Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations
Cite this dataset
Bourgeois, Yann; Ruggiero, Robert; Hariyani, Imtiyaz; Boissinot, Stephane (2020). Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations [Dataset]. Dryad. https://doi.org/10.5061/dryad.wpzgmsbjw
TEs were called using MELT (https://melt.igs.umaryland.edu/), using the consensus sequences found in the file TE_consensus_for_MELT.fasta. Information about TE counts, lengths, and densities were extracted from the VCF files using VCFTools and BEDTOOLs. A file with the average effective recombination rate divided by nucleotide diversity in 1Mb windows is also provided. Because the effective recombination rate depends on the effective population size, it is directly correlated to local reduction of diversity due to linked selection. Thus, a low value may be due to either low diversity due to linked selection or to reduced recombination (r). Since nucleotide diversity is an estimator of 4Nm,with m the mutation rate and N the local effective population size, this statistic can be seen as the ratio between r and the mutation rate m.
VCF files contain TE genotypes without missing data for the 29 individuals included in the study. The file Correspondance_individuals_VCF_clades.txt details to which genetic cluster/species each individual belongs.