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168 results for “evolutionary genetics”
Data from: Genetic ancestry and population differences in levels of inflammatory cytokines in women: role for evolutionary selection and environmental factors
Background: Selection pressure due to exposure to infectious pathogens endemic to Africa may explain distinct genetic variations in immune response genes. However, the impact of those genetic variations on human immunity remains understudied, especially within the context of modern lifestyles and living environments, which are drastically different from early humans in sub Saharan Africa. There are few data on population differences in constitutional immune environment, where genetic ancestry and environment are likely two primary sources of variation. Methods and Findings: In a study integrating genetic, molecular and epidemiological data, we examined population differences in plasma levels of 14 cytokines involved in innate and adaptive immunity, including those implicated in chronic inflammation, and possible contributing factors to such differences, in 914 AA and 855 EA women. We observed significant differences in 7 cytokines, including higher plasma levels of CCL2, CCL11, IL4 and IL10 in EAs and higher levels of IL1RA and IFNα2 in AAs. Analyses of a wide range of demographic and lifestyle factors showed significant impact, with age, education level, obesity, smoking, and alcohol intake, accounting for some, but not all, observed population differences for the cytokines examined. Levels of two pro-inflammatory chemokines, CCL2 and CCL11, were strongly associated with percent of African ancestry among AAs. The signal was pinpointed through admixture mapping to local ancestry at 1q23, with fine-mapping analysis refined to the Duffy-null allele of rs2814778. In AA women, this variant was a major determinant of systemic levels of CCL2 (p=1.1e-58) and CCL11 (p=2.2e-110), accounting for 19% and 40% of the phenotypic variance, respectively. Conclusion: Our data reveal strong ancestral footprints in inflammatory chemokine regulation. The Duffy-null allele may indicate a loss of the buffering function for chemokine levels. The substantial immune differences by ancestry may have broad implications to health disparities between AA and EA populations.
Data from: Mate competition and evolutionary outcomes in genetically modified Zebrafish (Danio rerio)
Demonstrating relationships between sexual selection mechanisms and trait evolution is central to testing evolutionary theory. Using zebrafish, we found that wild-type males possessed a significant advantage in mate competition over transgenic RFP Glofish™ males. In mating trials, wild-type males were aggressively superior to transgenic males in male-male chases and male-female chases; as a result, wild-type males sired 2.5x as many young as did transgenic males. In contrast, an earlier study demonstrated that female zebrafish preferred transgenic males as mates when mate competition was excluded experimentally. We tested the evolutionary consequence of this conflict between sexual selection mechanisms in a long-term study. The predicted loss of the transgenic phenotype was confirmed. More than 18,500 adults collected from 18 populations across 15 generations revealed that the frequency of the transgenic phenotype declined rapidly and was eliminated entirely in all but one population. Fitness component data for both sexes indicated that only male mating success differed between wild-type and transgenic individuals. Our predictive demographic model based on fitness components closely matched the rate of transgenic phenotype loss observed in the long-term study, thereby supporting its utility for studies assessing evolutionary outcomes of escaped or released genetically modified animals.
Figure 6 from: Patterson BD, Webala PW, Lavery TH, Agwanda BR, Goodman SM, Kerbis Peterhans JC, Demos TC (2020) Evolutionary relationships and population genetics of the Afrotropical leaf-nosed bats (Chiroptera, Hipposideridae). ZooKeys 929: 117-161. https://doi.org/10.3897/zookeys.929.50240
Figure 6 Species tree Hipposideridae based on StarBEAST analysis of four introns. Posterior probabilities appear at all nodes.
Figure 5 from: Patterson BD, Webala PW, Lavery TH, Agwanda BR, Goodman SM, Kerbis Peterhans JC, Demos TC (2020) Evolutionary relationships and population genetics of the Afrotropical leaf-nosed bats (Chiroptera, Hipposideridae). ZooKeys 929: 117-161. https://doi.org/10.3897/zookeys.929.50240
Figure 5 Phylogeny of Hipposideridae based on Bayesian analysis of 103 concatenated nuclear intron sequences. Numbers denote posterior probabilities (BI) and bootstrap percentages (ML); red circles at more terminal nodes indicate BS ≥ 70%, PP ≥ 0.95.
Figure 4 from: Patterson BD, Webala PW, Lavery TH, Agwanda BR, Goodman SM, Kerbis Peterhans JC, Demos TC (2020) Evolutionary relationships and population genetics of the Afrotropical leaf-nosed bats (Chiroptera, Hipposideridae). ZooKeys 929: 117-161. https://doi.org/10.3897/zookeys.929.50240
Figure 4 Substitution network plots for Afrotropical hipposiderids AHipposideros caffer clades 1–4 BHipposideros caffer clades 5–8 CH. ruber clades.
GWAS summary statistics for The genetic architecture and evolutionary consequences of the human pelvic form
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Drivers of genetic differentiation and recent evolutionary history of an Eurasian wild pea
<p class="17"><strong><span>Aim:</span></strong> Genetic diversity is a major determinant for the capacity of species to persist and adapt to their environments. Unraveling the factors affecting genetic differentiation is crucial to understand how genetic diversity is shaped and species may react to changing environments. We investigated the drivers of genetic differentiation and their interplay with the evolutionary history in a wild pea to test how those may have affected the distribution of genetic diversity.</p> <p class="17"><strong><span>Location: </span></strong>Mediterranean basin, western Asia</p> <p class="17"><strong><span>Taxon: </span></strong><em><span>Pisum sativum </span></em>(Fabaceae)</p> <p class="17"><strong><span>Methods:</span></strong> We employed RAD-seqencing to test the influence of environmental factors on genetic differentiation in a collection of 81 wild pea samples. Demographic history and past expansion patterns were analyzed to test their effect on the current distribution of genetic diversity. Association of SNPs with environmental variables were analyses to find signatures of local adaptation.</p> <p class="17"><strong><span>Results:</span></strong> Genetic variation was geographically structured into six distinct genetic clusters. The effect of the tested factors influencing genetic differentiation was variable among genetic clusters. Climate predictors were most important in all clusters. Land use was more important in clusters from areas strongly influenced by human land use, especially by agriculture. We found statistically significant associations of 3,623 SNPs with environmental variables. Most of them were correlated with latitude followed by temperature. Wild peas went through a genetic bottleneck during the last glacial period followed by population recovery. The detected range expansion patterns suggested an eastward range expansion of the European cluster to Turkey and thereof southwards and eastwards.</p> <p class="17"><strong><span>Main conclusion:</span></strong> Our results suggest that it is insufficient to consider the present distribution of genetic diversity alone but rather consider it in conjunction with the evolutionary history of the respective species. Moreover, the distribution of genetic variation has to be viewed in the context of its hierarchical structure and the environment of its genetic entities to understand how this variation was shaped and may change in the future.</p>
Data from: Ultraconserved elements anchor thousands of genetic markers for target enrichment spanning multiple evolutionary timescales
Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with non-model organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota, because UCEs and phylogenetic relationships are well known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2,030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2,386 UCE-anchored loci from nine, non-model avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels.
Genetic diversity and evolutionary patterns of Taraxacum kok-saghyz Rodin
<p><i><span>Taraxacum kok-saghyz</span></i> Rodin (TKS) is an important potential alternative source of natural inulin and rubber production, which has great significance for the production of industrial products. In this study, we sequenced 58 wild TKS individuals collected from four different geography regions worldwide to elucidate the population structure, genetic diversity and the patterns of evolution. Also, the first flowering time, crown diameter, morphological characteristics of leaf and scape of all TKS individuals were measured and evaluated statistically. Phylogenetic analysis based on SNPs and cluster analysis based on agronomic traits showed that all 58 TKS individuals could be roughly divided into three distinct groups: I) Zhaosu county in Xinjiang (population AB, including a few individuals from population C and D); II) Tekes county in Xinjiang (population C); and III) Tuzkol lake in Kazakhstan (population D). Population D exhibited a closer genetic relationship with population C compared to population AB. Genetic diversity analysis further revealed that population expansion from C and D to AB occurred, as well as gene flow between them. Additionally, some natural selection regions were identified in AB population. Function annotation of candidate genes identified in these regions revealed that they mainly participated in biological regulation processes, such as transporter activity, structural molecule activity and molecular function regulator. We speculated that the genes identified in selective sweep regions may contributed to TKS adaptation to the Yili River Valley of Xinjiang. In general, this study provides new insights in clarifying population structure and genetic diversity analysis of TKS using SNP molecular markers and agronomic traits.</p>
Figure 3 from: Matern A, Drees C, Hardtle W, von Oheimb G, Assmann T (2011) Historical ecology meets conservation and evolutionary genetics: a secondary contact zone between Carabus violaceus (Coleoptera, Carabidae) populations inhabiting ancient and recent woodlands in north-western Germany. ZooKeys 100: 545-563. https://doi.org/10.3897/zookeys.100.1546
Figure 3 - Correlogram showing the result of spatial autocorrelation analysis at three allozyme loci. Genetic distances D (Nei 1972) are indicated for the population pairs of the respective distance classes (squares). Dashed lines show the 95% confidence interval (1000 permutations) under the null hypothesis of spatially random differentiation. Significant deviations from the mean are indicated by filled squares (p < 0.05).
Figure 4 from: Matern A, Drees C, Hardtle W, von Oheimb G, Assmann T (2011) Historical ecology meets conservation and evolutionary genetics: a secondary contact zone between Carabus violaceus (Coleoptera, Carabidae) populations inhabiting ancient and recent woodlands in north-western Germany. ZooKeys 100: 545-563. https://doi.org/10.3897/zookeys.100.1546
Figure 4 - Maximum width of the aedeagus tip A and the quotient of maximum and minimum width of the aedeagus tip B are plotted for each population. Boxes display 25–75%- quartiles and bars indicate medians. Whiskers show the total range of values without outliers. Outliers are indicated as circles and extreme outliers as diamonds. Numbers of measured individuals per population are shown in brackets. Pie charts show frequencies of elytral sculpture classes "0" (white), "1" (grey), and "2" (black) in each population. Significant differences between populations are indicated by the lines marked with asterisks.
Figure 1 from: Matern A, Drees C, Hardtle W, von Oheimb G, Assmann T (2011) Historical ecology meets conservation and evolutionary genetics: a secondary contact zone between Carabus violaceus (Coleoptera, Carabidae) populations inhabiting ancient and recent woodlands in north-western Germany. ZooKeys 100: 545-563. https://doi.org/10.3897/zookeys.100.1546
Figure 1 - Carabus violaceus populations studied and proportion of specimens with different elytron sculptures (pie charts). White sections indicate the frequencies of smooth elytra, black sections indicate the frequencies of more than three striae per elytron, and grey sections indicate the frequencies of intermediate phenotypes, i.e. class "1". Numbers next to the pie charts indicate population number followed by sample size in brackets. The location of the study area is indicated as a white square on the map of Germany. Woodlands in the study region northwest of the town of Bramsche according to TK 50 3512 Bramsche (Landesvermessungsamt Niedersachsen 1998) are presented as striped patches. Size and position of ancient woodlands (black patches) are taken from the map by LeCoq (1805). In this study, these are called "Börsteler Wald" (in the north) and "Gehn" (in the south). White patches within woodlands indicate openings. Hedges are not shown.
Figure 2 from: Matern A, Drees C, Hardtle W, von Oheimb G, Assmann T (2011) Historical ecology meets conservation and evolutionary genetics: a secondary contact zone between Carabus violaceus (Coleoptera, Carabidae) populations inhabiting ancient and recent woodlands in north-western Germany. ZooKeys 100: 545-563. https://doi.org/10.3897/zookeys.100.1546
Figure 2 - Aedeagus tip of Carabus violaceus. 1 Maximum aedeagus width (AedMax), 2 minimum aedeagus width (AedMin), and 3 preputial field.
Data from: Genetic and evolutionary correlates of fine-scale recombination rate variation in Drosophila persimilis
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Data from: Rate of evolutionary change in cranial morphology of the marsupial genus Monodelphis is constrained by the availability of additive genetic variation
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Data from: A dedicated target capture approach reveals variable genetic markers across micro- and macro-evolutionary time scales in palms
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Evolutionary rate and genetic load in an emblematic Mediterranean tree following an ancient and prolonged population collapse
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Evolutionary stability, landscape heterogeneity, and human land-usage shape population genetic connectivity in the Cape Floristic Region biodiversity hotspot
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Data from: Ultraconserved elements anchor thousands of genetic markers for target enrichment spanning multiple evolutionary timescales
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Drivers of genetic differentiation and recent evolutionary history of an Eurasian wild pea
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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)
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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.