Paul M. Oliver

Independent Transitions between Monsoonal and Arid Biomes Revealed by Systematic Revison of a Complex of Australian Geckos (Diplodactylus; Diplodactylidae)

How the widespread expansion and intensification of aridity through the Neogene has shaped the Austral biota is a major question in Antipodean biogeography. Lineages distributed across wide aridity gradients provide opportunities to examine the timing, frequency, and direction of transitions between arid and mesic regions. Here, we use molecular genetics and morphological data to investigate the systematics and biogeography of a nominal Australian gecko species (Diplodactylus conspicillatus sensu lato) with a wide distribution spanning most of the Australian Arid Zone (AAZ) and Monsoonal Tropics (AMT). Our data support a minimum of seven genetically distinct and morphologically diagnosable taxa; we thus redefine the type species, ressurrect three names from synonymy, and describe three new species. Our inferred phylogeny suggests the history and diversification of lineages in the AAZ and AMT are intimately linked, with evidence of multiple independent interchanges since the late Miocene. However, despite this shared history, related lineages in these two regions also show evidence of broadly contrasting intra-regional responses to aridification; vicarance and speciation in older and increasingly attenuated mesic regions, versus a more dynamic history including independent colonisations and recent range expansions in the younger AAZ.

Systematics of small Gehyra (Squamata: Gekkonidae) of the southern Kimberley, Western Australia: redescription of G . kimberleyi Börner & Schüttler, 1983 and description of a new restricted range species

Ongoing fieldwork and molecular research continues to reveal that the monsoonal tropics of northern Australia contain more vertebrate species than currently recognised. Here we focus on two morphologically distinctive, yet unrecognised forms in the genus Gehyra from the southern Kimberley region and surrounding deserts. We base our descriptions on a combination of unpublished genetic data and a morphological examination of voucher specimens. We recognise and redescribe G. kimberleyi, a species with a broad distribution extending over most of the south-west Kimberley, across the Great Sandy Desert and into the far northern Pilbara. This species has been previously assigned to G. pilbara owing to its frequent occurrence on termite mounds and short snout, but can be distinguished from G. pilbara and other regionally sympatric Gehyra by its moderate body size, moderate number of pre-cloacal pores in males (12-17) and aspects of dorsal colouration. We also describe G. girloorloo sp. nov., a small rock-dwelling species with a short snout, low number of pre-cloacal pores in males (8-11) and pinkish-grey dorsal colouration with alternating series of indistinct pale spots and irregular transversely-aligned dark blotches. The new species appears to be restricted to a relatively small region of exposed limestone karst in the south-west Kimberley and is entirely circumscribed by morphologically similar congeners.

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

Abstract. Species are a fundamental unit for all fields of biology but conceptual and practical limitations have hampered the process of identifying and describing species in many organismal groups. One outcome of these challenges is the accumulation of genetically divergent lineages and morphologically distinctive populations that are ‘known’, but remain of uncertain taxonomic status and evolutionary significance. These lineages are also currently not effectively incorporated into evolutionary studies or conservation planning and management. Here we suggest three ways to address this issue. First, there is a need to develop improved frameworks to systematically capture taxonomically unrecognised lineage diversity. Second, increased utilisation of metadata frameworks will allow better recording and dissemination of biodiversity information. Finally, emerging genomic and analytical techniques will provide powerful new tools to improve our identification and understanding of evolutionary lineages.

Systematic revision of the marbled velvet geckos ( Oedura marmorata species complex, Diplodactylidae) from the Australian arid and semi-arid zones

Lizards restricted to rocky habitats often comprise numerous deeply divergent lineages, reflecting the disjunct nature of their preferred habitat and the capacity of rocky habitats to function as evolutionary refugia. Here we review the systematics and diversity of the predominantly saxicoline Australian marbled velvet geckos (genus Oedura) in the Australian arid and semi-arid zones using newly-gathered morphological data and previously published genetic data. Earlier work showed that four largely allopatric and genetically divergent lineages are present: Western (Pilbara and Gascoyne regions), Gulf (west and south of the Gulf of Carpentaria), Central (central ranges) and Eastern (Cooper and Darling Basins). None of these four populations are conspecific with true O. marmorata, a seperate species complex that is restricted to the Top End region of the Northern Territory. Top End forms share a short, bulbous tail whereas the other four lineages treated here possess a long, tapering tail. Morphological differences among the arid and semi-arid lineages include smaller body size, tapering lamellae and a shorter tail for the Gulf population, and a partially divided rostral scale in the Western population compared to the Central and Eastern populations. Accordingly, we resurrect O. cincta de Vis from synonymy for the Central and Eastern lineages, and regard this species as being comprised of two evolutionary significant units. We also describe the Gulf and Western lineages as new species: Oedura bella sp. nov. and O. fimbria sp. nov., respectively. We note that a predominantly arboreal lineage (the Eastern lineage of O. cincta) is more widely distributed than the other lineages and is phylogenetically nested within a saxicoline clade, but tends to have a deeper head and shorter limbs, consistent with morphological variation observed in other lizard radiations including both saxicoline and arboreal taxa.

Mass turnover and recovery dynamics of a diverse Australian continental radiation

Trends in global and local climate history have been linked to observed macroevolutionary patterns across a variety of organisms. These climatic pressures may unilaterally or asymmetrically influence the evolutionary trajectory of clades. To test and compare signatures of changing global (Eocene‐Oligocene boundary cooling) and continental (Miocene aridification) environments on a continental fauna, we investigated the macroevolutionary dynamics of one of Australias most diverse endemic radiations, pygopodoid geckos. We generated a time‐calibrated phylogeny (>90% taxon coverage) to test whether (i) asymmetrical pygopodoid tree shape may be the result of mass turnover deep in the groups history, and (ii) how Miocene aridification shaped trends in biome assemblages. We find evidence of mass turnover in pygopodoids following the isolation of the Australian continental plate ∼30 million years ago, and in contrast, gradual aridification is linked to elevated speciation rates in the young arid zone. Surprisingly, our results suggest that invasion of arid habitats was not an evolutionary end point. Instead, arid Australia has acted as a source for diversity, with repeated outward dispersals having facilitated diversification of this group. This pattern contrasts trends in richness and distribution of other Australian vertebrates, illustrating the profound effects historical biome changes have on macroevolutionary patterns.

Cryptic lineage diversity, body size divergence, and sympatry in a species complex of Australian lizards (Gehyra ): SIZE CONSERVATISM IN PARAPATRIC SPECIES COMPLEX

Understanding the joint evolutionary and ecological underpinnings of sympatry among close relatives remains a key challenge in biology. This problem can be addressed through joint phylogenomic and phenotypic analysis of complexes of closely related lineages within, and across, species and hence representing the speciation continuum. For a complex of tropical geckos from northern Australia—Gehyra nana and close relatives—we combine mtDNA phylogeography, exon‐capture sequencing, and morphological data to resolve independently evolving lineages and infer their divergence history and patterns of morphological evolution. Gehyra nana is found to include nine divergent lineages and is paraphyletic with four other species from the Kimberley region of north‐west Australia. Across these 13 taxa, 12 of which are restricted to rocky habitats, several lineages overlap geographically, including on the diverse Kimberley islands. Morphological evolution is dominated by body size shifts, and both body size and shape have evolved gradually across the group. However, larger body size shifts are observed among overlapping taxa than among closely related parapatric lineages of G. nana, and sympatric lineages are more divergent than expected at random. Whether elevated body size differences among sympatric lineages are due to ecological sorting or character displacement remains to be determined.

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

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.

Stripes, jewels and spines: further investigations into the evolution of defensive strategies in a chemically defended gecko radiation (Strophurus, Diplodactylidae)

The geckos in the genus Strophurus (Diplodactylidae) are one of only two squamate lineages with specialized caudal defensive glands. Many species in this genus also have distinctive caudal ornamentation combined with bright and/or contrasting colour pattern elements on the iris, tail and especially the lining of the mouth that are hypothesized to be adaptations for specialized (e.g. deimatic) defensive functions. We present the first multilocus, phylogenetic analysis of the biogeography and evolution of all recognized taxa of Strophurus. Contrary to previous phenotypic and ecological assessments, our phylogenetic analyses delineate four divergent lineages. Three lineages are relatively small (snout‐vent length [SVL] 40–60 mm), species‐poor (<5 recognized taxa), cryptically coloured (either striped or spotted) and lack precloacal pores (a secondary sexual trait) and putative deimatic elements. In contrast, the remaining lineage is comparatively species rich (at least 14 taxa), attains a larger body size (SVL 60–90 mm), possesses precloacal pores and shows extensive variation in caudal ornamentation and often bright and/or contrasting eye, tail and mouth colouration. The three less diverse lineages have smaller distributions and tend to be associated with spinifex (e.g. Triodia) hummock grasses or rocks, whereas the fourth lineage is much more widespread (including multiple biomes) and consistently reported to utilize more exposed diurnal microhabitats on shrubs and trees. Biogeographical analyses also indicate that – in contrast to many other Australian radiations – the arid biome is the ancestral area of occupation for Strophurus, with multiple inferred shifts into surrounding sclerophyll and monsoon biomes. This study emphasizes that – independent of caudal defensive glands – it appears to be a shift in microhabitat use that correlates with the accumulation of bright and contrasting colouration elements, secondary sexual characters and the widest geographic distribution.

The Knight and the King: two new species of giant bent-toed gecko (Cyrtodactylus, Gekkonidae, Squamata) from northern New Guinea, with comments on endemism in the North Papuan Mountains

Abstract The diverse biota of New Guinea includes many nominally widespread species that actually comprise multiple deeply divergent lineages with more localised histories of evolution. Here we investigate the systematics of the very large geckos of the Cyrtodactylus novaeguineae complex using molecular and morphological data. These data reveal two widespread and divergent lineages that can be distinguished from each other, and from type material of Cyrtodactylus novaeguineae, by aspects of size, build, coloration and male scalation. On the basis of these differences we describe two new species. Both have wide distributions that overlap extensively in the foothill forests of the North Papuan Mountains, however one is seemingly restricted to hill and lower montane forests on the ranges themselves, while the other is more widespread throughout the surrounding lowlands. The taxon endemic to the North Papuan Mountains is related to an apparently lowland form currently known only from Waigeo and Batanta Island far to the west – hinting at a history on island arcs that accreted to form the North Papuan Mountains.

Mountain colonisation, miniaturisation and ecological evolution in a radiation of direct-developing New Guinea Frogs (Choerophryne, Microhylidae)

Aims Mountain ranges in the tropics are characterised by high levels of localised endemism, often-aberrant evolutionary trajectories, and some of the world’s most diverse regional biotas. Here we investigate the evolution of montane endemism, ecology and body size in a clade of direct-developing frogs (Choerophryne, Microhylidae) from New Guinea. Methods Phylogenetic relationships were estimated from a mitochondrial molecular dataset using Bayesian and maximum likelihood approaches. Ancestral state reconstruction was used to infer the evolution of elevational distribution, ecology (indexed by male calling height), and body size, and phylogenetically corrected regression was employed to examine the relationships between these three traits. Results We obtained strong support for a monophyletic lineage comprising the majority of taxa sampled. Within this clade we identified one subclade that appears to have diversified primarily in montane habitats of the Central Cordillera (>1,000 m a.s.l.), with subsequent dispersal to isolated North Papuan Mountains. A second subclade (characterised by moderately to very elongated snouts) appears to have diversified primarily in hill forests (<1,000 m a.s.l.), with inferred independent upwards colonisations of isolated montane habitats, especially in isolated North Papuan Mountains. We found no clear relationship between extremely small body size (adult SVL less than 15 mm) and elevation, but a stronger relationship with ecology—smaller species tend to be more terrestrial. Conclusions Orogeny and climatic oscillations have interacted to generate high montane biodiversity in New Guinea via both localised diversification within montane habitats (centric endemism) and periodic dispersal across lowland regions (eccentric endemism). The correlation between extreme miniaturisation and terrestrial habits reflects a general trend in frogs, suggesting that ecological or physiological constraints limit niche usage by miniaturised frogs, even in extremely wet environments such as tropical mountains.