New approaches to cataloguing and understanding evolutionary diversity: a perspective from Australian herpetology

McDonald²

2016

R. Soc. open sci.

Climatic change, and in particular aridification, has played a dominant role in shaping Southern Hemisphere biotas since the mid-Neogene. In Australia, ancient and geologically stable ranges within the vast arid zone have functioned as refugia for populations of mesic taxa extirpated from surrounding areas, yet the extent to which relicts may be linked to major aridification events before or after the Pliocene has not been examined in detail. Here we use molecular phylogenetic and morphological data to show that isolated populations of saxicoline geckos in the genus Oedura from the Australian Central Uplands, formerly confounded as a single taxon, actually comprise two divergent species with contrasting histories of isolation. The recently resurrected Oedura cincta has close relatives occurring elsewhere in the Australian arid biomes with estimated divergence dates concentrated in the early Pliocene. A new taxon (described herein) diverged from all extant Oedura much earlier, well before the end of the Miocene. A review of data for Central Uplands endemic vertebrates shows that for most (including Oedura cincta), gene flow with other parts of Australia probably occurred until at least the very late Miocene or Pliocene. There are, however, a small number of palaeoendemic taxa—often ecologically specialized forms—that show evidence of having persisted since earlier intensification of aridity in the late Miocene.

Section: Resultsmentioning

confidence: 98%

Young relicts and old relicts: a novel palaeoendemic vertebrate from the Australian Central Uplands

McDonald²

2016

R. Soc. open sci.

“…Globally, ongoing integrated assessments of evolutionary diversity in many orders of life (including vertebrates) continue to reaffirm that biodiversity remains seriously underestimated (Pfenninger & Schwenk, ; Vieites et al ., ; Poulin, ; Pawlowski et al ., ; Adams et al ., ). Taxonomically unrecognized and often morphologically cryptic taxa pose major challenges for evolutionary biologists and conservation management (Bickford et al ., ; Oliver et al ., ). While in most cases assessments of cryptic diversity are taxonomically focused, at least theoretically, where evolutionary processes such as refugial dynamics and allopatric diversification are acting in concert across landscapes, geographically concordant clusters of unrecognized diversity in unrelated lineages may go undetected.…”

Section: Introductionmentioning

confidence: 97%

A novel hotspot of vertebrate endemism and an evolutionary refugium in tropical Australia

Diversity and Distributions

Laver

Martins

et al. 2016

Aim In lineages or regions that are rife with morphologically cryptic taxa, hotspots of local endemism may remain overlooked when genetic data are unavailable. Here we examine the genetic diversity and evolutionary origins of lizard communities occurring in a relatively restricted, isolated and heretofore poorly surveyed region of limestone karst in northern Australia.Location The Devonian Reef System (DRS), an iconic range of exposed weathered limestone at the margin of the Australian Arid Zone (AAZ) and Monsoonal Tropics (AMT) in north-west Australia, that is widely recognized for its cultural, geological and palaeontological significance.Methods In collaboration with local landowners, we sampled four different gecko genera at sites spanning the DRS and adjacent biomes. We then used measures of genetic divergence, neutrality tests, Bayesian dating and hierarchical approximate Bayesian computational (HABC) approaches to identify divergent lineages, test for shared biogeographic history and compare patterns of genetic differentiation in lineages with different ecologies (saxicoline, arboreal and terrestrial).Results Amongst saxicoline taxa, we identified 11 genetically divergent lineages that appear to be endemic to the DRS. Generalists and arboreal lineages showed no evidence of endemism in the DRS. Estimated divergence dates and patterns of distribution indicate that endemic lineages have persisted since the Plio-Pleistocene (or even earlier). Taxa in an old endemic Australian Gondwanan radiation showed evidence of longer persistence and isolation than those in radiations with more recent immigrant origins.Main Conclusions The DRS is a heretofore overlooked hotspot of vertebrate endemism and persistence. Areas with distinctive underlying geology that provide microrefugia (such as karst) in tropical regions across the globe are likely important refugia for biodiversity at both ecological and evolutionary scales. They warrant further focused survey efforts (including genetics-based assessments of diversity) and ongoing conservation attention.

“…Documenting and describing morphologically similar, yet genetically and evolutionarily distinctive cryptic species poses well-recognised, but ongoing challenges for systematists, evolutionary biologists and conservation managers (Bickford et al, 2007;Oliver, Keogh & Moritz, 2015;Singhal et al, 2018). The existence of multiple species within the G. australis group was not apparent based on prima-facie morphological data.…”

Section: Discussionmentioning

confidence: 99%

“…Integrative taxonomic analyses utilise multiple independent data sources to illuminate patterns of phenotypic and genetic differentiation (De Queiroz, 2007;Padial et al, 2010). Thus, in addition to the traditional morphological characters upon which taxonomy was founded hundreds of years ago, systematists in recent decades have progressively added a growing battery of genetic approaches to analyse evidence from karyotypes, allozymes, mtDNA sequence data and, increasingly common, loci from the nuclear genome (Oliver, Keogh & Moritz, 2015). However, genetic species delimitation methods can incorrectly diagnose distinct populations as 'species', especially where dispersal rates are low or sampling is sparse (Carstens et al, 2013;Sukumaran & Knowles, 2017;Leaché et al, 2018;Singhal et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Crypsis and convergence: integrative taxonomic revision of the Gehyra australis group (Squamata: Gekkonidae) from northern Australia

Prasetya

Tedeschi

et al. 2020

PeerJ

Self Cite

For over two decades, assessments of geographic variation in mtDNA and small numbers of nuclear loci have revealed morphologically similar, but genetically divergent, intraspecific lineages in lizards from around the world. Subsequent morphological analyses often find subtle corresponding diagnostic characters to support the distinctiveness of lineages, but occasionally do not. In recent years it has become increasingly possible to survey geographic variation by sequencing thousands of loci, enabling more rigorous assessment of species boundaries across morphologically similar lineages. Here we take this approach, adding new, geographically extensive SNP data to existing mtDNA and exon capture datasets for the Gehyra australis and G. koira species complexes of gecko from northern Australia. The combination of exon-based phylogenetics with dense spatial sampling of mitochondrial DNA sequencing, SNP-based tests for introgression at lineage boundaries and newly-collected morphological evidence supports the recognition of nine species, six of which are newly described here. Detection of discrete genetic clusters using new SNP data was especially convincing where candidate taxa were continuously sampled across their distributions up to and across geographic boundaries with analyses revealing no admixture. Some species defined herein appear to be truly cryptic, showing little, if any, diagnostic morphological variation. As these SNP-based approaches are progressively applied, and with all due conservatism, we can expect to see a substantial improvement in our ability to delineate and name cryptic species, especially in taxa for which previous approaches have struggled to resolve taxonomic boundaries.