Multilocus phylogeography, population genetics and niche evolution of Australian brown and black-tailed treecreepers (Aves:Climacteris)

Abstract

The Carpentarian barrier across north-eastern 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 modelling of brown and black-tailed treecreepers (Climacteris picumnus and Climacteris 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 revealed a signature of a recent selective sweep in C. picumnus. 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. Palaeoecological niche models show that both range size as measured by available habitat and estimated historical population sizes of both species declined in the past ~600 kyr and that the area of interspecific 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.

Estimating Genome-wide Phylogenies Using Probabilistic Topic Modeling

“…2c show the trees generated by TopicContml for the 9 locations where the birds were collected for unaligned and aligned sequences, respectively. Inspection of the clades reveals that our trees recover the expected geographic relationship within each species (Edwards et al 2023;Cracraft 1986), and the locations are separated by species. Aligned and non-aligned trees are similar, although some locations, such as Sedan, Bourke, and Noonbah, are placed differently in the two trees.…”

“…Relationship tree of 9 populations of two Australian treecreeper species reconstructed. (a) The map of Australia shows the locations; the black disks mark Climacteris melanurus , and the white disks mark Climacteris picumnus (Edwards et al 2023). (b) The best phylogeny constructed by T opic C ontml from unaligned sequences with bootstrap support.…”

“…Real data.-Bird data set: The first data set of nine populations of two bird species, Australian brown treecreepers (Climacteris picumnus) and black-tailed treecreepers (Climacteris melanurus) (Edwards et al 2023). The DNA sequences consist of 14 loci and 9 different geographic locations.…”

“…The data of nine populations of two bird species, Australian brown and black-tailed treecreepers (Climacteris picumnus and melanurus, respectively), were previously published by Edwards et al (2023). The DNA sequences consist of 14 loci and 9 different geographic locations.…”

“…simulated data was used to show the effects of the number of loci and the divergence times within the true genealogy of 40 individuals from 4 species or populations.Real data set.-The data of nine populations of two bird species, Australian brown and black-tailed treecreepers (Climacteris picumnus and melanurus, respectively), were previously published byEdwards et al (2023). The DNA sequences consist of 14 loci and 9 different geographic locations.…”