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119 results for “ecological genomics”
Data from: Genomic architecture of ecologically divergent body shape in a pair of sympatric crater lake cichlid fishes
Determining the genetic bases of adaptations and their roles in speciation are prominent issues in evolutionary biology. Cichlid fish species flocks are a prime example of recent rapid radiations often associated with adaptive phenotypic divergence from a common ancestor within a short period of time. In several radiations of freshwater fishes divergence in eco-morphological traits including body shape, color, lips and jaws, are thought to underlie their ecological differentiation, specialization and – ultimately – speciation. The Midas cichlid species complex (Amphilophus spp.) of Nicaragua provides one of the few known examples of sympatric speciation where species have rapidly evolved different but parallel morphologies in young crater lakes. This study identified significant QTL for body shape, using SNPs generated via ddRAD sequencing and geometric morphometric analyses of a cross between two ecologically and morphologically divergent, sympatric cichlid species endemic to crater Lake Apoyo: an elongated limnetic species (A. zaliosus) and a high-bodied benthic species (A. astorquii). A total of 453 genome-wide informative SNPs were identified in 240 F2 hybrids. These markers were used to construct a genetic map in which 25 linkage groups were resolved. Seventy-two segregating SNPs were linked to 11 QTL. By annotating the two most highly supported QTL-linked genomic regions, genes that might contribute to divergence in body shape along the benthic-limnetic axis in Midas cichlid sympatric adaptive radiations were identified. These results suggest that few genomic regions of large effect contribute to early-stage divergence in Midas cichlids.
Data from: The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record
Background: The highly derived morphology and astounding diversity of snakes has long inspired debate regarding the ecological and evolutionary origin of both the snake total-group (Pan-Serpentes) and crown snakes (Serpentes). Although speculation abounds on the ecology, behavior, and provenance of the earliest snakes, a rigorous, clade-wide analysis of snake origins has yet to be attempted, in part due to a dearth of adequate paleontological data on early stem snakes. Here, we present the first comprehensive analytical reconstruction of the ancestor of crown snakes and the ancestor of the snake total-group, as inferred using multiple methods of ancestral state reconstruction. We use a combined-data approach that includes new information from the fossil record on extinct crown snakes, new data on the anatomy of the stem snakes Najash rionegrina, Dinilysia patagonica, and Coniophis precedens, and a deeper understanding of the distribution of phenotypic apomorphies among the major clades of fossil and Recent snakes. Additionally, we infer time-calibrated phylogenies using both new 'tip-dating' and traditional node-based approaches, providing new insights on temporal patterns in the early evolutionary history of snakes. Results: Comprehensive ancestral state reconstructions reveal that both the ancestor of crown snakes and the ancestor of total-group snakes were nocturnal, widely foraging, non-constricting stealth hunters. They likely consumed soft-bodied vertebrate and invertebrate prey that was subequal to head size, and occupied terrestrial settings in warm, well-watered, and well-vegetated environments. The snake total-group – approximated by the Coniophis node – is inferred to have originated on land during the middle Early Cretaceous (~128.5 Ma), with the crown-group following about 20 million years later, during the Albian stage. Our inferred divergence dates provide strong evidence for a major radiation of henophidian snake diversity in the wake of the Cretaceous-Paleogene (K-Pg) mass extinction, clarifying the pattern and timing of the extant snake radiation. Although the snake crown-group most likely arose on the supercontinent of Gondwana, our results suggest the possibility that the snake total-group originated on Laurasia. Conclusions: Our study provides new insights into when, where, and how snakes originated, and presents the most complete picture of the early evolution of snakes to date. More broadly, we demonstrate the striking influence of including fossils and phenotypic data in combined analyses aimed at both phylogenetic topology inference and ancestral state reconstruction.
Data from: Genomic data detect corresponding signatures of population size change on an ecological time scale in two salamander species
Understanding the demography of species over recent history (e.g., < 100 years) is critical in studies of ecology and evolution, but records of population history are rarely available. Surveying genetic variation is a potential alternative to census-based estimates of population size, and can yield insight into the demography of a population. However, to assess the performance of genetic methods it is important to compare their estimates of population history to known demography. Here, we leveraged the exceptional resources from a wetland with 37 years of amphibian mark-recapture data to study the utility of genetically-based demographic inference on salamander species with documented population declines (Ambystoma talpoideum) and expansions (A. opacum); patterns that have been shown to be correlated with changes in wetland hydroperiod. We generated ddRAD data from two temporally sampled populations of A. opacum (1993, 2013) and A. talpoideum (1984, 2011) and used coalescent-based demographic inference to compare alternate evolutionary models. For both species, demographic model inference supported population size changes that corroborated mark-recapture data. Parameter estimation in A. talpoideum was robust to our variations in analytical approach, while estimates for A. opacum were highly inconsistent, tempering our confidence in detecting a demographic trend in this species. Overall, our robust results in A. talpoideum suggest that genome-based demographic inference has utility on an ecological scale, but researchers should also be cognizant that these methods may not work in all systems and evolutionary scenarios. Demographic inference may be an important tool for population monitoring and conservation management planning.
Three reference genomes for freshwater diatom ecology and evolution
<p>This repository contains the genome assemblies and gene models provided for "Three reference genomes for freshwater diatom ecology and evolution"</p> <p>Authors:</p> <p>Wade R. Roberts (email: wader [at] uark [dot] edu)</p> <p>Andrew J. Alverson (email: aja [at] uark [dot] edu)</p> <p> </p> <p>The Whole Genome Shotgun (WGS) projects are available from NCBI GenBank under accession JALLPB020000000 (C. tholiformis), JALLBG020000000 (D. pseudostelligera), and JALLAZ020000000 (P. triporus).<strong></strong></p> <p><br>The following files are included:</p> <p>Cyclostephanos tholiformis strain AJA228-03</p> <p> aja228-03.consensus.fasta</p> <p> aja228-03.consensus.gff3<br> <br> aja228-03.consensus.proteins.fasta</p> <p> aja228-03.consensus.combined_uniprot_annotation.csv</p> <p> aja228-03.consensus.panther_annotation.csv</p> <p> aja228-03.consensus.pfam_annotation.csv</p> <p> </p> <p>Discostella pseudostelligera strain AJA232-27</p> <p> aja232-27.consensus.fasta</p> <p> aja232-27.consensus.gff3<br> <br> aja232-27.consensus.proteins.fasta</p> <p> aja232-27.consensus.combined_uniprot_annotation.csv</p> <p> aja232-27.consensus.panther_annotation.csv</p> <p> aja232-27.consensus.pfam_annotation.csv</p> <p> </p> <p>Praestephanos triporus strain AJA276-08</p> <p> aja276-08.consensus.fasta</p> <p> aja276-08.consensus.gff3<br> <br> aja276-08.consensus.proteins.fasta</p> <p> aja276-08.consensus.combined_uniprot_annotation.csv</p> <p> aja276-08.consensus.panther_annotation.csv</p> <p> aja276-08.consensus.pfam_annotation.csv</p> <p> </p> <p>R code and phylogenetic tree to reproduce Figure 1 in the manuscript</p> <p> plot-figure-1.R</p> <p> busc.prot.concat.partition.rooted.tree</p> <p> </p>
Data from: A migratory divide spanning two continents is associated with genomic and ecological divergence
<p>Migratory divides are contact zones between breeding populations with divergent migratory strategies during the non-breeding season. These locations provide an opportunity to evaluate the role of seasonal migration in the maintenance of reproductive isolation, particularly the relationship between population structure and features associated with distinct migratory strategies. We combine light-level geolocators, genomic sequencing, and stable isotopes to investigate the timing of migration and migratory routes of individuals breeding on either side of a migratory divide coinciding with genomic differentiation across a hybrid zone between barn swallow (<i>Hirundo rustica</i>) subspecies in China. Individuals west of the hybrid zone, with <i>H. r. rustica</i> ancestry, had comparatively enriched carbon isotope values and overwintered in eastern Africa, while birds east of the hybrid zone, with <i>H. r. gutturalis </i>ancestry, had depleted isotope values and migrated to southern India. The two subspecies took divergent migratory routes around the high-altitude Karakoram Range and arrived on the breeding grounds over three weeks apart. These results indicate that assortative mating by timing of arrival and/or selection against hybrids with intermediate migratory traits may maintain reproductive isolation between the subspecies, and that inhospitable geographic features may have contributed to the diversification of Asian avifauna by influencing migratory patterns.</p>
Ecological genomics of distinct bleaching tolerances among cryptic coral species
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Data from: Genomic architecture of ecologically divergent body shape in a pair of sympatric crater lake cichlid fishes
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Data from: Shared patterns of genome-wide differentiation are more strongly predicted by geography than by ecology.
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Data from: The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record
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Data from: Ecological constraints associated with genome size across salamander lineages
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Data from: Assessing the utility of whole genome amplified DNA for next-generation molecular ecology
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Data from: The genomic and ecological context of hybridization affects the probability that symmetrical incompatibilities drive hybrid speciation
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Data from: Genomic evidence for ecological divergence against a background of population homogeneity in the marine snail Chlorostoma funebralis
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Data from: Genomic data detect corresponding signatures of population size change on an ecological time scale in two salamander species
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Data from: A migratory divide spanning two continents is associated with genomic and ecological divergence
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Widespread and adaptive alterations in genome-wide gene expression associated with ecological divergence of two Oryza species
GEO Series GSE71044. Oryza rufipogon; Oryza nivara. 42 samples. Type: Expression profiling by high throughput sequencing.
Data from: The role of recombination, niche-specific gene pools and flexible genomes in the ecological speciation of bacteria
Bacteria diversify into genetic clusters analogous to those observed in sexual eukaryotes, but the definition of bacterial species is an ongoing problem. Recent work has focused on adaptation to distinct ecological niches as the main driver of clustering, but there remains debate about the role of recombination in that process. One view is that homologous recombination occurs too rarely for gene flow to constrain divergent selection. Another view is that homologous recombination is frequent enough in many bacterial populations that barriers to gene flow are needed to permit divergence. Niche‐specific gene pools have been proposed as a general mechanism to limit gene flow. We use theoretical models to evaluate additional hypotheses that evolving genetic architecture, specifically the effect sizes of genes and gene gain and loss, can limit gene flow between diverging populations. Our model predicts that (a) in the presence of gene flow and recombination, ecological divergence is concentrated in few loci of large effect and (b) high rates of gene flow plus recombination promote gene loss and favor the evolution of niche‐specific genes. The results show that changing genetic architecture and gene loss can facilitate ecological divergence, even without niche‐specific gene pools. We discuss these results in the context of recent studies of sympatric divergence in microbes.
Genomic Tools for Studying the Ecology of the Human Vaginal Microflora
ClinicalTrials.gov study NCT00576797. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Data from: The role of recombination, niche-specific gene pools and flexible genomes in the ecological speciation of bacteria
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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.