Tuesday, July 3, 2018

[Herpetology • 2018] Speciation in the Mountains and Dispersal by Rivers: Molecular Phylogeny of Eulamprus Water Skinks and the Biogeography of Eastern Australia


Top left is a topographic map of the Australian continent (red = high, green = low, major drainage lines = white). 
Bottom left map shows finer‐scale drainage lines (Global Map Australia 1M 2001, Geoscience Australia) overlain on to a digital elevation model image (Shuttle Radar Topography Mission) where light grey equates to areas of high elevation, and dark grey equates to areas of low elevation. 

Right panel shows the distribution of the five Eulamprus species; E. quoyii (A, purple), E. kosciuskoi and E. leuraensis (B, yellow and red, respectively), E. heatwolei (C, green) and E. tympanum (D, pink). 
(Photos: Stephen Zozaya & Stewart Macdonald).

in Pepperm, Sumner, Brennan, et al., 2018.
  DOI: 10.1111/jbi.13385  


Abstract
Aim: 
To develop a robust phylogeny for the iconic Australian water skinks (Eulamprus) and to explore the influence of landscape evolution of eastern Australia on phylogeographic patterns.

Location: Eastern and south‐eastern Australia.

Methods: 
We used Sanger methods to sequence a mitochondrial DNA (mtDNA) locus for 386 individuals across the five Eulamprus species to elucidate phylogeographic structure. We also sequenced a second mtDNA locus and four nuclear DNA (nDNA) loci for a subset of individuals to help inform our sampling strategy for next‐generation sequencing. Finally, we generated an anchored hybrid enrichment (AHE) approach to sequence 378 loci for 25 individuals representing the major lineages identified in our Sanger dataset. These data were used to resolve the phylogenetic relationships among the species using coalescent‐based species tree inference in *BEAST and ASTRAL.

Results: 
The relationships between Eulamprus species were resolved with a high level of confidence using our AHE dataset. In addition, our extensive mtDNA sampling revealed substantial phylogeographic structure in all species, with the exception of the geographically highly restricted E. leuraensis. Ratios of patristic distances (mtDNA/nDNA) indicate on average a 30‐fold greater distance as estimated using the mtDNA locus ND4.

Main conclusions: 
The major divergences between lineages strongly support previously identified biogeographic barriers in eastern Australia based on studies of other taxa. These breaks appear to correlate with regions where the Great Escarpment is absent or obscure, suggesting topographic lowlands and the accompanying dry woodlands are a major barrier to dispersal for water skinks. While some river corridors, such as the Hunter Valley, were likely historically dry enough to inhibit the movement of Eulamprus populations, our data indicate that others, such as the Murray and Darling Rivers, are able to facilitate extensive gene flow through the vast arid and semi‐arid lowlands of New South Wales and South Australia. Comparing the patristic distances between the mitochondrial and AHE datasets highlights the continued value in analysing both types of data.

Keywords: anchored hybrid enrichment, Eastern Australia, gene flow, great dividing range, Murray–Darling Basin, Newer Volcanics Province


Figure 1: Phylogenomic analyses provide consistent support of interspecific relationships among Eulamprus water skinks, regardless of reconstruction method. Lizard images to the left depict the relative size and appearance of each species. The first and third trees in this figure were constructed using anchored phylogenomics data (nuclear exons—nDNA), resulting in identical topologies between the full (378) and filtered (281) datasets. On these two trees (nDNA starBEAST and nDNA ASTRAL), nodes labelled with a white circle denote fully supported relationships (posterior probability = 1, bootstrap = 100), with all other nodes labelled according to estimated support. Note terminal branch lengths in ASTRAL analysis are fixed, and not to scale. The middle phylogeny has been reconstructed using the mitochondrial locus ND4 (mtDNA), with nodes labelled by a red circle constrained to match the nuclear species tree topology. Intraspecific relationships of the mtDNA tree remained unconstrained, and are used to illustrate the sampling depth and relative diversity of each species. Labels on the far right of this figure match the nDNA ASTRAL tree, run on phased haplotype data, where each taxon is represented by two terminal tips representing the phased alleles. Sampling data for each individual can be found in Table S1. Colours designated for each species correspond to sampling maps in Figure 2, and intraspecific mtDNA phylogenies in supplemental materials (Figures S1–S4)

Figure 2: Top left is a topographic map of the Australian continent (red = high, green = low, major drainage lines = white). Bottom left map shows finer‐scale drainage lines (Global Map Australia 1M 2001, Geoscience Australia) overlain on to a digital elevation model image (Shuttle Radar Topography Mission) where light grey equates to areas of high elevation, and dark grey equates to areas of low elevation. Thick dark grey lines indicate biogeographic barriers mentioned in the text. Stippled blue lines indicate the major rivers; Darling River (DR), Lachlan River (LR), Murrumbidgee River (MBR) and Murray River (MR). Coloured symbols represent sampling localities for two clades that use rivers to facilitate long‐distance gene flow. Purple triangles indicate one of the E. quoyii clades, while green circles representing our sample localities for one of the E. heatwolei clades. State boundaries are shown by thin grey lines. QLD = Queensland, SA = South Australia, NSW = New South Wales, ACT = Australian Capital Territory, VIC = Victoria.

Right panel shows the distribution of the five Eulamprus species; E. quoyii (A, purple), E. kosciuskoi and E. leuraensis (B, yellow and red, respectively), E. heatwolei (C, green) and E. tympanum (D, pink). Different coloured shapes on each map refer to major clades within each species, whereas small black + symbols refer to museum locality records. Relevant biogeographic barriers from the larger map to the left have been overlain 
(Photo credit: Stephen Zozaya & Stewart Macdonald).


Mitzy Pepperm, Joanna Sumner, Ian G. Brennan, Kate Hodges, Alan R. Lemmon, Emily Moriarty Lemmon, Garry Peterson, Daniel L. Rabosky, Lin Schwarzkopf, Ian A. W. Scott, Glenn Shea and J. Scott Keogh. 2018. Speciation in the Mountains and Dispersal by Rivers: Molecular Phylogeny of Eulamprus Water Skinks and the Biogeography of Eastern Australia. Journal of Biogeography. DOI: 10.1111/jbi.13385

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