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8 results for “Coalescence time”
Data and software associated with the paper "Bayesian Inference of Joint Coalescence Times of Sampled Sequences"
<p>1. Data files and run logs produced for the paper "Bayesian Inference of Joint Coalescence Times of Sampled Sequences".</p> <p>2. Software script versions used in the above.</p>
SINGER-inferred targets for exceptional population differentiation in coalescence times in African populations in 1000 Genomes Project
<p>This repo saves the gene targets which shows the signal of population differentiation in coalescence times in African populations in 1000 Genomes Project. </p> <p>Here are the detailed explanations for the header of the files:</p> <p>chrom The chromosome where the genomic window is located (e.g., chr1, chrX).<br>window_start The 0-based start position of the genomic window being analyzed.<br>window_end The 1-based end position of the genomic window (exclusive).<br>score Ratio between the overall diversity and the population specific diversity, in the genomic window.<br>transcript_chrom The chromosome where the transcript is located.<br>transcript_start The 0-based start position of the transcript.<br>transcript_end The 1-based end position of the transcript (exclusive).<br>transcript_id The unique identifier for the transcript (e.g., Ensembl or RefSeq ID).<br>strand The strand of the transcript: "+" for forward, "-" for reverse.<br>coding_start The start position of the coding region of the transcript (if applicable).<br>coding_end The end position of the coding region of the transcript (if applicable).<br>RGB The RGB color used for visualization in genome browsers (format: R,G,B).<br>block_count The number of exons in the transcript.<br>block_sizes Comma-separated list of exon lengths (in base pairs).<br>block_starts Comma-separated list of exon start positions relative to transcript_start.</p>
Supplementary material for: Impact of ghost introgression on coalescent-based species tree inference and estimation of divergence time
<p><span>The species studied in any evolutionary investigation generally constitute a small proportion of all the species currently existing or that have gone extinct. It is therefore likely that introgression, which is widespread across the tree of life, involves "ghosts," i.e., unsampled, unknown, or extinct lineages. However, the impact of ghost introgression on estimations of species trees has rarely been studied and is poorly understood. Here, we use mathematical analysis and simulations to examine the robustness of species tree methods based on the multispecies coalescent model to introgression from a ghost or extant lineage. We found that many results originally obtained for introgression between extant species can easily be extended to ghost introgression, such as the strongly interactive effects of incomplete lineage sorting (ILS) and introgression on the occurrence of anomalous gene trees (AGTs). The relative performance of the summary species tree method (ASTRAL) and the full-likelihood method (*BEAST) varies under different introgression scenarios, with the former being more robust to gene flow between non-sister species whereas the latter performing better under certain conditions of ghost introgression. When an outgroup ghost (defined as a lineage that diverged before the most basal species under investigation) acts as the donor of the introgressed genes, the time of root divergence among the investigated species generally was overestimated, whereas ingroup introgression, as commonly perceived, can only lead to underestimation. In many cases of ingroup introgression that may or may not involve ghost lineages, the stronger the ILS, the higher the accuracy achieved in estimating the time of root divergence, although the topology of the species tree is more prone to be biased by the effect of introgression.</span></p>
Supplementary material for: Impact of ghost introgression on coalescent-based species tree inference and estimation of divergence time
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Data from: Coalescence times, life history traits and conservation concerns: an example from four coastal shark species from the Indo-Pacific
<p><span><span><span><span><span><span><span><span><span><span><span>Dispersal abilities play a crucial role in shaping the extent of population genetic structure, with more mobile species being panmictic over large geographic ranges and less mobile ones organized in meta-populations exchanging migrants to different degrees. In turn, population structure directly influences the coalescence pattern of the sampled lineages, but the consequences on the estimated variation of the effective population size<i> </i>(<i>Ne</i>) over time obtained by means of <i>unstructured</i>demographic models remain poorly understood. However, this knowledge is crucial for biologically interpreting the observed <i>Ne </i>trajectory and further devising conservation strategies in endangered species. Here we investigated the demographic history of four shark species (<i>Carharhinus melanopterus</i>, <i>Carharhinus limbatus</i>, <i>Carharhinus amblyrhynchos</i>, <i>Galeocerdo cuvier</i>) with different degrees of endangered status and life history traits related to dispersal distributed in the Indo-Pacific and sampled off New Caledonia. We compared several evolutionary scenarios representing both <i>structured</i> (meta-population) and<i> unstructured</i> models and then inferred the <i>Ne</i> variation through time. By performing extensive coalescent simulations, we provided a general framework relating the underlying population structure and the observed <i>Ne</i> dynamics. On this basis, we concluded that the recent decline observed in three out of the four considered species when assuming <i>unstructured</i> demographic models can be explained by the presence of population structure. Furthermore, we also demonstrated the limits of the inferences based on the sole site frequency spectrum and warn that statistics based on linkage disequilibrium will be needed to exclude recent demographic events affecting meta-populations.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Coalescence times, life history traits and conservation concerns: an example from four coastal shark species from the Indo-Pacific
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Estimating uncertainty in divergence times among three-spined stickleback clades using the multispecies coalescent
<p>Incomplete lineage sorting (ILS) can lead to biased divergence time estimates. To explore if and how ILS has influenced the results of a recent study of worldwide phylogeny of three-spined sticklebacks (Gasterosteus aculeatus), we estimated divergence times among major clades by applying both a concatenation approach and the multispecies coalescent (MSC) model to single-nucleotide polymorphisms. To further test the influence of different calibration strategies, we applied different calibrations to the root and to younger nodes in addition to the ones used in the original study. Both the updated calibrations and the application of the MSC model influenced divergence time estimates, sometimes significantly. The new divergence time estimates were more ancient than in the previous study for older nodes, whereas the estimates of younger nodes were not strongly affected by the re-analyses. However, given the applied MSC method employs a simple substitution model and cannot account for changes in population size, we suggest that different analytical approaches and calibration strategies should be used in order to explore uncertainty in divergence time estimates. This study provides a valuable reference timeline for the ages of worldwide three-spined stickleback populations and emphasizes the need to embrace, rather than obscure, uncertainties around divergence time estimates.</p>
Estimating uncertainty in divergence times among three-spined stickleback clades using the multispecies coalescent
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