DOI: 10.5061/dryad.z34tmpgp2
title: Data from: The great rift valley is a greater biogeographic barrier than the blue Nile Valley for six Ethiopian highland passerines in the Eastern Afromontane biodiversity hotspot

description: The Ethiopian Highlands are divided by lowland biogeographic barriers,
 including the Blue Nile Valley (BNV) and Great Rift Valley (GRV). We show
 that the GRV is a more pronounced phylogeographic break than the BNV for
 six focal passerines. Previous research suggests that the BNV greatly
 shaped phylogeographic patterns in relatively sedentary montane taxa such
 as frogs and rodents, whereas the GRV shaped phylogeographic patterns in
 volant taxa such as birds. However, no previous research simultaneously
 compares the impact of each valley on phylogeographic patterns in birds,
 and as these barriers vary in geographic extent and topography, the
 relative extent of their effects on gene flow is unclear. Using whole
 genome resequencing, we quantified genetic variation in six montane forest
 passerines in the Ethiopian Highlands and found that their phylogeographic
 patterns varied, with general trends distinct from those of taxa that were
 previously studied across the same barriers. Genetic variation was
 assessed by estimating genome-wide genetic diversity (HO), demographic
 history, phylogeographic structure, and phylogeographic concordance among
 taxa. Population pairs flanking the GRV showed higher FST and more
 distinct population clusters in PCA than those separated by the BNV. HO
 was broadly consistent across populations, excluding noticeable reductions
 in two populations (one population each in two separate species). The
 overall phylogenetic signature and concordance across study taxa supported
 populations separated by the BNV as sister and populations southeast of
 the GRV as most distinct.
description: Blood was sampled from six species for downstream molecular
 analyses: <em>Cossypha</em> <em>semirufa</em>,
 <em>Crithagra </em><em>tristriata</em>,
 <em>Melaenornis</em> <em>chocolatinus</em>,
 <em>Sylvia</em> <em>galinieri</em>,
 <em>Turdus abyssinicus</em>, and
 <em>Zosterops</em> <em>poliogastrus</em>. Of
 these, <em>S. galinieri</em>, <em>C.
 tristriata</em>, <em>M. chocolatinus</em>, and
 <em>Z. poliogastrus </em>are endemic to high elevations in the
 Horn of Africa.<em> C. semirufa </em>and <em>T.
 abyssinicus</em> are found throughout much of the EABH. Permit
 limitations led to n ≤ 3 individuals captured per species per region. All
 sampling took place with permissions from the Ethiopian Wildlife
 Conservation Authority and local landowners. DNA was extracted from blood
 samples using the QIAGEN (Hilden, Germany) DNeasy Blood and Tissue Kit
 following manufacturer protocols. DNA samples were sent to the Oklahoma
 Medical Research Foundation (OMRF) Clinical Genomics Center for Illumina
 shotgun sequencing on either the HiSeq3500 or NovaSeq6000. Samples were
 multiplexed on flow cells with libraries from other projects and sequenced
 with a target of ~10–20× genomic coverage.
description: # The Great Rift Valley is a greater biogeographic barrier than the Blue
 Nile Valley for six Ethiopian Highland passerines in the eastern
 Afromontane biodiversity hotspot
 [https://doi.org/10.5061/dryad.z34tmpgp2](https://doi.org/10.5061/dryad.z34tmpgp2) Illumina shotgun WGS raw reads in FASTQ format for individual bird blood samples.  ## Description of the data and file structure Raw sequencing data were previously uploaded to NCBI and are found at the NCBI links provided in the Sharing/Access information section. Each blood sample has an NCBI SRA number within each BioProject provided in either link (PRJNA948542 and PRJNA605410). Within each SRA, the FASTQ files have a library name that includes the species name and sampling ID of each bird sampled  (e.g. "Zosterops_poliogastrus_EB049"). The sampling IDs correspond to those in the paper.  ## Sharing/Access information Links to NCBI data locations: * [https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA948542](https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA948542) (Choke Mountains FASTQ files from this project)  * [https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA605410](https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA605410) (Previously uploaded Bale and Menagesha FASTQ files from Manthey et al. 2022)  ## Code/Software Code was written in R and Shell. Each code file that corresponds to a particular analysis will have that analysis name at the beginning on the file name.