Population Genetic Diversity Research Articles

The influence of elevation on genetic structure and variability in a wetland crucifer of the Rocky Mountains.

In mountain ecosystems, environmental conditions (e.g., temperature, ultraviolet radiation) covary with elevation, potentially limiting gene flow over steep gradients. We hypothesized that, (1) due to stark elevational differences in environmental factors, populations from dissimilar elevations (e.g., montane versus alpine) are more strongly differentiated than populations from similar elevations; (2) patterns of migration reflect downslope dispersal more than upslope dispersal; and (3) alpine populations at the cold edge show evidence of expansion, while montane populations at the warm edge have declined. DNA polymorphisms in whole-genome sequences were studied from 6-10 genotypes each in populations of Cardamine cordifolia found at three montane sites (ranging from 2200 to 2800 m a.s.l.) and three alpine sites (ranging from 3000 to 3500 m a.s.l.). Statistical analyses assessed patterns of population structure, genetic diversity, migration, and historical demography since the Pleistocene. Populations maintained very high levels of nucleotide diversity (π range: 0.062-0.071) and were weakly differentiated (pairwise FST = 0.027) on average. Migration among alpine populations was also inferred, with no directionality of migration across elevation bands. Demographic inference suggests that both montane and alpine populations have declined in size since the Pleistocene. Environmental differences across elevation represent diffuse barriers to gene flow. Recent polyploidy and clonal reproduction likely explain excess heterozygosity and high nucleotide diversity within populations. The genetic similarity of populations across elevation suggests highly connected refugia during the Pleistocene; such results may indicate that montane and alpine populations will respond similarly to changing environmental conditions associated with climate change.

Evaluation of the conservation value and conservation difficulty of local populations of the rare plant Viola raddeana based on genetic diversity and gene expression information using next‐generation sequencers

AbstractRare plant species identified in project areas where land is to be developed or altered may need to be extracted for ex situ conservation under human control. During ex situ conservation, it is important to minimize the impact of adverse factors including the potentially limited environmental adaptability of rare plants under cultivation and possible losses of genetic diversity due to inbreeding if the number of conserved individuals is low. Here we evaluate the conservation difficulty and genetic diversity of populations of the rare plant Violα raddeana at five sites based on harmful gene accumulation and gene duplication data gathered using RNA‐seq. Additionally, we evaluate the genetic diversity and structure of these populations using single‐nucleotide polymorphism (SNP) data acquired by multiplexed inter‐simple sequence repeat genotyping by sequencing (MIG‐seq). The results obtained indicate that the V. raddeana populations have declined but remain robust toward environmental changes and can undergo voluntary mating at all sites. Moreover, we observed clear genetic differentiation between two populations in close geographic proximity. We considered that if the majority of the remaining individuals of V. raddeana in each genetically related population were transplanted and cultivated, it would be possible to maintain their genetic diversity through ex situ conservation. It is important that V. raddeana be kept under ex situ conservation management. In order to achieve this, we should work with public organizations such as local government agencies and botanical gardens.

Evaluating the Centre‐Periphery Hypothesis Through Genomic Phylogeographical Comparisons of Two Sister Species of Liquidambar in East Asia's Tertiary Relict Forests

ABSTRACTAimUnderstanding the spatial distribution of genetic variation within species is a central tenet in evolutionary biology and conservation biology. This study explores how historical demographic processes and/or environmental factors interact to affect contemporary genetic variation and adaptive potential, with a specific focus on testing the ‘centre‐periphery’ hypothesis (CPH).LocationSubtropical China.Taxon Liquidambar. MethodsWe combined comparative phylogeography, landscape genomics and niche modelling to investigate the interplay between demographic history and past/current environmental factors in shaping genetic variation in Liquidambar formosana and L. acalycina, a sister pair of East Asia's Tertiary relict forests.ResultsIn both species, core populations occupied highly suitable habitats at highest densities. Consistent with the CPH, population genetic diversity decreased, and differentiation increased, from centre to margin in L. acalycina, but not in L. formosana, likely reflecting different demographic histories and different relative contributions of geography, past (LGM) and current climates to their present‐day genetic variation. In addition, L. formosana showed higher adaptive potential to future climate change than L. acalycina.Main ConclusionsThis study demonstrates that differences in contemporary genetic variation and adaptability among closely related species can be explained by contrasting demographic responses to multiple geographic/climatic factors. In turn, it should also expand our understanding of the CPH, while informing future conservation efforts for these two study species.

Genomic exploration of Thuja plicata indicates no loss of diversity from adults to offspring in UK Woodlands

Thuja plicata is a conifer tree that is valued for its cultural, ecological and wood quality features in its natural range in western North America and is used in Europe as an exotic timber species. It is increasingly used in mixed species forests in the UK that are managed using natural regeneration, raising questions about genetic diversity of both the adult trees and offspring of the species in these stands. We studied population structure and genetic diversity in four UK woodlands of both adults and naturally regenerated offspring of T. plicata. We discovered 194,154 Single Nucleotide Polymorphisms (SNPs) using Genotyping-by-Sequencing (GBS) and retained 655 SNPs across 598 genome sequence scaffolds for analysis. The majority of these scaffolds included only one SNP, suggesting that; the selected SNPs were widely distributed within the genome. We found many monomorphic sites, most of which were restricted to adults in a single woodland, indicative of a genetic differentiation among woodlands. We found three ancestral populations (K = 3) and low levels of admixture across the four sites, indicating that the starting materials were largely from single populations. Estimates of genetic diversity using heterozygosity (Ho) and nucleotide diversity (π) were low (overall Ho = 0.174, π = 0.00226) across all sites but slightly higher in juveniles at two sites. Our genotyping methods and results on standing genetic diversity in this important conifer provide insight into the ability of planted woodlands in the UK to face environmental shifts and disease threats.

Genetic diversity, population structure in a historical panel of Brazilian soybean cultivars.

Soybean [Glycine max (L.) Merrill] is one of the most widely grown legumes in the world, with Brazil being its largest producer and exporter. Breeding programs in Brazil have resulted from multiple cycles of selection and recombination starting from a small number of USA cultivar ancestors in the 1950s and 1960s years. This process has led to the successful adaptation of this crop to tropical conditions, a phenomenon known as tropicalization. Many studies describe a narrow genetic background in Brazilian soybean cultivars. Various factors can affect the genetic diversity in species, especially in cultivated crops, such as the reproduction type, artificial selection, and the number and sources of variability in the breeding programs. In turns, the genetic diversity can affect the linkage disequilibrium blocks (LD) patterns and, consequently, molecular breeding strategies for selection of target loci for agronomic traits. We used high-throughput genotyping with SoySNP50K Illumina SNP markers to assess a collection of 370 Brazilian soybean accessions covering more than 60 years of soybean breeding in Brazil. Our goal was to investigate population structure and genetic diversity in the Brazilian germplasm, detect patterns of LD blocks, and identify regions presenting signals of selective swaps linked with quantitative trait loci (QTLs) of agronomic interest. Population structure analysis revealed two major groups among all genotypes, primarily differentiated by the year of release, separating old and new cultivars (before and after 2000´s years), and by growth habit (stem termination type-SST). The group I comprises about 75% of the panel and includes cultivars release before 2000`s years, including the oldest cultivars released in Brazil, most of which exhibit a determinate growth habit and maturity groups VI and VII. Group II includes only 83 materials, but shows higher levels of diversity than group I, representing most recent introductions in Brazilian germplasm. Further analysis of substructure within Group I, identified seven subgroups with no clear trend for segregation based on maturity group, STT or year of release. Instead, these subgroups were based on the contribution of key donors of disease resistance and adaptability, as soybean cultivation expanded from the South to Central region of Brazil. This finding is consistent with the history of soybean expansion in Brazil. We identified 123 genomic regions under selection among the groups of Brazilian cultivars associated with 440 quantitative trait loci (QTLs), revealing regions fixed across the breeding process associated with yield, disease resistance, water efficiency use, and others.

High-throughput sequence-based microsatellite genotyping for the non-model Neotropical tree species Anadenanthera colubrina (Leguminosae)

Background and aims – Anadenanthera colubrina is a Neotropical native forest tree species with significant ecological importance in Seasonally Dry Tropical Forests. Developing genetic markers for this species is relevant for conservation, breeding, and evolutionary studies. Previously available genetic markers for A. colubrina consisted of a few microsatellites. Next-generation sequencing (NGS) strategies allow simple and cost-effective development of new SSR loci from low-coverage whole genome shotgun sequencing. The main aim was to develop microsatellite markers for sequence-based high-throughput genotyping (SSRseq) in the species and to characterize their information content against traditional capillary electrophoresis-based microsatellite data by estimating the amount of molecularly accessible size homoplasy of each locus. Additionally, the reliability of these markers for population genetic analysis was assessed by genotyping two age classes (reproductively mature trees and seedlings) in a typical location in Argentina. Key results – Sixty primer pairs targeting microsatellites were designed, of which 25 were validated with allelic error rates < 3% and genotype missingness < 20%. A significantly higher number of alleles per locus and heterozygosity was detected for SSRseq considering sequence polymorphisms compared to analysing the same data based on sequence size (length) only. Size homoplasy, calculated as the proportion of mismatches between datasets relative to the number of alleles differing in length, averaged 97.85% over all SSR loci. High levels of population genetic diversity were detected in adults and seedlings from Paranaense forests, exceeding those reported in previous studies of A. colubrina using traditional SSRs. The generated datasets increase the resolution of capillary-based microsatellite genotyping, allowing for more accurate inference of eco-evolutionary processes in non-model tree species.

Spatially explicit estimation of recent migration rates in plants using genotypic data.

We present a new hierarchical Bayesian method using multilocus genotypes to estimate recent seed and pollen migration rates in a spatially explicit framework that incorporates distance effects separately for each type of dispersal. The method additionally estimates population allelic frequencies, population divergence values, individual inbreeding coefficients, individual maternal and paternal ancestries, and allelic dropout rates. We conduct a numerical simulation analysis that indicates that the method can provide reliable estimates of seed and pollen migration rates and allow accurate inference of spatial effects on migration, at affordable sample sizes (25-50 individuals/population) when population genetic divergence is not low (FST≥0.05), or by increasing sampling (to at least 100 individuals/population) under weaker levels of divergence (FST=0.025). Simulations also show that the accuracy provided by assays with about one thousand unlinked polymorphic SNP loci may approach, for a given sample size, the theoretical maximum achievable under categorical origin discrimination. We apply our method to Taxus baccata data, revealing low but significant seed and pollen migration among nearby population remnants during the last generation, with a negative effect of interpopulation distance on migration that was detectable for pollen but not for seeds.

Population viability of the orchid Gymnadenia conopsea increases with population size but is not related to genetic diversity

Abstract Population size is a main indicator of conservation potential, thought to predict both current and long‐term population viability. However, few studies have directly examined the links between the size and the genetic and demographic properties of populations, using metrics that integrate effects across the whole life cycle. In this study, we combined 6 years of demographic data with SNP‐based estimates of genetic diversity from 18 Swedish populations of the orchid Gymnadenia conopsea. We assessed whether stochastic growth rate increases with population size and genetic diversity, and used stochastic life table response experiment (SLTRE) analysis to evaluate how underlying vital rates contribute to among‐population variation in growth rate. For each population, we also estimated the probability of quasi‐extinction (shrinking below a threshold size) and of a severe (90%) decline in population size, within the next 30 years. Estimates of stochastic growth rate indicated that 10 populations are declining, seven increasing and one population is approximately stable. SLTRE decomposition showed that low mean adult survival and growth characterized strongly declining populations, whereas high mean fecundity characterized strongly increasing populations. Stochastic growth rate increased with population size, mainly due to higher survival in larger populations, but was not related to genetic diversity. One third of the populations were predicted to go extinct and eight populations to undergo a 90% decrease in population size in the coming 30 years. Low survival in small populations most likely reflects a positive association between local environmental conditions and population size. Synthesis: The association between G. conopsea population size and viability was driven by variation in survival, and there was no sign that ongoing declines are due to genetic erosion. This suggests that large populations occur in favourable habitats that buffer effects of climatic variation. The results also illustrate that demographic metrics can be more informative than genetic metrics, regarding conservation priority.

Plastid genome comparison and phylogenetic analyses of the Chinese group of medicinal species and related taxa within Asparagus genus

BackgroundAsparagus L. is a large genus widely distributed across the continents of the Old World. Among its members, approximately 14 species found in China are recognized as popular herbal medicines. However, accurate authentication of these medicinal species and their phylogenetic relationships with related taxa remains unresolved.MethodsTo identify simple sequence repeats (SSRs) and divergence hotspot regions appropriate for future authentication studies, as well as to infer the phylogenetic relationships among Asparagus species, we employed a plastid genome (plastome) dataset consisting of 25 Asparagus species (21 newly sequenced and four retrieved from GenBank), encompassing 12 Chinese medicinal species, for comparative and phylogenetic analyses.ResultsAll Asparagus plastomes displayed a typical quadripartite structure with sizes ranging from 155,948 bp to 157,128 bp and harbored 114 unique genes (80 protein-coding genes, 30 tRNA genes, and four rRNA genes). IRscope and Mauve analyses indicated minimal structural variation among Asparagus plastomes. We detected between 79 to 95 SSRs across the plastomes; most were located in the large single-copy (LSC) region and primarily consisted of mono-nucleotide repeat sequences (especially A and T repeats). The genus displayed mono-, di-, tri-, tetra-, penta-, and hexa-nucleotide repeats, but with variations in types and numbers among different species. Additionally, we identified 12 special SSR motifs and seven divergent hotspot regions that may serve as potential molecular markers for future identification efforts. Phylogenetic analyses yielded a robust phylogeny for Asparagus taxa, which were split into Clades I, II, and III. Notably, medicinal Asparagus species were mainly found in Clade III. Although the phylogenetic relationships of most Asparagus species aligned with previous study findings, the phylogenetic positions of A. munitus, A. subscandens, A. gobicus, and A. dauricus were newly determined.ConclusionsThe plastomes of Asparagus are largely conserved in terms of genome structure, size, gene content, and arrangement. Nevertheless, SSRs analyses revealed significant interspecific polymorphism within Asparagus. In addition, special SSR motifs and divergent hotspot regions identified from Asparagus plastomes provided reference for subsequent identification investigations. The plastome-based phylogeny provided preliminary insights into the relationships among the Chinese group of medicinal species and related taxa within Asparagus. Overall, this study offers a wealth of informative genetic resources pertinent to Asparagus, thereby enhancing our understanding of its evolution and laying a foundation for species identification, assessment of genetic population diversity, as well as the exploration and conservation of germplasm resources.

Population genomics and genetic diversity of the invasive chrysanthemum lace bug (Corythucha marmorata) across its invasive range in Japan

The escalating global movement of alien species, facilitated by increased trade and travel, poses a pressing need to comprehend their invasive potential and the consequent ecological and economic ramifications. Despite a growing body of evidence on rapid evolutionary shifts in invasive species, comprehensive insights into the genetic variability underlying these adaptations are constrained by limited genomic resources. Understanding the role of genetic variation in the success or failure of biological invaders is thus crucial. This study focuses on the chrysanthemum lace bug, Corythucha marmorata, as a model system to investigate the interplay of genetic variation and invasion dynamics. Our analysis reveals moderate genetic structure among countries, with significant genetic differentiation observed within populations. Mitochondrial COI DNA and haplotype network analysis revealed shared haplotypes between Japan and North America, indicating recent events of introduction, while exclusive Japanese haplotypes and significant FST and GST values suggest local divergence. Phylogenetic and STRUCTURE analyses show genetic clusters unique to Japan, with populations like SAG and CER displaying higher divergence. Bottlenecks followed by divergence, as indicated by the DIYABC-RF analysis, point to a complex evolutionary history involving multiple introductions and subsequent local divergence in Japan.

Whole-genome resequencing landscape of adaptive evolution in Relict gull (Larus relictus)

BackgroundThe relict gull (Larus relictus, Charadriiformes, Laridae) classified as vulnerable in the IUCN Red List is defined as a first-class national protected bird in China. However, our knowledge of the evolutionary history of L. relictus is limited. Here, we performed whole-genome resequencing of L. relictus (n = 14) and L. brunnicephalus (n = 3) to explore the genetic relationships and population structures and understand their adaptive evolution.ResultsThe whole genome resequencing generated 667.55 Gb clean reads with an average sequencing depth of ~ 29×. The genomic variant analysis identified 13,717,267 heterozygous SNPs in the samples obtained from 17 individuals. Population genetic diversity analysis revealed that low nucleotide diversity (0.00029) and no obvious population structure in L. relictus. Demographic history revealed that from 180 to 5 kya (thousand years ago), the effective population size (Ne) of L. relictus exhibited declines (24,000 to 5,000), with a very low range population size (2,200 to 5,000). In contrast, from 100 to 80 kya, L. brunnicephalus peaked in ancestral Ne, followed by distinct declines at ~ 70 kya (100,000 to 16,000). The findings identified several genes associated with the correlated changed life-history traits of L. relictus, including BMP4 involved in beak adaptation; HAND2, NEUROG1, COL11A2, and EDNRB involved in the evolution of the palate, soft palate, and tongue; PIGR and PLCB2 involved in an enhanced response to bitter taste by sensing chemical secretions released by staple food substrate insects to activate protective mechanisms. Furthermore, thirty-four genes related to sperm development and activity, including KLHL10 and TEKT3, were identified in the expanded gene family. In addition, MED1, CNOT9, NR5A1, and PATZ1 were involved in enhanced male hormone secretion and a high density of candidate genes associated with embryonic development were identified. The findings indicated that the L. relictus population was in a male-biased diffusion mode; the function of the TEKT3 gene showed that males played a dominant role in brooding, which enhanced their attraction to females. Our study revealed that significant enrichment of olfactory signaling pathway genes, including OR14C36, OR14J1, OR14I1, and OR14A16; inner ear development-related, including PTN, PTPN11, GATA2, ATP8B1, and MYO15A; and those related to hypoxic adaptation to high-altitude breeding and iris colour.ConclusionsBased on the results and the knowledge of this organism biology and habitat use, we infer that less adaptive evolutionary pressure on vision in L. relictus were related with their feeding behaviour and adaptation. In summary, this comprehensive analysis provides insights into the evolutionary features of L. relictus and a new perspective for scientific research on L. relictus to effectively determine its future survival viability.

Population genetic structure of Uroteuthis edulis in the East China Sea based on the COI gene.

Uroteuthis edulis is a significant economic cephalopod resource utilized by mainland China, Taiwan, and Japan. Understanding the population genetic structure of U.edulis is essential to evaluate the changes of its resource abundance. In this study, we used the COI gene as a marker to evaluate the population structure of U.edulis. Molecular marker analysis indicated that the sampled individuals were categorized into three populations (ES1, ES2, and ES3). All populations exhibited high haplotype diversity indices (Hd) and low nucleotide diversity indices (Pi), with the ES2 population showing the lowest Hd and Pi values. Analysis of molecular variance (AMOVA) revealed that genetic variation among populations accounted for 89.06% of the total variation. The phylogenetic tree illustrated distinct lineage clustering, with each population forming a separate clade. Combined with the biological information, it was observed that the majority of female individuals were larger in size and exhibited high sexual maturity. Male individuals displayed notable differences across populations: ES1 individuals were primarily small to medium-sized with low sexual maturity, ES2 individuals were mainly medium-sized with a relatively even distribution of sexual maturity, and ES3 individuals were predominantly large-sized with high sexual maturity. The findings indicate substantial genetic differentiation and ecological variation among U.edulis. Strengthen monitoring of population resources and genetic diversity, long-term tracking of changes, and the timely formulation of scientifically sound conservation and management measures to ensure the sustainable development in future.

Genetic insights into the first detection of Paracoccus marginatus (Hemiptera: Pseudococcidae) in Australia.

Species spread in a new environment is often associated with founders' effect, and reduced effective population size and genetic diversity. However, reduced genetic diversity does not necessarily translate to low establishment and spread potential. Paracoccus marginatus Williams and Granara de Willink is a polyphagous pest that has invaded 4 continents in around 34 years. It was first detected in the Northern Territory, Australia in July 2023. Following this, we collected 45 specimens from 20 suburbs across 3 regions. Using mitochondrial cytochrome oxidase I and nuclear ribosomal RNA genes (18S and 28S), we examined molecular diagnostics robustness, genetic diversity, haplotype network, and demographics (Tajima D) of the recently detected Australian population. We compared our samples with publicly available sequences deposited on GenBank. All 3 genes were suitable for molecular diagnosis with a 100% identity score. For all 3 genes, we found low nucleotide diversity, haplotype diversity, and negative Tajima D in the newly detected P. marginatus population, suggesting a recent single founder event by a few individuals. Comparing our study's sequences with global sequences showed low haplotype diversity, nucleotide diversity, and Tajima's D, suggesting that despite low genetic diversity at the 3 genes, P. marginatus has successfully invaded South America, Africa, Asia, and Oceania. Our study highlights the role of demographic and life history traits in the species' invasion success. We provide a baseline dataset from the first detection of P. marginatus in Australia. Further analysis of the spread can provide insights into invasive species' adaptation in a novel environment.

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

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

RETRACTION: Investigating the Effectiveness of Forensic Genetics and Population Genetic Diversity Using a Multi-InDel System in Chinese Hezhou and Southern Shaanxi Han Populations.

Wang, X., Q. Lan, Y. Lin, etal. "Investigating the Effectiveness of Forensic Genetics and Population Genetic Diversity Using a Multi-InDel System in Chinese Hezhou and Southern Shaanxi Han Populations," Annals of Human Genetics (Early View): https://doi.org/10.1111/ahg.12553. The above article, published online on 20 May 2024, in Wiley Online Library (http://onlinelibrary.wiley.com/), has been retracted by an agreement between the authors; the journal's Editor in Chief, Dr. Rosemary Ekong; University College London; and John Wiley & Sons, Ltd. The authors reported that a number of errors had been included in the published article, which would require corrections to the abstract, results, and conclusions, as well as Figure 5. The editors confirmed these errors. The retraction has been agreed to because the corrections required to amend these major errors would require substantial changes to the results and conclusions in the article. The authors have agreed to submit the revised version of this article for evaluation by the journal.

Molecular Genetic Assessment Aids in Clarifying Phylogenetic Status of Iranian Kerman Wild Sheep.

Two species of wild sheep inhabit Iran: Asiatic mouflon (Ovis gmelini) and urial (O. vignei). Phylogenetic relationships between populations distributed in this country are complex and still remain unclear. This study aimed to clarify, by genetic assessment, the phylogenetic status of Kerman wild sheep, considered to be a hybrid of the two species. For this purpose, we created a dataset that included specimens of O. gmelini, O. vignei, and Kerman sheep. We applied genome-wide SNP genotyping technology to analyze population structure and genetic diversity of these groups. Using Neighbor-Net and PCA plots, it was demonstrated that Kerman sheep were differentiated from other groups and occupy an intermediate position between O. gmelini and O. vignei. Using Admixture analysis, two ancestral components were identified in this population; however, admixed ancestry was not confirmed by f3 statistics. Genetic diversity in Kerman wild sheep was significantly higher than in any group of O. vignei, but lower than in O. gmelini. Additionally, we examined complete mitochondrial genomes and it was demonstrated that the matrilineal ancestor of Kerman sheep belonged to O. vignei. Our results lead to the conclusion that Kerman wild sheep can be recognized as a separate subspecies of O. vignei.

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

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

Patterns of population structure and genetic variation within the Saudi Arabian population.

The Arabian Peninsula is considered the initial site of historic human migration out of Africa. The modern-day indigenous Arabians are believed to be the descendants who remained from the ancient split of the migrants into Eurasia. Here, we investigated how the population history and cultural practices such as endogamy have shaped the genetic variation of the Saudi Arabians. We genotyped 3,352 individuals and identified twelve genetic sub-clusters that corresponded to the geographical distribution of different tribal regions, differentiated by distinct components of ancestry based on comparisons to modern and ancient DNA references. These sub-clusters also showed variation across ranges of the genome covered in runs of homozygosity, as well as differences in population size changes over time. Using 25,488,981 variants found in whole genome sequencing data (WGS) from 302 individuals, we found that the Saudi tend to show proportionally more deleterious alleles than neutral alleles when compared to Africans/African Americans from gnomAD (e.g. a 13% increase of deleterious alleles annotated by AlphaMissense between 0.5 - 5% frequency in Saudi, compared to 7% decrease of the benign alleles; P < 0.001). Saudi sub-clusters with greater inbreeding and lower effective population sizes showed greater enrichment of deleterious alleles as well. Additionally, we found that approximately 10% of the variants discovered in our WGS data are not observed in gnomAD; these variants are also enriched with deleterious annotations. To accelerate studying the population-enriched deleterious alleles and their health consequences in this population, we made available the allele frequency estimates of 25,488,981 variants discovered in our samples. Taken together, our results suggest that Saudi's population history impacts its pattern of genetic variation with potential consequences to the population health. It further highlights the need to sequence diverse and unique populations so to provide a foundation on which to interpret medical- and pharmaco- genomic findings from these populations.

Areas with agroecological potential for Agave cupreata (Trel. &amp; Berger) plantations in Guerrero, Mexico

Objective: to determine areas with agroecological potential for Agave cupreata (Trel. &amp; Berger) plantations in the state of Guerrero, Mexico. Design/ Methodology/ Approach: fifty-four specimens of A. cupreata were characterized. For each specimen, phenotypical, agroclimatic and agroecological data were recorded. Information from 123 herbarium specimens and information available in the literature were consulted. In addition, representatives of the State Council of Mezcal in Guerrero and other companies were interviewed, in order to identify possible areas excluded in the field. As well as in the specimens reviewed at the herbarium, which were validated with field observations. This information was processed in ArcGIS© version 10.3.1 (Esri Inc., 1999-2015, United States), with which a geographic information system was built and the distribution map was obtained, as well as the soil and climate and agroecological requirements of A. cupreata in the state of Guerrero. This information allowed the delimitation of the optimal, suboptimal and marginal areas for establishing agave plants. The validation of the information was made through field trips to specific areas to validate the agroecological variables of the potential areas defined in this study. Results: areas comprising 673 084.16 ha with optimal agroecological potential, and 1 942 072.86 ha with suboptimal potential were determined. Limitations/ Implications of the study: it is suggested to complement with studies on productivity, population ecology, intra- and inter population genetic variability, in plantations and natural population (called in Mexico ‘magueyeras’) of A. cupreata. Findings/ Conclusions: in the state of Guerrero (Mexico), North, Central and Mountain regions were those with the highest number of optimal areas, which coincides with the areas where mezcal (a strong and dry alcoholic beverage distilled from the sap of Agave plants) production is concentrated.

A Post-Mortem Molecular Damage Profile in the Ancient Human Mitochondrial DNA.

Mitochondrial DNA (mtDNA) analysis is crucial for understanding human population structure and genetic diversity. However, post-mortem DNA damage poses challenges, that make analysis difficult. DNA preservation is affected by environmental conditions which, among other factors, complicates the differentiation of endogenous variants from artefacts in ancient mtDNA mix profiles. This study aims to develop a molecular damage profile for ancient mtDNA that can become a useful tool in analysing mtDNA from ancient remains. A dataset of 427 whole genomes or capture of mtDNA sequences from individuals representing different historical periods and climatic regions was compiled from the ENA database. Present-day and UDG-treated ancient samples were also included and used to establish levels of damaged reads. Results indicated that samples from cold regions exhibited the lowest percentage of damaged reads, followed by arid, cold, tropical and temperate regions, with significant differences observed between cold and temperate regions. A global damage profile was generated, identifying 2933 positions (25% of the positions considered) with damage in more than 23.8% of the samples analysed, deemed as damage hotspots. Notably, 2856 of these hotspots had never been reported as damage or mutational hotspots, or heteroplasmic positions. Damage hotspot frequency by position was slightly higher in the non-coding region compared with the coding region. In conclusion, this study provides a molecular damage profile for ancient mtDNA analysis that is expected to be a valuable tool in the interpretation of mtDNA variation in ancient samples.