Microsatellite Loci Research Articles

Polymorphism of microsatellite loci of yaroslavl cattle in herds of various breeding values

The paper presents the results of studying the polymorphism of microsattellite loci of Yaroslavl cattle in breeding herds of the Yaroslavl region. 115 alleles with different frequency of occurrence were identified for 15 microsatellite DNA loci. From 5 to 11 alleles were identified in each of the studied loci. The average number of alleles per locus was 6.41, the number of effective alleles was 3.58. The highest incidence (0.75) in the entire population was found in locus SPS115 with allele 248, its distribution ranged from 0.72 to 0.83 across farms. For the SPS115 locus, the rare alleles are 252, 254 and 256. 6 alleles were identified at the BM1818 locus. Allele 266 has the highest frequency of occurrence in all the studied herds, and alleles 262, 264 and 270 are present in sufficient numbers. The allele 182 has the highest frequency of occurrence in herds at the BM1824 locus (from 0.46 to 0.64), with an average of 0.51 in the sample. Rare alleles have been identified, which are present only in individual herds with a frequency of occurrence from 0.01 to 0.02. The average number of observed heterozygosity was 0.71, and the expected one was 0.60% less than the observed one. The study found that the first hard the heifers had the highest yield (6871 kg, p < 0.001), rare alleles were identified in this herd – 179 at the CSSM66 locus and 268 at the BM1818 locus. The largest number of alleles, which are not present in other herds, was revealed in the breeding herd III. The higher fat content was obtained from the first heifers of this herd – 4.36% and the higher protein content – 3.45%.The fixation index in all the studied herds was negative (-0.019), which indicates an excess of heterozygotes. The obtained data will allow controlling the level of homozygosity in herds, and taking into account the allelic polymorphism of the breeding stock when fixing bulls of producers to obtain breeding offspring and in custom mating.

An updated reference genome of Barbatula barbatula (Linnaeus, 1758)

The stone loach Barbatula barbatula is a benthic fish species widely distributed throughout Europe, primarily inhabiting stony upper sections of stream networks. This study presents an updated genome assembly of B. barbatula, contributing to the species’ available genomic resources for downstream applications such as conservation genetics. The draft assembly was 550 Mbp in size, with an N50 of 11.21 Mbp. We used the species’ available chromosome scaffolds to finish the genome. The final assembly had a BUSCO score of 96.7%. We identified 23270 protein-coding genes, and the proteome exhibited high completeness with BUSCO (93.1%) and OMArk (90.81%). Despite using multiple approaches to reduce duplicate contigs, we observed a relatively high duplicate ratio of 6.1% (BUSCO) and 8.52% (OMArk) in the annotations. We aimed to find microsatellite loci present in both the species’ publicly available genome and the new assembly to aid marker development for downstream analyses. This dataset serves as a reference for genomic analysis and is useful for developing markers to study the species’ biodiversity and support conservation efforts.

Range-wide understanding of genetic diversity and population structure of endangered Kashmir musk deer in North-Western Himalaya.

The endangered Kashmir musk deer (Moschus cupreus), native to high-altitude Himalayas, is an ecological significant and endangered ungulate, threatened by habitat loss and poaching for musk pod distributed in western Himalayan ranges of India, Nepal and Afghanistan. Despite its critical conservation status and ecological importance in regulating vegetation dynamics, knowledge gaps persist regarding its population structure and genetic diversity, hindering effective management strategies. We aimed to understand the population genetics of Kashmir musk deer in north-western Himalayas using two mitochondrial DNA (mtDNA) regions and 11 microsatellite loci. Total of 63 consensus sequences were analyzed, revealing 10 haplotypes with high haplotype diversity (Hd = 0.906 ± 0.031) and moderate nucleotide diversity (π = 0.00539 ± 0.004) at mitochondrial markers. Microsatellite analysis indicated moderate genetic variability, with observed heterozygosity (Ho = 0.445 ± 0.049) and expected heterozygosity (He = 0.764 ± 0.039), comparable to the forest musk deer but relatively lower than that observed in other ungulates. Population structure analysis identified three potential genetic clusters, with evidence of genetic admixture in the Lahaul Valley, possibly due to gene flow from neighboring areas. Historical demographic analyses using Bayesian skyline plots and mismatch distribution curves indicated stable population sizes in the past, followed by recent declines in maternal effective population size. Our findings highlight the necessity of preserving the genetic diversity of the Kashmir musk deer to ensure its long-term survival. We recommend expanding the geographic range of sampling to include regions such as Chamba and Kinnaur districts in Himachal Pradesh, potential areas in Jammu and Kashmir and Uttarakhand, for more comprehensive population-level analysis. Such efforts will be crucial for developing targeted conservation strategies and mitigating the impacts of human activities on this endangered species.

Comparing microsatellites and single nucleotide polymorphisms to evaluate genetic structure and diversity in wolverines (Gulo gulo) across Alaska and western Canada

Abstract The Wolverine (Gulo gulo) is a cold-adapted species of conservation interest because it is sensitive to human development, disturbance, exploitation, and climate warming. Wolverine populations have been studied across much of their distributional range to evaluate patterns of genetic diversity, genetic structure, and gene flow. Little population structure has been detected in northwestern North America with microsatellite loci, but low genomic diversity in wolverines may limit detection of genetic differences in this highly vagile species. Here, we genotyped a relatively large sample of wolverines from across Alaska (US) and adjacent Yukon (Canada) with 12 microsatellite loci (n = 501) and 4,222 single nucleotide polymorphisms (SNPs; n = 201) identified using restriction-site associated DNA sequencing. We compared the relative ability of our microsatellite and SNP datasets to evaluate population genetic structure, genetic diversity, differentiation, and isolation by distance (IBD). We predicted that the SNP dataset would detect a higher degree of genetic structure and provide more significant support for IBD. We found evidence for multiple genetic clusters, including genetic distinctiveness of wolverines in southeast Alaska and on the Kenai Peninsula. The SNP dataset detected additional genetic clusters that align largely with ecoregions, and the SNP dataset showed stronger evidence of IBD, while the 2 datasets were generally consistent in estimates of genetic diversity and differentiation among regional groups. Our results highlight the importance of genomic methods to assess gene flow in wolverines. Identifying population genetic structure allows an assessment of the potential impacts of conservation threats and is an important precursor for designing population monitoring programs.

Similar phylogeographic history in a fig species and its obligate pollinators forms parallel genetic structure

Abstract Closely related and co-distributed species usually share a common phylogeographic history, but it is still largely unclear whether ecologically interacting species can respond synchronously to historical climate changes. Here, we focused on a fig-pollinator mutualism comprising Ficus pumila var. pumila and its obligate pollinators (morphospecies Wiebesia pumilae), and collected samples across most of their distribution ranges. We employed both cytoplasmic DNA sequences and nuclear microsatellite loci to reveal the species composition within the pollinator and to test whether the two mutualists exhibited similar postglacial phylogeographic patterns. In the three cryptic pollinator species observed here, two dominant cryptic species were parapatric, covering the north and the south of the plant’s distribution range, respectively. Similar current spatial genetic structure was detected in the two dominant cryptic pollinator species and the plant, with an eastern and a western genetic cluster. Moreover, for these three species, evidence for postglacial expansion was found, and their potential refugia at the last glacial maximum were located in the east and the west of their distribution ranges. These results suggest their synchronous responses to historical climate changes. Our study therefore shows congruent phylogeographic patterns between obligate mutualists and highlight the role of biogeographic factors in shaping the current biodiversity across trophic levels.

Parentage Verification and Segregation Distortion Patterns of Microsatellite Markers in Olive Flounder (Paralichthys olivaceus) Full-Sib Families.

Microsatellite markers are widely used in aquaculture for genetic analysis and breeding programs, but challenges such as segregation distortion and allelic instability can impact their effectiveness in parentage verification and inheritance studies. This study evaluated 15 microsatellite loci in seven experimental olive flounder (Paralichthys olivaceus) families bred through 1:1 full-sibling crosses, assessing their utility for accurate parentage and inheritance stability. Parentage assignments were conducted within an expanded pool of 647 candidate parents (including the actual 14 parents), encompassing both closely related and moderately distant individuals. Despite increased genetic diversity, assignments maintained a high accuracy rate (99.6%), demonstrating marker robustness. Differences in delta values highlighted the influence of genetic backgrounds on assignment clarity, with some groups showing reduced distinctiveness in the expanded pool. Segregation distortion was observed at certain loci, deviating from Mendelian inheritance, likely due to meiotic drive and post-zygotic selection. These findings underscore the need for empirical validation of microsatellite loci for stable inheritance and reliable parentage in diverse breeding programs, especially with genetically similar spawners.

Genetic diversity and intercontinental dispersal of temperate and subarctic populations of Dibothriocephalus dendriticus (Cestoda; Diphyllobothriidea), a causative agent of dibothriocephalosis.

The diphyllobothriid tapeworm Dibothriocephalus dendriticus, one of the causative agents of the fish-borne zoonosis dibothriocephalosis, is mainly distributed in the Arctic/subarctic and temperate zones of the Northern Hemisphere (Europe, North America, and Asia), but also in the southern cone region of South America (Patagonia). The genetic structure and gene flow among 589 individuals of D. dendriticus, representing 20 populations, were studied using the mitochondrial cox1 gene as the first choice marker and 10 polymorphic nuclear microsatellite loci as a dominant molecular tool. The haplotype network of 30 cox1 haplotypes and Principal Coordinate Analysis/Structure analysis based on microsatellite data revealed close genetic relationships among populations within continents, namely northern and northwestern Europe (Norway, Finland, and UK/Scotland), North America (USA/Alaska, USA/Oregon, and Greenland), and South America (Argentina and Chile). The population from Iceland, located on the Mid-Atlantic Ridge between North America and Europe, was related to both Europe and North America. The mixed Nearctic and Palaearctic origin of D. dendriticus in Iceland was confirmed by a coalescent-based analysis of the microsatellite loci (in Migrate software). The most likely scenarios suggested that the Icelandic population is a genetic admixture of tapeworms from northwestern Europe and USA/Alaska. These findings corresponded with the distribution and migratory routes of piscivorous birds of the family Laridae, the main definitive hosts of D. dendriticus. The origin of an apparently non-native population of D. dendriticus in Patagonia was investigated in detail. The two most plausible hypotheses based on Migrate analysis represented different scenarios. One of them points to a European origin of the Patagonian population, the other to a North American origin. Future research with more extensive and a geographically broader sampling set is recommended to trace dispersal routes of D. dendriticus in Patagonia.

The impact of selective logging on the genetic diversity of Rubroshorea johorensis in the tropical rainforest

The tropical rainforest of Kalimantan, Indonesia, is dominated by a mixed dipterocarp forest. Rubroshorea johorensis is a commercial species of the Dipterocarpaceae family but is listed as vulnerable. So far, the management of natural forests through selective logging may have a negative impact on genetic diversity. Therefore, this study was conducted to determine the genetic diversity of R. johorensis in different forest types representing the management and silvicultural techniques in the tropical rainforest of Kalimantan, including virgin forest (V1-V4 populations), logged over area/LOA (L1-L3 populations), and stand established by enrichment planting after selective logging (E1-E3 populations). The study applied both expressed sequence tags microsatellite (EST-SSR) loci and genomic microsatellite loci. The AMOVA showed that genetic differences among forest types were minimal (2.48%), with most of the variation occurring within individuals (78.51%). All genetic diversity variables of R. johorensis were not significantly different among forest types, although with respect to all genetic variables, enrichment planting was the highest, and LOA was the lowest. The research suggested that selective logging slightly reduced the genetic diversity of R. johorensis, and the enrichment planting using intensive silvicultural technique could increase all genetic variables and the potential of residual stand. In addition, the established R. johorensis progeny trial using selected mother trees from the surrounding concession area is useful for improving the genetic quality and conserving genetic resources in the future. The success of massive rehabilitation in the LOA will promote the standing stock and maintain the forest genetic resources. Furthermore, the consistent involvement of forest concessionaires and government support is crucial for the sustainable management of R. johorensis in its natural habitat.

Assessing Genetic Diversity and Population Structure of Western Honey Bees in the Czech Republic Using 22 Microsatellite Loci.

To date, no study has been conducted to investigate the diversity in honeybee populations of Apis mellifera in the Czech Republic. Between 2022 and 2023, worker bees were collected from colonies distributed throughout the Czech Republic in 77 districts, and their genetic differences were examined using 22 microsatellite loci. The samples were obtained from hives (n = 3647) and through the process of capture on flowers (n = 553). Genetic diversity parameters were assessed for both populations in all 77 districts. The findings demonstrated that honeybee populations exhibit moderate genetic diversity, as evidenced by the number of observed alleles, the Shannon index, and heterozygosity values. There was no discrepancy in diversity between hive and flower samples. Diversity characteristics were determined: mean observed heterozygosity 0.55 (hives) and 0.56 (flowers), and fixation index 0.58 for both populations. The average number of alleles per locus was 13.77 and 11.18 from hives and flowers, respectively. The low FST and FIS values (they measured the level of genetic differentiation between populations and the level of inbreeding, respectively) suggest the absence or minimal genetic diversity within and among studied populations. The genetic variation was calculated as 2% and 1% between populations, 8% and 6% between individuals within populations, and 91% and 93% between all individuals in samples from hives and flowers, respectively. Cluster and DAPC (discriminant analysis principal component) analysis classified the bee samples collected from across the country into three and five to six distinguishable groups, respectively. The honeybee population in the Czech Republic displays sufficient diversity and a partial structure. However, there appears to be no correlation between the genetic groups and the geographic regions to which they are assigned.

Fine-Scale Genetic Structure of Small Fish Populations in Islands: The Case of Brook Charr Salvelinus fontinalis (Mitchill, 1814) in Saint-Pierre and Miquelon (France).

Island ecosystems, particularly vulnerable to environmental challenges, host many endangered native species. Diadromous fish, in particular, are threatened throughout their marine and freshwater habitats. The conservation of these species requires an in-depth understanding of their genetic diversity and structure, to better understand their adaptive potential. We investigated fine-scale population diversity and structure in native brook charr (Salvelinus fontinalis) by genotyping 10 microsatellite loci in 244 individuals at three spatial scales in Saint-Pierre and Miquelon, France. We found limited genetic variability across the archipelago, with particularly low genetic diversity in one island, Langlade. A significant difference in allelic richness was also detected among the three islands, indicating a difference in genetic composition across the archipelago, probably induced by historical stocking actions on both Saint-Pierre and Miquelon. Finally, a strong genetic structure was detected across the archipelago among hydrosystems (overall F ST = 0.19) and even within several of them. The presence of predominant interisland gene flow combined with complete genetic isolation from certain hydrosystems suggests that this contemporary genetic structure is the result of both natural demographic processes during the species postglacial colonization and recent restocking actions. The complex genetic structure of such isolated brook charr subpopulations highlights the importance of considering fine-scale genetic structure in conservation management.

Spatio-Temporal Patterns of Hybridization in an Alloploid Salamander (Ambystomatidae: Ambystoma) and Conservation Implications of Introgression in a Unisexual Vertebrate.

Maynard Smith's proposed two-fold cost of sex states that one of the disadvantages of clonal reproduction is the decreased ability to persist in dynamic ecosystems. However, the long-term persistence of some clonal alloploid lineages suggests that these lineages may not always be so ephemeral in nature. Understanding the stability of these lineages over time can inform our understanding of the advantages of an asexual mode of life. Here we investigate a gynogenetic allopolyploid triploid, the Silvery Salamander (LJJ-historically referred to as Ambystoma platineum), an asexual lineage closely related to A. barbouri. However, in our focal populations, neither parental species is present, and another sexual host, A. texanum (TT), is a required sperm donor. Gynogenetic reproduction involving LJJ and its host A. texanum should result in a clone of the mother (LJJ); however, with the occurrence of kleptogenesis, it often can result in tetraploid hybrids (LJJT). LJJ is considered endangered in this population due to its restricted range coupled with concerns that the cryptic tetraploid (LJJT) could completely replace LJJ. Here we assess the level of LJJ × A. texanum hybridization in nine ephemeral wetland populations in east central Illinois. Using species-specific microsatellite loci, we compared the prevalence of LJJ and LJJT genotypes across localities and years. We find variation across ponds and developmental stages but suggest relative stability over time. Given the considerable amount of environmental degradation and loss, we suggest continued monitoring of this unique segment of biodiversity to ensure its persistence into the future.

Characterization of nuclear microsatellites in Marchantia polymorpha (liverwort) with additional trans-specific analyses.

Microsatellites are present in mitochondria, chloroplast, and nuclear DNA, but nuclear microsatellites are more useful genetic tools than those in plastids or mitochondria. Plastid and mitochondrial microsatellites have been identified in the model plant Marchantia polymorpha (liverwort), but no laboratory has published information on nuclear microsatellite loci. The aim of this study was to detect novel nuclear markers in the most commonly employed liverwort species, design PCR primers that would allow amplification, and characterize the subsequently generated loci. We detected 18 polymorphic nuclear loci in M. polymorpha, amplifiable by PCR across all chromosomes. Additionally, trans-specific amplification of the eighteen loci was characterized in the closely related taxa Marchantia emarginata and Marchantia paleacea. All loci were present in M. paleacea, whereas 17 of 18 primer pairs were amplified in M. emarginata.

Genetic Diversity of Bali Cattle Base on Two Microsatellite Loci - INRA032 and BM2113

Genetic Diversity of Bali Cattle Base on Two Microsatellite Loci - INRA032 and BM2113

Genome-Wide In Silico Analysis of Microsatellite Loci in Rabbits.

This study aimed to characterize microsatellites in the rabbit genome using an in silico approach and to develop and validate microsatellite markers. Blood samples were collected from 15 Baladi rabbits and 18 New Zealand White (NZW rabbits). The GMATA software was used to define SSRs in the extracted sequences. Twelve primer pairs were used to validate the loci identified and the primers developed. The total number of the detected microsatellite loci overall chromosomes was 1,136,253. The di-nucleotide microsatellite repeats dominated and exceeded 88% of the detected microsatellites in all chromosomes. There were no microsatellites detected in mitochondrial DNA. The highest relative microsatellite abundance was obtained for chromosome 19, followed by 13 and 6. The highest estimated SSR density was obtained for chromosome 14, and the lowest was for mitochondrial DNA, followed by chromosome 13. The polymorphism was 81.63% and 75.51% for Baladi and NZW rabbits, respectively. The number of detected alleles ranged between two and seven alleles/loci, and polymorphic information content was from 35% to 71%. The AMOVA analysis showed that the total variance of all levels of population structure was 15.734. The results definitely confirmed higher genetic diversity in Baladi compared with NZW rabbits.

Chromosome-Level Genome Assembly and Genetic Maker System of the Endangered Largemouth Bronze Gudgeon (Coreius guichenoti) with Focus on Conservation Applications.

The largemouth bronze gudgeon (Coreius guichenoti), an endemic fish species, is distributed in the upper Yangtze River drainage. Due to anthropogenetic factors such as water pollution, overfishing, and dam construction, the wild populations of C. guichenoti have dramatically declined in recent decades. In this study, we generated a reference chromosomal-level genome assembly of C. guichenoti on the basis of PacBio HiFi sequencing and Hi-C scaffolding technologies. The final genome assembly was 1.10 Gb in length (contig N50: 28.64 Mb; scaffold N50: 42.39 Mb) with 25 chromosomes. The completeness score of the C. guichenoti genome was 96.4%, and high synteny was detected compared with Danio rerio and Ictalurus punctatus genomes. A total of 24325 PCGs were annotated for the C. guichenoti genome. Comparative genomics analysis identified 986 expanded gene families in C. guichenoti, which were significantly enriched in GO items associated with the development and interaction of sperm and egg as well as immunity. Furthermore, positively selected genes (PSGs) detected in C. guichenoti were mainly associated with DNA repair, ATP binding, mitochondrion, and lipid homeostasis. Based on the reference genome and resequencing data, the polymorphic microsatellite (SSR) loci were comprehensively analyzed for C. guichenoti, and the top 15 tetra-nucleotide SSR loci were selected for the construction of the genetic maker system after validation through PCR and genotyping. All of these 15 tetra-nucleotide SSR loci without Hardy-Weinberg equilibrium (HWE) deviation showed high polymorphism, good amplification stability, and selective neutrality. The PID (sibs) curves revealed that the subset of four tetra-nucleotide SSR loci (cgui1, cgui5, cgui3, cgui13) was sufficient for accurate identification of C. guichenoti individuals (PIDsib < 0.01). These 15 tetra-nucleotide SSR loci could also serve as genetic markers in subsequent parentage identification and genetic diversity analysis. The chromosome-level genome assembly and findings laid solid foundations for molecular breeding, genomic research, and biological conservation of C. guichenoti.

Genetic Characterization of Captive South American Fur Seals in Japan Based on Mitochondrial and Microsatellite DNA Analyses.

Molecular genetic analyses are effective in revealing the origin, kinship, and genetic diversity of zoo animals. In this study, we carried out the genetic characterization of captive founder individuals of the South American fur seal (Arctocephalus australis) in Japanese zoos and aquariums based on analyses of mitochondrial sequences and nuclear microsatellite loci. In mitochondrial DNA analysis, the haplotype diversity and nucleotide diversity of the overall population were 0.8949 and 0.0119, respectively. Microsatellite DNA analysis revealed that the observed heterozygosity within the overall population was 0.722. In addition, we did not detect genetic bottlenecks. The results from two kinds of DNA analyses indicated that the genetic diversity in this captive population was equivalent to that previously reported in wild populations. The detected mitochondrial haplotypes were the same as or phylogenetically close to those previously reported in wild populations in southern Brazil, Uruguay, Argentina, and southern Chile but diverged from those previously reported in a wild population in Peru. Genetic clustering analyses using microsatellite genotypes revealed that no clear genetic structures in this captive population.

Genetic Structure and Diversity of Eurasian Otter (Lutra lutra) in Northern Eurasia and Caucasus: Are There Any Differences Between the Two Subspecies?

The Eurasian otter (Lutra lutra) is a widespread semiaquatic carnivorous mammal in Eurasia. The nominate subspecies (L. l. lutra) occupies vast areas between Western Europe and the Russian Far East, but its phylogeography and genetic diversity are still unclear across Northern Eurasia. Another subspecies, L. l. meridionalis, located in the Caucasus mountains, is morphologically almost identical to L. l. lutra but needs genetic revision. We compared the genetic diversity of Eurasian otters from Russia and Armenia using a mtDNA fragment (820 bp) and 20 autosomal microsatellite loci (N = 117). A total of 32 haplotypes were observed with 17 novel haplotypes. The MtDNA median-joining network was mostly star-shaped with a branch of haplotypes from Far Eastern Russian otters. Both mtDNA analysis and Bayesian clustering of microsatellite data indicated that Far Eastern otters are more genetically differentiated than European and Siberian otters (Φst = 0.565 and 0.467; Rst = 0.306 and 0.256), as well as Caucasian otters (L. l. meridionalis) from Russia and Armenia (Φst = 0.515, Rst = 0.253). Haplotype and nucleotide diversities of Far Eastern otters are also the highest between sample groups (H = 0.882, π = 0.003) and, of Caucasian otters, the lowest (H = 0.464, π = 0.001). Our results suggest Caucasian otters are more similar to the otters from European Russia than to the other groups (but with lower genetic diversity) and lack the genetic variability typical to different subspecies. On the contrary, otters from the Russian Far East are more genetically differentiated, have higher genetic diversity than otters from Europe, and likely belong to another genetic lineage.

Population genetics of Salvator merianae (Reptilia, Teiidae) in its southernmost distribution

The black and white tegu (Salvator merianae, Duméril and Bibron, 1839) is the most widespread lizard species in the southern part of South America. This is an important species as a natural resource, traditionally used for food and traded as leather and pets, and this intensive exploitation can be important for regional economies in their range. We analyzed their genetic diversity, structure, and mating system in Argentina using the mitochondrial ND4 locus and 10 microsatellite loci. We hypothesized low genetic diversity, high levels of interpopulation structure, and multiple paternal contribution to clutches. Our results support our hypotheses, detecting two divergent mitochondrial haplogroups, low levels of allelic diversity and low to medium population structure values using microsatellites, and that S. merianae is both polygynous and has multiple paternal contributions to the clutches we analyzed. These results are informative for the on-going sustainable use-based management of S. merianae, ensuring the sustainability of its commercially exploited populations and the habitats on which they depend.

Genetic variability of Scots pine (&lt;i&gt;Pinus sylvestris&lt;/i&gt; L.) plus trees in the Middle and Upper Volga Region based on polymorphism of nSSR markers

BACKGROUND: One of the key issues in the area of forest selection is how to mitigate the risks evolving changes in the genetic structure and loss of diversity of future artificial forests due to the use of plus trees for seed production. Therefore, there should be studies aiming at assessing the genetic variability of plus trees selected for phenotypic traits in natural populations. AIM: The aim of this study is to examine of variability and differentiation of Scots pine plus trees selected for phenotypic traits from the Chuvash Republic, the Republic of Tatarstan and the Republic of Mari El with the use of nSSR markers. MATERIALS AND METHODS: Using five microsatellite loci, the authors assessed 207 plus trees of Scots pine from the Chuvash Republic, the Republic of Tatarstan and the Republic of Mari El. RESULTS: The number of alleles differed from 33 to 37 for various groups of plus trees. Thus, plus trees from the Mar El Republic are specified by a reduced level of diversity (Na = 6.6; Ne = 3.5; Ho = 0.361; He= 0.687) as compared to trees from the Chuvash Republic (Na = 7.4; Ne = 4.8; Ho = 0.503; He= 0.778) and the Republic of Tatarstan (Na = 6.8; Ne = 4.4; Ho = 0.570; He = 0.739). The groups of plus trees are slightly differentiated, and the genetic subdivision index equaled to 0.023. The major part of the nSSR marker polymorphism is within the groups of plus trees (98.0 %). CONCLUSIONS: The plus trees under study differ in the level of genetic variability. Relatively low allelic diversity and a large deficit of heterozygote are typical for all groups. Thus, we may conclude that the plus trees are compatible with natural populations of Scots pine grown in the Middle and Upper Volga Region in terms of distribution of genetic variability and differentiation.

Paleoclimate Fluctuations Facilitate the Biogeographical History of Endemic Species of Freshwater Crabs in China via Cycles of Introgressive Hybridisation and Habitat Isolation

ABSTRACTAimThe impact of Pleistocene climate fluctuations on the biogeographical history of aquatic species has been a topic of enduring debate. This issue poses particular challenges for parapatric closely related species, especially those situated in transition zones where species assemblages occur between distinct zoogeographic boundaries.LocationEastern China.TaxonFive closely related Sinopotamon species and subspecies, S. shensiense, S. honanense, S. y. yangtsekiense, S. y. shanxianense, and S. y. tongbaiense.MethodsThese parapatric Sinopotamon species and subspecies, distributed along the boundary between the Palaearctic and Oriental realms in eastern China, offer an ideal model for addressing these challenges. We explored the biogeographic history of these species by conducting a comparative phylogeographic analysis using nine microsatellite loci and two mitochondrial DNA sequences, combined with morphological variation and fine‐tuned ecological niche modelling.ResultsOur phylogeographic analyses consistently revealed two well‐supported clades: clade A, for S. y. yangtsekiense, and clade B, which includes other species showing polyphyletic patterning and significant gene introgression. The Nanyang Basin and surrounding mountains regions (NBSM) was identified as a critical shared refuge and hybrid zone, facilitating interspecific introgression through at least two putative hybridisation events. During the Late Pleistocene glacial cycles, introgressive hybridisation of these species occurred in the NBSM, followed by rapid expansion and colonisation of heterogenous habitats during interglacial cycles, with dispersal corridors largely aligning with the local river system. In particular, the diffusion corridor of S. honanense significantly disrupted the continuous distribution of S. y. shanxianense and S. y. tongbaiense, indicating that S. honanense has replaced S. y. shanxianense and S. y. tongbaiense in the NYSM and caused a disruption in its distribution.Main ConclusionsThe biogeographic histories of the species in clade B are consistent with a mixing–isolation–mixing model, which suggests that populations experienced repeated introgressive hybridisation during glacial periods and regional habitat isolation during interglacial periods. Our findings represent a classic case of fine tracking biogeographical scenarios in parapatric species and provide unprecedented insights into the evolutionary radiation of the freshwater fauna that occupies zoogeographic boundaries.