High Genetic Diversity Research Articles

Development of targeted whole genome sequencing approaches for Crimean-Congo haemorrhagic fever virus (CCHFV)

Crimean-Congo haemorrhagic fever (CCHF) is the most prevalent human tick-borne viral disease, with a reported case fatality rate of 30 % or higher. The virus contains a tri-segmented, negative-sense RNA genome consisting of the small (S), medium (M) and large (L) segments encoding respectively the nucleoprotein (NP), the glycoproteins precursor (GPC) and the viral RNA-dependent RNA polymerase (RDRP). CCHFV is one of the most genetically diverse arboviruses, with seven distinct lineages named after the region they were first reported in and based on S segment phylogenetic analysis.Due to the high genetic divergence of the virus, a single targeted tiling PCR strategy to enrich for viral nucleic acids prior to sequencing is difficult to develop, and previously we have developed and validated a tiling PCR enrichment method for the Europe 1 genetic lineage.We have developed a targeted, probe hybridisation capture method and validated its performance on clinical as well as cell-cultured material of CCHFV from different genetic lineages, including Europe 1, Europe 2, Africa 2 and Africa 3. The method produced over 95 % reference coverages with at least 10x sequencing depth. While we were only able to recover a single complete genome sequence from the tested Europe 1 clinical samples with the capture hybridisation protocol, the data provides evidence of its applicability to different CCHFV genetic lineages.CCHFV is an important tick-borne human pathogen with wide geographical distribution. Environmental as well as anthropogenic factors are causing increased CCHFV transmission. Development of strategies to recover CCHFV sequences from genetically diverse lineages of the virus is of paramount importance to monitor the presence of the virus in new areas, and in public health responses for CCHFV molecular surveillance to rapidly detect, diagnose and characterise currently circulating strains.

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

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

Genomes of Aegilops umbellulata provide new insights into unique structural variations and genetic diversity in the U-genome for wheat improvement.

Aegilops umbellulata serve as an important reservoir for novel biotic and abiotic stress tolerance for wheat improvement. However, chromosomal rearrangements and evolutionary trajectory of this species remain to be elucidated. Here, we present a comprehensive investigation into Ae. umbellulata genome by generating a high-quality near telomere-to-telomere genome assembly of PI 554389 and resequencing 20 additional Ae. umbellulata genomes representing diverse geographical and phenotypic variations. Our analysis unveils complex chromosomal rearrangements, most prominently in 4U and 6U chromosomes, delineating a distinct evolutionary trajectory of Ae. umbellulata from wheat and its relatives. Furthermore, our data rectified the erroneous naming of chromosomes 4U and 6U in the past and highlighted multiple major evolutionary events that led to the present-day U-genome. Resequencing of diverse Ae. umbellulata accessions revealed high genetic diversity within the species, partitioning into three distinct evolutionary sub-populations and supported by extensive phenotypic variability in resistance against several races/pathotypes of five major wheat diseases. Disease evaluations indicated the presence of several novel resistance genes in the resequenced lines for future studies. Resequencing also resulted in the identification of six new haplotypes for Lr9, the first resistance gene cloned from Ae. umbellulata. The extensive genomic and phenotypic resources presented in this study will expedite the future genetic exploration of Ae. umbellulata, facilitating efforts aimed at enhancing resiliency and productivity in wheat.

Population genetics analysis of Diospyrosmun A.Chev. ex Lecomte (Ebenaceae) based on EST-SSR markers derived from a novel transcriptome.

Diospyrosmun A.Chev. ex Lecomte (Ebenaceae), a native evergreen tree in Vietnam, has important economic and ecological values. The absence of effective and reliable molecular markers has hampered the study of D.mun's genetic diversity and population structure, even though it is an endemic and endangered species. Therefore, significant enrichment of genomic resources is urgently needed to uncover and better understand the genetic architecture of D.mun. This study aims to demonstrate an efficient and reliable tool to explore the polymorphism within D.mun germplasm. It provides a valuable platform for the breeding and conservation of this species and other endangered species worldwide. The Illumina HiSeq™ 4000 sequencing technology was applied for the transcriptomic analysis, genetic differentiation and population structure of D.mun in Vietnam. In this study, the transcriptomes of D.mun were analysed using the Illumina HiSeqTM 4000 sequencing system and a total of 5,588,615,700 base pairs were generated. De novo assembly indicated that 91,134 unigenes were generated (average length = 645.55 bp, N50 = 957 bp, Q20 = 98.08% and Q30 = 94.51%). A total of 92,798 and 21,134 unigenes had significant similarities amongst Nr and Swiss-Prot, respectively. In the GO database, 19,929 unigenes were annotated and these genes were divided into three major categories and 50 subcategories. In the KOG analysis, 18,499 unigenes were annotated and divided into 25 gene function categories. In the KEGG analysis, 12,017 unigenes were annotated. According to the related pathways involved, they could be classified into 56 subclasses. In this study, we have identified a total of 9,391 EST-SSR markers. Ten microsatellite loci were employed to assess the genetic diversity and structure of 82 adult D.mun trees across three populations in Vietnam. The results indicated moderate levels of genetic diversity with PIC = 0.77, NA = 3.9, NE = 2.8, Ho = 0.56 and HE = 0.58 and the fixation index value was recorded as positive for three populations (NS, NH and CP). Genetic differentiation among populations was low (FST = 0.045), suggesting limited gene flow (Nm = 5.34). This result indicates gene exchange between the populations of ancient D.mun from different geographical areas and regions. The analysis of molecular variance (AMOVA) showed that high genetic variation existed within individuals (91%) compared to amongst populations (4%). Genetic structure analysis, DAPC and the NJ tree indicated that the three populations were divided into three main clusters. With this study, we provide a molecular resoureces for the breeding and conservation of D.mun.

Genetic Diversity of Common Bean (Phaseolus vulgaris L.) Landraces Based on Morphological Traits and Molecular Markers.

The objective of this study was to evaluate the genetic diversity among traditional common bean accessions through morphological descriptors and molecular markers. Sixty-seven common bean accessions from the Germplasm bank of the Instituto Federal of Espírito Santo-Campus de Alegre were evaluated. For this, 25 specific morphological descriptors were used, namely 12 quantitative and 13 qualitative ones. A diversity analysis based on morphological descriptors was carried out using the Gower algorithm. For molecular characterization, 23 ISSR primers were used to estimate dissimilarity using the Jaccard Index. Based on the dendrograms obtained by the UPGMA method, for morphological and molecular characterization, high genetic variability was observed between the common bean genotypes studied, evidenced by cophenetic correlation values in the order of 0.99, indicating an accurate representation of the dissimilarity matrix by the UPGMA clustering. In the morphological characterization, high phenotypic diversity was observed between the accessions, with grains of different shapes, colors, and sizes, and the accessions were grouped into nine distinct groups. Molecular characterization was efficient in separating the genotypes in the Andean and Mesoamerican groups, with the 23 ISSR primers studied generating an average of 6.35 polymorphic bands. The work identified divergent accessions that can serve different market niches, which can be indicated as parents to form breeding programs in order to obtain progenies with high genetic variability.

A wide range of abiotic habitat factors and genetic diversity facilitate expansion of Trapa natans within its native range

Climate change and intense human activity are exacerbating changes in species' ranges. While the rapid spread of invasive alien species is well documented worldwide, the phenomenon of the spread of native species is poorly understood. To explain the problem of rapidly spreading species in the changing world, it is necessary to understand their ecology, genetic diversity and habitat limitation. The aim of our study was to analyze the ecological requirements and genetic diversity in the population of the macrophyte Trapa natans s. l., an invasive alien species in North America but native in Europe and Asia. We investigated the populations in its native range (Central and Northeastern Europe), where the species is defined as rare or extinct. We found the occurrence of T. natans in Northeastern Europe aquatic habitats where, up to now, it was described as an extinct species. The results of our environmental studies showed that the species has a wide range of tolerance to habitat conditions and lives in medium to highly nutrient-rich water with low and high salinity. Using Amplified Fragment Length Polymorphism (AFLP) analysis, we revealed high genetic variability within populations with relatively limited differentiation between populations. We showed that some populations are highly diverse (possibly refugia; Central Europe) and others are homogeneous (new sites, commercial reintroduction; Northeastern Europe). Conservation status of T. natans in its native range should be reconsidered, as the species has spread rapidly in recent decades and could be detrimental to aquatic habitats. The conclusion is that expansion/invasion can start from small populations, but under favorable conditions these populations spread rapidly. The introduction of species (even native) should be done carefully, if at all, as uncontrolled introduction to new locations, e.g. private ponds, could be the start of dispersal (native habitats) or invasion (non-native area).

Characterization of Genetic Diversity in the Capsid Protein Gene of Grapevine Fleck Virus and Development of a New Real-Time RT-PCR Assay.

The grapevine fleck virus (GFkV) is a ubiquitous grapevine-infecting virus found worldwide, is associated with the grapevine fleck complex, and is often found in mixed infections with viruses of the grapevine leafroll complex and/or vitiviruses. Although GFkV has been studied for a long time, limited sequence information is available in the public databases. In this study, the GFkV sequence data available in GenBank and data generated at the Foundation Plant Services, University of California, Davis, were used to perform nucleotide sequence comparisons, construct a phylogenetic tree, and develop a new RT-qPCR assay. Sequence comparisons showed high genetic diversity among the GFkV isolates, and the phylogenetic analyses revealed a new group comprised of GFkV isolates identified in the present study. A new assay, referred to as GFkV-CP, was designed and validated using an existing GFkV positive control together with 11 samples known to be infected with combinations of different marafiviruses and maculaviruses but not GFkV. In addition, the newly designed assay was used in a field survey to screen grapevines from diverse geographical locations that are maintained at the United States Department of Agriculture (USDA) National Clonal Germplasm Repository (NCGR) in Winters, CA.

Assessment of Population Genetic Diversity of Medicinal Meconopsis integrifolia (Maxim.) Franch. Using Newly Developed SSR Markers.

Meconopsis integrifolia is an endangered Tibetan medicinal plant with significant medicinal and ornamental value. Understanding its genetic diversity and structure is crucial for its sustainable utilization and effective conservation. Here, we develop a set of SSR markers based on transcriptome data to analyze the genetic diversity and structure of 185 individuals from 16 populations of M. integrifolia. The results indicate that M. integrifolia exhibits relatively high genetic diversity at the species level (the percentage of polymorphic bands PPB = 91.67%, Nei's genetic diversity index He = 0.2989, Shannon's information index I = 0.4514) but limited genetic variation within populations (PPB = 12.08%, He = 0.0399, I = 0.0610). The genetic differentiation among populations is relatively high (the coefficient of gene differentiation GST = 0.6902), and AMOVA analysis indicates that 63.39% of the total variation occurs among populations. This suggests that maintaining a limited number of populations is insufficient to preserve the overall diversity of M. integrifolia. Different populations are categorized into four representative subclusters, but they do not cluster strictly according to geographical distribution. Limited gene flow (Nm = 0.2244) is likely the main reason for the high differentiation among these populations. Limited seed and pollen dispersal abilities, along with habitat fragmentation, may explain the restricted gene flow among populations, highlighting the necessity of conserving as many populations in the wild as possible.

Murine astrovirus (MuAstV) infection in mouse facilities in Brazil: First South American report.

This study aimed to investigate the presence of murine astrovirus (MuAstV) in Brazil. Fecal samples from mice belonging to four Brazilian animal facilities were collected and tested for MuAstV using real-time polymerase chain reaction. Of the 162 samples tested, 38 (23.5%) were positive for MuAstV, 33 (91.7%) of which came from specific-pathogen free colonies. Although most of the samples were obtained from asymptomatic animals, three mice presented diarrheal symptoms, and MuAstV was the only agent detected by molecular assay. Phylogenetic analysis revealed similarities between the MuAstV strains from this study and prototypes from the USA. MuAstV's high prevalence, environmental stability, genetic diversity and potential for persistent infections must be considered when evaluating health monitoring programs for laboratory rodents.

Genomic selection strategies for the German Merino sheep breeding programme - A simulation study.

Genomic selection is widely implemented in livestock breeding programmes across species. Its potential is also evident for sheep breeding; however, it has several limitations, particularly because of the high genetic diversity across and within sheep breeds. In Germany, the predominant sheep breed is the Merino sheep. Until now, there has been no use of genomic selection in the German Merino sheep breeding programme. In this simulation study, different genomic selection strategies were compared with a reference scenario with a breeding value estimation based on pedigree BLUP. A simplified version of the German Merino sheep breeding programme, including a health and a production trait in the breeding goal, was simulated via the R package Modular Breeding Program Simulator (MoBPS). Real genotype data were used to create a population specific simulation. The reference scenario was compared with several alternative scenarios in which selection was based on single-step GBLUP (ssGBLUP) breeding value estimation with varying genotyping strategies. In addition to scenarios in which all male and all male plus all female lambs were genotyped, scenarios with a preselection of lambs, that is only a certain proportion (top 25%, top 50%) genotyped, were simulated. The results revealed that genetic gain increased with increasing numbers of available genotypes. However, marginal gains decreased with increasing numbers of genotypes. Compared with the reference scenario, genotyping the top 25% of male lambs increased the genetic gain for the breeding ram population by 13% for both traits whereas genotyping the top 50% of male lambs or all male lambs led to increases of 18% (17%) or 26% (21%) for the health (production) trait, respectively. The potential of genotyping females in addition to male lambs was less evident on the male side with no significant differences between the scenarios with different proportions of genotyped females. The results have shown that genomic selection can be a valuable tool to increase genetic gain in the German Merino sheep population and that the genotyping of a certain proportion of animals might lead to substantial improvement over pedigree-based breeding value estimation. Nevertheless, further studies, especially economic evaluations, are needed before practical implementation.

Use of Phenomics in the Selection of UAV-Based Vegetation Indices and Prediction of Agronomic Traits in Soybean Subjected to Flooding

Flooding is a frequent environmental stress that reduces soybean growth and grain yield in many producing areas in the world, such as the United States, Southeast Asia, and Southern Brazil. In these regions, soybean is frequently cultivated in lowland areas in crop rotation with rice, which provides numerous technical, economic, and environmental benefits. In this context, the identification of the most important spectral variables for the selection of more flooding-tolerant soybean genotypes is a primary demand within plant phenomics, with faster and more reliable results enabled using multispectral sensors mounted on unmanned aerial vehicles (UAVs). Accordingly, this research aimed to identify the optimal UAV-based multispectral vegetation indices for characterizing the response of soybean genotypes subjected to flooding and to test the best linear model fit in predicting tolerance scores, relative maturity group, biomass, and grain yield based on phenomics analysis. Forty-eight soybean cultivars were sown in two environments (flooded and non-flooded). Ground evaluations and UAV-image acquisition were conducted at 13, 38, and 69 days after flooding and at grain harvest, corresponding to the phenological stages V8, R1, R3, and R8, respectively. Data were subjected to variance component analysis and genetic parameters were estimated, with stepwise regression applied for each agronomic variable of interest. Our results showed that vegetation indices behave differently in their suitability for more tolerant genotype selection. Using this approach, phenomics analysis efficiently identified indices with high heritability, accuracy, and genetic variation (>80%), as observed for MSAVI, NDVI, OSAVI, SAVI, VEG, MGRVI, EVI2, NDRE, GRVI, BNDVI, and RGB index. Additionally, variables predicted based on estimated genetic data via phenomics had determination coefficients above 0.90, enabling the reduction in the number of important variables within the linear model.

Genetic homogeneity and weak signatures of local adaptation in the marine mussel Mytilus chilensis

The natural populations of the marine mussel Mytilus chilensis and the associated aquaculture industry forms a sensitive social-ecological system that relies on the released propagules for cultivation in the highly heterogeneous environment (temperature, productivity, and salinity) of northern Patagonia (42–44 °S). We assessed spatial genetic structure, signals of local adaptation, and population assignment of M. chilensis analyzing 5963 SNPs from 125 individuals across six natural populations sampled over two consecutive years along the southeast Pacific coast (39° 25′ to 43° 07′ S, ~ 430 km). Neutral and putatively adaptive loci revealed high genetic diversity and low genetic differentiation among populations. Of the whole dataset, less than 1% (50) of loci were identified as putatively adaptive through multiple approaches, with only 0.1% detected in by all of them, and only two loci of them were correlated with environmental variables. No evidence of Isolation by Environment (IBE) was found, albeit a slight differentiation in the southern sampling location (Yaldad). These results suggest that the genetic structure observed is primarily shaped by neutral processes with weak signals of local adaptation. Gene-flow appears to be the main evolutionary force influencing the species’ population genetic structure. Because of the importance for the industry, the probability of correct assignment of individuals to their population of origin using allelic frequencies was evaluated. Analyses exhibited relatively low probabilities (< 50% for four out of six sites) of accurately assigning individuals to their geographic origin, with a limited success of SNP markers the for such purposes. Likely, species' high dispersal capacity, seed translocation, and the spill-over effect of mussel aquaculture prevents population genetic differentiation through high effective gene flow, hindering local genetic adaptation.

Genetic diversity and incidence of cassava bacterial blight (CBB) caused by Xanthomonas phaseoli pv. manihotis in Burkina Faso

AbstractCassava bacterial blight (CBB), caused by Xanthomonas phaseoli pv. manihotis (Xpm), poses a significant threat to cassava production in Burkina Faso. Prior to this study, the geographical distribution, incidence and origin of CBB introductions were poorly understood. In this investigation, we assessed the incidence of CBB in major cassava‐cropping regions and analysed the genetic diversity of 344 Xpm strains collected from 19 fields between 2015 and 2016, using a multilocus variable number of tandem repeat analysis (MLVA) scheme targeting 14 microsatellite markers. Our results reveal the presence of CBB in three out of four cropping regions, with incidences ranging from 0% to 100% at locality and variety scale. Burkina Faso's Xpm strains exhibited high genetic diversity at multiple levels, including country scale (He = 0.6), cropping region (0.43 to 0.57), locality (0.25 to 0.50) and field (0.25 to 0.52). Pairwise comparisons among populations from different cropping areas indicated a strong genetic differentiation. The categorical minimum spanning tree reveals that the Cascades region has the higher diversity indices and consequently could be the origin site of dispersion of Xpm in the other cropping regions of cassava. Human activities play a major role in the dissemination of Xpm through cassava cuttings. The importance of the sanitary state of cuttings must be emphasized in order to avoid CBB and ensure good cassava production.

Identification of Capsicum species from Colombia by DNA barcoding and high resolution melting (HRM) analysis

AbstractDNA barcoding allows the use of molecular markers to differentiate the species of an interest group. This is especially useful when morphological characters are insufficient due to high similarity between species. The genus Capsicum contains some species that are difficult to determine by taxonomic means, in particular the annuum complex. Thus, the objective of this study was to investigate the discriminatory ability of two molecular markers in Colombian Capsicum accessions, including three wild species belonging to the Andean clade of the genus. A total of 95 Capsicum accessions, representing eight species, were genotyped by high resolution melting analysis (HRM) using the Waxy and C2_At5g04590 markers. Waxy could discriminate the Andean clade species (C. rhomboideum, C. dimorphum and C. lycianthoides), C. baccatum, C. pubescens and C. chinense, while C2_At5g04590 could discriminate C. frutescens, C. annuum var. annuum and C. annuum var. glabriusculum. Hence, a combination of the two markers could be used for discrimination of the eight species including the wild variety of C. annuum: C. annuum var. glabriusculum. Most nucleotide substitutions and indels were found in the sequences of the three Andean species, indicating that the Andean clade has a high genetic diversity compared to the other species. The incorporation of more wild species and varieties in this study allowed to correct the power of both markers to discriminate Capsicum species, besides the registration of new haplotypes.

MtDNA genetic diversity and phylogeographic insights into giant domestic pigeon (Columba livia domestica) breeds: connections between Central Europe and the Middle East

Humans have selectively bred domestic pigeons (Columba livia domestica) to create breeds with a diversity of shapes, colors and other attributes. Since Darwin, the domestic pigeon has always been a popular model species for scientific research because of its richness of form, colouration and behaviour. It is believed that the world's squab pigeon industry uses breeds and hybrids from the Mediterranean region. An exception is the indigenous giant pigeon breeds of the Carpathian Basin, whose origin is not known. Therefore, our aims were 1) to understand the phylogenetic relationships of giant pigeons, which sheds light on the origin of Hungarian breeds and their relationship to the Mediterranean giant pigeon breed group; 2) to contribute molecular genetic data to the genealogy of 2 Iraqi pigeon breeds close to the pigeon domestication center, including the culturally important Iraqi Red Pigeon, and 3) to compare the genetic diversity of European and Middle Eastern domestic pigeon populations and to draw conclusions on the phylogenetic relationships between pigeon breeds and molecular clues to their different breeding practices of both regions. A 655-bp-long sequence of the cytochrome oxidase 1 (COI) region of the mitochondrial DNA was studied in a total of 276 pigeons (19 breeds). A total of 27 haplotypes were found, of which 22 were unique. The highest genetic diversity was found in the Carpathian Basin, and the lowest in the Iraqi region. STRUCTURE analysis revealed low structurality, K=3 was the most likely. The majority of the samples belong to the most ancient haplotype H_2=219, however the Jacobin pigeon is on a very separate evolutionary branch with a large number of mutations. None of the 19 breeds investigated in this study have been previously studied in phylogenetics, and most of these breeds have potential as squab pigeons, and have good meat forms for utilization, therefore the results of this study may also be of help to the squab pigeon industry.

Population genomics of Streptococcus mitis in UK and Ireland bloodstream infection and infective endocarditis cases

Streptococcus mitis is a leading cause of infective endocarditis (IE). However, our understanding of the genomic epidemiology and pathogenicity of IE-associated S. mitis is hampered by low IE incidence. Here we use whole genome sequencing of 129 S. mitis bloodstream infection (BSI) isolates collected between 2001–2016 from clinically diagnosed IE cases in the UK to investigate genetic diversity, antimicrobial resistance, and pathogenicity. We show high genetic diversity of IE-associated S. mitis with virtually all isolates belonging to distinct lineages indicating no predominance of specific lineages. Additionally, we find a highly variable distribution of known pneumococcal virulence genes among the isolates, some of which are overrepresented in disease when compared to carriage strains. Our findings suggest that S. mitis in patients with clinically diagnosed IE is not primarily caused by specific hypervirulent or antimicrobial resistant lineages, highlighting the accidental pathogenic nature of S. mitis in patients with clinically diagnosed IE.

GENETIC DIVERSITY AND POPULATION STRUCTURE OF JUNIPERUS SERAVSCHANICA KOM. IN CENTRAL ASIA REVEALED BY MICROSATELLITE MARKERS

Juniperus seravschanica Kom. is a widely distributed and significant tree species in Central Asia, thriving in the mountain ranges from Oman to Uzbekistan, Kyrgyzstan, and Kazakhstan. It plays a vital role in forming shrub-forest massifs in mountainous regions, contributing to soil drainage and stabilization at medium to high altitudes. To gain a detailed understanding of the current status of J. seravschanica and to develop effective conservation strategies, a comprehensive study of the species' genetic diversity and population structure was conducted. Leaf samples were collected from 15 J. seravschanica populations across Uzbekistan, Kyrgyzstan, and Kazakhstan to assess genetic diversity and population structure. Using 11 polymorphic simple sequence repeat (SSR) markers, genetic diversity parameters such as the number of alleles, the number of effective alleles, the percentage of polymorphic loci, and Nei's genetic diversity index were evaluated. Nei's genetic diversity index for J. seravschanica populations averaged 0.450, ranging from 0.407 to 0.566. The AMOVA revealed that 90.3% of the total genetic variation was within populations, indicating a high level of genetic diversity within each population. Gene flow, calculated using alleles from all populations, was estimated at 4.654. Population structure analysis showed weak clustering among the studied populations, supporting the AMOVA findings. This study provides valuable insights into the genetic diversity and population structure of J. seravschanica in Central Asia. The high genetic diversity within populations suggests a strong adaptive capacity to environmental changes. These findings can be effectively utilized to develop conservation strategies for J. seravschanica, ensuring the long-term sustainability of this important tree species in Central Asia. This work was supported by Grant No.AP09259027 of the Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan.

Genetic variation in phenology of wild Arabidopsis thaliana plants.

Phenology and the timing of development are often under selection, but at the same time influence selection on other traits by controlling how traits are expressed across seasons. Plants often exhibit high natural genetic variation in phenology when grown in controlled environments, and many genetic and molecular mechanisms underlying phenology have been dissected. There remains considerable diversity of germination and flowering time within populations in the wild and the contribution of genetics to phenological variation of wild plants is largely unknown. We obtained collection dates of naturally inbred Arabidopsis thaliana accessions from nature and compared them to experimental data on the descendant inbred lines that we synthesized from two new and 155 published controlled experiments. We tested whether the genetic variation in flowering and germination timing from experiments predicted the phenology of the same inbred lines in nature. We found that genetic variation in phenology from controlled experiments significantly, but weakly, predicts day of collection from the wild, even when measuring collection date with accumulated photothermal units. We found that experimental flowering time breeding values were correlated to wild flowering time at location of origin estimated from herbarium collections. However, local variation in collection dates within a region was not explained by genetic variation in experiments, suggesting high plasticity across small-scale environmental gradients. This apparent low heritability in natural populations may suggest strong selection or many generations are required for phenological adaptation and the emergence of genetic clines in phenology.

Earthworm (Oligochaeta, Lumbricidae) intraspecific genetic variation and polyploidy.

Earthworms are known for their intricate systematics and a diverse range of reproduction modes, including outcrossing, self-fertilization, parthenogenesis, and some other modes, which can occasionally coexist in a single species. Moreover, they exhibit considerable intraspecific karyotype diversity, with ploidy levels varying from di- to decaploid, as well as high genetic variation. In some cases, a single species may exhibit significant morphological variation, contain several races of different ploidy, and harbor multiple genetic lineages that display significant divergence in both nuclear and mitochondrial DNA. However, the relationship between ploidy races and genetic lineages in earthworms remains largely unexplored. To address this question, we conducted a comprehensive review of available data on earthworm genetic diversity and karyotypes. Our analysis revealed that in many cases, a single genetic lineage appears to encompass populations with different ploidy levels, indicating recent polyploidization. On the other hand, some other cases like Octolasion tyrtaeum and Dendrobaena schmidti/D. tellermanica demonstrate pronounced genetic boundaries between ploidy races, implying that they diverged long ago. Certain cases like the Eisenia nordenskioldi complex represent a complex picture with ancient divergence between lineages and both ancient and recent polyploidization. The comparison of phylogenetic and cytological data suggests that some ploidy races have arisen independently multiple times, which supports the early findings by T.S. Vsevolodova-Perel and T.V. Malinina. The key to such a complex picture is probably the plasticity of reproductive modes in earthworms, which encompass diverse modes of sexual and asexual reproduction; also, it has been demonstrated that even high-ploidy forms can retain amphimixis.

Mitochondrial phylogeography of grassland caterpillars (Lepidoptera: Lymantriinae: Gynaephora) endemic to the Qinghai-Tibetan plateau.

Grassland caterpillars (Lepidoptera: Lymantriinae: Gynaephora) are the most damaging pests to alpine meadows in the Qinghai-Tibetan Plateau (QTP). Here, we conducted extensive sampling from 39 geographic populations covering almost the entire distribution of the eight QTP Gynaephora (Hübner) species to investigate phylogeographic patterns and speciation based on two mitochondrial genes (COI and ND5). A total of 40 haplotypes were detected in the 39 populations, with >70% of all haplotypes not shared between populations. The monophyletic QTP Gynaephora migrated from non-QTP regions during the Pliocene, corresponding to the uplift of the QTP, suggesting a mode of transport into the QTP. Among the eight QTP Gynaephora species described by morphological characteristics, two species (G. alpherakii and G. menyuanensis) were recovered as monophyletic groups (Clades B and C), while the remaining six formed two monophyletic clades: Clade A (G. qinghaiensis, G. jiuzhiensis, and G. qumalaiensis) and Clade D (G. aureata, G. ruoergensis, and G. minora). These results suggested that the number of the QTP Gynaephora species may be overestimated and further studies based on both morphological and nuclear gene data are needed. Genetic differentiation and speciation of the QTP Gynaephora were likely driven by the QTP uplifts and associated climate fluctuations during the Pleistocene, indicated by divergence time estimation, suggesting that isolation and subsequent divergence was the dominant mode of speciation. The Sanjiangyuan region (i.e., Clade A, characterized by high genetic diversity) may have been a glacial refugium of the QTP Gynaephora, as supported by analyses of gene flow and biogeography. High levels of genetic diversity were found in QTP Gynaephora, without population expansion, which may explain the high-altitude adaptation and outbreaks of grassland caterpillars in alpine meadows of the QTP. This study provides the largest phylogeographic analysis of QTP Gynaephora and improves our understanding of the diversity and speciation of QTP insects.