rpba_trim_noogmiss_200loci

SNAPP input file for species delimitation analyses based on 200 loc

RedpollFilteredStructureTranscriptome

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

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

RNASeqShellScripts

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

README.txt

README file that explains the contents of this submission

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

Demographic parameter estimates with 90% highest posterior density intervals for divergence of blue-footed and Peruvian boobies.

<p>t  =  years since divergence from common ancestor, N  =  effective population size, 2Nm  =  per generation population migration rate.</p

Evidence for Asymmetrical Divergence-Gene Flow of Nuclear Loci, but Not Mitochondrial Loci, between Seabird Sister Species: Blue-Footed (<i>Sula nebouxii</i>) and Peruvian (<i>S. variegata</i>) Boobies

<div><p>Understanding the process of speciation requires understanding how gene flow influences divergence. Recent analyses indicate that divergence can take place despite gene flow and that the sex chromosomes can exhibit different levels of gene flow than autosomes and mitochondrial DNA. Using an eight marker dataset including autosomal, z-linked, and mitochondrial loci we tested the hypothesis that blue-footed (<i>Sula nebouxii</i>) and Peruvian (<i>S. variegata</i>) boobies diverged from their common ancestor with gene flow, paying specific attention to the differences in gene flow estimates from nuclear and mitochondrial markers. We found no gene flow at mitochondrial markers, but found evidence from the combined autosomal and z-linked dataset that blue-footed and Peruvian boobies experienced asymmetrical gene flow during or after their initial divergence, predominantly from Peruvian boobies into blue-footed boobies. This gene exchange may have occurred either sporadically between periods of allopatry, or regularly throughout the divergence process. Our results add to growing evidence that diverging species can remain distinct but exchange genes.</p></div