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1,659 results for “structured population”
Nuclear genetic diversity and structure of Anastrepha ludens wild populations evidenced by microsatellite markers
<p class="MsoNormal"><span>The Mexican fruit fly, <em>Anastrepha ludens </em>is an important pest that causes widespread damage to a number of fruit crops in Mexico. The Sterile Insect Technique (SIT) is commonly used for its control. However, the existence of natural barriers can give rise to a population structure in neutral loci and possibly behavioral or adaptive traits that interfere with SIT. For this reason, it is important to understand the genetic diversity and structure of<em> A. ludens </em>populations and to better understand the evolutionary ecology and population processes in view of possible expansions and possible host shifts due to climate change. We genotyped nine nuclear DNA (nDNA) microsatellite loci among fruit fly populations collected from five biogeographic areas within Mexico, Mexican Plateau, the Northeastern Coastal Plain, the Pacific Coast, the Gulf Coast of Mexico, the Soconusco and a laboratory strain. The nuclear genetic diversity was moderate (from <em>H</em>e = 0.34 to <em>H</em>e = 0.39) within the wild mexfly population. We found that populations were clustered in three genetic groups (<em>K</em>=3). The diversity and genetic structure of <em>A. ludens</em> are produced by environmental and geological conditions as well as local conditions like anthropogenic perturbation which would produce population expansion and the existence of possible predators that would affect the population density. Gene flow showed recent migration among populations. The laboratory strain showed less diversity than the wild samples. Large values of current and ancestral population size suggest high resistance to climatic changes, probably due to biological attributes, such as its polyphagous, multivoltine and high dispersal characteristics. In particular ecosystem fragmentation and perturbation as well as the existence of new plant hosts all of which would probably increase the abundance of flies.</span></p>
Population genetic structure and demographic history of Rhodeus atremius suigensis, an endangered bitterling in Japan
<p><span>Demographic events can shape genetic diversity through genetic drift, often leaving a persistent signal in the genetic characteristics of species. <em>Rhodeus atremius suigensis</em> is an endangered bitterling fish endemic to the Okayama Plain, Japan. In this study, we inferred its demographic history and genetic structure using a comprehensive analysis of the mtDNA ND1 gene, microsatellite marke</span>rs<span> (MS) and MHC class IIB gene. Based on mtDNA, <em>R. a. suigensis</em> included two sublineages; A and B. While <a name="OLE_LINK85"></a><a name="OLE_LINK88"></a>the former was widely distributed, the latter was restricted to eastern populations<a name="OLE_LINK11"></a><a name="OLE_LINK12"></a> that were monomorphic in MHC. Phylogenetic analysis revealed that <em>R. a. suigensis</em>, together with <em>R. a. atremius</em>, experienced a substantial bottleneck in the middle Pleistocene. In MS and MHC, genetic diversity was low in all populations; ranked as the lowest among bitterling species. Bayesian clustering suggested that two clusters of MS had been widely introgressed in the centre of its distribution. These clusters seem to have been formed by the disruption of the distribution in the last Pleistocene, and later admixed by a large-scale reclamation in the Okayama Plain since the 16th century, which triggered a decline in effective population size (<em>N</em><sub>e</sub>) in many populations. Based on coalescence analysis, all populations reached their lowest <em>N</em><sub>e</sub> around the middle of the 20th century. Accordingly, <em>R.</em> <em>a</em>. <em>suigensis</em> seems to have experienced two large bottlenecks in the past. While the first bottleneck was probably due to climatic changes in the middle Pleistocene, the second is due to anthropogenic degradation and fragmentation of habitats in recent years.</span></p>
Genetic Population Structure of the Waved Whelk (Buccinum undatum) in the western North Atlantic
<p>R studio script files that includes original SNP data files used to determine the spatial genetic structure of <strong><em>Buccinum undatum </em></strong>in the western North Atlantic. Attached R-code is used to generate population genetic analyses, including a pairwise F<sub>ST</sub> heatmap, principal component analyses, and admixture analyses.</p>
Population structure and demographic history of the gastropod Thaisella chocolata (Duclos, 1832) from the Southeast Pacific inferred from mitochondrial DNA analyses
<p>The present-day population structure of a species reflects the combination of oceanographic currents, life-history traits, and historical events. However, little is known about the mechanisms that have shaped the gene lineage distribution of marine species inhabiting the Southeast Pacific. Here we provide a comprehensive phylogeographical study of a species distributed along the Southeast Pacific coastal region by analyzing the endemic gastropod Thaisella chocolata (Duclos, 1832). Sequencing of mitochondrial cytochrome c oxidase subunit 1 (CO1) and 16S rRNA revealed strikingly high haplotypic nucleotide and genetic diversity but a lack of significant population differentiation within the survey area. In addition, a star-shaped phylogeny and significantly negative Tajima's D and Fu's Fs tests of neutrality suggested historical occurrence of rapid demographic expansion. Mismatch distributions and Bayesian inference analyses also confirmed T. chocolata to have undergone two ancestral demographic expansions. Calculations suggested that these expansions began in the lower and middle Pleistocene epoch, likely due to continental shelf development and climatic conditions. These findings could help establish a genetic baseline for T. chocolata as the first step toward sustainable spatial management of this species, as well as understand this species' response to future climate change.</p>
Data from: Population genomics reveal deep divergence and strong geographical structuring in the Hengduan Mountains
<p>We used restriction site-associated DNA sequencing to generate 1,907 single nucleotide polymorphisms (SNPs) and four-kb of plastid sequence in species of the <em>Gentiana hexaphylla</em> complex (Gentianaceae). We performed genetic clustering with spatial and non-spatial models, phylogenetic reconstructions, and ancestral range estimation, with the aim of addressing the processes influencing the diversification of <em>G</em>. <em>hexaphylla</em> in the HM. Here, the SNP data and plastid sequence alignments are provided.</p>
Weak population genetic structure in Eurasian spruce bark beetle over large regional scales in Sweden
<p class="MsoNormal"><span>The Eurasian spruce bark beetle, <em>Ips typographus</em>, is a major pest, capable of killing spruce forests during large population outbreaks. Recorded dispersal distances of individual beetles are typically within hundreds of meters or a few </span>kilometres<span>. However, the connectivity between populations at larger distances and longer time spans and how this is affected by the habitat is less studied, despite its importance for understanding at which distances local outbreaks may spread. Previous population genetic studies in <em>I. typographus </em>typically used low resolution markers. Here, we use genome-wide data to assess population structure and connectivity of<em> I. typographus </em>in Sweden. We used 152 individuals from 19 population samples, distributed over 830 km from Strömsund (63º 46' 8'' N) in the north to Nyteboda (56º 8'</span> <span>50'' N) in the south, to capture processes at a large regional scale, and a transect sampling design adjacent to a recent outbreak to capture processes at a smaller scale (76 km). Using restriction site-associated DNA sequencing (RADseq) markers capturing 1409-1997 SNPs throughout the genome, we document a weak genetic structure over the large scale, potentially indicative of high connectivity with extensive gene flow. No differentiation was detected at the smaller scale. We find indications of isolation-by-distance both for relative (F<sub>ST</sub>) and absolute divergence (Dxy). The two northernmost populations are most differentiated from the remaining populations, and diverge in parallel to the southern populations for a set of outlier loci. In conclusion, the population structure of <em>I. typographus </em>in Sweden is weak, suggesting a high capacity to disperse and establish outbreak populations in new territories.</span></p>
High-density genomic data reveal fine-scale population structure and pronounced islands of adaptive divergence in lake whitefish (Coregonus clupeaformis) from Lake Michigan
<p>Understanding patterns of genetic structure and adaptive variation in natural populations is crucial for informing conservation and management. Past genetic research using 11 microsatellite loci identified six genetic stocks of lake whitefish (<em>Coregonus clupeaformis</em>) within Lake Michigan, USA. However, ambiguity in genetic stock assignments suggested those neutral microsatellite markers did not provide adequate power for delineating lake whitefish stocks in this system, prompting calls for a genomics approach to investigate stock structure. Here, we generated a dense genomic dataset to characterize population structure and investigate patterns of neutral and adaptive genetic diversity among lake whitefish populations in Lake Michigan. Using Rapture sequencing, we genotyped 829 individuals collected from 17 baseline populations at 197,588 SNP markers after quality filtering. Although the overall pattern of genetic structure was similar to the previous microsatellite study, our genomic data provided several novel insights. Our results indicated a large genetic break between the northwestern and eastern sides of Lake Michigan, and we found a much greater level of population structure on the eastern side compared to the northwestern side. Collectively, we observed five genomic islands of adaptive divergence on five different chromosomes. Each island displayed a different pattern of population structure, suggesting that combinations of genotypes at these adaptive regions are facilitating local adaptation to spatially heterogenous selection pressures. Additionally, we identified a large linkage disequilibrium block of ~8.5 Mb on chromosome 20 that is suggestive of a putative inversion but with a low frequency of the minor haplotype. Our study provides a comprehensive assessment of population structure and adaptive variation that can help inform management of Lake Michigan's lake whitefish fishery and highlights the utility of incorporating adaptive loci into fisheries management. </p>
Data from: Linking environmental stability with genetic diversity and population structure in two Atlantic Forest palm trees
<p><span>Spatial patterns of biodiversity in the Atlantic Forest of Brazil are well characterized. However, there is no consensus on the biological processes underlying these patterns, and multiple competing hypotheses have been proposed, several of which center on climatic stability. Here, we ask if Late Quaternary climatic stability predicts contemporary population structure and genomic-level diversity in two palm species: </span><span>Syagrus botryophora </span><span>and S. pseudococos (Arecaceae)</span></p> <p><span>We first use species occurrence data to model the distribution of suitable environments in 62 time-slice climate projections over the last 120 thousand years, and summarize stability over that period. We then use >25,000 RADseq-generated SNPs to i) describe the spatial patterns of genomic variation in both species, ii) test how well genomic variation is explained by isolation by distance and by the environmental resistance imposed by historical instability (isolation by resistance) and iii) test for a correlation between genetic diversity and historical stability.</span></p> <p><span>The contemporary range of S. botryophora has been relatively stable over the last 30 thousand years and there are two isolated regions of high stability for S. pseudococos. The genomic data recovers a clear pattern of isolation by distance in S. botryophora and two structured populations in S. pseudococos. Consequently, the contribution of isolation by resistance to overall genetic structure is much higher in S. pseudococos. Genetic diversity is not significantly correlated with historical stability in either species.</span></p> <p><span>Based on the concordance between historical stability and genetic structure, Late Quaternary climate stability may have maintained population connectivity within S. botryophora and promoted intraspecific divergence in S. pseudococos. Conversely, historical stability does not seem to be driving spatial patterns of genetic diversity. This study supports the primary role of climatic stability in determining spatial population structure, but not genetic diversity, in the Atlantic Forest.</span></p>
Data and scripts from: Microbiome composition is shaped by geography and population structure in the parasitic wasp Asobara japonica, but not in the presence of the endosymbiont Wolbachia
<p>The microbial community composition is crucial for diverse life-history traits in many organisms. However, we still lack a sufficient understanding of how the host microbiome is acquired and maintained, a pressing issue in times of global environmental change. Here we investigated to what extent host genotype, environmental conditions, and the endosymbiont <em>Wolbachia</em> influence the bacterial communities in the parasitic wasp <em>Asobara japonica</em>. We sampled multiple wasp populations across ten locations in their natural distribution range in Japan and sequenced the host genome (whole genome sequencing) and microbiome (16S rRNA gene). We compared the host population structure and bacterial community composition of wasps that reproduce sexually and are uninfected with <em>Wolbachia</em> with wasps that reproduce asexually and carry <em>Wolbachia</em>. The bacterial communities in asexual wasps were highly similar due to a strong effect of <em>Wolbachia</em> rather than host genomic structure. In contrast, in sexual wasps, bacterial communities appear primarily shaped by a combination of population structure and environmental conditions. Our research highlights that multiple factors shape the bacterial communities of an organism and that the presence of a single endosymbiont can strongly alter their compositions. This information is crucial to understanding how organisms and their associated microbiome will react in the face of environmental change.</p>
Dataset for "Genetic diversity and population structure of a wide Pisum spp. core collection."
<p>Silico-DArT and SNP datasets of the IAS pea core collection.</p> <p>Each file contain key information of the molecular markers used to establish the population structure and genetic diversity of the IAs pea core collection.</p>
Population genetic structure of the gastropod species Bulinus truncatus
<p class="MsoNormal"><strong><span>Background:</span></strong><span> Gastropod snails remain strongly understudied, despite their important role in transmitting parasitic diseases. Knowledge on their distribution and population dynamics increases our understanding of processes driving disease transmission. This is the first study using High Throughput Sequencing (HTS) to elucidate the population genetic structure of the hermaphroditic snail <em>Bulinus truncatus </em>(Gastropoda, Heterobranchia) on a regional (17 to 150 km) and an inter-regional (1,000 – 5,400 km) scale. This snail species acts as an intermediate host of <em>Schistosoma haematobium </em>and <em>Schistosoma bovis</em>, which cause human and animal schistosomiasis respectively<em>. </em></span></p> <p class="MsoNormal"><strong><span>Methods:</span></strong><span> <em>Bulinus truncatus </em>snails were collected in Senegal, Cameroon, Egypt and France and identified through DNA barcoding. A single-end Genotyping by Sequencing (GBS) library, comprising of 87 snail specimens from the respective countries, was built and sequenced on an Illumina HiSeq 2000 platform. Reads were mapped against <em>S. bovis </em>and <em>S. haematobium </em>reference genomes to identify schistosome infections and Single Nucleotide Polymorphisms (SNPs) were scored using the Stacks pipeline. These SNPs were used to estimate genetic diversity, assess population structure and to construct phylogenetic trees of <em>Bulinus truncatus</em>. </span></p> <p class="MsoNormal"><strong><span>Results:</span></strong><span> A total of 10,750 SNPs were scored and used in downstream analyses. The phylogenetic analysis identified five clades, each consisting of snails from a single country but with two distinct clades within Senegal. Genetic diversity was low in all populations, reflecting high selfing rates, but varied between locations due to habitat variability. Significant genetic differentiation and isolation by distance patterns were observed at both spatial scales, indicating that gene flow is not strong enough to counteract the effects of population bottlenecks, high selfing rates and genetic drift. Remarkably, the population genetic differentiation on a regional scale (i.e. within Senegal) was as large as between populations on an inter-regional scale. The blind GBS technique was able to pick up parasite DNA in snail tissue, demonstrating the potential of HTS techniques to further elucidate the role of snail species in parasite transmission.</span></p> <p class="MsoNormal"><strong><span>Conclusions</span></strong><span>:</span><span> HTS techniques offer a valuable toolbox to further investigate the population genetic patterns of schistosome intermediate host snails and the role of snail species in parasite transmission. </span></p>
Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds
<p><strong>Summary</strong></p> <p>Uganda is endowed with a large population of goats from predominantly indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture of the exotic breed Boer is still limited. Using a medium density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six Ugandan goat breeds. Samples from five indigenous Ugandan goat breeds including Mubende (n=29), Kigezi (n=29), Small East African (n=29), Sebei (n=29) and Karamojong (n=15), and the exotic breed Boer (n=13) from different agro-ecological regions of Uganda were genotyped using the GoatSNP50 BeadChip. Analysis of genotype data revealed high levels of polymorphism with the proportion of polymorphic SNPs ranging from 0.885 in Kigezi to 0.928 in Sebei. The overall mean genetic diversity indices across breeds for <em>H<sub>O</sub></em> and <em>H<sub>E</sub></em> was 0.355±0.147 and 0.384±0.143 respectively. Principle components, genetic distances and ADMIXTURE analyses revealed weak population sub-structuring among the breeds. Principle components separate Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong are tightly entangled together while Mubende occupies a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. ADMIXTURE and four population test analyses further revealed gene-flow from Boer to Ugandan indigenous goat breeds and varying levels of admixture among the Ugandan indigenous breeds. Generally, moderate to high levels of genetic variability were observed in the Ugandan goat breeds. Our findings provide useful insight to devise strategies to maintain genetic diversity in local goat breeds from Uganda and to design appropriate breeding programs to exploit within breed diversity and heterozygote advantage in cross-breeding schemes.</p>
Genome-wide single nucleotide polymorphisms reveal the genetic diversity and population structure of Creole goats from northern Peru
<p>Goat farming constitutes a significant source of income for farmers in northern Peru. There is currently an absence of information about the genetics of Peruvian Creole goats that would enable us to understand their origins and genetic spread. The objective of this study was to estimate the genetic diversity of Creole goats from northern Peru using SNP markers. This study involved the collection of 192 male Creole goats from three key goat production regions in northern Peru. These goat samples were genotyped using the GGPGoat70k SNP panel. To explore the genetic influence of other breeds on Peruvian Creole goats, our dataset was combined with previously published SNP genotypes. External data set includes multiple breeds genotypes sampled from Argentina, Brazil, Spain, and Alpine breed from Italy, France, and Switzerland. After quality control 52,832 autosomal SNPs were used to assess genetic diversity in the Peruvian goats. For the population structure analysis of the merged data 20,513 common SNPs were used. Estimations for expected heterozygosity (H<sub>e</sub>), observed heterozygosity (H<sub>o</sub>), and inbreeding coefficient (F<sub>IS</sub>) were computed for the Peruvian groups. AMOVA, principal component analysis and ADMIXTURE were conducted to evaluate the population structure in the two data sets, Peru and merged. The results revealed a considerable genetic diversity, with H<sub>o</sub> values ranging from 0.40 to 0.41 for the Peruvian sampling groups, and inbreeding coefficient was notably low for Peruvian goat. The population structure analysis demonstrated a distinction (p< 0.05) from other breeds. These findings suggest a level of genetic differentiation of the Peruvian goat population among other breeds, although further research is needed considering samples from other Peruvian areas. We expect this study will contribute to define genetic management strategies to prevent the loss of genetic diversity in Peruvian goat populations and for upcoming advancements in this field.</p>
Data from: The basic-reproduction number of infectious diseases in spatially structured host populations
<p>The spatial structure of a host population has a profound effect on the dynamics of infectious diseases. The basic reproduction number, a central quantity in the study of epidemic dynamics, is affected by host clustering as well as host density. Several authors have developed methods to quantify the basic reproduction number in a spatially structured host population. The methods used and the expressions derived are however difficult to apply to real life spatial host structures. In this paper we introduce an explicit expression for the basic reproduction number using the O-ring statistic, developed in spatial statistics, that quantifies the host density as a function of the distance from a randomly selected host individual. The O-ring statistic is frequently used in the study of the ecology of spatially structured plant populations, being a convenient summary of the properties of a landscape by way of a single function. The connection we develop between spatial statistics and epidemic dynamics can be used to study the effect of host spatial pattern on the basic reproduction number of infectious diseases. As well as showing how explicit expressions for the basic reproduction number can be derived for landscapes with standard structures, our expression for the basic reproduction number is tested against a simulation model. The model structure in our simulation is motivated by the spread of a plant disease epidemic, although it is applicable more broadly. The agreement between our analytic expression for the basic reproduction number and the corresponding numeric quantity extracted from simulations is close to perfect across a wide range of landscape structures and model parameterisations, and including cases in which more than one species of host is at risk of infection.</p>
Genetic variability and Population structure of two sympatric cownose rays Rhinoptera (Myliobatiformes, Rhinopteridae) in the Western Atlantic Ocean
<p><em><span><span>We analyzed sequences of COI and Cytb genes for Rhinoptera bonasus (COI: 230; 11 haplotypes, Cytb: 108; 12 haplotypes) and R. brasiliensis (COI: 181; 10 haplotypes, Cytb: 105; eight haplotypes ) to investigate the genetic diversity and their relationship with environmental variables, genetic structure, as well as demographic parameters. </span></span></em></p>
Data from: Responses of population structure and genomic diversity to climate change and fishing pressure in a pelagic fish
<p><span>The responses of marine species to environmental changes and anthropogenic pressures (e.g. fishing) interact with ecological and evolutionary processes that are not well understood. Knowledge of changes in the distribution range and genetic diversity of species and their populations into the future is essential for the conservation and sustainable management of resources.</span><span> Almaco jack (<em>Seriola rivoliana</em>) is<em> </em>a pelagic fish with high importance to fisheries and aquaculture in the Pacific Ocean. </span><span>In this study, we assessed contemporary genomic diversity and structure in loci that are putatively under selection (outlier loci) and determined their potential functions. Utilizing a combination of genotype-environment association, spatial distribution models, and demogenetic simulations, we modeled the effects of cl</span><span>imate change (under three different RCP scenarios) and fishing pressure on the species' geographic distribution and genomic diversity and structure to 2050 and 2100.</span><span> Our results show that most of the outlier loci identified were related to biological and metabolic processes that may be associated with temperature and salinity. Contemporary genomic structure showed three populations—two in the Eastern Pacific (</span><span>Cabo San Lucas </span><span>and Eastern Pacific) and one in the Central Pacific (</span><span>Hawaii</span><span>). Future projections suggest a loss of suitable habitat and potential range contractions for most scenarios, while fishing pressure decreased population connectivity. Our results suggest that future climate change scenarios and fishing pressure will affect the genomic structure and genotypic composition of <em>S. rivoliana</em> and lead to loss of genomic diversity in populations distributed in the eastern-central Pacific Ocean, which could have profound effects in fisheries that depend on this resource.</span></p>
Fig. 4 in Age Structure In A Declining Population Of Rana Temporaria From Northern Italy
Fig. 4. Age distribution of male (filled bars) and female (empty bars) Rana temporaria
An assemblage-level comparison of genetic diversity and population genetic structure between island and mainland ant populations
<p>Island biotas provide unparalleled opportunities to examine evolutionary processes. Founder effects and bottlenecks, for example, typically decrease genetic diversity in island populations, while selection for reduced dispersal can increase population structure. Given that support for these generalities mostly comes from single-species analyses, assemblage-level comparisons are needed to clarify how (i) colonization affects the gene pools of interacting insular organisms, and (ii) patterns of genetic differentiation vary within assemblages of organisms. Here, we use genome-wide sequence data from ultraconserved elements (UCEs) to compare genetic diversity and population structure of mainland and island populations of nine ant species in coastal southern California with respect to genetic diversity and population structure. As expected, island populations (from Santa Cruz Island) had lower than expected heterozygosity and Watterson's theta compared to mainland populations (from the Lompoc Valley). Island populations, however, exhibited smaller genetic distances among samples, indicating less population subdivision and a higher capacity for dispersal compared to mainland populations. Within the focal assemblage, pairwise F<sub>st</sub> values revealed pronounced interspecific variation in mainland-island differentiation, which increases with gyne body size. Our results reveal differences in genetic diversity and population genetic structure across an assemblage of interacting species, and illuminate general patterns of insularization in ants. Compared to single-species studies, our analysis of nine species pairs from the same island-mainland system offers a powerful approach to studying fundamental evolutionary processes.</p>
Fig. 2 in Altitudinal Variation In Population Density, Body Size And Morphometric Structure In C A R A B U S O D O R At U S S H I L, 1996 (C O L E O P T E R A: Carabidae)
Fig. 2. Sampling localities of C. odoratus.
Fig. 8 in Phenology And Population Structure Of Forest Herbaceous Species In Artificial And Natural Communities In The Steppe Zone Of Ukraine
Fig. 8. Dates of onset and duration of budding (1) and flowering (2).
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.