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424 results for “Ecological genetics”
Loss of ecologically important genetic variation in late generation hybrids reveals links between adaptation and speciation
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Data and supplementary materials from: Large genetic divergence underpins cryptic local adaptation across ecological and evolutionary gradients
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Data from: Functional vertebrate group diversity, tick-borne pathogen ecology and genetic diversity
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Ecological, genetic and geographical divergence explain differences in sunbird (Nectariniidae) colouration
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Considerable genetic diversity and structure despite narrow endemism and limited ecological specialization in the Hayden's ringlet, Coenonympha haydenii
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Genetic and ecological drivers of molt in a migratory bird
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A machine learning approach to integrating genetic and ecological data in tsetse flies (Glossina pallidipes) for spatially explicit vector control planning
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Ecological basis and genetic architecture of crypsis polymorphism in the desert clicker grasshopper (Ligurotettix coquilletti)
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Data from: Ecological speciation in sympatric palms: 3. genetic map reveals genomic islands underlying species divergence in Howea
Although it is now widely accepted that speciation can occur in the face of continuous gene flow, with little or no spatial separation, the mechanisms and genomic architectures that permit such divergence are still debated. Here, we examined speciation in the face of gene flow in the Howea palms of Lord Howe Island, Australia. We built a genetic map using a novel method applicable to long-lived tree species, combining it with double digest restriction-site associated DNA sequencing of multiple individuals. Based upon various metrics, we detected 46 highly differentiated regions throughout the genome, some of which contained genes with functions that are particularly relevant to the speciation scenario for Howea, specifically salt and drought tolerance.
Identification of a genetic network for an ecologically relevant behavioral phenotype in Drosophila melanogaster
<p>Pupation site choice of <i>Drosophila </i>third-instar larvae is critical for the survival of individuals, as pupae are exposed to various biotic and abiotic dangers while immobilized during the 3-4 days of metamorphosis. This singular behavioural choice is sensitive to both environmental and genetic factors. Here we developed a high-throughput phenotyping approach to assay the variation in pupation height in <i>Drosophila melanogaster, </i>while controlling for possibly confounding factors. We find substantial variation of mean pupation height among sampled natural stocks and we show that the <i>Drosophila</i> Genetic Reference Panel (DGRP) captures this variation. Using the DGRP stocks for genome wide association (GWA) mapping, 16 loci involved in determining pupation height could be resolved. The candidate genes in these loci are enriched for high expression in the larval central nervous system. A genetic network could be constructed from the candidate loci, which places <i>scrib</i> at the centre, plus other genes known to be involved in nervous system development, such as <i>Egfr</i> and <i>p53</i>. Using gene disruption lines, we could functionally validate several of the initially identified loci, as well as additional loci predicted from network analysis. Our study shows that the combination of high throughput phenotyping with a genetic analysis of variation captured from the wild can be used to approach the genetic dissection of an environmentally relevant behavioural phenotype.</p>
Data from: Population genetic structures of two ecologically distinct species Betula platyphylla and B. ermanii inferred based on nuclear and chloroplast DNA markers
Climatic oscillations during the last glacial maximum (LGM) significantly affected the distribution patterns and genetic structure of extant plants. Northeast China (NEC) is a major biodiversity center in East Asia, and the influence of historical climate change on NEC populations is critical for understanding species responses to future climate change. However, only a few phylogeographic studies of cool-temperate deciduous tree species have been conducted in the area, and results are inconsistent for species with different niches or distribution areas. We employed multiple chloroplast and nuclear markers to investigate the genetic structure of two ecologically contrasting species, Betula platyphylla and B. ermanii, in NEC. Rare haplotypes were identified in the chloroplast genome of these species, and both exhibited high levels of nucleotide diversity based on a fragment of the nuclear gene G3PDH and microsatellites. Moreover, significant phylogeographic structure was detected for B. platyphylla, suggesting that these populations had recolonized from independent glacial refuges, whereas no genetic structure was found for B. ermanii.
Unique genetic signatures of local adaptation over space and time for diapause, an ecologically relevant complex trait, in Drosophila melanogaster
<p>Organisms living in seasonally variable environments utilize cues such as light and temperature to induce plastic responses, enabling them to exploit favorable seasons and avoid unfavorable ones. Local adapation can result in variation in seasonal responses, but the genetic basis and evolutionary history of this variation remains elusive. Many insects, including <i>Drosophila melanogaster,</i> are able to undergo an arrest of reproductive development (diapause) in response to unfavorable conditions. In <i>D. melanogaster</i>, the ability to diapause is more common in high latitude populations, where flies endure harsher winters, and in the spring, reflecting differential survivorship of overwintering populations. Using a novel hybrid swarm-based genome wide association study, we examined the genetic basis and evolutionary history of ovarian diapause. We exposed outbred females to different temperatures and day lengths, characterized ovarian development for over 2800 flies, and reconstructed their full phased genomes. We found that diapause scored at two different developmental cutoffs has modest heritability, and we identified hundreds of SNPs associated with each of the two phenotypes. Alleles associated with one of the diapause phenotypes tend to be more common at higher latitudes, but these alleles do not show predictable seasonal variation. The collective signal of many small-effect, clinally varying SNPs can plausibly explain latitudinal phenotypic variation seen in North America. SNPs associated with diapause do not exhibit signs of recent selective sweeps, but most are segregating at relatively high frequencies in Africa, suggesting that variation in diapause relies on ancestral polymorphisms. Finally, we utilized outdoor mesocosms to track diapause under natural conditions. We found that hybrid swarms reared outdoors evolved increased propensity for diapause in late fall, whereas indoor control populations experienced no such change. Our results indicate that diapause is a complex, quantitative trait with different evolutionary patterns across time and space.</p>
Data from: Physical and ecological isolation contribute to maintain genetic differentiation between fire salamander subspecies
<p>Landscape features shape patterns of gene flow among populations, ultimately determining where taxa lay along the continuum between panmixia to complete reproductive isolation. Gene flow can be restricted leading to population differentiation in two non-exclusive ways: "physical isolation", in which geographic distance in combination with the landscape features restricts movement of individuals promoting genetic drift, and "ecological isolation", in which adaptive mechanisms constrain gene flow between different environments via divergent natural selection. In central Iberia, two fire salamander subspecies occur in parapatry across elevation gradients along the Iberian Central System mountains, while in adjacent Mountains of Toledo Region only one of them occurs. By integrating population and landscape genetic analyses, we show a ubiquitous role of physical isolation between and within mountain ranges, with unsuitable landscapes increasing differentiation between populations. However, across the Iberian Central System, we found strong support for a significant contribution of ecological isolation, with low genetic differentiation in environmentally homogeneous areas, but high differentiation across sharp transitions in precipitation seasonality. These patterns are consistent with a significant contribution of ecological isolation in restricting gene flow among subspecies. Overall, our results suggest that ecological divergence contributes to reduce genetic admixture, creating an opportunity for lineages to follow distinct evolutionary trajectories.</p>
FIGURE 4 in First record of Branchipodopsis affinis Sars, 1901 (Crustacea: Anostraca) in Iran (Bazargan, West Azerbaijan): Ecology, Morphology and Genetics
FIGURE 4. Female of Branchipodopsis affinis. A, dorsal view of head. B, lateral view of genital segments. C, cercopods. Scale bars: 200μm.
FIGURE 3 in First record of Branchipodopsis affinis Sars, 1901 (Crustacea: Anostraca) in Iran (Bazargan, West Azerbaijan): Ecology, Morphology and Genetics
FIGURE 3. Male of Branchipodopsis affinis. A1, dorsal view of clypeus, arrow indicates small projection on apex of outer lobe of basal process. A2, variability of the basal antennal processes in adults. B, cercopods, arrow indicates spines on ventral surface of last abdominal segment. C, ventral view of gonopods, arrow indicates peg-like projection distally on lateral margin. Scale bars: 200μm.
FIGURE 2 in First record of Branchipodopsis affinis Sars, 1901 (Crustacea: Anostraca) in Iran (Bazargan, West Azerbaijan): Ecology, Morphology and Genetics
FIGURE 2. Proportional abundance (%) of the main zooplankton groups in temporary pools. The size of pools increases from left to right. For the codes see table 1.
FIGURE 5 in First record of Branchipodopsis affinis Sars, 1901 (Crustacea: Anostraca) in Iran (Bazargan, West Azerbaijan): Ecology, Morphology and Genetics
FIGURE 5. Neighbor-Joining tree based on the mitochondrial data set of Branchipodopsis species. Artemia urmiana. is used as outgroup. The numbers at the nodes indicate levels of bootstrap support (%).
Data from: Hybridization between genetically modified Atlantic salmon and wild brown trout reveals novel ecological interactions
Interspecific hybridization is a route for transgenes from genetically modified (GM) animals to invade wild populations, yet the ecological effects and potential risks that may emerge from such hybridization are unknown. Through experimental crosses, we demonstrate transmission of a growth hormone transgene via hybridization between a candidate for commercial aquaculture production, GM Atlantic salmon (Salmo salar), and closely related wild brown trout (S. trutta). Transgenic hybrids were viable and grew more rapidly than transgenic salmon and other non-transgenic crosses in hatchery-like conditions. In stream mesocosms designed to more closely emulate natural conditions, transgenic hybrids appeared to express competitive dominance and suppressed the growth of transgenic and non-transgenic (wild-type) salmon by 82% and 54%, respectively. To the best of our knowledge, this is the first demonstration of environmental impacts of hybridization between a GM animal and a closely related species. These results provide empirical evidence of the first steps towards introgression of foreign transgenes into the genomes of new species and contribute to the growing evidence that transgenic animals have complex and context-specific interactions with wild populations. We suggest that interspecific hybridization be explicitly considered when assessing the environmental consequences should transgenic animals escape to nature.
Data from: Genetic relationships and ecological divergence in Salix species and populations in Taiwan
Linking ecology with evolutionary biology is important to understand how environments drive population and species divergence. Phenotypically diverse Salix species, such as lowland riparian willow trees and middle- to high-elevation multistemmed shrubs and alpine dwarf shrubs, provide opportunities for studying genetic divergence driven by ecological factors. We used amplified fragment length polymorphism (AFLP) to quantify the genetic variation of 185 individuals from nine populations of four Salix species in Taiwan. Our phylogenetic analyses distinguished two riparian species and the separation of riparian species from multistemmed and dwarf shrub species. Variance partitioning for the total data found that environment explained a substantially larger proportion of genetic variation than geography. However, no genetic variation was explained by geography alone when only compared within and between species. Spatially structured regional environmental effects explained more variation than pure environments in most comparisons within and between species, suggesting that unmeasured environmental variables and/or past demographic histories played important roles in shaping population and species divergence. Based on forward selection analysis, annual mean temperature, aspect, and fraction of absorbed photosynthetically active radiation were the most influential ecological factors in shaping genetic variation within and between species. Nevertheless, different combinations of environmental variables correlated significantly with genetic variation within and between species. We identified eight AFLP loci that potentially evolved under selection intraspecifically using different outlier detection methods. These loci correlated with more than one environmental variable, suggesting local adaptation along environmental gradients at the population level.
Data from: Blind to morphology: genetics identifies several widespread ecologically common species and few endemics among Indo-Pacific cauliflower corals (Pocillopora, Scleractinia)
AIM: Using high-resolution genetic markers on samples gathered from across their wide distributional range, we endeavoured to delimit species diversity in reef-building Pocillopora corals. They are common, ecologically important, and widespread throughout the Indo-Pacific, but their phenotypic plasticity in response to environmental conditions and their nearly featureless microskeletal structures confound taxonomic assignments and limit an understanding of their ecology and evolution. LOCATION: Indo-Pacific, Red Sea, Arabian/Persian Gulf. METHODS: Sequence analysis of nuclear ribosomal (internal transcribed spacer 2, ITS2) and mitochondrial (open reading frame) loci were combined with population genetic data (seven microsatellite loci) for Pocillopora samples collected throughout the Indo-Pacific, Red Sea and Arabian Gulf, in order to assess the evolutionary divergence, reproductive isolation, frequency of hybridization and geographical distributions of the genus. RESULTS: Between five and eight genetically distinct lineages were identified that appear comparable to species with minimal or no hybridization. Colony morphology was generally incongruent with genetics across the full range of sampling, and the total number of species is apparently consistent with lower estimates from competing morphologically based hypotheses (c. seven or eight taxa). The most commonly occurring genetic lineages were widely distributed and exhibited high dispersal and gene flow, factors that have probably minimized allopatric speciation. Uniquely among scleractinian genera, this genus contains a monophyletic group of broadcast spawners that evolved recently from an ancestral brooder. MAIN CONCLUSIONS: The delineation of species diversity guided by genetics fundamentally advances our understanding of Pocillopora geographical distributions, ecology and evolution. Because traditional diagnostic features of colony and branch morphology are proving to be of limited utility, the identification of Pocillopora species for future ecological and experimental work should rely on genetic characters that will improve research and aid in conservation strategies for these and other reef-building corals, including the detection of real and mistaken endemic populations.
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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.