This repository contains the research data associated with the article "The late blooming amphipods: global change promoted post-Jurassic ecological radiation despite Palaeozoic origin". It contains a concatenated alignment (COI, H3, 28S and 18S markers) in nexus format, a chronogram obtained with BEAST in nexus format, and a maximum likelihood phylogram obtained with IQTREE in newick format.
Contributors:Wilson Guillory, Jason Brown, Steffen Reichle, Stefan Lötters, Connor French, Andrew Whitworth, Ignacio de La Riva, Ivan Prates, Shirley Jennifer Serrano Rojas, Rudolf von May, Evan Twomey, german chavez
Supplemental data for the manuscript "Phylogenetic relationships and systematics of the Amazonian poison frog genus Ameerega using ultraconserved genomic elements". Contains per-locus alignments, tree files, and instructional code.
Contributors:Rafael Acuna, Tilo Henning, Maximilian Weigend, Federico Luebert
Concatenated alignment used to infer the divergence times and biogeographic history of Loasoideae
and maximum clade credibility trees of Cornales in .tre format for callibration schemes A, B and C.
Refer to the main article: Acuña, Luebert, Henning & Weigend. Major lineages of Loasaceae subfam.
Loasoideae diversified during the Andean uplift. Molecular Phylogenetics and Evolution, for details.
Contributors:White N.D., Braun M.J.
The data associated with the article "Extracting Phylogenetic Signal from Phylogenomic Data:
Higher-Level Relationships of the Nightbirds (Strisores)" published in 2019 in Molecular
Phylogenetics and Evolution by Noor D. White and Michael J. Braun includes the following files:
Matrices_phylip.tar.gz: Concatenated nucleotide matrices used in this study, including character sets detailing individual UCE loci
Tree files are those found in Figure 5 of the manuscript. They include:
Trees_concatenated_ACGT.tar.gz: Results of the concatenated analysis of nucleotide matrices
Trees_concatenated_RY.tar.gz: Results of the concatenated analysis of RY-coded matrices
Trees_gene_tree_sum_ACGT.tar.gz: Results of the gene tree summarization of nucleotide matrices
Trees_gene_tree_sum_RY.tar.gz: Results of the gene tree summarization of RY-coded matrices
Trees_Low_GC_Variance.tar.gz: Results of the concatenated analysis of nucleotide matrices containing only UCE loci with low GC variance (10% highest GC variant loci removed)
Trees_Part_by_Locus.tar.gz: Results of the concatenated analysis of nucleotide matrices partitioned by UCE locus
Contributors:Jun Sato, Gerardo Begué-Quiala, Tessa Bradford, Nobiyuki Yamaguchi, Son Truong Nguyen, steve donnellan, Jorgelino Gámez-Díez, Kyle Armstrong, Satoshi Ohdachi, Lazaro Echenique-Diaz, Masaki Kita