Molecular Phylogenetics and Evolution

Dataset used to reconstruct the phylogenetic relationships among Aciculata (Annelida). The datasets comprise transcriptomic matrices, species trees (ASTRAL and concatenated supermatrix) and gene trees used for data exploration.

RAD datamatrix

13+2BIalignment.nex: sequence alignment of 13 PCGs + 2 rRNAs NT dataset for BI reconstruction including mrbayes model. 13+2BI.result: BI result tree of 13 PCGs + 2 rRNAs NT dataset. 13+2NT.phy: sequence alignment (Phylip format) of 13 PCGs + 2 rRNAs dataset for ML reconstruction. 13+2RAxML_bipartitions.result: ML result tree of 13 PCGs + 2 rRNAs NT dataset. 13AA.phy: sequence alignment of 13 PCGs AA dataset. 13AABI.tre: result BI tree based on 13 PCGs AA dataset. 13AARAxML_bipartitions.result: result ML tree based on 13 PCGs AA dataset. 13NT.phy: sequence alignment of 13 PCGs NT dataset. 13NTBI3.tre: result BI tree based on 13 PCGs NT dataset. 13NTRAxML_bipartitions.result: result ML tree based on 13 PCGs NT dataset. BMPmatric.nex: data matric for BMP analysis. BMPtree.tre: result tree of BMP analysis. EMPmatric.nex: data matric for EMP analysis. EMPtree.tre: result tree of EMP analysis. LeuAlignment.nex: sequence alignment for trnLs phylogenetic. LeuTree.tre: result tree of trnLs phylogenetic. NCR.phy: sequence alignment for mNCRs phylogenetic. NCRml.tre: result tree of mNCRs phylogenetic. trexinput1~8.txt: input files for TreeREx analyses. trex1~8.dot, trex1~8.out, trex1~8.pdf: output files of TreeREx analyses.

The vcf file of the SNP calls and the abc scripts for EST-SSR data used in this study

Gene sequences for the studied four sister bird pairs in the present study.

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.

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.

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

Research data: 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.

Data matrix composed of 16 taxa and 639 UCE loci (138,146 bp) which I based on when inferring phylogenies.