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637 results for “Population analysis”
Fig. 1 in Multilocus population analysis of Gavia immer (Aves: Gaviidae) mtDNA reveals low genetic diversity and lack of differentiation across the species breeding range
Fig. 1 Haplotype network constructed using the median joining method. Haplotype numbers are indicated. Circle patterns represent coastal sampling locations: GZ Galicia, Spain, MX Mexico, GE Germany, NJ New Jersey, US, MI Michigan, US, CA Canada, FL Florida, US. Circle surfaces are roughly proportional to the number of individuals with each haplotype (Table 3)
FIGURE 1 in Combining morphology and population genetic analysis uncover species delimitation in the widespread African tree genus Santiria (Burseraceae)
FIGURE 1. Genetic clusters (GC) detected in Santiria samples from western Central Africa. Bayesian clustering analyses were performed on 479 individuals genotyped at 10 microsatellites loci. A. Variation in means of Ln (likelihood) of the data as a function of the number of hypothetical genetic clusters (K), showing a plateau at K=3. B. Histogram of genetic assignment of the 481 individuals at K = 3. C. Distribution of the three genetic clusters in western Central Africa, and delimitation of the distribution of each genetic cluster (dotted line: GC1, solid line: GC2, dashed line: GC3). We extended the distribution ranges of GC2 and GC3 because morphotypes of both genetic clusters were observed in the south of the Republic of the Congo. Note: Interm. GCx and GCy = intermediate individuals between GCx and GCy.
FIGURE 2 in Combining morphology and population genetic analysis uncover species delimitation in the widespread African tree genus Santiria (Burseraceae)
FIGURE 2. Extended Principal Component Analysis (the Hill-Smith ordination) of quantitative and qualitative traits assessed in 103 Santiria herbarium samples assigned to GC1 (N = 46, open circles), GC2 (N = 21, stars) and GC3 (N = 36, open triangles). Note: NL = number of leaflets per leaf; LL = length of leaves; LP = length of petiole; WP = width of petiole; LP/WP = ratio between LP and WP; TPeL = terminal petiolule length; TLL = terminal leaflet length; TLW = terminal leaflet width; TLL/TLW = ratio between TLL and TLW; TLWe = terminal leaflet weight dry portion; AL = apex length; GD = glandular dots; Le = lenticels.
Tree germination sensitivity to increasing temperatures: a global meta-analysis across biomes, species and populations.
<p>The dataset contains the files used for the meta-analysis on the role of temperature increases on the germination of tree species from different biomes around the world.</p> <p>This meta-analysis is accepted for publication in Global Ecology and Biography (MS reference number: GEB-2024-0273.R1 ; Article DOI: 10.1111/geb.13921).</p> <p>Files S6 and S7 gather data of germination percentage and time, respectively, at population scale. File S5 is a summary of the publications used as data sources for the meta-analysis. The whole dataset comprises 50 papers addressing 63 species and 250 populations, it covers boreal, temperate, Mediterranean and tropical-subtropical biomes, and a time period between 1996 and 2024.</p>
Data from: Population genetic analysis of white sturgeon (Acipenser transmontanus) in the Fraser River
White sturgeon (Acipenser transmontanus) in the Fraser River are listed as imperiled (the second highest possible rating) by the British Columbia Conservation Data Centre. A difficulty in trying to protect this species in the Fraser River and elsewhere is the lack of knowledge regarding their population biology. Variation in the mitochondrial DNA control region and at four microsatellite loci was examined in order to characterize white sturgeon samples from throughout the Fraser River mainstem and from a major tributary, the Nechako River. Samples from the adjacent Columbia River were analyzed for comparison. In contrast to previous work, present data indicate that white sturgeon population structure in this region reflects post-glacial dispersal more than it does recent anthropogenic effects. The data divided the Fraser into four biogeographic regions: (i) the lower Fraser, below Hell's Gate; (ii) the middle Fraser, between Hell's Gate and river km 553; (iii) the upper Fraser, above the Nechako confluence; and (iv) the Nechako River. These four groups are concordant with those suggested by tag and recapture and catch per unit effort data, and are separated by what have been identified as barriers to white sturgeon migration. Based on concordance between these different types of data, it is argued that the four groups identified here merit evolutionarily significant unit (ESU) status.
Data from: Genomic analysis reveals depression due to both individual and maternal inbreeding in a free-living mammal population
There is ample evidence for inbreeding depression manifested as a reduction in fitness or fitness-related traits in the focal individual. In many organisms, fitness is not only affected by genes carried by the individual, but also by genes carried by their parents, for example if receiving parental care. While maternal effects have been described in many systems, the extent to which inbreeding affects fitness directly through the focal individual, or indirectly through the inbreeding coefficients of its parents, has rarely been examined jointly. The Soay sheep study population is an excellent system in which to test for both effects, as lambs receive extended maternal care. Here, we tested for both maternal and individual inbreeding depression in three fitness-related traits (birthweight and weight and hindleg length at 4 months of age) and three fitness components (first-year survival, adult annual survival and annual breeding success), using either pedigree-derived inbreeding or genomic estimators calculated using ~37 000 SNP markers. We found evidence for inbreeding depression in 4-month hindleg and weight, first-year survival in males, and annual survival and breeding success in adults. Maternal inbreeding was found to depress both birthweight and 4-month weight. We detected more instances of significant inbreeding depression using genomic estimators than the pedigree, which is partly explained through the increased sample sizes available. In conclusion, our results highlight that cross-generational inbreeding effects warrant further exploration in species with parental care and that modern genomic tools can be used successfully instead of, or alongside, pedigrees in natural populations.
Data from: Sixty years of anthropogenic pressure: a spatio-temporal genetic analysis of brown trout populations subject to stocking and population declines
Analyses of historical samples can provide invaluable information on changes to the genetic composition of natural populations resulting from human activities. Here, we analyze 21 microsatellite loci in historical (archived scales from 1927-1956) and contemporary samples of brown trout (Salmo trutta) from six neighbouring rivers in Denmark, to compare the genetic structure of wild populations before and after population declines and stocking with non-local strains of hatchery trout. We show that all populations have been strongly affected by stocking, with admixture proportions ranging from 14 to 64%. Historical population genetic structure was characterized by isolation-by-distance and by positive correlations between historical effective population sizes and habitat area within river systems. Contemporary population genetic structure still showed isolation-by-distance, but also reflected differences among populations in hatchery trout admixture proportions. Despite significant changes to the genetic composition within populations over time, dispersal rates among populations were roughly similar before and after stocking. We also assessed whether population declines or introgression by hatchery strain trout should be the most significant conservation concern in this system. Based on theoretical considerations, we argue that population declines have had limited negative effects for the persistence of adaptive variation, but admixture with hatchery trout may have resulted in reduced local adaptation. Collectively, our study demonstrates the usefulness of analyzing historical samples for identifying the most important consequences of human activities on the genetic structure of wild populations.
Phylogenetic analysis of HIV-1 shows frequent cross-country transmission and local population expansions
<p>Understanding of pandemics depends on characterization of pathogen collections from well-defined and demographically diverse cohorts. Since its emergence in Congo almost a century ago, HIV-1 has geographically spread and genetically diversified into distinct viral subtypes. Phylogenetic analysis can be used to reconstruct the ancestry of the virus to inform on the origin and distribution of subtypes.</p> <p>We sequenced two 3.6 kb amplicons of HIV-1 genomes from 3,197 participants in a clinical trial with consistent and uniform sampling at sites across 35 countries and analyzed our data with another 2,632 genomes that comprehensively reflects the HIV-1 genetic diversity. We used maximum likelihood phylogenetic analysis coupled with geographical information to infer the state of ancestors.</p> <p>The majority of our sequenced genomes (n=2,501) were either pure subtypes (A-D, F, G) or CRF01_AE. The diversity and distribution of subtypes across geographical regions differed; United States showed the most homogenous subtype population, whereas African samples were most diverse. We delineated transmission of the four most prevalent subtypes in our dataset (A, B, C, and CRF01_AE), and our results suggest both continuous and frequent transmission of HIV-1 over country borders, as well as single transmission events being the seed of endemic population expansions.</p> <p>Overall, we show that coupling of genetic and geographical information of HIV-1 can be used to understand origin and spread of pandemic pathogens.</p> <p> </p>
Data from: Biosystematics of Platanthera bifolia s.l. (Orchidaceae): Inferences from analysis of Scandinavian population samples
<p>Over the years, various authors have (sub)divided the Eurasian moth pollinated Platanthera bifolia into several taxa. Advanced studies using multivariate morphometric analysis and/or genetic fingerprinting have all included regions where the situation appears particularly complex. With the aim to resolve variation patterns in a region where the situation seems less complex, we analysed morphometric and AFLP data from 13 Scandinavian populations using a range of uni- and multivariate statistical methods. Variation was largely continuous, though with (individuals from) short-spurred and long-spurred populations, respectively, forming loose groups. Provided that successful pollinator shifts usually occur between moth species with small difference in proboscis length, this pattern is congruent with the hypothesis that spur length in P. bifolia s.l. has mainly evolved through pollinator shifts followed by selection in response to proboscis length of the prevailing local pollinator species. Acknowledging an important adaptive role of spur length, observing that spur length was among the main contributors to morphological variation, and noting this pattern to be congruent with both AFLP patterns and habitat requirements, we advocate the formal distinction between a short-spurred and a long-spurred taxon. Adopting the operational definitions of species, subspecies and variety provided in Flora Nordica, the two taxa should be recognized as P. bifolia var. bifolia and P. bifolia var. latissima, respectively. A key to the varieties is provided.</p>
Figure 1 in Genetic diversity of Atherina hepsetus (Osteichthyes: Atherinidae) populations as determined by RFLP analysis of three mtDNA regions
Figure 1. Sampling sites: Monastiraki (MON), Panagopoula (PAN), Kiparissi (KIP), Tinos (TIN), Naxos (NAX), Samos (SAM), Nissiros (NIS), Leipsi (LEI), Kos (KOS), Lesvos (MYT) and Evvoia (EVV).
Figure 3 in Genetic diversity of Atherina hepsetus (Osteichthyes: Atherinidae) populations as determined by RFLP analysis of three mtDNA regions
Figure 3. Dollo parsimony (Farris 1977) dendrogram showing the relationships between the 15 mtDNA haplotypes detected. Numbers indicate the bootstrap support (10,000 replicates) of each node of the majority-rule consensus tree.
Oxytenanthera abyssinica (A. Rich.) Munro; lowland bamboo (Poaceae, Bambusinea) in Ethiopia: Genetic diversity, population structure and gene flow analysis
<p><span>As one of the most important non-timber forest resources, a potential alternative to wood and wood product and fastest-growing plant in the world (91 cm (35 in) per day), bamboo is a member of the grass family (Poaceae) and constitutes a single subfamily Bambusoideae. 67% of total area of bamboo in Africa and 7% of world total is contributed by Ethiopia giving more than 1.44 million hectares. Silica gel dried young fresh leaves from 130 individuals of O. abyssinica were collected for DNA extraction and PCR amplification. Each of the PCR amplified ISSR fragments using 19 ISSR primers were used to study band pattern and heterozigosity, level of polymorphism, calculating marker efficiency, Nei`s (H) and Shannon (I) genetic diversity, analysis of molecular variance (AMOVA), analysis for cluster, principal coordinates (PCoA) and admixture results. High genetic variation at species level was observed with the percentage of the polymorphic loci (PPL) = 84.48%. The H, I, observed number of alleles (Na) and effective number of alleles (Ne) at species level was 0.2702, 0.4061, 1.8448, and 1.4744, respectively, showing a relatively high level of genetic diversity. However, the genetic differentiation at the population level was relatively low. AMOVA using grouped populations revealed that, most of the diversity was distributed within the populations (61.05%) with F<sub>ST</sub> = 0.38949, F<sub>SC</sub> = 0.10486 and F<sub>CT</sub> = 0.31797. Cluster analysis grouped the populations into sharply distinct clusters, which could be attributed to cross pollination nature of the plant and long lived to the area. STRUCTURE analyses for all population and excluding Gambella population gives different result K = 2 and K = 11. Using these markers, we find strong evidence linking geographic origin of diversity and samples from Gambella Region found different from others and might tell the availability of additional bamboo species in the country.</span></p>
Data and scripts from: Exploratory analysis of multi-trait coadaptations in the light of population history
<p><span>During the process of range expansion, populations encounter a variety of environments. They respond to the local environments by modifying their mutually interacting traits. Common approaches of landscape analysis include first focusing on the genes that undergo diversifying selection or directional selection in response to environmental variation. To understand the whole history of populations, it is ideal to capture the history of their range expansion with reference to the series of surrounding environments and to infer the multi-trait coadaptation. To this end, we propose a complementary approach; it is an exploratory analysis using up-to-date methods that integrates population genetic features and features of selection on multiple traits. First, we conduct correspondence analysis of site frequency spectra, traits and environments with auxiliary information of population-specific fixation index (FST). This visualizes the structure and the ages of populations and helps infer the history of range expansion, encountered environmental changes and selection on multiple traits. Next, we further investigate the inferred history using an admixture graph that describes the population split and admixture. Finally, principal component analysis of the </span><span>selection on edge-by-trait (SET) matrix identifies multi-trait coadaptation and the associated edges of the admixture graph. We introduce a newly defined factor loadings of environmental variables in order to identify the environmental factors that caused the coadaptation. A numerical simulation of one-dimensional stepping-stone population expansion showed that the exploratory analysis reconstructed the pattern of the environmental selection that was missed by analysis of individual traits. Analysis of a public dataset of natural populations of black cottonwood in northwestern America identified the first principal component (PC) coadaptation of photosynthesis- vs growth-related traits responding to the geographical clines of temperature and daylength. The second PC coadaptation of volume-related traits suggested that soil condition was a limiting factor for above-ground environmental selection.</span></p>
FIG. 1 in Effect of Season on Analysis of Growth in a Population of the Western Lesser Siren, Siren intermedia nettingi, in Northwestern Louisiana
FIG. 1. First season capture SVL (mm) frequency (n ¼ 881) for all individuals of Siren intermedia over the seven years of the study (1992– 1998).
FIG. 2 in Effect of Season on Analysis of Growth in a Population of the Western Lesser Siren, Siren intermedia nettingi, in Northwestern Louisiana
FIG. 2. Graph of interaction among years, seasons, and sex on growth in mass of Siren intermedia as calculated by increase in g per day. See Table 3 for statistics.
FIG. 4 in Effect of Season on Analysis of Growth in a Population of the Western Lesser Siren, Siren intermedia nettingi, in Northwestern Louisiana
FIG. 4. Number of Siren intermedia captured per season and year over the five years of the study that sampled all four seasons.
FIG. 3 in Effect of Season on Analysis of Growth in a Population of the Western Lesser Siren, Siren intermedia nettingi, in Northwestern Louisiana
FIG. 3. Graph of interaction among years, seasons, and sex on growth in SVL of Siren intermedia as calculated by increase in mm per day. See Table 4 for statistics.
Fig. 4 in An analysis of variations in morphological characteristics, essential oil content, and genetic sequencing among and within major Iranian Juniper (Juniperus spp.) populations
Fig. 4. (A) A map of Iran showing the relative geographic location of each habitat, (B) Representative of DNA fragments generated by the UBC807 primer in the nine juniper populations. The left-most (L) column corresponds to the biological ruler (Ladder) and the right-most column () is a negative control., (C) Dendrogram obtained from five ISSR primers using UPGMA method by Dice similarity coefficient for 27 juniper genotypes (D) Principal Component Analysis based on Dice matrix for 27 juniper genotypes.
Fig. 2 in An analysis of variations in morphological characteristics, essential oil content, and genetic sequencing among and within major Iranian Juniper (Juniperus spp.) populations
Fig. 2. (A): Cluster analysis using an average of 40 compounds identified in the 27 individuals from across the Juniperus genus. (B): Cluster analysis dendrogram of juniper populations evaluated based on 13 morphological characters using SPSS 0.16 and Average Linkage method (Within Group). The abbreviations of the labels are given in Table S6.
Fig. 1 in An analysis of variations in morphological characteristics, essential oil content, and genetic sequencing among and within major Iranian Juniper (Juniperus spp.) populations
Fig. 1. Typical representative GC-MS chromatograms of EOs collected from (A1): J. excelsa of Torbat-Heydaryeh (JET1), (A2): J. sabina of Ramsar (JSR) and (A3): J. communis of Tooskestan (JCT), (B1): Analysis of EO percentage among the studied populations (B2,3): Mean comparison of top 10 EO constituents.
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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.