RedpollFilteredStructureTranscriptome

Structure file generated by calling SNPs from the de novo transcriptome presented in Mason and Taylor using the GAT

README.txt

README file that explains the contents of this submission

RedpollOnly_m5M5n5r0.8_20kSNPs

Genepop formatted file that contains information for 20,712 SNPs generated using Stacks with a ddRAD-Seq pipeline. Stacks was run with -m 5, -M 5, -n

RedpollSNAPP_200loci

Output of SNAPP species tree analysis run using 200 loci

redpoll_wOG_1587SNPs

Genepop formatted file for 1587 SNPs for redpolls and two outgroup (Loxia) individuals. SNPs were assembled using the stacks pipeline

rpba_trim_nomiss_35loci

SNAPP input file for species delimitation analyses based on 35 loci with no missing dat

RNASeqShellScripts

This zip file contains shell scripts used in the RNA-Seq portion of this study

Geographic distribution of Acorn Woodpecker (<i>Melanerpes formicivorus</i>).

<p>An expert range map of Acorn Woodpecker from BirdLife International is shown in light blue. Inset shows a male Acorn Woodpecker (photograph by Walt Koenig). Reprinted under a CC BY license, with permission from Walt Koenig, original copyright 2011.</p

Relative contributions of variables in “abiotic only” species distribution model for Acorn Woodpeckers (<i>Melanerpes formicivorus</i>).

<p>This model does not include the presence of the Colombian oak (<i>Quercus humboldtii</i>). Variables with values > 7.5% for either percent contribution to the species distribution model or permutation importance are included.</p><p>Relative contributions of variables in “abiotic only” species distribution model for Acorn Woodpeckers (<i>Melanerpes formicivorus</i>).</p

Performance indices of species distribution models of Acorn Woodpeckers.

<p>The three species distribution models we compared were constructed from abiotic data alone, <i>Quercus</i> occurrence points alone, and abiotic data in combination with <i>Quercus</i> occurrence points. Higher scores indicate increased model performance for AUC of ROC, AUC of Kappa, AUC of Overall Performance and Pearson’s correlation coefficient. Lower scores indicate increased model performance for AUC of Commission Index and AUC of Omission index. For each parameter, the best performing models are highlighted in bold. Thus, species distribution models that include <i>Quercus</i> occurrence points perform consistently better across a variety of performance indices, particularly with respect to the AUC of Commission Index, which is important for evaluating which factors contribute to the southern distribution limits of Acorn Woodpecker.</p><p>Performance indices of species distribution models of Acorn Woodpeckers.</p