding sequences of AMY1 copies are evolving under negative selection. Genomic analyses of these haplotypes in archaic hominins and ancient human genomes suggest that a common three-copy haplotype, dating as far back as 800 KYA, has seeded rapidly evolving rearrangements through recurrent non-allelic homologous recombination. Additionally, haplotypes with more than three AMY1 copies have significantly increased in frequency among European farmers over the past 4,000 years, potentially as an adaptive response to increased starch digestion.