Speciational History of Australian Grass Finches (Poephila) Inferred From Thirty Gene Trees*

Abstract

Multilocus genealogical approaches are still uncommon in phylogeography and historical demography, fields which have been dominated by microsatellite markers and mitochondrial DNA, particularly for vertebrates. Using 30 newly developed anonymous nuclear loci, we estimated population divergence times and ancestral population sizes of three closely related species of Australian grass finches (Poephila) distributed across two barriers in northern Australia. We verified that substitution rates were generally constant both among lineages and among loci, and that intralocus recombination was uncommon in our dataset, thereby satisfying two assumptions of our multilocus analysis. The reconstructed gene trees exhibited all three possible tree topologies and displayed considerable variation in coalescent times, yet this information provided the raw data for maximum likelihood and Bayesian estimation of population divergence times and ancestral population sizes. Estimates of these parameters were in close agreement with each other regardless of statistical approach and our Bayesian estimates were robust to prior assumptions. Our results suggest that black-throated finches (Poephila cincta) diverged from long-tailed finches (P. acuticauda and P. hecki) across the Carpentarian Barrier in northeastern Australia around 0.6 million years ago (mya), and that P. acuticauda diverged from P. hecki across the Kimberley Plateau-Arnhem Land Barrier in northwestern Australia approximately 0.3 mya. Bayesian 95% credibility intervals around these estimates strongly support Pleistocene timing for both speciation events, despite the fact that many gene divergences across the Carpentarian region clearly predated the Pleistocene. Estimates of ancestral effective population sizes for the basal ancestor and long-tailed finch ancestor were large (about 521,000 and about 384,000, respectively). Although the errors around the population size parameter estimates are considerable, they are the first for birds taking into account multiple sources of variance.

MTML-msBayes: Approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity

“…Additionally we include an empirical analysis of three Australian avian taxon-pairs that are hypothesized to have arisen simultaneously from three codistributed ancestral species due to the emergence of the Carpentarian barrier in northern Australia [51,52]. Specifically, the three taxon-pairs consist of the red backed fairy wren, Malurus melanocephalus melanocephalus and M. m. cruentatus (37 loci of 58 - 467 base pairs and mean of 27.8 individuals per descendent sister taxon), the black-throated and long-tailed finches, Poephila cincta and P. acuticauda (30 loci of 216 - 650 base pairs and one individual collected per descendent sister taxon) and the brown and black-tailed treecreepers, Climacteris picumnus and C. melanura (15 loci of 201 - 358 base pairs and mean of 9.5 individuals per descendent sister taxon).…”

“…To demonstrate how MTML-msBayes can test for simultaneous divergence given large numbers of loci and post-divergence migration, we used 15-37 loci collected from three bird taxon-pairs all of which consist of sister taxon-pairs that presently span the Carpentarian barrier in northern Australia [51,52]. This includes the brown and black-tailed treecreepers ( Climacteris picumnus and C. melanura ), the black-throated and long-tailed finches ( Poephila cincta and P. acuticauda ) and the eastern and western ssp.…”

Experimental evidence that extra-pair mating drives asymmetrical introgression of a sexual trait

“…The subspecies are genetically differentiated at multiple nuclear and mitochondrial loci across the Carpentarian Barrier, with an estimated divergence time of 270 000 years ago [20]. The Carpentarian Barrier is a prominent arid and sparsely vegetated zoogeographic barrier for many other Australian taxa, and is thought to have been a particularly impermeable barrier during the Pleistocene [21][22][23]. The current continuous distribution of the red-backed fairy-wren across the Carpentarian Barrier probably resulted from secondary contact as the species re-colonized this area after refugial isolation in coastal northern and southeastern Australia [20,21].…”

Phylogeography of the antilopine wallaroo (Macropus antilopinus) across tropical northern Australia

“…2012). Many studies have highlighted the importance of the Carpentarian barrier in shaping species distribution and diversification (Cracraft 1986; Cardinal and Christidis 2000; Jennings and Edwards 2005; Lee and Edwards 2008; Kearns et al. 2011).…”

“…Phylogeographic studies on a range of taxa confirm the importance of the Carpentarian barrier in dividing western and eastern populations across northern Australia (Cardinal and Christidis 2000; Jennings and Edwards 2005; Braby 2008; Lee and Edwards 2008; Toon et al. 2010; Kearns et al.…”