Data from: Acquisition of germ plasm accelerates vertebrate evolution.

Evans, Teri, University of Nottingham

Wade, Christopher M., University of Nottingham

Chapman, Frank A., University of Florida

Johnson, Andrew D., University of Nottingham

Loose, Matthew, University of Nottingham

Published Apr 09, 2015 on Dryad. https://doi.org/10.5061/dryad.rd70f

Cite this dataset

Evans, Teri et al. (2015). Data from: Acquisition of germ plasm accelerates vertebrate evolution. [Dataset]. Dryad. https://doi.org/10.5061/dryad.rd70f

Abstract

Primordial germ cell (PGC) specification occurs either by induction from pluripotent cells (epigenesis) or by a cell-autonomous mechanism mediated by germ plasm (preformation). Among vertebrates, epigenesis is basal, whereas germ plasm has evolved convergently across lineages and is associated with greater speciation. We compared protein-coding sequences of vertebrate species that employ preformation with their sister taxa that use epigenesis and demonstrate that genes evolve more rapidly in species containing germ plasm. Furthermore, differences in rates of evolution appear to cause phylogenetic incongruence in protein-coding sequence comparisons between vertebrate taxa. Our results support the hypothesis that germ plasm liberates constraints on somatic development and that enhanced evolvability drives the evolution of germ plasm.

Usage notes

Scripts for Analyses

This file contains the instructions for generating the appropriate mySQL databases and the scripts required to process this data and recreate the analyses described in Evans et al.

Scripts.tar.gz

Alignment Files

This file contains the folder system storing the alignments (*.nex) and Maximum-Likelihood tree files (*_tree.tre) for the sequences presented in Evans et al. Each file is named according to the seq_number information as in the database basic_db.sql (also contained within this DataDryad submission). Each alignment contains only the sequence from the first two codon positions as reported in Evans et. al.

Alignment_files.tar.gz

mySQL Database including data

This file contains a mySQL database including all the data used in Evans et al. It is in the same format as the database which can be created using the files available in the Scripts package associated with this datadryad package.

basic_db.sql