GENE_TREES_STAR_SP_TREE

RAxML gene trees and STAR species tree (newick format)

Supplementary_Table_1_Dryad_Synapomorphies

Supplementary Table 1. List of 51 unambiguous molecular synapomorphies supporting pleuronectiform monophyly. The list was extracted from PAUP* using the topology obtained under maximum parsimony in TNT. Character number refers to the position in the concatenated alignment

Fossil-based comparative analyses reveal ancient marine ancestry erased by extinction in ray-finned fishes

<p>ABSTRACT</p> <p>The marine-freshwater boundary is a major biodiversity gradient and few groups have colonized both systems successfully. Fishes have transitioned between habitats repeatedly, diversifying in rivers, lakes, and oceans over evolutionary time. However, their history of habitat colonization and diversification is unclear based on available fossil and phylogenetic data. We estimate ancestral habitats and diversification and transition rates using a large-scale phylogeny of extant fish taxa and one containing a massive number of extinct species. Extant-only phylogenetic analyses indicate freshwater ancestry, but inclusion of fossils reveal strong evidence of marine ancestry in lineages now restricted to freshwaters. Diversification and colonization dynamics vary asymmetrically between habitats, as marine lineages colonize and flourish in rivers more frequently than the reverse. Our study highlights the importance of including fossils in comparative analyses, showing that freshwaters have played a role as refuges for ancient fish lineages, a signal erased by extinction in extant-only phylogenies.</p

List_Genes_260C_131S

List of genes in the 260C and 131S set

Stevardiinae trees

Stevardiinae phylogenies reconstructed with the software's: RAxML (concatenated and gene trees), Garli, STAR and TNT. Trees were rooted in Serrasalmus sp. and bootstraps support are shown when available

Datasets from Salichos & Rokas (2013)

The files include individual gene (protein) alignments for the 1070 genes as well as RAxML gene tree

Concatenation and species tree methods exhibit statistically indistinguishable accuracy under a range of simulated conditions

<p>50speciesTrees: Fifty species trees of eight taxa. Trees are in newick format but .nex extension needed for simulation script to work</p> <p>simulation.pl : Perl script to simulate 540 gene trees with corresponding 1000bp sequences for all 50 species trees at both tree depths and with varying number of individuals per species. Requires seqgen and ms in same directory to run</p> <p>mbconcat2.py : Python script to concatenate by three, nine and 27 and run MrBayes. Nexus files for each species tree must be in own directory. Input and output directories need to be provided</p

Stevardiinae concatenated alignment

Concatenated alignment with all sequences generated to reconstruct the phylogeny of Stevardiinae. The gene partitions are: myh6 = 1 - 621; ptr = 622 - 1158; rag1 = 1159 - 2520; rag2 = 2521 - 3291; coi = 3292 - 3813; 16s = 3814 - 4387; 12s = 4388 - 4816. Also, all taxa listed are identified by its name and voucher number

Trees_TD_ND

Trees_TD_N

MrBayes_ND_Commands

MrBayes_ND_Command