Data from: Worldwide phylogeny of three-spined sticklebacks ...

• Main Authors: Fang, Bohao, Merilä, Juha, Ribeiro, Filipe, Alexandre, Carlos M., Momigliano, Paolo
• Format: Dataset
• Language: English
• Published: Dryad 2019
• Subjects: Pleistocene to Holocene.; Gasterosteus; Gasterosteus aculeatus; Arctic; Arctic Ocean; Kya; Pacific
• Online Access: https://dx.doi.org/10.5061/dryad.2529hr1; https://datadryad.org/stash/dataset/doi:10.5061/dryad.2529hr1

Stickleback fishes in the family Gasterosteidae have become model organisms in ecology and evolutionary biology. However, even in the case of the most widely studied species in this family – the three-spined stickleback (Gasterosteus aculeatus) – the worldwide phylogenetic relationships and colonization history of the different populations and lineages remain poorly resolved. Using a large collection of samples covering most parts of the species distribution range, we subjected thousands of single nucleotide polymorphisms to coalescent analyses in order to reconstruct a robust worldwide phylogeny of extant G. aculeatus populations, as well their ancestral geographic distributions using Statistical-Dispersal Vicariance and Bayesian Binary MCMC analyses. The results suggest that contemporary populations originated from the Pacific Ocean in the late Pleistocene, and the Atlantic was colonized through the Arctic Ocean by a lineage that diverged from Pacific sticklebacks ca 44.6 Kya. This lineage contains two ... : Worldwide phylogenetic tree of Gasterosteus aculeatusThe time-calibrated worldwide phylogenetic tree of Gasterosteus aculeatus.World_3sp.treeVCF file for all samplesVCF file for all samples. It consists of 126 Gasterosteus aculeatus and 2 individuals of G. nipponicus, a sister species of G. aculeatus.128IDs_full_chrs_ref.vcfAlignments_load_to_BEASTSequence alignments used for phylogenomic analyses. The alignments include 8079 concatenated SNPs.Assembly parameters for ipyrad programAssembly parameters for the ipyrad program in the study.ipyrad_params.txtTime verification tree built from 1000 concatenated RAD lociTime verification tree built from1000 concatenated RAD loci. The tree was built for exclusively calculating divergence times given the tree topology estimated using the SNP data, and solely for the purpose of confirming divergence time estimates generated with the SNP dataset.1000_concat_loci_for_time_verification.tree ...