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data employed for studies on phylogenetics and elevational distributions of birds in the genus Scytalopus
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README.md
Scyt90_forBeast_corrected_March2019.fasta
Scytalopus309_ND2-revised-May2019.phy
Scytalopus_ElevationData_47taxa.csv
Scytalopus_ElevationData_57taxa.csv
alignment_subset_fasta.zip
scytalopus.jpg

README.md

Introduction

This repository contains data employed for studies on phylogenetics and elevational distributions of birds in the genus Scytalopus.

The molecular datasets were used for analyses of phylogeny and diversification in:

Cadena, C. D., A. M. Cuervo, L. N. Céspedes, G. A. Bravo, N. Krabbe, T. S. Schulenberg, 
G. E. Derryberry, L. F. Silveira, E. P. Derryberry, R. T. Brumfield & J. Fjeldså. 2019. 
Systematics, biogeography and diversification of Scytalopus tapaculos (Rhinocryptidae), 
an enigmatic radiation of Neotropical montane birds.
https://www.biorxiv.org/content/10.1101/600775v1

Data on elevational distributions were analyzed in:

Cadena, C. D. & L. N. Céspedes. 2019. Origin of elevational replacements in a clade of nearly 
flightless birds – most diversity in tropical mountains accumulates via secondary contact 
following allopatric speciation. In press in: Rull, V. & Carnaval, A. (eds.), 
Neotropical diversification. Springer, Berlin.
https://www.biorxiv.org/content/10.1101/606558v2

Data

DNA Sequence Data

We constructed phylogenies of most Scytalopus and their near relatives using sequences of a total of 1,246,332 base pairs of nuclear DNA sequences corresponding to regions flanking 1,833 ultra conserved elements (UCEs; 1,201,528 bp) and 80 exons (44,804 bp). The file aligment_subset_fasta-zip contains alignments for each of these regions which we used to construct phylogenies in concatenated and species-tree analyses. Raw data will be made available once a large-scale project on the phylogeny of suboscine birds led by M. Harvey et al. is completed.

We also conducted phylogenetic analyses based on sequences of the mitochondrial ND2 gene for close to 300 specimens. The file Scytalopus309_ND2-revised-May2019.phy contains the ND2 alignment we employed for analyses aimed at reconstructing phylogenetic relationships using maximum-likelihood and Bayesian inference in RAxML and MrBayes, respectively. The file Scyt90_forBeast_corrected_March2019 corresponds to the aligment we employed to construct a BEAST tree for 90 tips, which we used in diversification analyses. Individual ND2 sequences were also submitted to GenBank.

Elevational Distributions

The file Scytalopus_ElevationData_47taxa.csv contains minimum and maximum elevation for the 47-taxa dataset described in the manuscript. The file Scytalopus_ElevationData_57taxa.csv contains minimum and maximum elevation for the 57-taxa dataset, as well as information on the specimens used to construct the phylogeny based on ND2 mitochondrial sequences, and the name with which each taxon is labeled on the tree in Figure 3.


Watercolor by John Fjeldså

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