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Data from: Multiple lines of evidence indicate ongoing allopatric and parapatric diversification in an Afromontane sunbird (Cinnyris reichenowi)

Citation

Cooper, Jacob C.; Maddox, J. Dylan; McKague, Kellie; Bates, John M. (2021), Data from: Multiple lines of evidence indicate ongoing allopatric and parapatric diversification in an Afromontane sunbird (Cinnyris reichenowi), Dryad, Dataset, https://doi.org/10.5061/dryad.34tmpg4j0

Abstract

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.

Methods

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 et al. (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). As such, not all distributional data, ecological variables, nor genetic data are included in this data upload. 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.

Usage Notes

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.

Funding

University of Chicago Hinds Fund

University of Chicago Committee on Evolutionary Biology

Field Museum H. B. Conover Fund

Pritzker Laboratory for Molecular Systematics and Evolution

University of Chicago Hinds Fund

University of Chicago Committee on Evolutionary Biology

Field Museum H. B. Conover Fund

Pritzker Laboratory for Molecular Systematics and Evolution