Genetic Subdivision Research Articles

Blocks identical by descent in the genomes of the indigenous population of Siberia demonstrate genetic links between populations.

The gene pool of the indigenous population of Siberia is a unique system for studying population and evolutionary genetic processes, analyzing genetic diversity, and reconstructing the genetic history of populations. High ethnic diversity is a feature of Siberia, as one of the regions of the peripheral settlement of modern human. The vast expanses of this region and the small number of aboriginal populations contributed to the formation of significant territorial and genetic subdivision. About 40 indigenous peoples are settled on the territory of the Siberian historical and ethnographic province. Within the framework of this work, a large-scale population study of the gene pool of the indigenous peoples of Siberia was carried out for the first time at the level of high-density biochips. This makes it possible to fill in a significant gap in the genogeographic picture of the Eurasian population. For this, DNA fragments were analyzed, which had been inherited without recombination by each pair of individuals from their recent common ancestor, that is, segments (blocks) identical by descent (IBD). The distribution of IBD blocks in the populations of Siberia is in good agreement with the geographical proximity of the populations and their linguistic affiliation. Among the Siberian populations, the Chukchi, Koryaks, and Nivkhs form a separate cluster from the main Siberian group, with the Chukchi and Koryaks being more closely related. Separate subclusters of Evenks and Yakuts, Kets and Chulyms are formed within the Siberian cluster. Analysis of SNPs that fell into more IBD segments of the analyzed populations made it possible to compile a list of 5358 genes. According to the calculation results, biological processes enriched with these genes are associated with the detection of a chemical stimulus involved in the sensory perception of smell. Enriched for the genes found, molecular pathways are associated with the metabolism of linoleic, arachidonic, tyrosic acids and by olfactory transduction. At the same time, an analysis of the literature data showed that some of the selected genes, which were found in a larger number of IBD blocks in several populations at once, can play a role in genetic adaptation to environmental factors.

Assessing population substructure in the Lebanese population: A population study using data on 23 autosomal short tandem repeats.

Understanding the genetic substructure of a population is essential for proper forensic genetic analysis. The Lebanese population has a high rate of endogamous and consanguineous marriages and is segregated based on religious belongings. However, no genetic population studies have been performed up to date to estimate the degree of genetic substructure and inbreeding coefficients. The present study analyzed a compendium of 23 autosomal STRs typed in 1400 individuals belonging to the seven major Lebanese religious subcommunities. Inbreeding coefficients such as F statistics were estimated. Results showed a Fst (theta) value of 0.002, indicating a low genetic subdivision within the Lebanese population. This study aimed at assessing the genetic substructure of the Lebanese population by analyzing 1400 Lebanese citizens' samples using 23 STR markers. F statistics were computed to evaluate the degree of genetic substructure. Results showed a Fst value of 0.002, indicating a low genetic subdivision within the Lebanese population.

Entomological parameters and population structure at a microgeographic scale of the main Colombian malaria vectors Anopheles albimanus and Anopheles nuneztovari.

Population subdivision among several neotropical malaria vectors has been widely evaluated; however, few studies have analyzed population variation at a microgeographic scale, wherein local environmental variables may lead to population differentiation. The aim of the present study was to evaluate the genetic and geometric morphometric structure of Anopheles nuneztovari and Anopheles albimanus in endemic localities of northwestern Colombia. Genetic and phenetic structures were evaluated using microsatellites markers and wing geometric morphometrics, respectively. In addition, entomological indices of importance in transmission were calculated. Results showed that the main biting peaks of Anopheles nuneztovari were between 20:00 and 22:00, whereas Anopheles albimanus exhibited more variation in biting times among localities. Infection in An. nuneztovari by Plasmodium spp. (IR: 4.35%) and the annual entomological inoculation rate (30.31), indicated high vector exposure and local transmission risk. We did not detect Plasmodium-infected An. albimanus in this study. In general, low genetic and phenetic subdivision among the populations of both vectors was detected using a combination of phenotypic, genetic and environmental data. The results indicated high regional gene flow, although local environmental characteristics may be influencing the wing conformation differentiation and behavioral variation observed in An. albimanus. Furthermore, the population subdivision detected by microsatellite markers for both species by Bayesian genetic analysis provides a more accurate picture of the current genetic structure in comparison to previous studies. Finally, the biting behavior variation observed for both vectors among localities suggests the need for continuous malaria vector surveys covering the endemic region to implement the most effective integrated local control interventions.

Genomic analyses indicate resilience of a commercially and culturally important marine gastropod snail to climate change.

Genomic vulnerability analyses are being increasingly used to assess the adaptability of species to climate change and provide an opportunity for proactive management of harvested marine species in changing oceans. Southeastern Australia is a climate change hotspot where many marine species are shifting poleward. The turban snail, Turbo militaris is a commercially and culturally harvested marine gastropod snail from eastern Australia. The species has exhibited a climate-driven poleward range shift over the last two decades presenting an ongoing challenge for sustainable fisheries management. We investigate the impact of future climate change on T. militaris using genotype-by-sequencing to project patterns of gene flow and local adaptation across its range under climate change scenarios. A single admixed, and potentially panmictic, demographic unit was revealed with no evidence of genetic subdivision across the species range. Significant genotype associations with heterogeneous habitat features were observed, including associations with sea surface temperature, ocean currents, and nutrients, indicating possible adaptive genetic differentiation. These findings suggest that standing genetic variation may be available for selection to counter future environmental change, assisted by widespread gene flow, high fecundity and short generation time in this species. We discuss the findings of this study in the content of future fisheries management and conservation.

Microsatellite DNA variation in Spalacopus cyanus, a social subterranean rodent endemic to Chile (Rodentia: Octodontidae)

We used five polymorphic microsatellite loci to examine patterns of genetic variation within and among colonies of coruros (Spalacopus cyanus) at three localities in central Chile. Detailed comparisons of genetic variation at two locations, Los Maitenes in the northern portion of the species’ range and El Alamo in the south, displayed very different patterns of variation. Overall variation (alleles per locus and heterozygosity) within and among colonies at Los Maitenes was several times higher than observed at El Alamo, with the latter showing patterns of variation more consistent with a social species of subterranean rodent. Comparisons among Los Maitenes, El Alamo, and Los Vilos, another northern population, revealed a distinct genetic subdivision between northern and southern localities, indicating little evidence of genetic exchange between these two regions. We discuss these patterns of variation in relation to previous genetic research on Spalacopus and other subterranean rodents.

Cryptic Lineage and Genetic Structure of Acanthopagrus pacificus Populations in a Natural World Heritage Site Revealed by Population Genetic Analysis

Recent studies have revealed extensive genetic differentiation among some populations of marine taxa that were previously believed to be essentially homogeneous because larvae are widely dispersed in ocean currents. Acanthopagrus pacificus is a commercially and ecologically important teleost fish that is endemic to shallow coastal waters and estuaries of some tropical and sub-tropical areas in the West Pacific Ocean. Here, we examined genetic structure and the inferred demographic history of A. pacificus populations from mtDNA control region sequence data. A 677–678 base-pair fragment was sequenced from 159 individuals sampled at three localities across the West Pacific Ocean. Haplotype diversity was high, ranging from 0.915 to 0.989, while nucleotide diversity was low to medium, ranging from 0.8% to 2.60%. Analysis of molecular variance (AMOVA) showed significant genetic subdivision (FST = 0.155, p < 0.05) among sampled populations while pairwise FST estimates also revealed strong genetic differentiation among populations indicating that gene flow was restricted. Two distinct cryptic lineages were identified that were estimated to have diverged during the Pleistocene. In summary, contemporary factors including regional oceanic currents and self-recruitment are considered to have played significant roles in producing the population structure in this fish. In particular, the genetic information generated in the current study will allow appropriate fisheries management and conservation strategies to be developed for this important local fish in the waters around Iriomotejima Island, a World Heritage site.

Interpopulation variation in inbreeding is primarily driven by tolerance of mating with relatives in a spermcasting invertebrate.

The degree to which individuals inbreed is a fundamental aspect of population biology shaped by both passive and active processes. Yet, the relative influences of random and non-random mating on the overall magnitude of inbreeding are not well characterized for many taxa. We quantified variation in inbreeding among qualitatively accessible and isolated populations of a sessile marine invertebrate (the colonial ascidian Lissoclinum verrilli) in which hermaphroditic colonies cast sperm into the water column for subsequent uptake and internal fertilization. We compared estimates of inbreeding to simulations predicting random mating within sites to evaluate if levels of inbreeding were (1) less than expected because of active attempts to limit inbreeding, (2) as predicted by genetic subdivision and passive inbreeding tolerance, or (3) greater than simulations due to active attempts to promote inbreeding via self-fertilization or a preference for related mates. We found evidence of restricted gene flow and significant differences in the genetic diversity of L. verrilli colonies among sites, indicating that on average colonies were weakly related in accessible locations, but their levels of relatedness matched that of first cousins or half-siblings on isolated substrates. Irrespective of population size, progeny arrays revealed variation in the magnitude of inbreeding across sites that tracked with the mean relatedness of conspecifics. Biparental reproduction was confirmed in most offspring (86%) and estimates of total inbreeding largely overlapped with simulations of random mating, suggesting that interpopulation variation in mother-offspring resemblance was primarily due to genetic subdivision and passive tolerance of related mates. Our results highlight the influence of demographic isolation on the genetic composition of populations, and support theory predicting that tolerance of biparental inbreeding, even when mates are closely related, may be favoured under a broad set of ecological and evolutionary conditions.

Comparative genomics of Sarcoptes scabiei provide new insights into adaptation to permanent parasitism and within-host species divergence.

Sarcoptes scabiei is the causative agent of a highly contagious skin disease in humans and more than 100 mammals. Here, we reported the first chromosome-level reference genome of S. scabiei isolated from rabbits, with a contig N50 size of 5.92Mb, a total assembled length of 57.30Mb, ∼12.65% repetitive sequences and 9333 predicted protein-coding genes. The phylogenetic tree based on 1338 shared high-confidence single-copy orthologous genes estimated that the mammalian ectoparasite S. scabiei and the plant-feeding mite Tetranychus urticae separated ∼340 million years ago. Both neighbour-joining tree and principal component analysis of 20 mite populations isolated from four hosts (humans, pigs, dogs and rabbits) distributed in three countries (China, Australia and the USA) consistently supported genetic subdivisions according to host species rather than geographical location. The demographic history of S. scabiei reconstructed by multiple sequentially Markovian coalescent analysis suggested that S. scabiei isolated from rabbits, humans, dogs and pigs diverged ∼5000 years ago. Investigation of the homeobox (Hox) genes revealed that S. scabiei contains 8 of 10 canonical Hox genes that are present in the arthropod ancestor, and the absence of the Abd-A gene may correlate with the long gap between their front and back legs. Comparative genomics demonstrated that genes specific to scabies mites were mainly enriched in nutrition digestive systems, whereas genes in the families that involved detoxification (cytochrome P450, carboxyl/cholinesterases and the ATP-binding cassette transporter C group) were extremely contracted compared with that of other mites analysed in this study. Selective sweep analysis of mite populations from various pairs of two out of the four host species revealed that the strongest selective sweep signals were mainly enriched in cysteine-type peptidase activity and apoptosis. The results provided clues for the mechanisms of S. scabiei adaptation to a permanent parasitic lifestyle and knowledge that would enable further control of this highly contagious skin disease.

Intraspecific differentiation of Allium canadense var. canadense (Amaryllidaceae) across the North American Coastal Plain

AbstractPolyploidy increases genetic variation in plants, leading to adaptations allowing expansion into novel habitats and increased genetic differentiation among populations isolated by barriers to dispersal. Allium canadense var. canadense is a polyploid taxon distributed within the North American Coastal Plain (NACP) biodiversity hotspot. It is the only one of six varieties in a species complex of wild onions native to North America that exhibits bulbils responsible for vegetative reproduction, which may lead to low levels of genetic variation within populations. Despite its threatened/endangered status in the northeast United States and noxious weed listing in Arkansas, USA, little is known about intraspecific differentiation among populations which may be impacted by riverine barriers or seasonal latitudinal gradients. We used sequences of one nuclear (ITS) and two chloroplast (trnL‐F and rpl32‐trnL) DNA regions generated from eight populations in the NACP and one population in Kansas, USA to examine genetic diversity and population structure of A. canadense var. canadense. A total of 12 ITS ribosomal and 10 chloroplast DNA haplotypes were identified. Phylogenetic analyses indicated two major lineages which corresponded to the genealogical relationships identified in the population structure analyses. Significant genetic subdivision among populations was detected across all populations by analysis of molecular variance. Overall, geographic structuring is apparent among populations of A. canadense var. canadense and populations showed moderate levels of gene diversity. These findings are indicative of the complex nature of polyploids and their contribution to genetic diversity among populations with mating systems that might otherwise have no phylogeographic structure.

Genomics reveal population structure, evolutionary history, and signatures of selection in the northern bottlenose whale, Hyperoodon ampullatus.

Information on wildlife population structure, demographic history, and adaptations are fundamental to understanding species evolution and informing conservation strategies. To study this ecological context for a cetacean of conservation concern, we conducted the first genomic assessment of the northern bottlenose whale, Hyperoodon ampullatus, using whole-genome resequencing data (n=37) from five regions across the North Atlantic Ocean. We found a range-wide pattern of isolation-by-distance with a genetic subdivision distinguishing three subgroups: the Scotian Shelf, western North Atlantic, and Jan Mayen regions. Signals of elevated levels of inbreeding in the Endangered Scotian Shelf population indicate this population may be more vulnerable than the other two subgroups. In addition to signatures of inbreeding, evidence of local adaptation in the Scotian Shelf was detected across the genome. We found a long-term decline in effective population size for the species, which poses risks to their genetic diversity and may be exacerbated by the isolating effects of population subdivision. Protecting important habitat and migratory corridors should be prioritized to rebuild population sizes that were diminished by commercial whaling, strengthen gene flow, and ensure animals can move across regions in response to environmental changes.

Community Characteristics and Genetic Diversity of Macrobenthos in Haima Cold Seep

Knowledge about community structure and genetic diversity can help assess the potential for change in the loss and restoration of biodiversity, thereby facilitating effective management and ecosystem protection. Macroinvertebrate communities are an important biotic component of deep sea cold seep ecosystems. As Haima cold seep is increasingly being assessed for its potential gas hydrate mineral wealth, knowledge of community characteristics and genetic diversity of macrobenthos is needed to anticipate the potential impacts on biodiversity. In this study, we examined species diversity and community structure at five sites in the Haima cold seep using a remote-operated vehicle (ROV) for in situ surveying. The results identified 12 macrobenthic species from 5 phyla and 12 families. The macrobenthos community could be divided into two communities (H1 and H2=mussel bed community, and H3 and H4= vesicomyid clams community) based on CLUSTER and NMDS analyses. Gigantidas haimaensis (Mollusca), Branchipolynoe pettiboneae (Annelida), and Histampica haimaensis (Echinodermata) were most dominant within their respective phyla, with values of the dominance of 0.160, 0.021 and 0.114, respectively. The genetic diversity of these three typical macrobenthic species in the Haima cold seep was evaluated using the mitochondrial cytochrome c oxidase subunit I (COI) gene, haplotype, and nucleotide diversity values were 0.651 to 0.912 and 0.00148 to 0.00812, respectively, representing high haplotype diversity but low nucleotide diversity. Finally, mitochondrial concatenated dataset (MCD) sequences from three mitochondrial genes (ATP6, COI, and NAD4) and 294,734 genome-wide single nucleotide polymorphisms (SNPs) from restriction site-associated DNA-sequencing (RAD-seq) data were obtained from 60 individuals from two sites (H1 and H2), providing deep insight into the genetic diversity and structure of G. haimaensis, the engineer species in Haima cold seep. No significant genetic differentiation between G. haimaensis in H1 and H2 was detected based on MCD sequences. Nevertheless, when using SNP datasets, a small but clear genetic subdivision between G. haimaensis in the two sites as revealed by STRUCTURE and principal component analysis (PCA). The results comprehensively illuminate macrobenthos biodiversity in the Haima cold seep ecosystem and provide a baseline against which population dynamics may be assessed in the future.

Assessment of Genetic Diversity of the Salangid, Neosalanx taihuensis, Based on the Mitochondrial COI Gene in Different Chinese River Basins.

Simple SummaryIn the current study, we estimate the genetic diversity of the salangid Neosalanx taihuensis sampled from 11 populations in the six typical river basins of China. Using the COI gene sequencing technology, the N. taihuensis population’s genetic difference within and between river basins was investigated. Significant levels of genetic subdivision were detected among populations within basins rather than between basins. Population history dynamics showed that N. taihuensis populations experienced a population expansion during the glacial period in the late Pleistocene. These results suggest that different populations should be considered as different management units to achieve effective conservation and management purposes.The salangid Neosalanx taihuensis (Salangidae) is a commercially important economical fish endemic to China and restricted to large freshwater systems with a wide-ranging distribution. This fish species has continuous distribution ranges and a long-introduced aquaculture history in Chinese basins. However, the research on its population genetic differentiation within and between basins is very limited. In this regard, 197 individuals were sampled from 11 populations in the Nenjiang River Basin (A1–A4), Songhua River Basin (B1), Yellow River Basin (C1–C2), Yangtze River Basin (D1), Lanchang River Basin (E1–E2) and Huaihe River Basin (F1). Based on the COI sequence, the N. taihuensis population’s genetic difference within and between river basins was investigated. The haplotypes and their frequency distributions were strongly skewed, with most haplotypes (n = 13) represented only in single samples each and thus restricted to a single population. The most common haplotype (H4, 67/197) was found in all individuals. The analysis of molecular variance (AMOVA) revealed a random pattern in the distribution of genetic diversity, which is inconsistent with contemporary hydrological structure. The mismatch between the distribution and neutrality tests supported the evidence of a population expansion, which occurred during the late Pleistocene (0.041–0.051 million years ago). Significant levels of genetic subdivision were detected among populations within basins rather than between the six basins. Population history dynamics showed that N. taihuensis experienced an expansion during the glacial period in the late Pleistocene. Therefore, different populations should be considered as different management units to achieve effective conservation and management purposes. These results have great significance for the evaluation and exploitation of the germplasm resources of N. taihuensis.

Population genetic characterization of the endangered dung beetle Copris tripartitus (Coleoptera: Scarabaeidae) using novel microsatellite markers

• We studied the genetic diversity of endangered C. tripartitus populations in Korea. • All populations showed higher H O than H E and no inbreeding. • Only one among two gene pools was detected in some populations. • These results suggest prolonged conservation efforts for C. tripartitus . The dung beetle Copris tripartitus (Coleoptera: Scarabaeidae) has long been considered an endangered insect in South Korea; the detection of recent population increases leaves its endangered status uncertain. Population genetic analysis subsequent to development of molecular markers is essential for establishing proper conservation strategies. In this study, we developed ten microsatellite markers specifically for C. tripartitus . Sixty-eight individuals of C. tripartitus collected from six South Korean localities were genotyped to validate these markers and preliminarily assess population genetic characteristics. Per-locus observed number of alleles, observed heterozygosity ( H O ), and expected heterozygosity ( H E ) ranged from 5–12, 0.499–0.958, and 0.54–0.743, respectively. All populations showed higher H O than H E , negative values of inbreeding coefficient, and, overall, no sign of recent population bottlenecks (excluding one population, Seosan). This suggests that C. tripartitus did not suffer from genetic drift and inbreeding, which are typically severe in small, isolated populations. Nevertheless, detection of only one of the two gene pools in some populations and resultant genetic subdivision into two population groups may suggest that the population size is not enough to cover both gene pools. Thus, a more extended period of protection may be required to ensure higher genetic diversity of widespread populations and achieve the long-term conservation goal.

Genomic legacy of migration in endangered caribou.

Wide-ranging animals, including migratory species, are significantly threatened by the effects of habitat fragmentation and habitat loss. In the case of terrestrial mammals, this results in nearly a quarter of species being at risk of extinction. Caribou are one such example of a wide-ranging, migratory, terrestrial, and endangered mammal. In populations of caribou, the proportion of individuals considered as “migrants” can vary dramatically. There is therefore a possibility that, under the condition that migratory behavior is genetically determined, those individuals or populations that are migratory will be further impacted by humans, and this impact could result in the permanent loss of the migratory trait in some populations. However, genetic determination of migration has not previously been studied in an endangered terrestrial mammal. We examined migratory behavior of 139 GPS-collared endangered caribou in western North America and carried out genomic scans for the same individuals. Here we determine a genetic subdivision of caribou into a Northern and a Southern genetic cluster. We also detect >50 SNPs associated with migratory behavior, which are in genes with hypothesized roles in determining migration in other organisms. Furthermore, we determine that propensity to migrate depends upon the proportion of ancestry in individual caribou, and thus on the evolutionary history of its migratory and sedentary subspecies. If, as we report, migratory behavior is influenced by genes, caribou could be further impacted by the loss of the migratory trait in some isolated populations already at low numbers. Our results indicating an ancestral genetic component also suggest that the migratory trait and their associated genetic mutations could not be easily re-established when lost in a population.

Infirm effect of phylogeny on morphometric features in a cryptic Gobio species complex

Abstract Several recent notes prove that taxonomic relations of close relative animal groups (species complexes or cryptic species) can be revealed by the combined use of genetic and morphologic methodologies. At the same time scarce information can be found about how phylogeny, population origin, and sexual dimorphism affect the morphometric features of these species. In our present work, we performed simultaneous phylogenetic and morphological studies on the taxonomically still questionable Carpathian stream dwelling gudgeons (Cyprinidae, Gobio) by using two different methodologies (distance based and geometric morphometry). Our results were in correspondence with the previous findings, showing the presence of three phylogenetically more or less distinct groups in the area. The results of the whole-body geometric and the traditional, distance-based morphometry reflected the extent of phylogenetic differences. While the results of geometric scale morphometry did not correspond with the genetic subdivisions. Results of three way PERMANOVA analyses showed that the phylogenetic effects on morphometry is less considerable as the population origin or the sexual dimorphism at these cyprinid taxa. Our investigation contributed to the better understanding of the taxonomy of fish stocks in the Carpathian Basin, and to their conservation, but additional investigations will be needed to clarify the exact taxonomic position of the gudgeons (’Gobio sp1’) dominating the eastern part of the studied drainage.

Genomic survey of edible cockle (Cerastoderma edule) in the Northeast Atlantic: A baseline for sustainable management of its wild resources.

Knowledge on correlations between environmental factors and genome divergence between populations of marine species is crucial for sustainable management of fisheries and wild populations. The edible cockle (Cerastoderma edule) is a marine bivalve distributed along the Northeast Atlantic coast of Europe and is an important resource from both commercial and ecological perspectives. We performed a population genomics screening using 2b‐RAD genotyping on 9309 SNPs localized in the cockle's genome on a sample of 536 specimens pertaining to 14 beds in the Northeast Atlantic Ocean to analyse the genetic structure with regard to environmental variables. Larval dispersal modelling considering species behaviour and interannual/interseasonal variation in ocean conditions was carried out as an essential background to which compare genetic information. Cockle populations in the Northeast Atlantic displayed low but significant geographical differentiation between populations (F ST = 0.0240; p < 0.001), albeit not across generations. We identified 742 and 36 outlier SNPs related to divergent and balancing selection in all the geographical scenarios inspected, and sea temperature and salinity were the main environmental correlates suggested. Highly significant linkage disequilibrium was detected at specific genomic regions against the very low values observed across the whole genome. Two main genetic groups were identified, northwards and southwards of French Brittany. Larval dispersal modelling suggested a barrier for larval dispersal linked to the Ushant front that could explain these two genetic clusters. Further genetic subdivision was observed using outlier loci and considering larval advection. The northern group was divided into the Irish/Celtic Seas and the English Channel/North Sea, while the southern group was divided into three subgroups. This information represents the baseline for the management of cockles, designing conservation strategies, founding broodstock for depleted beds and producing suitable seed for aquaculture production.

Population structure of lake whitefish (Coregonus clupeaformis) from the Mississippian lineage in North America

The lake whitefish ( Coregonus clupeaformis) is a commercially valuable freshwater species with a broad distribution in North America. Some phylogeographic work has been done on this species, but little is known about genetic population subdivision among populations of the widely dispersed Mississippian lineage. We used 3,173 single nucleotide polymorphisms in 508 lake whitefish from 22 different lakes to examine population structure across central Canada and the United States. Bayesian clustering, ordination, and fixation indices identified population subdivision that largely reflected geographic distance and hydrological connectivity, with greater differentiation between lakes that are farther apart. Population subdivision was hierarchical, with greater differentiation between Canadian provinces and less differentiation based on river basins within provincial boundaries. Interestingly, isolation by distance alone was not sufficient to account for all of the observed genetic differentiation among populations. We conclude that important components of lake whitefish genetic diversity are present at different spatial scales, and that populations within the Mississippian lineage have differentiated widely across their range.

Türkiye’nin farklı coğrafi bölgelerinden toplanan Tetranychus urticae popülasyonlarındaki gen akışı ve popülasyon yapıları

Tetranychus urticae Koch (Acari: Tetranychidae) is a devastating agricultural pest that can feed on more than 1000 host plants. This extremely polyphagous nature of this pest may allow random disperse of them. Although population movement and structure are of vital importance to design area-wide pest control programs, there is no such study focusing on this issue in Turkey. The present study showed that there was no genetic subdivision among T. urticae the populations collected from four geographic regions of Turkey (FST=0.090, p&gt;0.05), based on cytochrome c oxidase subunit I (COI). In addition, the haplotype network supported these results since no clustering pattern was present. However, Black Sea populations had high genetic differentiation with other populations. This might be due to its isolated geography, different climate conditions, and limited sampling area. A high level of gene-flow between the Mediterranean and Aegean/Central Anatolian populations was determined. It is known that geography alone is not enough to explain population structure and genetic variation when excluding other ecological factors. Therefore, other factors such as current and historical climate data should be integrated to assess gene-flow in future studies.

Migration without interbreeding: Evolutionary history of a highly selfing Mediterranean grass inferred from whole genomes.

Wild plant populations show extensive genetic subdivision and are far from the ideal of panmixia which permeates population genetic theory. Understanding the spatial and temporal scale of population structure is therefore fundamental for empirical population genetics – and of interest in itself, as it yields insights into the history and biology of a species. In this study we extend the genomic resources for the wild Mediterranean grass Brachypodium distachyon to investigate the scale of population structure and its underlying history at whole‐genome resolution. A total of 86 accessions were sampled at local and regional scales in Italy and France, which closes a conspicuous gap in the collection for this model organism. The analysis of 196 accessions, spanning the Mediterranean from Spain to Iraq, suggests that the interplay of high selfing and seed dispersal rates has shaped genetic structure in B. distachyon. At the continental scale, the evolution in B. distachyon is characterized by the independent expansion of three lineages during the Upper Pleistocene. Today, these lineages may occur on the same meadow yet do not interbreed. At the regional scale, dispersal and selfing interact and maintain high genotypic diversity, thus challenging the textbook notion that selfing in finite populations implies reduced diversity. Our study extends the population genomic resources for B. distachyon and suggests that an important use of this wild plant model is to investigate how selfing and dispersal, two processes typically studied separately, interact in colonizing plant species.

Genetic differentiation between and within Northern Native American language groups: an argument for the expansion of the Native American CODIS database

The National Research Council recommends that genetic differentiation among subgroups of ethnic samples be lower than 3% of the total genetic differentiation within the ethnic sample to be used for estimating reliable random match probabilities for forensic use. Native American samples in the United States’ Combined DNA Index System (CODIS) database represent four language families: Algonquian, Na-Dene, Eskimo-Aleut, and Salishan. However, a minimum of 27 Native American language families exists in the US, not including language isolates. Our goal was to ascertain whether genetic differences are correlated with language groupings and, if so, whether additional language families would provide a more accurate representation of current genetic diversity among tribal populations. The 21 short tandem repeat (STR) loci included in the Globalfiler® PCR Amplification Kit were used to characterize six indigenous language families, including three of the four represented in the CODIS database (i.e. Algonquian, Na-Dene, and Eskimo-Aleut), and two language isolates (Miwok and Seri) using major population genetic diversity metrics such as F statistics and Bayesian clustering analysis of genotype frequencies. Most of the genetic variation (97%) was found to be within language families instead of among them (3%). In contrast, when only the three of the four language families represented in both the CODIS database and the present study were considered, 4% of the genetic variation occurred among the language groups. Bayesian clustering resulted in a maximum posterior probability indicating three genetically distinct groups among the eight language families and isolates: (1) Eskimo, (2) Seri, and (3) all other language groups and isolates, thus confirming genetic subdivision among subgroups of the CODIS Native American database. This genetic structure indicates the need for an increased number of Native American populations based on language affiliation in the CODIS database as well as more robust sample sets for those language families. Supplemental data for this article is available online at https://doi.org/10.1080/20961790.2021.1963088 .