DOI: 10.5061/dryad.bcc2fqzgt
title: Multilocus phylogeography, population genetics and niche evolution of Australian Brown and Black-tailed Treecreepers (Aves: Climacteris)

description: The Carpentarian barrier across northeastern Australia is a major
 biogeographic barrier and a generator of biodiversity within the
 Australian Monsoonal Tropics. Here we present a continent-wide analysis of
 mitochondrial (control region) and autosomal (14 anonymous loci) sequence
 and indel variation and niche modeling of Brown and Black-tailed
 Treecreepers (Climacteris
 picumnus and C. melanurus), a clade with a
 classic distribution on either side of the Carpentarian barrier. mtDNA
 control region sequences exhibited reciprocal monophyly and strong
 differentiation (Fst = 0.91), and reveals a signature of a recent
 selective sweep in C. picumnus. No loci among 14
 anonymous autosomal markers exhibited reciprocal monophyly between
 species, and a variety of tests support an isolation-with-migration model
 of divergence, albeit with low levels of gene flow across the Carpentarian
 barrier and a divergence time between species of ~1.7 – 2.8 MYA, depending
 on the model and assumptions about generation time. Paleo-ecological niche
 models show that both range size as measured by available habitat and
 estimated historical population sizes of both species declined in the last
 ~600 kyr and that the area of range overlap was never historically large,
 perhaps decreasing opportunities for extensive gene flow. The relatively
 long divergence time and low opportunity for gene flow may have
 facilitated speciation more so than in other co-distributed bird taxa
 across the Australian Monsoonal Tropics.
description: Avian tissue was collected in Australia under appropriate
 permits. Total genomic DNA was extracted from heart, liver or muscle
 tissue using phenol chloroform methods. To generate nuclear loci, we
 constructed a plasmid library from total genomic DNA from a single
 female <em>C. picumnus</em>, shearing, repairing and
 size-selecting the DNA into 2-3 kb fragments using methods. We used PCR to
 amplify a 363 base-pair segment of region 1 of the mitochondrial control
 region (CR1) and amplification conditions for each anonymous locus was
 optimized by thermal gradient PCR and annealing temperatures for PCR
 varied from 50 – 55ºC.  Sequences were trimmed, aligned and edited, and
 putatively heterozygous sites identified, using Aliview. Unphased diploid
 DNA sequences for each locus were phased using Phase 2.0. Phased
 haplotypes were converted into Nexus and Phylip formats for subsequent
 analyses.  Standard population genetic statistics, such as genetic
 diversity within and between populations and species , Tajima’s D
 and <em>F</em><sub>st</sub> among populations
 based on pairwise differences of haplotypes, were calculated using the R
 package PopGenome v. 2.7.5. Gene trees were constructed using the maximum
 likelihood algorithm in IQ-TREE v. 1.6.12, using best substitution models
 for each locus as estimated in ModelFinder. Net nucleotide diversity
 between populations and species was calculated using PopGenome . Indels
 were scored as biallelic or multiallelic
 and <em>F</em><sub>st</sub> for each indel was
 calculated using the hierarchical method implemented in
 hier<em>F</em><sub>st</sub>at. We analyzed the
 data via principal components analysis (PCA) in smartpca v. 8000. We used
 STRUCTURE v. 2.3.2.1 to understand the basic population units within and
 between species. We used Phrapl to test hypotheses of major classes of
 phylogeographic models. We used bpp v. 4.3 to estimate the population
 phylogeny and divergence times. We used migrate-n (version 5.0, Beerli
 & Felsenstein, 1999; Beerli, 2006) to conduct additional
 phylogeographic model selection (divergence with gene flow) using the full
 data set as well as equilibrium models of gene flow within <em>C.
 picumnus</em> and <em>C.</em> <em>melanurus</em> separately. The between-species analyses using migrate-n utilized the full sequence data from <em>C. picumnus</em> and <em>C. melanurus</em>, treating each species as a panmictic population.  For each species, we used ENMeval to test the best model parameters for species distribution models and downstream analysis with Maxent v. 3.4.1. We used Stairway plots to estimate variation in effective population size through time for <em>C. picumnus </em>and<em> C. melanurus.</em>
description: Phrapl (R package)   
 https://github.com/bomeara/phrapl<br>PopGenome (R package)   
 https://github.com/pievos101/PopGenome<br>Structure   
 https://web.stanford.edu/group/pritchardlab/structure.html<br>Stairwayplot2    https://github.com/xiaoming-liu/stairway-plot-v2<br>Aliview    https://github.com/AliView/AliView<br>Bayesian Phylogeography and Phylogenetics (bpp)    https://github.com/bpp/bpp<br>hierfstat (R package)    https://github.com/jgx65/hierfstat<br>IQ-TREE    http://www.iqtree.org/<br>migrate-n    https://peterbeerli.com/migrate-html5/<br>ms    https://uchicago.app.box.com/s/l3e5uf13tikfjm7e1il1eujitlsjdx13<br>smpartpca    https://github.com/chrchang/eigensoft/blob/master/POPGEN/README Maxent  https://github.com/mrmaxent/Maxent