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15 results for “microevolution”
Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non-model organisms
<p>Despite the increasing accessibility of high-throughput sequencing, obtaining high-quality genomic data on non-model organisms without proximate well-assembled and annotated genomes remains challenging. Here we describe a workflow that takes advantage of distant genomic resources and ingroup transcriptomes to select and jointly enrich long open reading frames (ORFs) and ultraconserved elements (UCEs) from genomic samples for integrative studies of microevolutionary and macroevolutionary dynamics. This workflow is applied to samples of the African unionid bivalve tribe Coelaturini (Parreysiinae) at basin and continent-wide scales. Our results indicate that ORFs are efficiently captured without prior identification of intron-exon boundaries. The enrichment of UCEs was less successful but nevertheless produced substantial datasets. Exploratory continent-wide phylogenetic analyses with ORF supercontigs (> 515,000 parsimony informative sites) resulted in a fully resolved phylogeny, the backbone of which was also retrieved with UCEs (> 11,000 informative sites). Variant calling on ORFs and UCEs of Coelaturini from the Malawi Basin produced ~2,000 SNPs per population pair. Estimates of nucleotide diversity and population differentiation were similar for ORFs and UCEs. They were low compared to previous estimates in mollusks, but comparable to those in recently diversifying Malawi cichlids and other taxa at an early stage of speciation. Skimming off-target sequence data from the same enriched libraries of Coelaturini from the Malawi Basin, we reconstructed the maternally-inherited mitogenome, which displays the gene order inferred for the most recent common ancestor of Unionidae. Overall, our workflow and results provide exciting perspectives for integrative genomic studies of microevolutionary and macroevolutionary dynamics in non-model organisms.</p>
Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non-model organisms
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Data from: REvoSim: organism-level simulation of macro and microevolution
Macroevolutionary processes dictate the generation and loss of biodiversity. Understanding them is a key challenge when interrogating the earth-life system in deep time. Model-based approaches can reveal important macroevolutionary patterns, and generate hypotheses on the underlying processes. Here we present and document a novel model called REvoSim (Rapid Evolutionary Simulator) coupled with a software implementation of this model. The latter is available here as both source code (C++/Qt, GNU General Public License), and as distributables for a variety of operating systems. REvoSim is an individual-based model with a strong focus on computational efficiency. It can simulate populations of 105–107 digital organisms over geological timescales on a typical desktop computer, and incorporates spatial and temporal environmental variation, recombinant reproduction, mutation and dispersal. Whilst microevolutionary processes drive the model, macroevolutionary phenomena such as speciation and extinction emerge. We present results and analysis of the model focussing on validation, and note a number potential applications. REvoSim can serve as a multipurpose platform for studying both macro- and microevolution, and bridges this divide. It will be continually developed by the authors to expand its capabilities and hence its utility.
Data from: Microevolution in time and space: SNP analysis of historical DNA reveals dynamic signatures of selection in Atlantic cod
Little is known about how quickly natural populations adapt to changes in their environment and how temporal and spatial variation in selection pressures interact to shape patterns of genetic diversity. We here address these issues with a series of genome scans in four overfished populations of Atlantic cod (Gadus morhua) studied over an 80-year period. Screening of >1000 gene-associated single-nucleotide polymorphisms (SNPs) identified 77 loci that showed highly elevated levels of differentiation, likely as an effect of directional selection, in either time, space or both. Exploratory analysis suggested that temporal allele frequency shifts at certain loci may correlate with local temperature variation and with life history changes suggested to be fisheries induced. Interestingly, however, largely nonoverlapping sets of loci were temporal outliers in the different populations and outliers from the 1928 to 1960 period showed almost complete stability during later decades. The contrasting microevolutionary trajectories among populations resulted in sequential shifts in spatial outliers, with no locus maintaining elevated spatial differentiation throughout the study period. Simulations of migration coupled with observations of temporally stable spatial structure at neutral loci suggest that population replacement or gene flow alone could not explain all the observed allele frequency variation. Thus, the genetic changes are likely to at least partly be driven by highly dynamic temporally and spatially varying selection. These findings have important implications for our understanding of local adaptation and evolutionary potential in high gene flow organisms and underscore the need to carefully consider all dimensions of biocomplexity for evolutionarily sustainable management.
Data from: Microevolution of S-allele frequencies in wild cherry populations: respective impacts of negative frequency dependent selection and genetic drift
Negative frequency dependent selection (NFDS) is supposed to be the main force controlling allele evolution at the gametophytic self-incompatibility locus (S-locus) in strictly outcrossing species. Genetic drift also influences S-allele evolution. In perennial sessile organisms, evolution of allelic frequencies over two generations is mainly shaped by individual fecundities and spatial processes. Using wild cherry populations between two successive generations, we tested whether S-alleles evolved following NFDS qualitative and quantitative predictions. We showed that allelic variation was negatively correlated with parental allelic frequency as expected under NFDS. However, NFDS predictions in finite population failed to predict more than half all S-allele quantitative evolution. We developed a spatially-explicit mating model which included the S-locus. We studied the effects of self-incompatibility and local drift within populations due to pollen dispersal in spatially distributed individuals, and variation in male fecundity on male mating success and allelic frequency evolution. Male mating success was negatively related to male allelic frequency as expected under NFDS. Spatial genetic structure combined with self-incompatibility resulted in higher effective pollen dispersal. Limited pollen dispersal in structured distributions of individuals and genotypes, non-random distribution of individuals and unequal pollen production significantly contributed to S-allele frequency evolution by creating local drift effects strong enough to counteract the NFDS effect on some alleles.
Microevolution Hypothesis of the Obesity Epidemic Dataset
<p>Includes all data used in study titled: "The Microevolutionary Hypothesis of the Obesity Epidemic" including National obesity rates, Maternal Death Rates, Maternal Morality, GDP, calorie intake, physical inactivity, antibiotic use</p>
Data from: Selection and microevolution of coat pattern are cryptic in a wild population of sheep
Understanding the maintenance of genetic variation in natural populations is a core aim of evolutionary genetics. Insight can be gained by quantifying selection at the level of the genotype, as opposed to the phenotype. Here, we show that in a natural population of Soay sheep which is polymorphic for coat pattern, recessive genetic variants at the causal gene, agouti signalling protein (ASIP), are associated with reduced lifetime fitness. This was due primarily to a reduction in juvenile survival of uniformly coloured (self-type) sheep, which are homozygous recessive, and occurs despite significantly higher reproductive success in surviving self-type adults. Consistent with their relatively low fitness, we show that the frequency of self-type individuals has declined from 1985 to 2008. Remarkably though, the frequency of the underlying self-allele has increased, because the frequency of heterozygous individuals (who harbour the majority of all self alleles) has increased. Indeed, the ratio of observed:expected heterozygous individuals has increased during the study, such that there is now a significant excess of heterozygotyes. By employing gene-dropping simulations, we show that microevolutionary trends in the frequency and excess of ASIP heterozygotes are too pronounced to be caused by genetic drift. Studying this polymorphism at the level of phenotype rather than underlying genotype would have failed to detect cryptic fitness differences. We would also have been unable to rule out genetic drift as an evolutionary force driving genetic change. This highlights the importance of resolving the underlying genetic basis of phenotypic variation in explaining evolutionary dynamics.
Data from: Microevolution in time and space: SNP analysis of historical DNA reveals dynamic signatures of selection in Atlantic cod
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Data from: REvoSim: organism-level simulation of macro and microevolution
Open the record for dataset details and reuse information.
Data from: Selection and microevolution of coat pattern are cryptic in a wild population of sheep
Open the record for dataset details and reuse information.
Data from: Microevolution of S-allele frequencies in wild cherry populations: respective impacts of negative frequency dependent selection and genetic drift
Open the record for dataset details and reuse information.
Purifying selection acting on the sequence of highly expressed proteins in the microevolution
GEO Series GSE189008. Escherichia coli. 7 samples. Type: Expression profiling by array.
Looking for local adaptation: convergent microevolution in Aleppo pine (Pinus halepensis).
<p>SNP dataset in Aleppo pine (<em>Pinus halepensis</em>) published in <em>Genes</em> <strong>2019</strong>, <em>10</em>(9), 673; https://doi.org/10.3390/genes10090673</p>
Microevolution of Candida albicans in macrophages restores filamentation in a nonfilamentous mutant
GEO Series GSE56174. Candida albicans. 12 samples. Type: Expression profiling by high throughput sequencing.
Microevolution of Cryptococcus neoformans in high CO2 converges on mutations isolated from patients with relapsed cryptococcosis
GEO Series GSE284927. Cryptococcus neoformans. 18 samples. Type: Expression profiling by high throughput sequencing.
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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.