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2,445 results for “Genetics: population”
Western redcedar single nucleotide polymorphism (SNP) genotyping data for genomic selection and population genetics
<p>Western redcedar (<em>Thuja plicata</em>) Single Nucleotide Polymorphism (SNP) data in Variant Call Format (VCF) for genomic selection training and target populations, genomic selection parents, and self-fertilized (selfing) lines, comprising 4,833 trees.</p> <p>Targeted sequencing-based genotyping was done by Capture-Seq methodology at Rapid Genomics (Neves est al. 2013). A set of 57,000 probes as designed for initial marker discovery, from which a panel of 20,858 probes was selected for genotyping. A set of transcriptomes (Shalev et al. 2018) (PRJNA704616) was aligned to the reference genome to identify SNPs. Candidate probes (120 nt) were initially designed in silico and 57,000 selected by removing candidates with poor base composition for hybridization (GC content <0.2 and >0.6, high G content >0.2 and long homopolymers >7), followed by removing probes aligning to more than one position on the reference genome (≥90% identity and length). The 57,000 probes represent 14,517 scaffolds (average 3.9 probes/scaffold), with 37,275 targeting at least one SNP and 19,725 mapping to intergenic regions not containing pre-identified SNPs. A set of 128 individuals were selected to validate the 57,000 probe panel and associated polymorphisms. Genomic DNA (0.5 ug) was fragmented (mean size 300 bp), followed by repair of ends, phosphorylation, adenylation, ligation of Illumina compatible adapters containing 8bp indexes and 5’ T-overhang, and 10 cycles PCR amplification with universal primers to produce sequencing-ready libraries. Libraries were quantified using PicoGreen. Libraries from 16 samples were pooled, hybridized to the 120 nt RNA probes following Agilent’s SureSelect Target Enrichment System (Agilent Technologies) and sequenced on an Illumina HiSeq X machine with paired-end 150bp cycle for an average sequencing depth per sample of 15X. Sequence data were aligned to the reference genome with BWA-MEM (http://arxiv.org/abs/1303.3997) and sets of four samples were combined to increase sequencing depth for identifying markers. Putative SNPs were identified using Freebayes (http://arxiv.org/abs/1207.3907) in 150bp on either side of the 57,000 probes and filtered probes that had more than 17 SNPs per 420 bp target region (150bp + 120bp + 150bp). The sequencing depth of the probes was used to select the final set of 20,885 probes, removing probes on both sides of the distribution (low and high sequencing depth), for Capture-Seq on the remainder of the samples.</p>
Population genetic and environmental data for Chamaecrista fasciculata
<p><em>Chamaecrista fasciculata</em> is a widely distributed, phenotypically variable species in the eastern U.S. Whereas studies have demonstrated genetic structure and local adaptation in northern areas of its distribution, there has been no comparison of genetic variability among populations at the southern extent where phenotypic variation is more complex. We characterized genetic variation at 14 microsatellite loci for populations in Mississippi and Alabama and compared this to variation in a phenotypic trait, leaf pubescence. Geographic distance, climatic variables, and elevation were evaluated as factors to explain the observed patterns of genetic diversity. A significant amount of variation (19%) resided among populations, but most variation (68%) was among individuals. Assignment of individuals into genetic groups suggests two primary clusters, but these groups are not concordant with known geographical or ecological breaks, nor phenotypic variants. Genetic structure at a regional scale can be characterized as isolation by distance, while environmental factors may play a secondary role in limiting gene flow at local scales. Mean population FST is strongly associated with allelic diversity and heterozygosity, suggesting that genetic drift influences population variation. Despite the presence of genetic and phenotypic variation in southern populations of <em>C. fasciculata</em>, the lack of concordant patterns between these types of variation indicate that they are not driven by the same factors. This study demonstrates how local factors differentially influence the maintenance of intraspecific variation and suggest the southern distributional range is an active area of evolution for <em>C. fasciculata</em></p>
Life-history stage and the population genetics of the tiger mosquito Aedes albopictus at a fine spatial scale
<p>As a widespread vector of disease, the mosquito species <em>Aedes albopictus </em>Skuse<em> </em>(Diptera: Culicidae) is a high priority for both public health and invasive species research and management. Like all mosquitoes, <em>A. albopictus </em>has a complex life history with aquatic egg, larval, and pupal stages and a terrestrial adult stage. This requires targeted management strategies for each life stage, coordinated across time and space. Researchers use population genetics to inform control of <em>A. albopictus</em>. However, these studies do not consider the impact on life stage on population genetic characteristics and subsequent conclusions. Our objective was to examine whether the life stage impacted patterns of <em>A. albopictus </em>genetic diversity and differentiation at a spatial scale relevant to management efforts. We first conducted a literature review of field-caught <em>A. albopictus </em>population genetic papers and identified 74 peer-reviewed publications, none of which compared results between life stages.<em> </em>We them examined population genetic patterns of egg and adult <em>A. albopictus </em>at five sites in Wake County, North Carolina USA using 8,425 single nucleotide polymorphisms. We found that level of genetic diversity and connectivity between sites varied between adults and eggs. This warrants further study and is critical for research aimed at informing local management.</p>
Genotype data for: Population genetics reveals divergent lineages and ongoing hybridization in a declining migratory fish species complex
<p>Deciphering the effects of historical and recent demographic processes responsible for the spatial patterns of genetic diversity and structure is a key objective in evolutionary and conservation biology. Using population genetic analyses, we investigated the demographic history, the contemporary genetic diversity and structure, and the occurrence of hybridization and introgression of two species of anadromous fish with contrasting life history strategies and which have undergone recent demographic declines, the allis shad (<em>Alosa alosa</em>) and the twaite shad (<em>Alosa fallax</em>). We genotyped 706 individuals from 20 rivers and 5 sites at sea in Southern Europe at thirteen microsatellite markers. Genetic structure between populations was lower for the nearly semelparous species <em>A. alosa</em>, which disperses greater distances compared to the iteroparous species, <em>A. fallax</em>. Individuals caught at sea were assigned at the river level for <em>A. fallax</em> and at the region level for A. alosa. Using an approximate Bayesian computation framework, we inferred that the most likely long term historical divergence scenario between both species and lineages involved historical separation followed by secondary contact accompanied by strong population size decline. Accordingly, we found evidence for contemporary hybridization and bidirectional introgression due to gene flow between both species and lineages. Moreover, our results support the existence of at least one distinct species in the Mediterrannean sea: <em>A. agone</em> in Golfe du Lion area, and another divergent lineage in Corsica. Overall, our results shed light on the interplay between historical and recent demographic processes and life history strategies in shaping population genetic diversity and structure of closely related species. The recent demographic decline of these species' populations and their hybridization should be carefully considered while implementing conservation programs.</p>
Population genetic and geographic data of six Neotropical plant species
<p>We examined population genetic structure and fine-scale spatial genetic structure (FSGS) in six perennial understory angiosperms in Andean cloud forests of northwestern Ecuador. Species belong to three families (Gesneriaceae, Melastomataceae, and Rubiaceae), and within each family we paired one insect-pollinated with one hummingbird-pollinated species, predicting that insect-pollinated species have greater population differentiation (as quantified with the F<sub>ST</sub> statistic) and stronger FSGS (as quantified with the S<sub>P</sub> statistic) than hummingbird-pollinated species.</p>
Genetic structure and dispersal in peripheral populations of a marine fish (Pacific cod, Gadus macrocephalus) and their importance for adaptation to climate change
<p>Small and isolated peripheral populations, which are often remnants of glacial refugia, offer an opportunity to determine the magnitude and direction of fine-scale connectivity in high gene flow marine species. When located at the equatorial edge of a species' range, these populations may also harbor genetic diversity related to survival and reproduction at higher temperatures, a critical resource for marine species facing warming ocean temperatures. Pacific cod (Gadus macrocephalus), a marine fish in the North Pacific, has already experienced major shifts in biomass and distribution linked to climate change. We estimated the magnitude and direction of connectivity between peripheral populations of Pacific cod at the southern edge of the species' range, by conducting restriction site-associated DNA (RAD) sequencing and individual assignment on fish collected around the Korean Peninsula during the spawning season. Three populations on the western, eastern, and southern Korean coasts were highly differentiated (FST =0.025 – 0.042) and relatively small (Ne = 433-1777). Ten putative dispersers and estimates of contemporary migration rates revealed asymmetrical, west-to-east movement around the Korean Peninsula, at a higher rate than predicted by indirect estimates of connectivity (FST). Allele frequencies at 87 RAD loci were decisively correlated with strong marine temperature gradients between the warmer southern coast and the cooler waters of the eastern and western coasts. Despite relatively small sample sizes, our data suggest asymmetrical dispersal and gene flow, potentially involving adaptive alleles, between peripheral populations inhabiting markedly different thermal regimes. Our study emphasizes the conservation value of peripheral populations in high gene flow marine fish species.</p>
Data from: Using a reference population yardstick to calibrate and compare genetic diversity reported in different studies: an example from the brown bear.
In species with large geographic ranges, genetic diversity of different populations may be well studied, but differences in loci and sample sizes can make the results of different studies difficult to compare. Yet, such comparisons are important for assessing the status of populations of conservation concern. We propose a simple approach of using a single well-studied reference population as a "yardstick" to calibrate results of different studies to the same scale, enabling comparisons. We use a well-studied large carnivore, the brown bear (Ursus arctos), as a case study to demonstrate the approach. As a reference population, we genotyped 513 brown bears from Slovenia using 20 polymorphic microsatellite loci. We used this dataset to calibrate and compare heterozygosity and allelic richness for 30 brown bear populations from 10 different studies across the global distribution of the species. The simplicity of the reference population approach makes it useful for other species, enabling comparisons of genetic diversity estimates between previously incompatible studies and improving our understanding of how genetic diversity is distributed along a species range.
Population genetic structure of wolves in the northwestern Dinaric-Balkan region
<p><span>The Balkan Peninsula and the Dinaric Mountains possess extraordinary biodiversity and </span>support one of the largest and most diverse wolf (<em>Canis lupus</em>) populations in Europe. Results obtained with diverse genetic markers show west-east substructure, also seen in various other species, despite the absence of obvious barriers to movement. However, the spatial extent of the genetic clusters remains unresolved, and our aim was to combine fine-scale sampling with population and spatial genetic analyses to improve resolution of wolf genetic clusters. We analyzed 16 autosomal microsatellites from 255 wolves sampled in Slovenia, Croatia, Bosnia and Herzegovina (BIH), and Serbia, and documented three genetic clusters. These comprised (1) Slovenia and the regions of Gorski kotar and Lika in Croatia, (2) the region of Dalmatia in southern Croatia and BIH, and (3) Serbia. <span>When we mapped the clusters geographically, we observed west-east genetic structure across the study area, together with some specific structure in BIH – Dalmatia. </span>We observed that cluster 1 had a smaller effective population size, consistent with earlier reports of population recovery since the 1980s. Our results provide foundation for future genomic studies that would further resolve the observed west-east population structure and its evolutionary history in wolves and other taxa in the region, and identify focal areas for habitat conservation. They also have immediate importance for conservation planning for the wolves in one of the most important parts of the species' European range.</p>
Genetic admixture and population structure analysis of Indian water buffaloes (Bubalus bubalis) using STR markers
<p><span>We generated genetic diversity data for 10 different buffalo populations of India using 20 highly polymorphic microsatellite markers. The buffalo populations of Odisha were the primary focus, viz. Chilika, Paralakhemundi, Kalahandi, Sambhalpuri, and Manda. The total observed number of alleles ranged between 143 (Manda) and 301 (Paralakhemundi) with an average of 204 alleles per breed. The minimal spanning network based on Bruvo's distance, PCA based on the Fst values, and genetic admixture analysis using both the STRUCTURE and 'snapclust' could identify the Manda population distinct from other Odisha buffalo breeds as well as Chhattisgarhi buffalo breed. The Sambhalpuri buffalo population also clustered into two separate subpopulations, half of the unique sub-population located geographically south-wards displayed no admixture with any of the adjacent buffalo populations. The Sambhalpuri population requires elaborate analysis to confirm the existence of two distinct sub-populations and if they could be recognized as separate breeds. The limited number of sires in the Manda population has resulted in excess of heterozygosity. Furthermore, the Manda population is left with very little allelic richness and this poses a huge threat to the population's existence. In another way, the study has led to the identification of the Manda buffalo as a distinct population, and the germplasm has been registered based on the study.</span></p>
Spatial pattern of genetic diversity in field populations of Fusarium incarnatum-equiseti species complex
<p><i>Fusarium</i> is associated with a number of wilt, blight, scab and rot diseases in a range of economically important staple food crops worldwide. An assessment of the genetic structure and population stratification of <i>Fusarium incarnatum-equiseti</i> species complex (FIESC) pathogen populations is important to understand the evolutionary potential of such populations in adapting to environmental change. Based on inter-simple sequence repeat polymerase chain reaction (ISSR-PCR), it was found that the pathogen population was structured into three genetic clusters for which genetic differentiation was higher within than among populations. There was high intra-population genetic diversity for population 1 (94.63%) which consisted largely of isolates collected from North Trinidad. Populations 2 and 3 had a low level of admixture among the populations based on overall population differentiation. Population 1 accounted for the highest amount of genetic variation (95.82%) followed by populations 2 and 3. Population stratification was reflected in the dendrogram topology, which consisted of three main genetic clusters and which coincided with the outcome of Bayesian and PCoA analyses. The populations were isolated by distance and Voronoi tessellations indicated physical or structural barriers to gene flow which contributed to restricted admixture between two of three populations. These findings suggest a high evolutionary potential for this FIESC pathogen population, the implications of which directly affect disease management strategies.</p>
Distribution. SE Guinea, E Liberia, and SW Ivory Coast in West Africa; the species may be found in Sierra Leone, but this population has not been genetically investigated and could be either the Ivory Coast White-toothed Shrew or the West African Pygmy White-toothed Shrew (C. obscurior). in Soricidae
Distribution. SE Guinea, E Liberia, and SW Ivory Coast in West Africa; the species may be found in Sierra Leone, but this population has not been genetically investigated and could be either the Ivory Coast White-toothed Shrew or the West African Pygmy White-toothed Shrew (C. obscurior).
Distribution. SE Guinea, E Liberia, S Ivory Coast, and W Ghana; populations ofeither this species, the Ivory Coast White-toothed Shrew (C. eburnea), or both species are found in S Sierra Leone and are included in the range map ofthis species but have not been investigated genetically and could represent either species. There are apparently records that represent this species from S Nigeria, although further research is needed to confirm thatthis speciesis truly found there. in Soricidae
Distribution. SE Guinea, E Liberia, S Ivory Coast, and W Ghana; populations ofeither this species, the Ivory Coast White-toothed Shrew (C. eburnea), or both species are found in S Sierra Leone and are included in the range map ofthis species but have not been investigated genetically and could represent either species. There are apparently records that represent this species from S Nigeria, although further research is needed to confirm thatthis speciesis truly found there.
Spatio-temporal dynamics of genetic variation at the quantitative and molecular levels within a natural Arabidopsis thaliana population
<p><span>Evolutionary change begins at the population scale. Therefore, understanding adaptive variation requires the identification of the factors maintaining and shaping standing genetic variation at the within-population level. Spatial and temporal environmental heterogeneity represent ecological drivers of within-population genetic variation, determining the evolutionary trajectory of populations along with random processes. Here, we focused on the effects of </span><span>spatio-temporal heterogeneity on quantitative and molecular variation in a natural population of the annual plant <em>Arabidopsis thaliana</em>.</span></p> <p><span>We sampled 1,093 individuals from a Spanish <em>A. thaliana </em>population across an area of 7.4 ha for 10 years (2012-2021). Based on a sample of 279 maternal lines, we estimated spatio-temporal variation in life-history traits and fitness from a common garden experiment. We genotyped 884 individuals with nuclear microsatellites to estimate spatio-temporal variation in genetic diversity. We assessed spatial patterns by estimating spatial autocorrelation of traits and fine-scale genetic structure. We analyzed the relationships between phenotypic variation, geographic location and genetic relatedness, as well as the effects of environmental suitability and genetic rarity on phenotypic variation. </span></p> <p><span>The common garden experiment indicated that there was more temporal than spatial variation in life-history traits and fitness. Despite the differences among years, genetic distance in ecologically relevant traits (e.g. flowering time) tended to be positively correlated to genetic distance among maternal lines, whilst isolation by distance was less important. Genetic diversity exhibited significant spatial structure at short distances, which were consistent among years. Finally, genetic rarity, and not environmental suitability, accounted for genetic variation in life-history traits.</span></p> <p><span>Synthesis. Our study highlighted the importance of repeated sampling to detect the large amount of genetic diversity at the quantitative and molecular levels that a single <em>A. thaliana</em> population can harbor. Overall, population genetic attributes estimated from our long-term monitoring scheme (genetic relatedness and genetic rarity), rather than biological (dispersal) or ecological (vegetation types and environmental suitability) factors, emerged as the most important drivers of within-population structure of phenotypic variation in <em>A. thaliana.</em></span></p>
FIGURE 4 in Population Structure and Genetic Diversity in Delphinium (Ranunculaceae) Using Scot Molecular Markers
FIGURE 4: WARD tree of SCoT data revealing species delimitation in the Delphinium sp1= D. teheranicum; sp2= D. camptocarpum; sp3= D. lorestanicum; sp4= D. leptocarpum; sp5= D. persicum; sp 6= D. aucheri; sp7= D. anthoroideum; sp8= D. hohenackeri; sp9= D. stocksianum; sp10: D. rugulosum; sp11: D. ambiguum; sp12= D. ajacis; sp13= D. consolida; sp14= D. oliverianum; sp15= D. flavum; sp16= D. trigonelloides; sp17= D. oliganthum; sp18= D. linarioides; sp19= D. paradoxum.
FIGURE. 3 in Population Structure and Genetic Diversity in Delphinium (Ranunculaceae) Using Scot Molecular Markers
FIGURE. 3. Electrophoresis gel of studied ecotypes from DNA fragments produced by SCoT-15. sp1= D. teheranicum; sp2= D. camptocarpum; sp3= D. lorestanicum; sp4= D. leptocarpum; sp5= D. persicum; sp 6= D. aucheri; sp7= D. anthoroideum; sp8= D. hohenackeri; sp9= D. stocksianum; sp10: D. rugulosum; sp11: D. ambiguum; sp12= D. ajacis; sp13= D. consolida; sp14= D. oliverianum; sp15= D. flavum; sp16= D. trigonelloides; sp17= D. oliganthum; sp18= D. linarioides; sp19= D. paradoxum. L = Ladder 100 bp,
FIGURE 2 in Population Structure and Genetic Diversity in Delphinium (Ranunculaceae) Using Scot Molecular Markers
FIGURE 2: PCA plot of morphological characters revealing species delimitation in the Delphinium species; sp1= D. teheranicum; sp2= D. camptocarpum; sp3= D. lorestanicum; sp4= D. leptocarpum; sp5= D. persicum; sp 6= D. aucheri; sp7= D. anthoroideum; sp8= D. hohenackeri; sp9= D. stocksianum; sp10: D. rugulosum; sp11: D. ambiguum; sp12= D. ajacis; sp13= D. consolida; sp14= D. oliverianum; sp15= D. flavum; sp16= D. trigonelloides; sp17= D. oliganthum; sp18= D. linarioides; sp19= D. paradoxum.
FIGURE. 1 in Population Structure and Genetic Diversity in Delphinium (Ranunculaceae) Using Scot Molecular Markers
FIGURE. 1. Map of Iran shows the collection sites and provinces where Delphinium species were obtained for this study; sp1= D. teheranicum; sp2= D. camptocarpum; sp3= D. lorestanicum; sp4= D. leptocarpum; sp5= D. persicum; sp 6= D. aucheri; sp7= D. anthoroideum; sp8= D. hohenackeri; sp9= D. stocksianum; sp10: D. rugulosum; sp11: D. ambiguum; sp12= D. ajacis; sp13= D. consolida
Panicum hallii RIL population (HAL2 X FIL2 ) genetic map
<p>This project represents the method of constructing genetic map for the <em>Panicum hallii</em> Recombinant Inbreed Line (RIL) population. This population is a cross between one inland (HAL2) and one coastal (FIL2) natural accession of <em>P. hallii</em>. This map compromise of 441 RIL individuals genotyped for 901 markers. The raw sequences for RIL individuals are available in NCBI SRA archive Umbrella project PRJNA701489. </p>
Holocene climate changes explain the spatial pattern in genetic diversity in populations of Cyperus papyrus from Southeast Africa wetlands
<p>Wetlands are one of the most threatened ecosystems in the world because more than 70% of the area worldwide has been lost since 1900. Wetland plant species rely greatly on water for seeds and propagules, which may lead to a downstream unidirectional dispersal and accumulation of genetic diversity downstream. However, several species show no support for unidirectional genetic diversity, revealing the complexity of population dynamics and gene flow in wetlands. Here, we used microsatellite loci to address how the past demographic dynamics shaped the contemporary spatial pattern in genetic diversity and population structure of <em>Cyperus papyrus</em> in wetlands of Southeast Africa. Using spatially explicit analysis and coalescent modelling we found no support for unidirectional dispersal. Instead, we found higher genetic diversity in populations upstream than downstream in the river basin. We also found high admixture among populations, most likely due to connections between adjacent river basins during sporadic floods, and ongoing gene flow due to bird-mediated seed dispersal. Our results suggest stepping-stone migration due to strong isolation-by-distance, but not necessarily unidirectional. Moreover, the past demographic dynamics in the Holocene shaped the current pattern of genetic diversity and structure, leading to higher genetic diversity in populations upstream of the Zambezi river basin. Our results also point to the very low genetic diversity of <em>C</em>. <em>papyrus</em> populations in Southeast Africa and the need for management and conservation strategies to guarantee the long-term persistence of the species in the region.</p>
Data from: Breeding system and geospatial variation shape the population genetics of Triodanis perfoliata
<p><span>Both intrinsic and extrinsic forces work together to shape connectivity and genetic variation in populations across the landscape. Here we explored how geography, breeding system traits, and environmental factors influence the population genetic patterns of <em>Triodanis perfoliata</em>, a widespread mix-mating annual plant in the contiguous US. By integrating population genomic data with spatial analyses and modeling the relationship between breeding system and genetic diversity, we illustrate the complex ways in which these forces shape genetic variation. Specifically, we used 4,705 single nucleotide polymorphisms to assess genetic diversity, structure, and evolutionary history among 18 populations. Populations with more obligately selfing flowers harbored less genetic diversity (π: R<sup>2</sup> = 0.63, P = 0.01, n = 9 populations), and we found significant population structuring (F<sub>ST</sub> = 0.48). Both geographic isolation and environmental factors played significant roles in predicting the observed genetic diversity: we found that corridors of suitable environment appear to facilitate gene flow between populations, and that environmental resistance is correlated with increased genetic distance between populations. Last, we integrated our genetic results with species distribution modeling to assess likely patterns of connectivity among our study populations. Our landscape and evolutionary genetic results suggest that <em>T. perfoliata</em> experienced a complex demographic and evolutionary history, particularly in the center of its distribution. As such, there is no singular mechanism driving this species' evolution. Together, our analyses support the hypothesis that breeding system, geography, and environmental variables shape the patterns of diversity and connectivity of <em>T. perfoliata</em> in the US. </span></p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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