DOI: 10.5061/dryad.57f48
title: Data from: Speciation in Western Scrub-Jays, Haldane’s rule, and genetic clines in secondary contact

description: Background: Haldane’s Rule, the tendency for the heterogametic sex to show
 reduced fertility in hybrid crosses, can obscure the signal of gene flow
 in mtDNA between species where females are heterogametic. Therefore, it is
 important when studying speciation and species limits in
 female-heterogametic species like birds to assess the signature of gene
 flow in the nuclear genome as well. We studied introgression of
 microsatellites and mtDNA across a secondary contact zone between coastal
 and interior lineages of Western Scrub-Jays (Aphelocoma californica) to
 test for a signature of Haldane’s Rule: a narrower cline of introgression
 in mtDNA compared to nuclear markers. Results: Our initial phylogeographic
 analysis revealed that there is only one major area of contact between
 coastal and interior lineages and identified five genetic clusters with
 strong spatial structuring: Pacific Slope, Interior US, Edwards Plateau
 (Texas), Northern Mexico, and Southern Mexico. Consistent with predictions
 from Haldane’s Rule, mtDNA showed a narrower cline than nuclear markers
 across a transect through the hybrid zone. This result is not being driven
 by female-biased dispersal because neutral diffusion analysis, which
 included estimates of sex-specific dispersal rates, also showed less
 diffusion of mtDNA. Lineage-specific plumage traits were associated with
 nuclear genetic profiles for individuals in the hybrid zone, indicating
 that these differences are under genetic control. Conclusions: This study
 adds to a growing list of studies that support predictions of Haldane’s
 Rule using cline analysis of multiple loci of differing inheritance modes,
 although alternate hypotheses like selection on different mtDNA types
 cannot be ruled out. That Haldane’s Rule appears to be operating in this
 system suggests a measure of reproductive isolation between the Pacific
 Slope and interior lineages. Based on a variety of evidence from the
 phenotype, ecology, and genetics, we recommend elevating three lineages to
 species level: A. californica (Pacific Slope); A. woodhouseii (Interior US
 plus Edwards Plateau plus Northern Mexico); A. sumicrasti (Southern
 Mexico). The distinctive Edwards Plateau population in Texas, which was
 monophyletic in mtDNA except for one individual, should be studied in
 greater detail given habitat threat.
description: Locality Info and
 Genetic and Phenotypic Data for Western Scrub-Jay Museum
 SpecimensThis Excel spreadsheet
 lists all 689 Western Scrub-Jay museum specimens used in the study. Museum
 abbreviations: Field Museum of Natural History (FMNH); Moore Laboratory of
 Zoology, Occidental College (MLZ); Museum of Vertebrate Zoology, Berkeley
 (MVZ). Haplotypes of the cytochrome B gene are coastal (C) or interior
 (I). Structure results refer to the raw results making up the different
 panels of Figure 3. The raw microsatellite data are listed in actual
 allele sizes after allele calling. For the phenotypic data: collar, vent,
 and eyestripe are qualitatively-scored categorical data ranging from 1 to
 6. Collar is the amount of blue coming down from the shoulders under the
 necklace with 1 = heavy collar (coastal) and 6 = little collar (interior).
 Vent is the amount of blue tinging to the feathers under the tail coverts,
 with 1 = white feathers (coastal) and 6 = heavily blue-tinged feathers
 (interior). Eyestripe is the boldness of the white stripe above the eye,
 with 1 = bold stripe (coastal) and 6 = small stripe (interior). Other
 phenotypic data are in the form of continuous variables measured in
 millimeters. Blank cells mean there is no data taken for that individual
 at that variable.All_Samples_Dryad.xlsxBayesian phylogeny of Aphelocoma from cytochrome b geneThis is a phylogeny generated in BEAST of the entire genus Aphelocoma (and outgroups) based on cytochrome b sequences from GenBank and those generated for Western Scrub-Jays for this study.Aphelocoma.consensus.tre