Janiak et al. 2022 Molecular Ecology - mtDNA of Amazonian primates

Files and data associated with the following publication: 

Janiak et al. (2022). 205 newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates. Molecular Ecology.

We assembled new mitochondrial genomes (with https://github.com/RemiAllio/MitoFinder) for platyrrhine primates, most from the Amazon and with known sampling locations and used the data to assess support for the long-standing Riverine Barrier Hypothesis (RBH), which proposes that river formation was a major driver of speciation in Amazonian primates. 

Mitochondrial genomes are available on GenBank (accession numbers OM328861-OM329065), underlying Illumina short reads are available at ENA project ID PRJEB49549, and scripts to run analyses are available on GitHub (https://github.com/MareikeJaniak/Platyrrhine-mtDNA) and archived at 10.6084/m9.figshare.19610187.

Files included:

mitoFinder_results_final_length_cov_MolEcol.txt - lengths and coverages of all final mitochondrial contigs assembled with MitoFinder

mitoFinder_results_multiple_contigs_all.txt - lengths and coverage of all contigs for samples for which multiple mitochondrial contigs were assembled by MitoFinder

mtDNA_plat.untrimmed.aln.fasta - full alignment of mitochondrial genomes newly assembled by us, published platyrrhine mitogenomes, and six non-platyrrhine outgroups

mtDNA_plat.July2021.trimmed.noND6.aln.nex - trimmed alignment of mitochondrial genomes newly assembled by us, published platyrrhine mitogenomes, and six non-platyrrhine outgroups with partitions, used as input to BEAUti to generate xml file for BEAST2 analysis

mtDNA_plat_bModelTest_relaxedClock.xml - input file for BEAST2 analysis generated with BEAUti

mtDNA_plat.trimmed.noND6.noProsim.aln.fasta - trimmed alignment used to build ML tree with RAxML and used as input for mPTP lineage delimitation

partitions.txt - used as input for RAxML

mtDNA_plat.trimmed.noND6.noProsim.tree - ML tree generated with RAxML, uesd as input for mPTP lineage delimitation

mtDNA.chain1chain2.combo.posterior.trees.tree - posterior trees from BEAST2 analysis, used to retrieve node age estimate distributions and to generate MCC tree

mtDNA.chain1chain2.combo.MCC.tree - maximum clade credibility tree from BEAST2 analysis, generated with TreeAnnotator

SupplementalData_metadata_mtDNA_full.xlsx - Complete metadata for all samples, including sequencing, sample, and voucher specimen IDs where available; GenBank accession numbers; geographic coordinates of sample locations