Plio-Pleistocene diversification and biogeographic barriers in southern Australia reflected in the phylogeography of a widespread and common lizard species

https://doi.org/10.1016/j.ympev.2018.12.014Get rights and content

Highlights

  • Mitochondrial and nuclear genetic data indicate strong phylogeographic structure.

  • Results consistent with biogeographic barriers at the Nullarbor Plain and Murray River.

  • Molecular clock analyses suggest diversification occurred in the Plio-Pleistocene.

  • Analyses indicate presence of one or more refugia associated with each of the three main populations.

Abstract

Palaeoclimatic events and biogeographical processes since the mid-Tertiary have played an important role in shaping the evolution and distribution of Australian fauna. However, their impacts on fauna in southern and arid zone regions of Australia are not well understood. Here we investigate the phylogeography of an Australian scincid lizard, Tiliqua rugosa, across southern Australia using mitochondrial DNA (mtDNA) and 11 nuclear DNA markers (nuDNA), including nine anonymous nuclear loci. Phylogenetic analyses revealed three major mtDNA lineages within T. rugosa, geographically localised north and south of the Murray River in southern Australia, and west of the Nullarbor Plain. Molecular variance and population analyses of both mtDNA and nuDNA haplotypes revealed significant variation among the three populations, although potential introgression of nuDNA markers was also detected for the Northern and Southern population. Coalescent times for major mtDNA lineages coincide with an aridification phase, which commenced after the early Pliocene and increased in intensity during the Late Pliocene-Pleistocene. Species distribution modelling and a phylogeographic diffusion model suggest that the range of T. rugosa may have contracted during the Last Glacial Maximum and the locations of optimal habitat appear to coincide with the geographic origin of several distinct mtDNA lineages. Overall, our analyses suggest that Plio-Pleistocene climatic changes and biogeographic barriers associated with the Nullarbor Plain and Murray River have played a key role in shaping the present-day distribution of genetic diversity in T. rugosa and many additional ground-dwelling animals distributed across southern Australia.

Introduction

Global climates have varied significantly over the periods during which present-day species originated and diversified. These fluctuations have affected the evolution and distributions of current species, particularly in the Northern Hemisphere where Ice-Age glaciations led to periodic range contractions followed by expansions of the range of species, which in turn led to genetic differentiation and diversification (Bhagwat and Willis, 2008, Cooper et al., 1995, Hewitt, 2000, Hewitt, 2004, Pielou, 1991, Taberlet et al., 1998). However, less is known about the effects of Plio-Pleistocene climate change on the present-day diversity of species in the Southern Hemisphere where the effect of glaciation was less pronounced and where processes may have been more complex (Byrne et al., 2008). This lack of knowledge is particularly true of southern Australia (Byrne et al., 2008), which is the focus of our study.

Phylogeography involves a study of the geographical distribution of genealogical lineages (Avise et al., 1987) and when applied in comparative multi-species studies, it can help deduce the historical processes that have shaped the evolution and distribution of species. Such studies provide valuable information for identifying refugia and biogeographic breaks within species, and hence for predicting how species may respond to future climate change (Scoble and Lowe, 2010). To date, there have been only a limited number of phylogeographic studies of species distributed in southern Australia. Many of these studies have been either regionally restricted (e.g. to south-western or south-eastern Australia; Byrne et al., 2011, Chapple et al., 2011, Chapple et al., 2005, Edwards et al., 2012, Schauble and Moritz, 2001, Symula et al., 2008) or have operated at the inter-species level (Dubey and Shine, 2010, Lanier et al., 2013, Rabosky et al., 2014), which may not have revealed recent evolutionary processes that have promoted genetic subdivision within species. Hence, there is a need for additional phylogeographic studies of southern Australian taxa with different ecologies, life histories and varying degrees of dispersal to fully understand the nature of refugia in past climates and the influence of biogeographical barriers in shaping their genetic structure and in speciation.

Two major barriers, the Nullarbor Plain and the Eyrean Barrier (Flinders Ranges–Lake Eyre Basin) (Fig. 1) have been proposed to play a key role in shaping the present-day diversity of fauna in southern Australia (Byrne et al., 2008, Dolman and Joseph, 2012, Dolman and Joseph, 2015). The Nullarbor Plain, a region in the centre of southern Australia spanning 700 km (Fig. 1), currently forms a major biogeographic barrier of unsuitable habitat for mesic adapted species between Australia's temperate mesic zones in the south-west and south-east (Crisp and Cook, 2007, Dolman and Joseph, 2012, Webb and James, 2006). This region has acted as a barrier since the late Miocene following the uplift of the Nullarbor Plain and the widespread development of aridity on the Australian continent (Bowler, 1976, Hill, 1994, McGowran et al., 2004). A proposed return to wetter conditions in the early Pliocene (Sniderman et al., 2016) may have enabled some geneflow and dispersal of mesic taxa across the Nullarbor, until aridity deepened once again during the Late Pliocene/Pleistocene. A major question, however, is whether the Nullarbor potentially acted as a biogeographic barrier for semi-arid and/or arid adapted species during Pleistocene glacial maxima. Pollen and diatom analyses, alluvial stratigraphy, and analyses of lake shorelines and desert dunes generally indicate that Australia was a significantly colder and drier landscape during glacial maxima (Byrne et al., 2008, Williams et al., 2009), with sea levels up to 125 m lower than current levels (Murray-Wallace and Woodroffe, 2014), exposing the continental shelf of the present day Great Australian Bight. Estimates of divergence times of populations of several bird species with continuous or patchily continuous distributions across the Nullarbor provided evidence for diversification during the Pleistocene and little evidence for gene flow across the exposed continental shelf during glacial maxima (Dolman and Joseph, 2012, Dolman and Joseph, 2015), suggesting that aridity/cold climatic conditions may have impacted the distribution of species.

The Lake Eyre Basin/Eyrean depression in South Australia has also been proposed as a Quaternary aridity barrier, largely from studies of bird species distributed across this region (Dolman and Joseph, 2015, Ford, 1987, Ford, 1974, Joseph et al., 2006, Keast, 1961, Schodde, 1982). The Flinders Ranges, located east of the barrier is a major upland region, has been proposed to have provided wetland conditions during glacial maxima (Williams et al., 2001), and hence may have acted as a possible refugium for plants and animals in the region following the expansion of arid conditions.

A lesser-known biogeographic break occurs in the Murray River basin, a region spanning 300,000 km2 in south-eastern Australia containing the outflow of the Murray River system (Fig. 1). The history of the basin was characterised by marine transgressions in the mid to late Miocene, an ancient Murray River system that was recently proposed to follow a course through western Victoria, followed by the establishment of a mega (50,000 km2) lake, Lake Bungunnia ∼2.5 Ma, until ∼700 Ka, when the modern Murray River was finally established (McLaren et al., 2011, Stephenson, 1986). The river now has highly variable flows, with large to medium floods occurring seven years per decade, but the river is also known to have extensively dried nearly once every century (Close, 1990), suggesting it would only be a semi-permeable barrier to gene flow. Nevertheless, major genetic discontinuities at the Murray basin/Murray River have been found in several organisms including marsupial dunnarts (Cooper et al., 2000), frogs (Schauble and Moritz, 2001, Symula et al., 2008), skinks (Chapple et al., 2011, Chapple et al., 2005), and grasshoppers (Kawakami et al., 2009), with divergence estimates for mtDNA lineages falling in the Plio-Pleistocene.

The monogamous skink Tiliqua rugosa, commonly known as the sleepy lizard, can be used to explore historical barriers and refuges due to its widespread distribution across semi-arid and mesic zone regions of southern Australia (Bull, 1987, Greer, 1989). Its current distribution crosses each of the above-proposed historical barriers (Fig. 1), providing an opportunity to further investigate their influence on the biogeographic history of southern Australian arid and semi-arid zone species.

We obtained DNA sequences using a mixture of Sanger and next generation sequencing (NGS) technology (Illumina Miseq) from T. rugosa across the entire current range of the species from one mitochondrial gene, NADH Dehydrogenase subunit 4 (ND4), and 11 nuclear genes including nine anonymous nuclear loci (ANL). We conducted a range of phylogenetic and population analyses to determine whether genetic discontinuities (distinct mtDNA clades or nuclear DNA haplotypes) are associated with each of the three biogeographic barriers in southern Australia referred to above (Nullarbor, Eyrean and Murray) and whether the time-course for genetic divergence is associated with climatic changes during the Pleistocene. We also used species distribution climatic and phylogeographic diffusion model analyses (Lemey et al., 2010) to determine whether there were putative historical refugia during glacial maxima and whether they coincided with the geographic location of lineage ancestors.

Section snippets

Sampling

We obtained frozen or alcohol-preserved tissue and blood samples from 76 specimens of T. rugosa from across the geographical range of the species in Australia held by the South Australian Museum (SAM) and the Australian Biological Tissue Collection (ABTC) (Fig. 1 and Table S1). All samples were collected under appropriate permits (approval no. E324).

DNA extraction and Sanger sequencing

DNA was extracted using a salting out extraction procedure (Miller et al., 1988) from frozen or alcohol-preserved tissues and blood samples. We

Sequence variability

The mitochondrial sequence data, collected from 76 individuals, comprised 438 base pairs (bp) of ND4 and 137 bp of tRNA, which included tRNA-His, tRNA-Ser and tRNA-Leu. This 575 bp fragment contained 95 variable sites, of which 66 were parsimony-informative, defining 45 mtDNA haplotypes (Table 1). Fewer individuals were sequenced successfully for the nuclear loci due to technical constraints (Table 1). The fragment size for each nuclear locus ranged between 119 bp (Tiru-16) to 748 bp (

Discussion

This study set out to determine whether genetic discontinuities (distinct mtDNA lineages or nuclear DNA haplotypes) were associated with each of three biogeographic barriers in southern Australia, and whether the time-course for genetic divergence was associated with climatic changes during the Pleistocene. We further aimed to determine whether there were putative historical refugia during glacial maxima and assess whether they coincided with the geographic location of lineage ancestors. Our

Conflict of interest

None.

Acknowledgments

This paper is dedicated to our colleague Professor Michael Bull, who passed away unexpectedly in November 2016, and whose inspirational research of the ecology and evolution of the sleepy lizard T. rugosa provided the foundation for the research reported here. Michael Bull also contributed to earlier drafts of this manuscript. Funding was received from the Sir Mark Mitchell Research Foundation, and support from South Australian Museum (SAM) staff for help with tissue sampling is gratefully

References (110)

  • M. Stephens et al.

    Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation

    Am. J. Hum. Genet.

    (2005)
  • M. Stephens et al.

    A new statistical method for haplotype reconstruction from population data

    Am. J. Hum. Genet.

    (2001)
  • A.E. Stephenson

    Lake Bungunnia—a Plio-Pleistocene megalake in southern Australia

    Palaeogeogr. Palaeoclimatol. Palaeoecol.

    (1986)
  • R. Symula et al.

    Ancient phylogeographic divergence in southeastern Australia among populations of the widespread common froglet, Crinia signifera

    Mol. Phylogenet. Evol.

    (2008)
  • T.H. Ansari et al.

    Data from: Plio-Pleistocene diversification and biogeographic barriers in southern Australia reflected in the phylogeography of a widespread and common lizard species

    Dryad Digital Repository

    (2019)
  • J.C. Avise et al.

    Intraspecific phylogeography – the mitochondrial-DNA bridge between population-genetics and systematics

    Annu. Rev. Ecol. Systemat.

    (1987)
  • S.A. Bhagwat et al.

    Species persistence in northerly glacial refugia of Europe: a matter of chance or biogeographical traits?

    J. Biogeogr.

    (2008)
  • F. Bielejec et al.

    SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics

    Bioinformatics

    (2011)
  • R. Bouckaert et al.

    BEAST 2: a software platform for bayesian evolutionary analysis

    PLoS Comput. Biol.

    (2014)
  • J.M. Bowler et al.

    Environmental evolution of the Mallee region, western Murray Basin

    Proc. Roy. Soc. Vic.

    (2006)
  • R.P. Brown et al.

    Phylogeography of skinks (Chalcides) in the Canary Islands inferred from mitochondrial DNA sequences

    Mol. Ecol.

    (1998)
  • C.M. Bull

    A population study of the viviparous Australian Lizard, Trachydosaurus rugosus (Scincidae)

    Copeia

    (1987)
  • C.M. Bull

    Population ecology of the sleepy lizard, Tiliqua rugosa, at Mt Mary, South Australia

    Aust. J. Ecol.

    (1995)
  • C.M. Bull et al.

    Relatedness and avoidance of inbreeding in the lizard, Tiliqua rugosa

    Behav. Ecol. Sociobiol.

    (1999)
  • C.M. Bull et al.

    Sexually dimorphic head sizes and reproductive success in the sleepy lizard Tiliqua rugosa

    J. Zool.

    (1996)
  • M. Byrne et al.

    Decline of a biome: evolution, contraction, fragmentation, extinction and invasion of the Australian mesic zone biota

    J. Biogeogr.

    (2011)
  • M. Byrne et al.

    Birth of a biome: insights into the assembly and maintenance of the Australian arid zone biota

    Mol. Ecol.

    (2008)
  • D.G. Chapple et al.

    Biogeographic barriers in south-eastern Australia drive phylogeographic divergence in the garden skink, Lampropholis guichenoti

    J. Biogeogr.

    (2011)
  • D.G. Chapple et al.

    Substantial genetic substructuring in southeastern and alpine Australia revealed by molecular phylogeography of the Egernia whitii (Lacertilia: Scincidae) species group

    Mol. Ecol.

    (2005)
  • Close, A., 1990. River salinity. In: Mackay, N., Eastburn, D. (Eds.), The Murray, Murray-Darling Basin Commission, pp....
  • S.J.B. Cooper et al.

    Phylogeography of the Australian dunnart Sminthopsis crassicaudata (Marsupialia: Dasyuridae)

    Aust. J. Zool.

    (2000)
  • S.J.B. Cooper et al.

    Postglacial expansion and genome subdivision in the European grasshopper Chorthippus parallelus

    Mol. Ecol.

    (1995)
  • G. Dolman et al.

    A species assemblage approach to comparative phylogeography of birds in southern Australia

    Ecol. Evol.

    (2012)
  • G. Dolman et al.

    Evolutionary history of birds across southern Australia: structure, history and taxonomic implications of mitochondrial DNA diversity in an ecologically diverse suite of species

    Emu

    (2015)
  • G. Dolman et al.

    Single copy nuclear DNA markers characterized for comparative phylogeography in Australian wet tropics rainforest skinks

    Mol. Ecol. Notes

    (2004)
  • A. Drummond et al.

    Relaxed phylogenetics and dating with confidence

    PLoS Biol.

    (2006)
  • A.J. Drummond et al.

    BEAST: Bayesian evolutionary analysis by sampling trees

    BMC Evol. Biol.

    (2007)
  • S. Dubey et al.

    Plio-Pleistocene diversification and genetic population structure of an endangered lizard (the Blue Mountains water skink, Eulamprus leuraensis) in south-eastern Australia

    J. Biogeogr.

    (2010)
  • D.L. Edwards et al.

    Effects of vicariant barriers, habitat stability, population isolation and environmental features on species divergence in the south-western Australian coastal reptile community

    Mol. Ecol.

    (2012)
  • A.J. Egan

    Reproduction in the Sleepy Lizard, Trachydosaurus rugosus

    (1984)
  • J. Elith et al.

    A statistical explanation of MaxEnt for ecologists

    Divers. Distrib.

    (2011)
  • R. Estes

    Fish, amphibians and reptiles from the Etadunna Formation, Miocene of South Australia

    Aust. Zool.

    (1984)
  • L. Excoffier et al.

    Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

    Mol. Ecol. Resour.

    (2010)
  • J. Ford

    Minor isolates and minor geographical barriers in avian speciation in continental Australia

    Emu

    (1987)
  • J.R. Ford

    Speciation in Australian birds adapted to arid habitats

    Emu

    (1974)
  • T. Fujioka et al.

    Global cooling initiated stony deserts in central Australia 2–4 Ma, dated by cosmogenic 21Ne-10Be

    Geology

    (2005)
  • M.G. Gardner et al.

    Tiliqua rugosa microsatellites: isolation via enrichment and characterisation of loci for multiplex PCR in T. rugosa and the endangered T. adelaidensis

    Conserv. Genet.

    (2008)
  • P.R. Gent et al.

    The community climate system model version 4

    J. Clim.

    (2011)
  • A. Greer

    The Biology and Evolution of Australian Lizards

    (1989)
  • G.R. Guerin et al.

    Multi-species distribution modelling highlights the Adelaide Geosyncline, South Australia, as an important continental-scale arid-zone refugium

    Austral Ecol.

    (2013)
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