An official website of the United States government
Abstract Wholeâgenome sequencing data allow survey of variation from across the genome, reducing the constraint of balancing genome subâsampling with estimating recombination rates and linkage between sampled markers and target loci. As sequencing costs decrease, lowâcoverage wholeâgenome sequencing of pooled or indexedâindividual samples is commonly utilized to identify loci associated with phenotypes or environmental axes in nonâmodel organisms. There are, however, relatively few publicly available bioinformatic pipelines designed explicitly to analyse these types of data, and fewer still that process the raw sequencing data, provide useful metrics of quality control and then execute analyses. Here, we present an updated version of a bioinformatics pipeline calledPoolParty2that can effectively handle either pooled or indexed DNA samples and includes new features to improve computational efficiency. Using simulated data, we demonstrate the ability of our pipeline to recover segregating variants, estimate their allele frequencies accurately, and identify genomic regions harbouring loci under selection. Based on the simulated data set, we benchmark the efficacy of our pipeline with another bioinformatic suite,angsd, and illustrate the compatibility and complementarity of these suites usingangsdto generate genotype likelihoods as input for identifying linkage outlier regions using alignment files and variants provided byPoolParty2. Finally, we apply our updated pipeline to an empirical dataset of lowâcoverage whole genomic data from population samples of Columbia River steelhead trout (Oncorhynchus mykiss), results from which demonstrate the genomic impacts of decades of artificial selection in a prominent hatchery stock. Thus, we not only demonstrate the utility ofPoolParty2for genomic studies that combine sequencing data from multiple individuals, but also illustrate how it compliments other bioinformatics resources such asangsd.
more »
« less
Estimating Genome-Wide Phylogenies Using Probabilistic Topic Modeling
Abstract Methods for rapidly inferring the evolutionary history of species or populations with genome-wide data are progressing, but computational constraints still limit our abilities in this area. We developed an alignment-free method to infer genome-wide phylogenies and implemented it in the Python package TopicContml. The method uses probabilistic topic modeling (specifically, Latent Dirichlet Allocation) to extract topic frequencies from k-mers, which are derived from multilocus DNA sequences. These extracted frequencies then serve as an input for the program Contml in the PHYLIP package, which is used to generate a species tree. We evaluated the performance of TopicContml on simulated datasets with gaps and three biological datasets: 1) 14 DNA sequence loci from two Australian bird species distributed across nine populations, 2) 5162 loci from 80 mammal species, and 3) raw, unaligned, nonorthologous PacBio sequences from 12 bird species. We also assessed the uncertainty of the estimated relationships among clades using a bootstrap procedure. Our empirical results and simulated data suggest that our method is efficient and statistically robust.
more »
« less
- Award ID(s):
- 2109989
- PAR ID:
- 10632663
- Editor(s):
- Hahn, Matthew
- Publisher / Repository:
- Oxford Journals
- Date Published:
- Journal Name:
- Systematic Biology
- ISSN:
- 1063-5157
- Subject(s) / Keyword(s):
- Alignmentâfree bootstrap CONTML đâmers LDA multilocus phylogeny NLP topic modelling
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
We developed a novel method for efficiently estimating time-varying selection coefficients from genome-wide ancient DNA data. In simulations, our method accurately recovers selective trajectories and is robust to misspecification of population size. We applied it to a large data set of ancient and present-day human genomes from Britain and identified seven loci with genome-wide significant evidence of selection in the past 4500 yr. Almost all of them can be related to increased vitamin D or calcium levels, suggesting strong selective pressure on these or related phenotypes. However, the strength of selection on individual loci varied substantially over time, suggesting that cultural or environmental factors moderated the genetic response. Of 28 complex anthropometric and metabolic traits, skin pigmentation was the only one with significant evidence of polygenic selection, further underscoring the importance of phenotypes related to vitamin D. Our approach illustrates the power of ancient DNA to characterize selection in human populations and illuminates the recent evolutionary history of Britain.more » « less
-
Ruane, Sara (Ed.)Abstract Comparisons of intraspecific genetic diversity across species can reveal the roles of geography, ecology, and life history in shaping biodiversity. The wide availability of mitochondrial DNA (mtDNA) sequences in open-access databases makes this marker practical for conducting analyses across several species in a common framework, but patterns may not be representative of overall species diversity. Here, we gather new and existing mtDNA sequences and genome-wide nuclear data (genotyping-by-sequencing; GBS) for 30 North American squamate species sampled in the Southeastern and Southwestern United States. We estimated mtDNA nucleotide diversity for 2 mtDNA genes, COI (22 species alignments; average 16 sequences) and cytb (22 species; average 58 sequences), as well as nuclear heterozygosity and nucleotide diversity from GBS data for 118 individuals (30 species; 4 individuals and 6,820 to 44,309 loci per species). We showed that nuclear genomic diversity estimates were highly consistent across individuals for some species, while other species showed large differences depending on the locality sampled. Range size was positively correlated with both cytb diversity (phylogenetically independent contrasts: R2 = 0.31, P = 0.007) and GBS diversity (R2 = 0.21; P = 0.006), while other predictors differed across the top models for each dataset. Mitochondrial and nuclear diversity estimates were not correlated within species, although sampling differences in the data available made these datasets difficult to compare. Further study of mtDNA and nuclear diversity sampled across speciesâ ranges is needed to evaluate the roles of geography and life history in structuring diversity across a variety of taxonomic groups.more » « less
-
Abstract The ant genus Tapinoma Foerster, 1850 is a moderately diverse group (81 valid species) that occurs worldwide. It includes the tramp species T. melanocephalum, whose evolutionary history, biogeographic origin, and population limits remain unclear. Here, we present a time-calibrated phylogeny and a biogeographic history inference of the genus based on thousands of Ultraconserved Element (UCE) loci. Focusing on T. melanocephalum, we used single nucleotide polymorphisms from UCE loci and COI sequences to analyze species boundaries based on nuclear and mitochondrial DNA. We recovered a monophyletic Tapinoma with an estimated crown age corresponding to middle Eocene (49.4 to 34.4 Ma). Phylogenomic data differentiated T. melanocephalum from T. jandai, a recently established species based on morphology, and revealed that the 2 species diverged âŒ12 Ma. Population genetic analyses identified considerable molecular divergence among sampled T. melanocephalum populations, and a heterogeneous genetic structure, showing a weak relationship between genetic differentiation and geographic distance. A phylogeographic comparison of habitat preferences of T. melanocephalum revealed an ecological shift from undisturbed to urban environments, a phenomenon which may have facilitated its ubiquitous and global distribution. Our study presents the first phylogenomic framework for this globally distributed ant genus and molecularly delineates a worldwide pest ant species.more » « less
-
Macdonald, S (Ed.)Abstract Quantitative genetics in Caenorhabditis elegans seeks to identify naturally segregating genetic variants that underlie complex traits. Genome-wide association studies scan the genome for individual genetic variants that are significantly correlated with phenotypic variation in a population, or quantitative trait loci. Genome-wide association studies are a popular choice for quantitative genetic analyses because the quantitative trait loci that are discovered segregate in natural populations. Despite numerous successful mapping experiments, the empirical performance of genome-wide association study has not, to date, been formally evaluated in C. elegans. We developed an open-source genome-wide association study pipeline called NemaScan and used a simulation-based approach to provide benchmarks of mapping performance in collections of wild C. elegans strains. Simulated trait heritability and complexity determined the spectrum of quantitative trait loci detected by genome-wide association studies. Power to detect smaller-effect quantitative trait loci increased with the number of strains sampled from the C. elegans Natural Diversity Resource. Population structure was a major driver of variation in mapping performance, with populations shaped by recent selection exhibiting significantly lower false discovery rates than populations composed of more divergent strains. We also recapitulated previous genome-wide association studies of experimentally validated quantitative trait variants. Our simulation-based evaluation of performance provides the community with critical context to pursue quantitative genetic studies using the C. elegans Natural Diversity Resource to elucidate the genetic basis of complex traits in C. elegans natural populations.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript
- Journal Article:
- https://doi.org/10.1093/sysbio/syaf015
