castanotum_EBSP

EBSP xml infile for Cinclosoma castanotum run in Beast v1.7.5. EBSP run uses mtDNA rate and one nuclear loci. This was chosen based on locus closest to average of all loci. All loci (except one) are within the bounds of the Ellegren (2013) Annual Review of Ecology and Systematics. The one outside is only a tiny fraction lower

Cinclosoma _Codominant

Geneland Infile: Diploid genotype file for has 22 columns (11 nulear loci), sequencing data converted to allelic data, missing data= NA, comma delimited

Cinclosoma Coordinates

Geneland Infile: Coordinates file has 2 columns for spatial coordinates (long, lat), with no missing data, comma delimite

clarum_noST_SB_EBSP

EBSP xml infile for Cinclosoma clarum (putative Cinclosoma clarum fordianum removed) run in Beast v1.7.5. EBSP run uses mtDNA rate and one nuclear loci. This was chosen based on locus closest to average of all loci. All loci (except one) are within the bounds of the Ellegren (2013) Annual Review of Ecology and Systematics. The one outside is only a tiny fraction lower

Cinclosoma_noST_SB_in

IMa2 infile with putative C. clarum fordianum removed: 2 populations (Cinclosoma castanotum and Cinclosoma clarum), 11 nuclear and 1 mtDNA locus

Summary of the thirteen loci included in the present study.

a<p>Locus information and chromosome number was inferred from the genome map of the chicken genome on GenBank.</p

Phylogenetic estimates of gene trees obtained via Bayesian and Maximum Likelihood analysis of individual loci.

<p>Locus acronyms follow <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031840#pone-0031840-t002" target="_blank">Table 2</a> and references therein. Nodal support is indicated by circles, where the upper half corresponds to Bayesian posterior probabilities (BPP) and the lower half depicts ML bootstrap values (MLBV). BPP support values greater than 95% are given in bold above branches, and indicated by dark upper half-circles. MLBV greater than 80 are in bold below branches, and indicated by dark lower half-circles. Support values below these thresholds are in regular font and depicted with an open circle half. Values below 50% BPP and 50 MLBV are denoted by double dashes or not at all where both algorithms failed to recover that value at a node. The mitochondrial protein coding genes ND2 and ND3 have been combined in a single partition, indicated as “mtDNA”. Mangrove specialists are highlighted in bold.</p

Phylogenetic hypothesis of relationships within the broader family Acanthizidae.

<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031840#s3" target="_blank">Results</a> are based on a three gene dataset (RAG1, RAG2, ND2) with extended taxon sampling derived from the study of Gardner et al. (2010). Nodal support in form of Bayesian posterior probabilities (BPP, above) and Maximum Likelihood bootstrap values (MLBV, below) are given at each node. Bold values are attributed to BPP >95% and MLBV >80, while regular font is used for values below this threshold. A double dash indicates support values below 50% BPP and 50 MLBV. Also illustrated are 95% confidence intervals around node heights as derived from the ultrametric tree generated in the program BEAST and calibrated using a normally distributed prior on ND2 mutation rates. The lower scale represents time in million years before present, and vertical dashed lines correspond to the onset of the Pliocene and Pleistocene epochs. Mangrove specialists are highlighted in bold. Placement of <i>Gerygone cinera</i> within <i>Acanthiza</i> is emphasized by a black bar.</p

Taxon sampling, voucher information, and locality information of <i>Gerygone</i> species included in the present study.

<p>Institutional abbreviations for voucher sources are as follows: American Museum of Natural History (AMNH), Australian National Wildlife Collection (ANWC), The University of Kansas Biodiversity Institute (KUBI), Massey University New Zealand (MUNZ), Western Australian Museum (WAM).</p

Map Making Scripts

This zip file contains within it three R scripts which are used to make the ASCII-formatted Raster files used in our manuscript. For the purposes of our research, these are used to describe IUCN status, within-species sampling, GenBank sampling, and species richness of parrot species per spatial grid cell