Search

High-altitude regions like the Himalaya, where various slopes are present on a very small spatial scale, are one of the best natural laboratories for investigating how genetic diversity and population structure are distributed across altitudinal gradients. In this study, we investigate the magnitude of genetic diversity and population structure of Rhododendron anthopogon D.Don along an altitudinal gradient in the Kashmir Himalaya. We used the start codon targeted (SCoT) marker to evaluate the genetic diversity and differentiation between different populations across five sites along an altitudinal gradient ranging from 3200 to 4000 m (amsl). Our results demonstrate that the magnitude of genetic diversity differs among the populations of R. anthopogon along the altitudinal gradient. We observed a decreasing trend in genetic diversity with increasing altitude from site-1 to site-3 (3200 to 3600 m), and an increasing trend from site-4 to site-5 (3601 to 4000 m). Furthermore, we also observed the highest genetic diversity at upper altitude (site-5) and the lowest at mid-altitude (site-3). Our results reveal a high genetic differentiation (Gst = 0.7349) and a low gene flow (Nm = 0.1804) among the populations. Analysis of molecular variance (AMOVA) reveals 71% variation among the populations and 29% variation within the populations. We also reveal positive associations between geographic and genetic distances, indicating isolation by distance effect across all altitudes. STRUCTURE and cluster analysis divided all the populations of R. anthopogon into five clusters according to their geographical location. Overall, the study adds to our understanding that altitude is the major driver of genetic variation and differentiation between populations of R. anthopogon which may help increase its range under ongoing projected climate change. Our study also reveals that populations at higher altitudes are not genetically isolated, suggesting that they might be an essential source for migration in the era of climate change. [ABSTRACT FROM AUTHOR]

The giant freshwater prawn, Macrobrachium rosenbergii, is one of the most crucial crustacean species cultured in China. However, in recent years, M. rosenbergii aquaculture in China has encountered several challenges, including low productivity and growth retardation. A decline in genetic variation has been implicated in this phenomenon. This study aims to develop microsatellite multiplex PCR panels to elucidate the genetic diversity and differentiation of cultured M. rosenbergii populations in China. Based on our previous transcriptome sequencing, we developed 24 polymorphic molecular markers. The average number of alleles (Na), observed heterozygosity (Ho), expected heterozygosity (He), and polymorphism information content (PIC) were 4.042, 0.535, 0.605, and 0.543, respectively. Two multiplex PCR panels involving six microsatellite loci were obtained by combining different amplicon lengths from these 24 loci. The panels were used to evaluate the genetic structure of six cultured M. rosenbergii populations in China, including one population in Guangxi (GX) and another in Guangdong (GD) province, along with two populations each in Jiangsu (JSA and JSB) and Zhejiang (ZJA and ZJB) provinces. Results revealed that the polymorphism among the six populations ranged from 0.365 to 0.682 with reduced genetic diversity in ZJA and JSB populations (PIC < 0.5). Pairwise FST, Nei's genetic distance, and STRUCTURE analysis revealed significant differentiation among the six cultured populations. ZJA and GD exhibited pronounced genetic distinctiveness from the other populations and were consequently assigned to distinct groups. Populations GX and JSB (FST=0.058, DA=0.045) and populations ZJB and JSA (FST=0.009, DA=0.016) were assigned to two clusters, respectively, suggesting they share similar origins. This study provided polymorphic microsatellite markers and genetic diversity assessment of cultured M. rosenbergii populations, laying a foundation for future breeding programs. [ABSTRACT FROM AUTHOR]

Assisted gene flow can restore genetic diversity when genetic drift has driven deleterious alleles to high frequencies in small, isolated populations. Previous crosses among 20 populations of Gymnadenia conopsea documented the strongest heterosis and the weakest inbreeding depression in sparse and small populations, consistent with fixation of mildly deleterious alleles by genetic drift. We genotyped the populations used for crosses, and used 1200–1728 SNPs to test the following predictions: (1) heterosis increases with genetic differentiation (FST) to donor populations and decreases with genetic diversity in the recipient population, (2) inbreeding depression increases with genetic diversity, and (3) genetic diversity increases, and mean FST to other populations decreases, with population size and density. Pairwise FST ranged from very low to moderate (0.005–0.20) and genetic diversity varied moderately among populations (proportion of polymorphic loci = 0.52–0.75). However, neither FST between populations, nor genetic diversity in the recipient population, were related to the strength of heterosis. There was also no association between genetic diversity and the strength of inbreeding depression. Genetic diversity increased and mean FST decreased with population size, consistent with reduced diversity and increased differentiation of small populations by genetic drift. The results indicate that the loci conferring heterosis are not mirrored by overall population differentiation, and limited additional information on potential source populations for genetic rescue is gained by the genetic data. Instead, the use of controlled crosses can directly reveal positive effects of introducing new genetic material, and is a simple method with high potential in conservation. [ABSTRACT FROM AUTHOR]

Aquaculture in sub‐Saharan African accounts for less than 2% of world aquaculture production. The use of unimproved species limits the growth of aquaculture. In order to increase production, there is a need to develop aquaculture species that show vigor and adapt to different culture conditions. A genetic improvement program for Oreochromis shiranus was initiated at the National Aquaculture Center (NAC), in Zomba, Malawi. The program used pedigree records during mate allocation to avoid mating of siblings. After six consecutive generations of selection, a sample of 32 fish was taken for genetic analysis using a panel of 16 microsatellite markers. Genetic diversity and population differentiation indices of the sixth filial generation (F6) were compared with wild fish populations sampled from the corresponding locations from which the initial brood stock was collected. The study results show that the genetic diversity of the F6 generation and wild populations was not significantly different after the Kruskal–Wallis tests. However, the number of private alleles was lower in generation F6 (0.80) than in the overall average for wild populations (1.28). Discriminant analysis of principal components (DAPCs) supported analysis of molecular variance (AMOVA) by showing that there were no significant overlaps of inertia ellipses among F6 generation and wild populations. The experimental population differentiated into a separate group because of the random brood stock contribution from only a few fish from the wild population. The results suggest that the initial genetic diversity of the brood stock was sufficient as shown by the high number of alleles and polymorphic information content (PIC) values which contributed to the success of the selection program. The selection program successfully produced large fish at harvest and ensured genetic diversity of the F6 generation. [ABSTRACT FROM AUTHOR]

The great web‐spinning sawfly Acantholyda posticalis is notorious for damaging Pinus forests across the Palearctic region. At present, uncertainties persist regarding its intraspecies variation and presumed subspecies. To use as tools for future studies, herein we developed genome‐wide microsatellite markers for A. posticalis. Through searching, rigorous manual screening, and amplification trial, 56 microsatellite markers were obtained from the genome sequences. We characterized these markers across two populations from Shandong province (SD) and Heilongjiang province (HLJ) in China, and carried out cross‐amplification in three related species. Out of the 56 markers tested, 10, 31, and 15 were categorized into high, moderate, and low polymorphic levels, respectively, based on their polymorphic information content (PIC) values. Meanwhile, 28, 19, and 4 microsatellite loci were successfully cross‐amplified in Cephalcia yanqingensis, C. chuxiongica, and C. infumata, respectively, which could serve as potential molecular markers for their further studies. STRUCTURE and PCoA analyses revealed two distinct clusters corresponding to SD and HLJ, respectively, indicating a high resolution of these markers. Therefore，the 56 microsatellite markers identified here have the potential to serve as efficient tools for unraveling intraspecies variation and evolutionary history of A. posticalis. [ABSTRACT FROM AUTHOR]

Human activity often has profound effects on plant growth and evolution. Orchids are the most diverse group of flowering plants and are threatened by habitat fragmentation, over-harvesting, and urbanization. A population of Phaius flavus from Beikengding Mount (BM) in the Fujian Province of China was divided into two patches by road construction. This study evaluated its genetic characteristics using restriction site-associated DNA sequencing (RAD-seq) data, more than seven years post-road construction. The purpose of this study was to explore the impact of road construction on the evolution of isolated patches within a population. The analysis revealed that the genetic diversity of patch B was slightly higher than that of patch A in the BM population of P. flavus. Principal component and phylogenetic analyses, genetic structure and genetic differentiation analysis, and bottleneck detection indicated relatively independent genetic differentiation between the two patches. Thus, the construction of the Y013 village road may have influenced different patches of this population on a genetic level. This study provides a case for understanding the impact of specific human activities on plant populations, and then biodiversity conservation. It is conducive to formulating more effective biological protection strategies to mitigate the damage inflicted by human activities on biodiversity. [ABSTRACT FROM AUTHOR]

This study aimed to compare and assess the genetic diversity and trends among the introduced family provenance, first-cycle superior trees breeding provenance, and improved-generation superior trees breeding provenance of Pinus elliottii using EST-SSR markers. The goal was to provide a foundation for advanced genetic improvement and sustainable utilization of P. elliottii in Jiangxi Province. A total of 417 individuals were analyzed for their genetic diversity and population structure using 19 pairs of SSR markers. The analysis identified 103 alleles across all the samples, with an average of 5.421 alleles per locus. Compared to other coniferous species, P. elliottii exhibited a moderate to high level of genetic diversity (I = 0.862, He = 0.457). Analysis of the molecular variance (AMOVA) revealed that 97.90% of the genetic variation occurred within provenances, consistent with a low genetic differentiation coefficient (Fst = 0.016 < 0.05) and high gene flow (Nm = 15.715) among provenances. In addition, analysis using STRUCTURE v. 2.3.4 software divided the 417 germplasm samples into two distinct groups, corroborating the results of the principal coordinates analysis (PCoA) and the unweighted pair group method with arithmetic (UPGMA) clustering analysis. Overall, the germplasm resources of P. elliottii exhibited rich genetic diversity, with the majority of the genetic variation occurring within provenances. For the genetic improvement of high-resin-yielding slash pines, breeding programs should prioritize populations with high genetic diversity while carefully selecting superior individuals from within those populations. These findings provide a solid foundation for breeding high-resin-yielding varieties and for future research on the sustainable utilization of these valuable resources. [ABSTRACT FROM AUTHOR]

Simple Summary: This study analyzes fecal samples from Siberian roe deer in the Greater Khingan Range of Heilongjiang Province, using mitochondrial DNA and microsatellite markers to explore the population's genetic characteristics. The findings indicate a high level of genetic diversity within the Siberian roe deer population, alongside notable genetic differentiation among groups. Furthermore, this research offers vital insights for the conservation and management of Siberian roe deer and provides valuable data for the protection of local Northeast tigers (Pantheratigris altaica). This study focuses on the Siberian roe deer population in the Greater Khingan Mountains, Northeast China. The cold temperate forest ecosystem in this area is distinctive. The Siberian roe deer is a crucial ecological indicator species, and its living conditions hold significant importance for ecological balance. From the winter of 2019 to 2022, 269 fecal samples of Siberian roe deer were collected from four protected areas in the northern part of the Greater Khingan Mountains, Heilongjiang Province. These samples were comprehensively analyzed using mitochondrial DNA and microsatellite markers, combined with conservation genetics evaluation methods. The results revealed that 244 individuals were identified in the fecal samples. The results of a Cyt b genetic analysis of the samples indicated that the haplotype and nucleotide diversity were 88.1% and 20.3%, respectively. The evaluation of 14 pairs of microsatellite loci showed that the average number of alleles was 11.2, and the average expected and observed heterozygosity were 0.672 and 0.506, respectively. Therefore, the overall genetic diversity level is high, but some populations of Siberian roe deer are at risk. AMOVA analysis and STRUCTURE Bayesian clustering confirmed the existence of obvious genetic differentiation among the populations. Historical studies have shown that the HZ and SH populations underwent the earliest diffusion events, and the BJC and SL populations also exhibited related signs (HZ: Huzhong Nature Reserve in the Greater Khingan Mountains; SH: Shuanghe National Nature Reserve in Heilongjiang Province; BJC: Heilongjiang Beijicun National Nature Reserve; SL: Songling District in Heilongjiang Province). Mismatch distribution and neutral tests indicated no expansion events or bottleneck effects in the population, and the inbreeding coefficient was positive, suggesting the possibility of inbreeding. The development potential of the population in the future varies among the various local populations. This study supports the biodiversity of Siberian roe deer at the genetic level to save the population and provides important scientific basis and reference for the protection and management of Siberian roe deer. [ABSTRACT FROM AUTHOR]

The results of a comparative study of the genetic structure, parameters of intraspecific genetic diversity, and spatial differentiation of 35 populations of Picea abies–P. obovata–P. koraiensis species complex, located within the areas of distribution of "pure" species and in the contact zones of their ranges were presented. P. abies populations from Eastern Europe (Belarus, Poland); spruce populations from the European part of Russia, the Urals, and the West Siberian Plain, located in the zone of P. abies and P. obovata introgressive hybridization; P. obovata populations from various parts of the extensive range of this species in Siberia and Mongolia; and P. koraiensis populations from the Russian Far East and Northeast China were analyzed. The study of genetic variability and differentiation of populations was based on the analysis of variability of three microsatellite loci: Pt63718, Pt71936, and Pt26081, developed on the basis of Pinusthunbergii Parl chloroplast genome. The use of these DNA markers made it possible to obtain data indicating a fairly high degree of P. koraiensis genetic divergence from two other spruce species included in the complex, P. abies and P. obovata. Korean spruce growing in the Far East differs significantly from the populations of these species in the number and composition of haplotypes, the level of genetic diversity, and population structure, which gives us reason to consider it as a separate species. [ABSTRACT FROM AUTHOR]

Pterocarpus santalinus L.f. is an endangered tree species that is cherished worldwide for its valuable deep red-colored heartwood, which has multiple uses. This species exhibits a wide range of medicinal properties and offers immense potential for the discovery of bioactive compounds of pharmacological importance. The overharvesting of this species for heartwood has led to a gradual decline in its natural populations, thereby depleting its genetic resources and contributing to the loss of genetic diversity. Therefore, it is essential to assess genetic diversity, as such information allows for the effective conservation and utilization of genetic resources. In the present study, the genetic diversity and population structure among 40 germplasm accessions originating from 8 populations of P. santalinus were analyzed using six cross-species simple sequence repeats (SSR), 20 each of inter simple sequence repeats (ISSR) and random amplified polymorphic DNA (RAPD) markers. SSR markers revealed higher polymorphism (100 %), followed by ISSRs (82.81 %) and RAPDs (67.50 %), across all the accessions. The mean values of the polymorphic information content (PIC), effective multiplex ratio (EMR), and marker index (MI) were higher for SSRs (0.84, 9.17, and 7.7), followed by ISSRs (0.262, 4.474, and 1.251) and RAPDs (0.204, 3.268 and 0.970, respectively), indicating the superiority of SSRs in detecting polymorphisms in red sanders. Similarly, the estimates of Nei's gene diversity (H) and Shannon's information index (I) varied across the studied accessions, with the highest values for SSRs (H = 0.528, I = 0.923), followed by ISSRs (H = 0.287, I = 0.428) and RAPDs (H = 0.206, I = 0.307). However, the genetic statistic (Gst) or fixation statistic (Fst) and gene flow (Nm) values were higher for RAPDs (0.455 and 0.598) and ISSRs (0.446 and 0.620) than for SSRs (0.383 and 0.489, respectively), indicating significant genetic differentiation of the populations and moderate gene flow among the populations. Analysis of molecular variance (AMOVA) with SSR, ISSR, and RAPD markers revealed that a greater proportion of genetic variation resided within populations (74 %, 69 %, and 66 %, respectively) than among populations (26 %, 31 %, and 34 %, respectively). Hierarchical clustering on the basis of RAPDs grouped most of the accessions according to the population of origin; however, this clustering was different for the ISSR and SSR markers. STRUCTURE analysis divided the accessions into four, two, and three groups with SSR, ISSR, and RAPD markers, respectively, with admixtures detected in all the groups pointing toward shared genetic lineages and diverse genetic ancestry among the accessions of different populations. Overall, the populations of Gumudipoondi of Tamil Nadu and K.V. Bhavi of Andhra Pradesh were genetically more diverse than other populations, as revealed by genetic diversity estimates obtained with SSR and ISSR marker systems; therefore, the accessions of these populations must be prioritized for conservation and utilization in breeding programs for genetic improvement. [Display omitted] • Genetic diversity was assessed among 40 accessions of P. santalinus using 6 cross-species SSR, 20 each of ISSR and RAPD primers. • Cross-species SSRs were more efficient in detecting genetic diversity in the studied populations than ISSRs and RAPDs. • The populations of Gumidipoondi of Tamil Nadu (GTN) and K.V. Bhavi of Andhra Pradesh (KAP) exhibited higher genetic diversity than other populations according to SSR and ISSR marker analysis. • Analysis of molecular variance with SSR, ISSR and RAPD markers showed that genetic variations within populations (74 %, 69 % and 66 %) were greater than among populations (26 %, 31 % and 34 %). • STRUCTURE analysis using SSR, ISSR and RAPD markers divided the populations into four, two and three genetic groups, respectively, with admixtures detected in all genetic groups. [ABSTRACT FROM AUTHOR]

Exserohilum turcicum is a devastating fungal pathogen that infects both maize and sorghum, leading to severe leaf diseases of the two crops. According to host specificity, pathogenic isolates of E. turcicum are divided into two formae spéciales, namely E. turcicum f. sp. zeae and E. turcicum f. sp. sorghi. To date, the molecular mechanism underlying the host specificity of E. turcicum is marginally known. In this study, the whole genomes of 60 E. turcicum isolates collected from both maize and sorghum were resequenced, which enabled identification of 233,022 single-nucleotide polymorphisms (SNPs) in total. Phylogenetic analysis indicated that all isolates are clustered into four genetic groups that have a close relationship with host source. This observation is validated by the result of principal component analysis. Analysis of population structure revealed that there is obvious genetic differentiation between two populations from maize and sorghum. Further analysis showed that 5,431 SNPs, including 612 nonsynonymous SNPs, are completely co-segregated with the host source. These nonsynonymous SNPs are located in 539 genes, among which 18 genes are predicted to encode secretory proteins, including six putative effector genes named SIX13-like, Ecp6, GH12, GH28-1, GH28-2, and CHP1. Sequence polymorphism analysis revealed various numbers of SNPs in the coding regions of these genes. These findings provide new insights into the molecular basis of host specificity in E. turcicum. [ABSTRACT FROM AUTHOR]

The Procambarus clarkii production sector in Sichuan Province, China, is experiencing rapid growth. However, the industry faces significant challenges, including on-farm breeding and the widespread "Catch Big, Keep Small" farming practice, which have led to substantial genetic degradation within P. clarkii populations. Moreover, the uncertainty surrounding the origins of breeding stocks poses an additional obstacle to the local selection and cultivation of high-quality juvenile P. clarkii. With the objective of inferring the genetic lineage of cultivated P. clarkii in Sichuan, twelve microsatellite loci were employed to investigate the genetic characters of six P. clarkii populations from Sichuan and two from Hubei Province, China. The results revealed that the Sichuan populations exhibited higher levels of heterozygosity (Ho = 0.549~0.699, He = 0.547~0.607) and genetic diversity than the Hubei populations (Na = 4.00~5.250, PIC = 0.467~0.535). Notably, the DY population located in northeastern Sichuan showed the highest heterozygosity (Ho = 0.699, He = 0.607) and genetic diversity (Na = 5.250, PIC = 0.535) among the eight populations. Population structure, principal coordinate analysis and clustering analysis illuminated a close genetic relationship between the Qionglai population in Sichuan and the Jianli population in Hubei. Additionally, the remaining five Sichuan populations (Luxian, Nanxi, Xingwen, Neijiang and Daying) exhibited strong genetic affinity with the QianJiang population in Hubei, and particularly high genetic exchange may have occurred between Daying and Qianjiang (Fst = 0.001, Nm = 217.141). These results suggest that the primary cultivated P. clarkii populations in Sichuan likely originated from Qianjiang and Jianli counties in Hubei, with Qianjiang contributing a more substantial proportion. The genetic diversity of Sichuan populations was higher than those of some other Chinese P. clarkii farming provinces and even some native populations. Specifically, the Daying population emerges as a potential breeding germplasm source for crayfish in Sichuan. In contrast, the Qionglai population exhibits relatively low genetic diversity, highlighting the need for strategic enhancement through interactions with other populations to promote diversity and resilience. Furthermore, fostering genetic exchange among locally cultivated populations within the southern Sichuan basin is strategic to elevate the quality of P. clarkii germplasm resources. [ABSTRACT FROM AUTHOR]

The Critically Endangered seventy-four seabream Polysteganus undulosus, a slow-growing sparid that forms spawning aggregations off South Africa, faced heavy exploitation from 1910 until a fishery moratorium was put in place in 1998. Utilising temporal samples from 1962/1963 (mid-collapse) and 2005/2006 (post-collapse), we assessed genetic diversity at six microsatellite loci. Amplification success for archived samples was low (43%), necessitating a rarefaction approach, revealing a 40% decrease in allelic diversity. Significant genetic differences between recent and archived samples confirmed the impact of overfishing. Simulation studies indicated that missing genotypes did not affect these tests, validating the genetic differences. Using a coalescent-based approach, a 10-fold decrease in effective population size (Ne) was estimated over this 43-year period (Ne = 43.88 to 4.76). Simulations provided corrected Ne of 36.86, accounting for missing genotypes that were responsible for inflated values. Assuming 25% of pristine levels in the 1960s, pristine Ne values ranged from 147 to 176 in 1910, suggesting a 96.8–98.3% genetic decline over 88 years of exploitation. This study emphasises severe genetic consequences of overfishing on P. undulosus diversity and effective population size. The results provide vital genetic baseline data for recovery assessment and conservation efforts, as well as an analytical framework to evaluate the stock decline using partial genotyping data gathered from degraded archived samples. [ABSTRACT FROM AUTHOR]

Background: Fighting cock breeds have considerable historical and cultural place in Thailand. Breeds such as Lueng Hang Khao (LHK) and Pradu Hang Dam (PDH) are known for their impressive plumage and unique meat quality, suggesting selection for fighting and other purposes. However, information regarding the genetic diversity and clustering in indigenous and local Thai chickens used for cockfighting is unclear. Objective: To investigates the genetic diversity and differentiation in Thai fighting cock breeds, including populations for cockfighting, ornamental aspects, and consumption. Methods: Thai fighting cook breeds, including LHK and PDH chickens were analyzed using genotyping with 28 microsatellite loci. Data were compared to a gene pool library from "The Siam Chicken Bioresource Project" to understand the impact of human selection on genetic differentiation. Fighting cock strains from different breeds may cluster owing to shared breeding goals. Result: The analysis of several chicken breeds showed subpopulation differentiation driven by artificial selection and genetic drift, affecting the genetic landscape and causing genetic hitchhiking. Eleven of 28 microsatellite loci showed hitchhiking selection, indicating directional selection in fighting cocks. Additionally, analyses revealed admixture with domestic chicken breeds and minimal influence of red junglefowl in the gene pool of Thai fighting chickens. These findings inform breed improvement, selection strategies, genetic resource management, and maintaining genetic diversity in fighting cocks. Conclusion: Analysis of Thai Fighting chicken breeds revealed a correlation between utilization and subpopulation differentiation. Specifically, selection for cockfighting and ornamental traits appears to explain the observed genetic structure within these breeds. [ABSTRACT FROM AUTHOR]

The Canary Islands have historically been a crossway among at least three continents; therefore, the genetic influences on their local animal breeds have been extremely diverse. In the Canarian chicken population, genetic diversity is evident but it has never been studied. The aim of this study was to assess the population structure and genetic diversity within the Canarian chicken population, as well as between the Canarian chicken population, the Spanish local populations, and the commercial chicken populations with microsatellites, with a view to reinforce the official recognition of the breed, for the design and development of a conservation program. Blood samples were collected at random from 198 animals of the Canarian and compared with Spanish local and commercial strains, in order to determine differentiation and genetic relatedness. The five phenotypic varieties of Canarian chicken, the population structure and genetic diversity within the Canarian chicken population had a higher unbiased expected heterozygosity than the observed heterozygosity. Comparing the Canarian vs other local Spanish breeds and commercial strains, FST was relatively high (0.179) (0.164 – 0.195), the neighborhood network showed that the Canarian varieties did not cluster with the other Spanish breeds. The STRUCTURE, confirmed that the Rubilana variety differed from the other four Canary Islands. We conclude that the Canary Islands chicken population shows a differentiated genetic profile, versus other Spanish and cosmopolitan breeds. The theory that the existence of genetic varieties is based on the color of feathers was definitively discarded, except in the Rubilana population, which could be admitted as a genetically different variety.

Abstract Elucidating biodiversity patterns and their background processes is critical in biodiversity science. Dissimilarity, which is calculated based on multivariate biological quantities, is a major component of biodiversity. As spatial and temporal biodiversity information availability increases, the scope of dissimilarity studies has been expanded to cover various levels and types of spatiotemporal biodiversity facets (e.g. gene, community and ecosystem function), and diverse pairwise dissimilarity indices have been developed. However, further development of the dissimilarity concept is required in comparative studies on spatiotemporal structures of biodiversity compositional patterns, such as those exploring commonalities of biogeographical boundaries among taxa, compared to the conventional ones to consider higher dimensions of dissimilarity: dissimilarity of dissimilarity structures. This study proposes a novel and general concept, higher‐order dissimilarity (HOD), for quantitatively evaluating the dissimilarities of spatial or temporal dissimilarity structures among different datasets, proposes specific implementations of HOD as operational indices, and illustrates the potential resolution of scientific and practical questions through HOD. We further demonstrate the advantages of the HOD concept by applying it to actual patterns, such as long‐term and/or large‐spatial hypothetical monitoring datasets. Our conceptual framework on HOD extends the existing framework of biodiversity science and is versatile, with many potential applications in acquiring more valuable information from ever‐increasing biodiversity data.

【Objective】The study was conducted to clarify the genetic structure characteristics, genetic diversity level and molecular variation of different geographical populations of Conopomorpha sinensis Bradely, with an aim to provide scientific evidence for the study of its origin and evolution and provide reference information for the control of this pest in different regions.【Method】Using the C. sinensis from5production areas in southern China as materials, using GBS (Genotyping-by-sequencing) technology was used for samples genotyping, then SNP locus was identified with SAMTOOLS software, and phylogenetic tree was constructed according to SNP genotyping results. Finally, principal component analysis was performed.【Result】Sequencing of C. sinensis from5regions was conducted by GBS technology. A total of 27.39 Gb of high-quality effective data were obtained, with an average of 5.48 Gb per sample. A total of 11 767 high-quality single nucleotide polymorphism (SNPs) loci were obtained. Phylogenetic tree analysis showed that the genetic relationship of Luzhou population was far from that of other populations. The results of principal component analysis showed that C. sinensis was divided into2groups in5regions, and the Luzhou population was significantly different from the other4populations. Both principal component analysis and phylogenetic tree analysis revealed that there were obvious differences in genetic level among C. sinensis from different geographical origins. The results of genetic diversity analysis showed that the observed heterozygosity was 0.2099-0.2531, the expected heterozygosity was 0.1937-0.2203, π was 0.2495-0.2748, indicating that the genetic diversity level of C. sinensis population was low. The results of AMOVA analysis showed that the genetic variation between populations (0.87%) was smaller than that within populations (99.13%), indicating that the variation mainly came from within populations rather than between populations.【Conclusion】The genetic diversity level of C. sinensis in different geographical populations was low, while the genetic differentiation degree of Luzhou population in Sichuan was high, and its genetic relationship was distant with other populations.

ABSTRACT: Buffaloes are vital contributors to the global dairy industry. Understanding the genetic basis of milk production traits in buffalo populations is essential for breeding programs and improving productivity. In this study, we conducted whole-genome resequencing on 387 buffalo genomes from 29 diverse Asian breeds, including 132 river buffaloes, 129 swamp buffaloes, and 126 crossbred buffaloes. We identified 36,548 copy number variants (CNV) spanning 133.29 Mb of the buffalo genome, resulting in 2,100 CNV regions (CNVR), with 1,993 shared CNVR being found within the studied buffalo types. Analyzing CNVR highlighted distinct genetic differentiation between river and swamp buffalo subspecies, verified by evolutionary tree and principal component analyses. Admixture analysis grouped buffaloes into river and swamp categories, with crossbred buffaloes displaying mixed ancestry. To identify candidate genes associated with milk production traits, we employed 3 approaches. First, we used Vst-based population differentiation, revealing 11 genes within CNVR that exhibited significant divergence between different buffalo breeds, including genes linked to milk production traits. Second, expression quantitative loci analysis revealed differentially expressed CNVR-derived genes (DECG) associated with milk production traits. Notably, known milk production-related genes were among these DECG, validating their relevance. Last, a GWAS identified 3 CNVR significantly linked to peak milk yield. Our study provides comprehensive genomic insights into buffalo populations and identifies candidate genes associated with milk production traits. These findings facilitate genetic breeding programs aimed at increasing milk yield and improving quality in this economically important livestock species.

Weather is an important short‐term, local driver of population size and dispersal, which in turn contribute to patterns of genetic diversity and differentiation within species. Climate change is leading to greater weather variability and more frequent extreme weather events. While the effects of long‐term and broad‐scale mean climate conditions on genetic variation are well studied, our understanding of the effects of weather variability and extreme conditions on genetic variation is less developed. We assessed the influence of temperature and snow depth on genetic diversity and differentiation of populations of the alpine butterfly, Parnassius smintheus. We examined the relationships between a suite of variables, including those representing extreme conditions, and population‐level genetic diversity and differentiation across 1453 single nucleotide polymorphisms, using both linear and gravity models. We additionally examined effects of land cover variables known to influence dispersal and gene flow in this species. We found that extreme low temperature events and the lowest recorded mean snow depth were significant predictors of genetic diversity. Extreme low temperature events, mean snow depth and land cover resistance were significant predictors of genetic differentiation. These results are congruent with known effects of early winter weather on population size and habitat connectivity on dispersal in P. smintheus. Our results demonstrate the potential for changes in the frequency or magnitude of extreme weather events to alter patterns of genetic diversity and differentiation. [ABSTRACT FROM AUTHOR]

【Objective】The study was conducted to clarify the genetic structure characteristics, genetic diversity level and molecular variation of different geographical populations of Conopomorpha sinensis Bradely, with an aim to provide scientific evidence for the study of its origin and evolution and provide reference information for the control of this pest in different regions.【Method】Using the C. sinensis from 5 production areas in southern China as materials, using GBS (Genotyping-by-sequencing) technology was used for samples genotyping, then SNP locus was identified with SAMTOOLS software, and phylogenetic tree was constructed according to SNP genotyping results. Finally, principal component analysis was performed.【Result】Sequencing of C. sinensis from 5 regions was conducted by GBS technology. A total of 27.39 Gb of highquality effective data were obtained, with an average of 5.48 Gb per sample. A total of 11 767 high-quality single nucleotide polymorphism (SNPs) loci were obtained. Phylogenetic tree analysis showed that the genetic relationship of Luzhou population was far from that of other populations. The results of principal component analysis showed that C. sinensis was divided into 2 groups in 5 regions, and the Luzhou population was significantly different from the other 4 populations. Both principal component analysis and phylogenetic tree analysis revealed that there were obvious differences in genetic level among C. sinensis from different geographical origins. The results of genetic diversity analysis showed that the observed heterozygosity was 0.2099-0.2531, the expected heterozygosity was 0.1937-0.2203, π was 0.2495-0.2748, indicating that the genetic diversity level of C. sinensis population was low. The results of AMOVA analysis showed that the genetic variation between populations (0.87%) was smaller than that within populations (99.13%), indicating that the variation mainly came from within populations rather than between populations.【Conclusion】The genetic diversity level of C. sinensis in different geographical populations was low, while the genetic differentiation degree of Luzhou population in Sichuan was high, and its genetic relationship was distant with other populations. [ABSTRACT FROM AUTHOR]

Turnip rape is a multi-purpose crop cultivated in temperate regions. Due to its ability to fit into crop rotation systems and its role as a food and feed source, spring-type turnip rape cultivation is on the rise. To improve the crop's productivity and nutritional value, it is essential to understand its genetic diversity. In this study, 188 spring-type accessions were genotyped using SeqSNP, a targeted genotyping-by-sequencing method to determine genetic relationships between various groups and assess the potential effects of mutations within genes regulating major desirable traits. Single nucleotide polymorphism (SNP) alleles at six loci were predicted to have high effects on their corresponding genes' functions, whereas nine loci had country/region-specific alleles. A neighbor-joining cluster analysis revealed three major clusters (I to III). About 72% of cluster-I accessions were of Asian origin, whereas 88.5% of European accessions and all North American accessions were placed in cluster-II or cluster-III. A principal coordinate analysis explained 65.3% of the total genetic variation. An analysis of molecular variance revealed significant differentiation among different groups of accessions. Compared to Asian cultivars, European and North American cultivars share more genetic similarities. Hence, crossbreeding Asian and European cultivars may result in improved cultivars due to desirable allele recombination. Compared to landraces and wild populations, the cultivars had more genetic variation, indicating that breeding had not caused genetic erosion. There were no significant differences between Swedish turnip rape cultivars and the NordGen collection. Hence, crossbreeding with genetically distinct cultivars could enhance the gene pool's genetic diversity and facilitate superior cultivar development. [ABSTRACT FROM AUTHOR]

The list of standard abbreviations for JDS is available at adsa.org/jds-abbreviations-24. Nonstandard abbreviations are available in the Notes. Buffaloes are vital contributors to the global dairy industry. Understanding the genetic basis of milk production traits in buffalo populations is essential for breeding programs and improving productivity. In this study, we conducted whole-genome resequencing on 387 buffalo genomes from 29 diverse Asian breeds, including 132 river buffaloes, 129 swamp buffaloes, and 126 crossbred buffaloes. We identified 36,548 copy number variants (CNV) spanning 133.29 Mb of the buffalo genome, resulting in 2,100 CNV regions (CNVR), with 1,993 shared CNVR being found within the studied buffalo types. Analyzing CNVR highlighted distinct genetic differentiation between river and swamp buffalo subspecies, verified by evolutionary tree and principal component analyses. Admixture analysis grouped buffaloes into river and swamp categories, with crossbred buffaloes displaying mixed ancestry. To identify candidate genes associated with milk production traits, we employed 3 approaches. First, we used Vst -based population differentiation, revealing 11 genes within CNVR that exhibited significant divergence between different buffalo breeds, including genes linked to milk production traits. Second, expression quantitative loci analysis revealed differentially expressed CNVR-derived genes (DECG) associated with milk production traits. Notably, known milk production-related genes were among these DECG, validating their relevance. Last, a GWAS identified 3 CNVR significantly linked to peak milk yield. Our study provides comprehensive genomic insights into buffalo populations and identifies candidate genes associated with milk production traits. These findings facilitate genetic breeding programs aimed at increasing milk yield and improving quality in this economically important livestock species. [ABSTRACT FROM AUTHOR]

Global climate change is expected to have a profound effect on species distribution. Due to the temperature constraints, some narrow niche species could shift their narrow range to higher altitudes or latitudes. In this study, we explored the correlation between species traits, genetic structure, and geographical range size. More specifically, we analyzed how these variables are affected by differences in fundamental niche breadth or dispersal ability in the members of two sympatrically distributed stream‐dwelling amphibian species (frog, Quasipaa yei; salamander, Pachyhynobius shangchengensis), in Dabie Mountains, East China. Both species showed relatively high genetic diversity in most geographical populations and similar genetic diversity patterns (JTX, low; BYM, high) correlation with habitat changes and population demography. Multiple clustering analyses were used to disclose differentiation among the geographical populations of these two amphibian species. Q. yei disclosed the relatively shallow genetic differentiation, while P. shangchengensis showed an opposite pattern. Under different historical climatic conditions, all ecological niche modeling disclosed a larger suitable habitat area for Q. yei than for P. shangchengensis; these results indicated a wider environment tolerance or wider niche width of Q. yei than P. shangchengensis. Our findings suggest that the synergistic effects of environmental niche variation and dispersal ability may help shape genetic structure across geographical topology, particularly for species with extremely narrow distribution. [ABSTRACT FROM AUTHOR]

We hypothesized that populations of ayu (Plecoglossus altivelis, an ecologically and commercially important fish) living in marginal habitats are under less favorable conditions, and are, thus, more vulnerable to extinction. To test this hypothesis, we analyzed the mitochondrial DNA control region of ayu collected from different localities, including central and marginal populations. The results showed that the ayu populations in southern marginal habitats (Tien Yen River in Vietnam; Yakugachi and Kawauchi Rivers in Amami-Oshima Island) displayed lower genetic diversity (haplotype diversity, h = 0.67; 0.54 and 0.80; nucleotide diversity, π = 0.006, 0.002, and 0.009, respectively) compared to the central populations. The genetic differences were highly significant between the southern marginal and the central populations (Fixation index (FST) values ranged from 0.412 to 0.543). However, ayu populations at the center of their distribution range (Shinano River in Honshu and Hamoji River in Sado Island) and the northern marginal habitats (Yoichi River in Hokkaido and Aonae River in Okushiri Island) exhibited high genetic diversity (h = 1 for all rivers; π = 0.024–0.029). The genetic differences between the populations in the central and northern marginal habitats were not significant (FST values ranged from 0.023 to 0.076). This study suggests that, in ayu, the central-marginal hypothesis is valid in the southern direction but invalid in the northern direction. Urgent conservation is needed for the genetically distinct populations in the degraded southern habitats with severely low genetic diversity. [ABSTRACT FROM AUTHOR]

Copyright of Methods in Ecology & Evolution is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Luculia yunnanensis is a vulnerable species endemic to Yunnan Province, Southwestern China, which has high ornamental value. Its wild population has not been fully protected and utilized for a long time, which is not conducive to the long-term stable development of this species. Genetic diversity assessment is the basis and prerequisite for the conservation of rare species. In this study, 21 phenotypic traits and 17 highly polymorphic EST-SSR markers were used to analyze the genetic diversity and genetic structure of 164 individuals from six L. yunnanensis populations. The coefficient of variation of 21 phenotypic traits ranged from 11.76% to 52.58% (mean=21.72%), and the coefficient of variation of 18 traits was less than 30%. The average values of Ne, I, Ho and He were 1.710, 0.619, 0.384, and 0.352, respectively. The genetic diversity of LLO (Ho = 0.476 and He = 0.426) and LCM (Ho = 0.424 and He = 0.381) populations in Lushui County was highest. The GDX populations (Ho = 0.335 and He = 0.269) isolated by Gaoligong Mountain had the lowest genetic diversity. The AMOVA results showed that 13.04% of the genetic variation was among populations and 86.96% was within populations. The average phenotypic differentiation coefficient of phenotypic traits among populations was 18.69%. The results of phenotypic and genetic variation analysis were consistent, indicating that the most of variation exists within population. Genetic structure, UPGMA clustering and PCA analysis results showed that the populations of L. yunnanensis had obvious geographical divisions, and the populations distributed in the southern region and distributed in the northern region of the Nujiang River clustered into one group respectively. Combining the results of phenotypic and molecular markers, we recommend that give priority to the protection of LLO, LCM and GDX population, in order to ensure the sustainable utilization of L. yunnanensis germplasm resources. [ABSTRACT FROM AUTHOR]

Over the past two decades, there has been a growing alarm about the role of unintended hybridization in shaping the current biodiversity. Major carps (Labeo rohita, Catla catla, and Cirrhina mrigala) are commercially important freshwater fish for aquaculture and are also found exclusively in the riverine ecosystems of Punjab, Pakistan. One of the main concerns is the genetic integrity of major carps. In this study, we employed both nuclear and mitochondrial DNA markers to determine the potential hybridization and patterns of genetic variation in major carps. Association tests of both nuclear and mtDNA markers provide evidence of recent hybridization, and patterns of genetic variations were also found consistent with observed pattern of admixture in major carps. In all hybridization events, L. rohita is detected to hybridize with C. catla and C. mrigala, whereas C. catla and C. mrigala are established to hybridize with L. rohita. Overall, two levels of hybridization; F1 hybrids reported in hatchery-reared stocks and few backcrosses individuals in wild populations suggest that anthropogenic or demographic dynamics accelerate inter-generic gene flow. Moreover, the disparity in amplified mtDNA COI subunit shows strong directional bias towards Labeo–Catla first-generation hybrids (100%) containing L. rohita maternal lineage while Labeo-Cirrhina hybrids (75%) exhibit C. mrigala maternal lineage. The results of this study endorse that culture-based fish farming and restocking activities of major carps in riverine ecosystems demand regular genetic monitoring of these species. The current genetic evidence and proclamation of practical information should encourage management and conservation efforts to strictly limit the genetic integrity of these species. [ABSTRACT FROM AUTHOR]

In migratory animals, high mobility may reduce population structure through increased dispersal and enable adaptive responses to environmental change, whereas rigid migratory routines predict low dispersal, increased structure, and limited flexibility to respond to change. We explore the global population structure and phylogeographic history of the bar‐tailed godwit, Limosa lapponica, a migratory shorebird known for making the longest non‐stop flights of any landbird. Using nextRAD sequencing of 14,318 single‐nucleotide polymorphisms and scenario‐testing in an Approximate Bayesian Computation framework, we infer that bar‐tailed godwits existed in two main lineages at the last glacial maximum, when much of their present‐day breeding range persisted in a vast, unglaciated Siberian‐Beringian refugium, followed by admixture of these lineages in the eastern Palearctic. Subsequently, population structure developed at both longitudinal extremes: in the east, a genetic cline exists across latitude in the Alaska breeding range of subspecies L. l. baueri; in the west, one lineage diversified into three extant subspecies L. l. lapponica, taymyrensis, and yamalensis, the former two of which migrate through previously glaciated western Europe. In the global range of this long‐distance migrant, we found evidence of both (1) fidelity to rigid behavioural routines promoting fine‐scale geographic population structure (in the east) and (2) flexibility to colonise recently available migratory flyways and non‐breeding areas (in the west). Our results suggest that cultural traditions in highly mobile vertebrates can override the expected effects of high dispersal ability on population structure, and provide insights for the evolution and flexibility of some of the world's longest migrations. [ABSTRACT FROM AUTHOR]

Failure of perennial ryegrass‐based pastures to persist beyond 3 years post‐sowing is an increasing threat to the sustainability of livestock industries in the north of New Zealand. Little is known of the long‐term responses of plants and populations to the environmental stresses responsible for persistence failure, or the effects of ryegrass genetics on those responses. Plants were collected from 10‐year‐old pastures sown in two environments (Waikato, North Island: warm‐temperate, summer/autumn dry; Canterbury, South Island: cool temperate, irrigated) to four ryegrass functional types and grazed by dairy cattle. Surviving plants in Canterbury pastures were almost all true‐to‐type for the original genotype, whereas there was substantial ingress of volunteer plants in the diploid cultivars in Waikato. Plants confirmed as true‐to‐type were compared to reference plants grown from the original seed lines. Leaf mass was lower in survivor plants than in reference plants for all functional types. This effect was reversed by recruitment of new plants from seed in a grazing deferment treatment applied at the Waikato site 18 months before plant collection, in a manner consistent with epigenetic control. Reproductive development was delayed by 4–6 days in survivors of mid‐ and late flowering diploid cultivars: this effect appeared to be the result of true genetic differentiation. There was less aftermath heading in the Canterbury survivors, but not Waikato survivors, compared with the reference plants. The relevance of these findings for ryegrass survival strategies and targeted selection of traits for improved persistence is discussed. [ABSTRACT FROM AUTHOR]

We present an overview of the morphology, biogeography, and ecology of the fern genus Osmunda (i.e. without previously included taxa of Claytosmunda , Osmundastrum , and Plenasium), with a focus on the American O. spectabilis Willd. and Old World O. regalis L. While genetic data supports the separation of these taxa, commonly used morphologic characters to distinguish between O. regalis and O. spectabilis (maximum frond size; pinnae sessile vs. stalked; pinnules opposite vs. alternate; general pinnule proportions) are not infallible. We recorded morphometric differences among and between O. regalis and O. spectabilis and correlated these with spatio-environmental gradients. Our work provides an updated taxonomic overview with full synonymy and diagnostic key of Osmunda. We preliminarily recognize six informal subtaxa in O. regalis ('regalis', 'abyssinica', 'huegeliana', 'longifolia', 'transvaalensis', 'obtusifolia') and three in O. spectabilis ('spectabilis', 'palustris', 'piresii') that separate in a morphological traits-based principal component analysis. The morphotaxa appeared geographically structured and their distribution showed significant correlations with elevation, mean annual precipitation, annual mean temperature, and temperature seasonality. The taxonomic rank and validity of the proposed subtaxa has to be tested through a large-scale sampling, e.g. with comparative cp/nr genomic and cytogenetic analyses. Such future analyses may help to ascertain whether the observed morphologic peculiarities are conditioned solely by abiotic factors (which would allow addressing them as forms) or are manifested in the genome. [ABSTRACT FROM AUTHOR]

Context: With growing World population, the demand for higher-yield crops becomes more evident. The genetic diversity, which is crucial for breeding superior cultivars, can be shown by using molecular techniques such as start codon targeted (SCoT) markers. Aims: The motivation of this study was to unfold the genetic diversity of Turkish germplasm. Methods: Ninety-four pea samples (90 landraces, 3 pea breeding materials, and 1 registered variety), were assessed for their diversity by using SCoT markers. Key results: Eight SCoT markers produced a total of 84 scorable bands, of which 74 (88.1%) were polymorphic. There was an average of 9.25 polymorphic bands per primer. The range of diversity indices evaluated, such as polymorphism information content (0.13–0.38), effective numbers of alleles (1.22–1.69), Shannon's diversity index (0.21–0.54), and gene diversity (0.13–0.38), showed great genetic variation in the germplasm under this study. STRUCTURE algorithm suggested the presence of two populations. Polymorphism percentage was 87% and 74%, whereas fixation index was 0.21 and 0.01 for population A and population B respectively. According to analysis of molecular variance, most of the difference was found to lie within population (99%) rather than between populations (1%). In contrast, principal coordinates analysis suggested separation into three populations. Conclusions: The Nei's genetic distance of 94 Turkish pea samples revealed that Antalya_2 and Canakkale_2 are genetically the most diverse and can be utilised as parental lines for breeding purposes. Implications: The wide range of pea varieties found in the Turkish germplasm can serve as a valuable genetic resource for the overall pea breeding efforts. Ensuring universal food security is a crucial concern for all of humanity. Pea, as one of the most important legumes, faces many growing challenges in the light of changing climate, whereas growing superior cultivars is a key strategy to meet the ever-growing demands. Turkish pea germplasm encompasses a rich diversity that can be utilised in breeding programs, particularly among the more diverse samples, to generate cultivars adapted to new changing environments. This article belongs to the Collection Plant breeding- and genetics-based tools for food security under changing climate. [ABSTRACT FROM AUTHOR]

The mite, Dermatophagoides farinae, is an allergen source that triggers allergy symptoms in humans. We studied how different habitats affect the genetic structure of D. farinae populations. We used 12 microsatellite loci to analyse the genetic structure of six D. farinae populations collected from four habitats: flour mill (FM), dormitory (DM), cotton mill (CM), and pillow (PL). The CM population had the highest genetic diversity (He = 0.641) while the FM population had less genetic diversity. AMOVA analysis showed 81% intrapopulation genetic variation and 19% interpopulation variation. The overall FST value of the six populations was 0.18531, indicating significant population genetic differentiation. Significant genetic differentiation occurred between the FM population and the other three habitat populations. Bayesian clustering analysis showed that the FM population was divided into two clusters. UPGMA tree and PCoA data supported the above results and indicated that the D. farinae populations from CM, PL, and DM1 had similar genetic ancestors. It was speculated that D. farinae could spread through the cotton-pillow-dormitory route. This study showed that D. farinae may have undergone habitat-associated differentiation and provides measures for preventing the dispersal of D. farinae. [ABSTRACT FROM AUTHOR]

Aim: Genetic diversity of marine forests results from complex interactions of eco‐evolutionary processes. Among them, oceanographic connectivity driven by dispersal through water transport is hypothesized to play a pivotal role, yet its relative contribution has not been addressed at the global scale. Here, we test how present‐day oceanographic connectivity is correlated with the distribution of genetic diversity of marine forests across the ocean. Location: Global. Time period: Contemporary. Major taxa studied: Marine forests of brown macroalgae (order: Fucales, Ishigeales, Laminariales and Tilopteridales). Methods: Through literature review, we compiled a comprehensive dataset of genetic differentiation, encompassing 699 populations of 30 species. A biophysical model coupled with network analyses estimated multigenerational oceanographic connectivity and centrality across the marine forest global distribution. This approach integrated propagule dispersive capacity and long‐distance dispersal events. Linear mixed models tested the relative contribution of site‐specific processes, connectivity and centrality in explaining genetic differentiation. Results: We show that spatiality‐dependent eco‐evolutionary processes, as described by our models, are prominent drivers of genetic differentiation in marine forests (significant models in 91.43% of the cases with an average R2 of 0.50 ± 0.07). Specifically, we reveal that 18.7% of genetic differentiation variance is explicitly induced by predicted contemporary connectivity and centrality. Moreover, we demonstrate that long‐distance dispersal is key in connecting populations of species distributed across large water masses and continents. Main conclusions: Our findings highlight the role of present‐day oceanographic connectivity in shaping the extant distribution of genetic diversity of marine forests on a global scale, with significant implications for biogeography and evolution. This understanding can pave the way for future research aimed at guiding conservation efforts, including the designation of well‐connected marine protected areas, which is particularly relevant for sessile ecosystems structuring species such as brown macroalgae. [ABSTRACT FROM AUTHOR]

Landscape genetics is a field dealing with local genetic differences and contributes to strategic conservation planning. Recently, environmental DNA (eDNA) metabarcoding has proven useful not only for detecting species but also for assessing genetic diversity and genetic structure on a large scale such as in phylogeography. However, it remains unclear whether eDNA analysis also has sufficient power to perform the landscape genetics, which focuses on a local scale. To reveal the applicability of eDNA to landscape genetics, we conducted an eDNA metabarcoding analysis of the mitochondrial DNA D‐loop region of the fluvial sculpin Cottus nozawae in the upper Sorachi River in Japan and compared the results with inferences based on traditional tissue‐based approaches by the same D‐loop region and genome‐wide SNP data. As a result, the spatial distribution of haplotypes was generally consistent between the eDNA‐ and tissue‐based approaches. In addition, the genetic differentiation statistics calculated using eDNA and tissue samples were highly correlated when comparing both in the D‐loop region. The removal of low‐frequency reads or the conversion to semi‐quantitative rankings of eDNA data did not alter the correlation of genetic diversity and differentiation statistics with tissue‐based approaches much. Finally, we confirmed that analyses using eDNA data can reveal patterns such as isolation‐by‐distance shown in previous studies on this species, indicating the applicability of eDNA to basic landscape genetics. Even though some limitations remain, eDNA may have great potential for conducting basic landscape genetics. [ABSTRACT FROM AUTHOR]

The inter- and intra-specific structure of genetic variability was studied using 18 microsatellite loci (nSSRs) in closely related roburoid white oaks in the Crimean-Caucasian region. The seven most widespread Quercus taxa in the region were studied in 29 morphologically pure populations from different parts of the North Caucasus, Transcaucasia, Crimea and northeastern Europe. Most taxa were studied using nSSR markers for the first time. Among the 492 trees studied, Bayesian clustering method implemented in STRUCTURE identified clusters corresponding to the pedunculate oak Quercus robur, the Hartwiss oak Q. hartwissiana, the Caucasian oak Q. macranthera, the downy oak Q. pubescens and three subspecies of sessile oak: Q. petraea ssp. petraea, Q. petraea ssp. iberica, Q. petraea ssp. medwediewii. Geographic structure was identified within Q. robur, Q. pubescens and Q. p. ssp. petraea. The 18 nSSR loci used are efficient in the taxonomic assignment of individuals, and identifying hybrids. The close relationship between the "long-peduncle" roburoid oaks (Q. robur and Q. hartwissiana) is shown, with a greater difference from other species. For one of the subspecies of sessile oak, widespread in the North Caucasus and Crimea Q. petraea ssp. medwediewii (syn. Q. calcarea), or limestone oak, significant differences from other taxa were found, reaching the inter-species level. The assumption of a possible hybrid origin of this taxon as a result of hybridization of Q. petraea and Q. pubescens is not confirmed by genetic analysis. The other two subspecies of Q. petraea (Q. p. ssp. petraea and Georgian durmast oak Q. p. ssp. iberica) are differentiated to a lesser extent and are related to each other, which confirms the legitimacy of distinguishing two geographically isolated taxa at the rank of subspecies. The highest variability was observed in Q. pubescens (He = 0.777). In Q. p. ssp. medwediewii variability was lower than in other widespread taxa (He = 0.652), and was approximately at the level of variability of Q. hartwissiana (He = 0.633) and Q. macranthera (He = 0.659). Clear differentiation of taxa by nuclear markers shows the limited introgression in closely related oak species in the Caucasus and Crimea. The identified genetic clusters can be used as reference groups for further population genetic studies of oaks in the Crimean-Caucasian region. [ABSTRACT FROM AUTHOR]

Phyllanthus emblica is a well-known medicinal and non-timber forest product species, widely distributed in the Indian subcontinent. Multiple disturbances like intensive fruit harvest, the spread of invasive species such as Lantana camara and Taxillus tomentosus, and other anthropogenic disturbances threaten population viability by altering ecological and genetic processes. Studying the genetic diversity and population structure of species harvested intensively and subjected to anthropogenic disturbances is crucial for evaluating their ability to survive under future environmental changes and for establishing conservation strategies. The genetic diversity and population structure of twelve populations of P. emblica that are harvested across three protected areas of the Western Ghats, the world’s most densely populated biodiversity hotspot was evaluated. Three hundred sixty samples were genotyped with nine simple sequence repeat markers. The changes in genetic diversity and genetic structure were assessed between generations by analyzing adults, seedlings, and juvenile samples. Despite intensive harvesting, the results found high genetic diversity in all the populations (mean/pop: Ho = 0.626; Hs = 0.722). However, genetic differentiation was significant between the study regions as well as between adult and seedling populations. The study also indicated a clear clustering of the twelve populations into three distinct genetic clusters. Neighbor-joining tree and hierarchical clustering analysis also showed the same pattern. The genetic data from the study provide information on how local disturbances including harvesting affect the population's genetic diversity and structure, which can provide a basis for implementing programs for conserving and sustainable utilization of P. emblica genetic resources in the future. [ABSTRACT FROM AUTHOR]

Quercus griffithii is an ecologically and economically important tree species utilized for firewood, fodder, compost, and building-making. It is also a good source of food for wildlife. The genetic diversity of Q. griffithii is poorly understood; therefore, in the present study, 16 polymorphic SSR markers were used to assess the extent and pattern of genetic diversity in Q. griffithii samples collected from the northeastern region of India. The SSR markers revealed significant discriminating power (PIC range, 0.15˗0.81) and resulted in the amplification of 119 alleles. At the species level, it showed moderate levels of genetic diversity (Ho = 0.47; He = 0.52) with low genetic differentiation (FST = 0.06) and high gene flow (Nm = 3.91). Two genetic clusters, with high admixture populations were estimated in the Bayesian analysis of STRUCTURE, which was in accordance with clusters of UPGMA and PCoA. This is the first study to assess genetic diversity using SSR markers in Q. griffithii. The genetic information generated in this study will be helpful in the future conservation and restoration of Q. griffithii in the northeastern region of India. [ABSTRACT FROM AUTHOR]

Copyright of South China Fisheries Science is the property of South China Fisheries Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

This article presents data on the polymorphism of intermicrosatellite sequences in the sterlet Acipenser ruthenus of the lower reaches of the Irtysh River and the middle reaches of the Ob River. We have assessed the intra- and interpopulation variability and genetic differentiation of A. ruthenus and revealed a high ISSR polymorphism in the species from the central part of the Ob-Irtysh basin. The proportion of polymorphic amplicons is 0.966, genetic diversity is 0.355, and the average number of alleles per locus is 1.97. The highest polymorphism is typical for the sterlet from the Tobol River at the confluence with the Irtysh River. The genetic differentiation between the sterlet groups of the Irtysh and Ob rivers is well pronounced, the interpopulation component accounts for 42% of variability (Gst = 0.42), and the gene flow is limited (Nm = 0.67). The sterlet groups inhabiting the Lower Irtysh from the mouth of the Tobol River to the mouth of the Konda River do not differ genetically and form one population (Gst = 0.08–0.12, Nm = 3.76–5.55). The sterlet from the Irtysh River within the Vagay region is genetically different from the other Irtysh samples (Gst = 0.22, Nm = 1.68) and belongs to a different population group. The differentiation between samples of sterlet from the Ob basin is higher than between samples from the Irtysh basin. Groups of sterlet from the Ob River and the Yuganskaya Ob canal are genetically different (Gst = 0.30, Nm = 1.19) and form various subpopulations. Spawning migrations, as well as confinement to wintering pits, play a decisive role in the formation of the sterlet population structure in the studied part of the distribution area. The sterlet population groups that are identified should be considered separate units of environmental and economic management. [ABSTRACT FROM AUTHOR]

Background and Aims The timing of flowering onset is often correlated with latitude, indicative of climatic gradients. Flowering onset in temperate species commonly requires exposure to cold temperatures, known as vernalization. Hence, population differentiation of flowering onset with latitude might reflect adaptation to the local climatic conditions experienced by populations. Methods Within its western range, seeds from Linum bienne populations (the wild relative of cultivated Linum usitatissimum) were used to describe the latitudinal differentiation of flowering onset to determine its association with the local climate of the population. A vernalization experiment including different crop cultivars was used to determine how vernalization accelerates flowering onset, in addition to the vernalization sensitivity response among populations and cultivars. Additionally, genetic differentiation of L. bienne populations along the latitudinal range was scrutinized using microsatellite markers. Key Results Flowering onset varied with latitude of origin, with southern populations flowering earlier than their northern counterparts. Vernalization reduced the number of days to flowering onset, but vernalization sensitivity was greater in northern populations compared with southern ones. Conversely, vernalization delayed flowering onset in the crop, exhibiting less variation in sensitivity. In L. bienne , both flowering onset and vernalization sensitivity were better predicted by the local climate of the population than by latitude itself. Microsatellite data unveiled genetic differentiation of populations, forming two groups geographically partitioned along latitude. Conclusions The consistent finding of latitudinal variation across experiments suggests that both flowering onset and vernalization sensitivity in L. bienne populations are under genetic regulation and might depend on climatic cues at the place of origin. The association with climatic gradients along latitude suggests that the climate experienced locally drives population differentiation of the flowering onset and vernalization sensitivity patterns. The genetic population structure suggests that past population history could have influenced the flowering initiation patterns detected, which deserves further work. [ABSTRACT FROM AUTHOR]

A subarctic Norwegian watercourse is known for its population of threespine sticklebacks (Gasterosteus aculeatus Linnaeus 1758) with unusual pelvic spine polymorphism; the upper lake contains a mixture of specimens that are normal-spined, asymmetric-spined, and spineless. In contrast, the downstream lakes and the nearby marine site contain only the normal spined morph. We investigated the maternal-line genetic structure in the watercourse using mitogenomics. A total of 242 sticklebacks representing two lakes and a marine site were assessed based on individual and pooled DNA sequencing. While two distinct mitogenome clades were detected in the upper lake (Lake Storvatnet), only one of these clades was present in the downstream lake. The marine site pooled DNA sample, however, contained several mitogenome haplotypes. We present mitogenome sequence features that include gene-specific single nucleotide polymorphisms, molecular phylogeny, and genetic differentiation assessments based on pairwise comparisons of pooled population samples from each site. The Lake Storvatnet mitogenomes belong to two distinct Euro-North American (ENA) clades; one of the ancestral lineages likely corresponds to the original maternal lineage in the watercourse, and the other was introduced more recently. We hypothesize that the second invader carried nuclear genomic features responsible for the observed present-day pelvic spine polymorphism in Lake Storvatnet. [ABSTRACT FROM AUTHOR]

[Display omitted] • Entamoeba nuttalli had a high degree of genetic differentiation between the host populations. • A novel ribosomal lineage of Entamoeba was identified and named RL13. • Low altitude populations of wild rhesus macaques had higher prevalence rates of Entamoeba than high altitude populations. Wild rhesus macaques are a potential source of zoonotic parasites for humans, and Entamoeba spp. are common intestinal parasites. To investigate the prevalence of Entamoeba in wild rhesus macaques in China and explore the genetic differentiation of the potentially pathogenic species Entamoeba nuttalli, a total of 276 fecal samples from five populations at high altitudes (HAG, 2,800–4,100 m above sea level) and four populations at low altitudes (LAG, 5–1,000 m above sea level) were collected. PCR methods based on the ssrRNA gene were used to detect Entamoeba infection. Genotyping of E. nuttalli was performed based on six tRNA-linked short tandem repeat (STR) loci for further genetic analyses. The results revealed that Entamoeba infection (69.2%) was common in wild rhesus macaques in China, especially in LAG which had a significantly higher prevalence rate than that in HAG (P < 0.001). Three zoonotic species were identified: Entamoeba chattoni (60.9%) was the most prevalent species and distributed in all the populations, followed by Entamoeba coli (33.3%) and Entamoeba nuttalli (17.4%). In addition, a novel Entamoeba ribosomal lineage named RL13 (22.8%) was identified, and phylogenetic analysis revealed a close genetic relationship between RL13 and Entamoeba. hartmanni. Genotyping of E. nuttalli obtained 24 genotypes from five populations and further analysis showed E. nuttalli had a high degree of genetic differentiation (F ST > 0.25, Nm < 1) between the host populations. The result of analysis of molecular variance (AMOVA) revealed that observed genetic differences mainly originate from differences among populations (F ST = 0.91). Meanwhile, the phylogenetic tree showed that these genotypes of E. nuttalli were clustered according to geographical populations, indicating a significant phylogeographic distribution pattern. Considering the potential pathogenicity of E. nuttalli , attention should be paid to its risk of zoonotic transmission. [ABSTRACT FROM AUTHOR]

The Yunnan‐Guizhou Plateau (YGP) is characterized by the distinctive isolated habitat of the limestone Karst Islands and features the Wumeng Mountains, which divide the YGP into the two Plateaus of Yunnan and Guizhou. This study aimed to assess the effects of geographic isolation and past climate fluctuation on the distribution of flora in the YGP. To achieve this, we carried out the phylogeographical pattern and genetic structure based on chloroplast and nuclear ribosomal DNA sequence in relation to past (Last Glacial Maximum) and present distributions based on ecological niche modeling for Morella nana, an important wild plant resource and endemic to the YGP once considered a vulnerable species. The results suggest that the genetic and chlorotype network structures of M. nana are divided into at least two groups: cpDNA chlorotype H2 (or dominant nrDNA haplotypes h1 and h2), distributed primarily to the east of the Wumeng Mountains, and cpDNA chlorotypes H1 and H3–H10 (or dominant nrDNA haplotype h2 and h3), distributed to the west of the Wumeng Mountains. A deep genetic split was noted within the two groups to reach 25 steps, especially for the cpDNA fragment variation. This east–west divergence reveals the existence of a natural geographical isolation boundary in the form of the Wumeng Mountains, and supports the existence of at least two glacial refuges during the Quaternary glacial period, along with two genetic diversity center, and at least two large geographic protection units for the important species of M. nana. This study indicates that the phylogeographical pattern of M. nana can be attributed to geographic/environmental isolation caused by the Wumeng Mountains and climate fluctuation during the last glacial maximum, and proposes an effective strategy to protecting this important plant resource. [ABSTRACT FROM AUTHOR]

Seed dispersal affects gene flow and hence genetic differentiation of plant populations. During the Late Quaternary, most fruit‐eating and seed‐dispersing megafauna went extinct, but whether these animals have left signatures in the population genetics of their food plants, particularly those with large, 'megafaunal' fruits (i.e. >4 cm—megafruits), remains unclear.Here, we assessed the population history, genetic differentiation and recent migration among populations of four animal‐dispersed palm (Arecaceae) species with large (Borassus madagascariensis), medium‐sized (Hyphaene coriacea, Bismarckia nobilis) and small (Chrysalidocarpus madagascariensis) fruits on Madagascar. We integrated double‐digest restriction‐site‐associated DNA sequencing (ddRAD) of 167 individuals from 25 populations with (past) distribution ranges for extinct (e.g., giant lemurs and elephant birds) and extant seed‐dispersing animals, landscape and human impact data, and applied linear mixed‐effects models to explore the drivers of genetic variation in Malagasy palms.Palm populations that shared more megafrugivore species in the past had lower genetic differentiation than populations that shared fewer megafrugivore species. This suggests that megafrugivore‐mediated seed dispersal in the past may have led to frequent gene flow among populations. In comparison, extant frugivore diversity only decreased genetic differentiation in the small‐fruited palm. Furthermore, genetic differentiation of all palm species decreased with landscape connectivity (i.e. environmental suitability, forest cover and river density) and human impact (i.e. road density), while migration rates of the small‐fruit palm increased with road density.Synthesis. Our results suggest that the legacy of megafrugivores regularly achieving long dispersal distances is still reflected in the population genetics of palms that were formerly dispersed by such animals. Furthermore, low genetic differentiation was possibly maintained after the megafauna extinctions through alternative dispersal (e.g. human‐ or river‐mediated), long generation times and long lifespans of these megafruit palms. Our study illustrates how species interactions that happened >1000 years ago can leave imprints in their population genetics. [ABSTRACT FROM AUTHOR]

Damage caused by the rice striped stem borer (SSB), Chilo suppressalis (Walker) (Lepidoptera: Pyralidae), is much more severe on indica/xian rice than on japonica/geng rice (Oryza sativa) which matches pest outbreak data in cropping regions of China. The mechanistic basis of this difference among rice subspecies remains unclear. Using transcriptomic, metabolomic and genetic analyses in combination with insect bioassay experiments, we showed that japonica and indica rice utilise different defence responses to repel SSB, and that SSB exploited plant nutrition deficiencies in different ways in the subspecies. The more resistant japonica rice induced patterns of accumulation of methyl jasmonate (MeJA—part of a defensive pathway) and vitamin B1 (VB1—a nutrition pathway) distinct from indica cultivars. Using gene‐edited rice plants and SSB bioassays, we found that MeJA and VB1 jointly affected the performance of SSB by disrupting juvenile hormone levels. In addition, genetic variants of key biosynthesis genes in the MeJA and VB1 pathways (OsJMT and OsTH1, respectively) differed between japonica and indica rice and contributed to performance differences; in indica rice, SSB avoided the MeJA defence pathway and hijacked the VB1 nutrition‐related pathway to promote development. The findings highlight important genetic and mechanistic differences between rice subspecies affecting SSB damage which could be exploited in plant breeding for resistance. Summary Statement: This manuscript demonstrates that striped stem borer (SSB) avoided one defence pathway and hijacked another nutrition‐related pathway to promote development. The findings highlight important genetic and mechanistic differences between rice subspecies affecting SSB damage which could be exploited in plant breeding for resistance. [ABSTRACT FROM AUTHOR]

Pleurotus tuoliensis is a unique species discovered in Xinjiang, China, which is recognized for its significant edible, medicinal, and economic value. It has been successfully incorporated into industrial production. Controversy has emerged concerning the evolution and environmental adaptability of this species due to inadequate interspecific ecology and molecular data. This study examines the germplasm resources of P. tuoliensis in the Xinjiang region. A total of 225 wild and cultivated strains of P. tuoliensis were gathered from seven representative regions. Phylogenetic analysis revealed that seven populations were notably segregated into three distinct groups, primarily attributed to environmental factors as the underlying cause for this differentiation. Population historical size data indicate that P. tuoliensis underwent two expansion events, one between 2 and 0.9 Mya (Miocene) and the other between 15 and 4 Mya (Early Pleistocene). The ancient climate fluctuations in the Xinjiang region might have contributed to the comparatively modest population size during the Pliocene epoch. Moreover, through the integration of biogeography and ancestral state reconstruction, it was determined that group C of P. tuoliensis emerged initially and subsequently dispersed to groups D and B, in that order. Subsequently, group D underwent independent evolution, whereas group B continued to diversify into groups A and EFG. The primary factor influencing this mode of transmission route is related to the geographical conditions and prevailing wind direction of each group. Subsequent research endeavors focused on assessing the domestication adaptability of P. tuoliensis to different substrates. It was found that the metabolic processes adapted during the domestication process were mainly related to energy metabolism, DNA repair, and environmental adaptability. Processes adapted to the host adaptability include responses to the host (meiosis, cell cycle, etc.) and stress in the growth environment (cysteine and methionine metabolism, sulfur metabolism, etc.). This study analyzed the systematic evolution and genetic differentiation of P. tuoliensis in Xinjiang. The identified loci and genes provide a theoretical basis for the subsequent improvement of germplasm resources and conducting molecular breeding. [ABSTRACT FROM AUTHOR]

Wetland ecosystems worldwide are threatened by habitat alteration, climate change and the introduction of invasive species, even within protected areas. Unravelling the reliance of sensitive wetland‐dwelling species, such as amphibians, on habitat characteristics is thus essential to identify conservation targets.Here we assess the distribution of genetic diversity of two strongly aquatic amphibians (Pelophylax perezi and Pleurodeles waltl) in association with habitat features across the most extensive, protected wetland of the Iberian Peninsula: Doñana National Park.Despite inhabiting a protected area free from anthropogenic barriers, the genetic diversity of P. perezi and P. waltl is not homogeneously distributed across the wetland, but instead concentrates in core areas, mainly in the northern zone. Both genetic diversity and connectivity (as opposed to genetic differentiation) showed significant positive associations with the area of the breeding sites and the flooded area surrounding the breeding sites within the dispersal potential of either species, that is nearby pond availability.Large water bodies connected to abundant temporary ponds are key for the maintenance of amphibian genetic diversity. Nevertheless, the core populations of our target species, which show markedly aquatic habits, are concentrated in areas colonised by invasive species, which could compromise their long‐term viability.Our results highlight that maintaining widely connected arrays of ponds of different hydroperiods, including large breeding sites free from invasive predators and competitors, is paramount for amphibian conservation in Mediterranean wetlands. [ABSTRACT FROM AUTHOR]

Understanding the driving forces of speciation is a central question in evolutionary biology. Cycas bifida (Dyer) K. D. Hill and Cycas micholitzii Dyer are two morphologically similar Cycas (Cycadaceae) species with deeply pectinate megasporophylls and dichotomously divided leaflets. Geographically, they are isolated by the Red River Fault Zone (RRFZ), which acts as a biogeographical barrier for many Cycas species. In this study, we investigated the divergence, genetic diversity, genetic structure, and demographic history of C. bifida and C. micholitzii to uncover the speciation mechanisms for the two endangered species. Results revealed high historical gene flow but low contemporary gene flow between the two species, with a deep divergence occurring in the Late Miocene. The long‐term geographical isolation and ecological niche differentiation were identified as important factors in driving the divergence of the two species, supported by significant isolation by distance testing, barrier analysis, and niche consistency detection. Geographical isolation by the RRFZ played a pivotal role in facilitating their divergence by constraining gene flow. Conservation genetic analyses indicated high genetic diversity within both species, coupled with disparate responses to Pleistocene climate fluctuations: C. micholitzii experienced population expansion, while C. bifida displayed a mild bottleneck effect. To ensure the protection and long‐term sustainability of two threatened species, relevant conservation guidelines were proposed based on the assessment of their genetic diversity and structure. This study furnishes valuable insights into the mechanisms underpinning species divergence and delivers actionable recommendations for cycad conservation. [ABSTRACT FROM AUTHOR]

Tropical and subtropical trees provide key ecosystem services but are facing global population decline due to logging, habitat degradation, land conversion, and climate change. Vatica guangxiensis used to be a characteristic timber species of China's tropical forests but is now terminally endangered (280 individuals) and fragmented into three relictual populations in southwest China. Generating genome‐wide DNA for ∼82% of all living tree individuals of this species complex, we found evidence for a late Pliocene division into two species‐level lineages that have not had gene flow for approximately 3 million years. All three relictual populations exhibited a loss of genetic diversity and recent bottlenecks. In addition, forward simulations indicated a likely population collapse in all three populations within the next century. Our study generates a model framework for the integration of genomic evidence—including evolutionary history, current genetic variation, and future projections—into conservation planning. [ABSTRACT FROM AUTHOR]