DOI: 10.5061/dryad.34tmpg4j0
title: Data from: Multiple lines of evidence indicate ongoing allopatric and parapatric diversification in an Afromontane sunbird (Cinnyris reichenowi)

description: Africa’s montane ecosystems are noteworthy not only for their isolation,
 but for their morphologically similar bird populations that inhabit
 geographically disparate localities. Many species possess range
 disjunctions in excess of 2,000 km and appear to represent populations
 that have been isolated since at least the last Ice Age, including the
 Northern Double-collared Sunbird (Cinnyris reichenowi). Recent work on
 other Afromontane birds has demonstrated substantial phylogeographic
 structure can exist in phenotypically similar populations, with cryptic
 species occurring parapatrically within the same mountain range. We
 explored genetic, morphological, and ecological diversity within C.
 reichenowi to assess whether cryptic regional diversification occurs
 across the disjunct portions of this species’ range. Within C. reichenowi,
 we find consistent patterns of morphological disparity that coincide with
 genetic diversification between xeric and wet montane populations within
 the Cameroon Line in the Western population, and clear genetic
 differentiation between Western and Eastern populations. Our research
 demonstrates that the geographically isolated populations of Cinnyris
 reichenowi represent different species, and that ecological
 diversification is shaping populations within Central Africa. We show here
 that two named populations should be recognized as members of a western
 species in the Northern Double-collared Sunbird complex: nominate Cinnyris
 preussi preussi in the Cameroon Line montane forests, and C. p.
 genderuensis in the more xeric hinterland of Cameroon and the Central
 African Republic, likely occurring in adjacent Nigeria as well.
description: Please see manuscript for
 full details. Ultra-conserved element (UCE) data were processed using the
 PHYLUCE
 pipeline (link active 11 November 2020) using remote servers
 provided by the Field Museum Grainger Bioinformatics Center and the
 University of Chicago Committee on Evolutionary Biology. We followed the
 methods of Zarza <em>et al</em>. (2016) to harvest single
 nucleotide polymorphisms (SNPs) from this dataset for populations
 analyses. Morphological data were obtained with permission from the
 relevent museum collections. Ecological niche modeling data were obtained
 from eBird (link
 active 11 November 2020) and from specimen localities georeferenced by
 Jacob C. Cooper. Ecological variables were downloaded directly from the
 ENVIREM
 repository (link active 11 November 2020). Genetic sequences are
 available from NCBI
 (link active 11 November 2020). <strong>As such, not all
 distributional data, ecological variables, nor genetic data are included
 in this data upload</strong>. Ecological niche analyses and modeling
 were performed via R 3.4.4 (R Core Team 2020); a full list of supporting
 programs and packages is listed in the manuscript and attached coding
 documents.
description: Not all files are included
 in this upload; unaltered eBird data files, ENVIREM environmental data
 files, and genetic sequences must be downloaded from their respective
 repositories. Almost all analyses and code were written for usage on Linux
 computers using Ubuntu, be they servers or personal computers. Therefore,
 code (specifically R code) must be reformatted for use on Mac or Windows
 computers. The packages, distributions, and specific programs used herein
 may be updated and require further investigation or alteration before
 use.