Renae C. Pratt

Molecular Phylogeny, Biogeography, and Habitat Preference Evolution of Marsupials

Marsupials exhibit great diversity in ecology and morphology. However, compared with their sister group, the placental mammals, our understanding of many aspects of marsupial evolution remains limited. We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species. This tree allows us to analyze the evolution of habitat preference and geographic distributions of marsupial species through time. We found a pattern of mesic-adapted lineages evolving to use more arid and open habitats, which is broadly consistent with regional climate and environmental change. However, contrary to the general trend, several lineages subsequently appear to have reverted from drier to more mesic habitats. Biogeographic reconstructions suggest that current views on the connectivity between Australia and New Guinea/Wallacea during the Miocene and Pliocene need to be revised. The antiquity of several endemic New Guinean clades strongly suggests a substantially older period of connection stretching back to the Middle Miocene and implies that New Guinea was colonized by multiple clades almost immediately after its principal formation.

Diversification of New Zealand weta (Orthoptera: Ensifera: Anostostomatidae) and their relationships in Australasia

New Zealand taxa from the Orthopteran family Anostostomatidae have been shown to consist of three broad groups, Hemiandrus (ground weta), Anisoura/Motuweta (tusked weta) and Hemideina–Deinacrida (tree–giant weta). The family is also present in Australia and New Caledonia, the nearest large land masses to New Zealand. All genera are endemic to their respective countries except Hemiandrus that occurs in New Zealand and Australia. We used nuclear and mitochondrial DNA sequence data to study within genera and among species-level genetic diversity within New Zealand and to examine phylogenetic relationships of taxa in Australasia. We found the Anostostomatidae to be monophyletic within Ensifera, and justifiably distinguished from the Stenopelmatidae among which they were formerly placed. However, the New Zealand Anostostomatidae are not monophyletic with respect to Australian and New Caledonian species in our analyses. Two of the New Zealand groups have closer allies in Australia and one in New Caledonia. We carried out maximum-likelihood and Bayesian analyses to reveal several well supported subgroupings. Our analysis included the most extensive sampling to date of Hemiandrus species and indicate that Australian and New Zealand Hemiandrus are not monophyletic. We used molecular dating approaches to test the plausibility of alternative biogeographic hypotheses for the origin of the New Zealand anostostomatid fauna and found support for divergence of the main clades at, or shortly after, Gondwanan break-up, and dispersal across the Tasman much more recently.

Evolution of a hotspot genus: geographic variation in speciation and extinction rates in Banksia (Proteaceae)

BackgroundHotspots of angiosperm species richness and endemism in Mediterranean-climate regions are among the most striking, but least well-understood, geographic patterns of biodiversity. Recent studies have emphasized the importance of rapid diversification within hotspots, compared to non-hotspot regions, as a major contributor to these patterns. We constructed the first near-complete phylogeny of Banksia (Proteaceae) to test whether diversification rates have differed between lineages confined to the southwest Australian hotspot and those found throughout southern, eastern and northern Australia. We then tested for variation in diversification rates among the bioclimatic zones within the southwest hotspot itself.ResultsAlthough Banksia species richness in the southwest is ten times that of the rest of the continent, we find little evidence for more rapid diversification in the southwest, although this result is inconclusive. However, we find firmer support for substantial rate variation within the southwest hotspot, with more rapid diversification in the semi-arid heaths and shrublands, compared to the high-rainfall forests. Most of the Banksia diversity of the southwest appears to be generated in the heaths and shrublands, with a high migration rate out of this zone boosting diversity of the adjacent forest zone.ConclusionsThe geographic pattern of diversification in Banksia appears more complex than can be characterized by a simple hotspot vs. non-hotspot comparison, but in general, these findings contrast with the view that the high diversity of Mediterranean hotspots is underpinned by rapid radiations. Steady accumulation of species at unexceptional rates, but over long periods of time, may also have contributed substantially to the great botanical richness of these regions.

Multilocus phylogeography reveals nested endemism in a gecko across the monsoonal tropics of Australia

Multilocus phylogeography can uncover taxonomically unrecognized lineage diversity across complex biomes. The Australian monsoonal tropics include vast, ecologically intact savanna‐woodland plains interspersed with ancient sandstone uplands. Although recognized in general for its high species richness and endemism, the biodiversity of the region remains underexplored due to its remoteness. This is despite a high rate of ongoing species discovery, especially in wetter regions and for rock‐restricted taxa. To provide a baseline for ongoing comparative analyses, we tested for phylogeographic structure in an ecologically generalized and widespread taxon, the gecko Heteronotia binoei. We apply coalescent analyses to multilocus sequence data (mitochondrial DNA and eight nuclear DNA introns) from individuals sampled extensively and at fine scale across the region. The results demonstrate surprisingly deep and geographically nested lineage diversity. Several intra‐specific clades previously shown to be endemic to the region were themselves found to contain multiple, short‐range lineages. To infer landscapes with concentrations of unique phylogeographic diversity, we probabilistically estimate the ranges of lineages from point data and then, combining these estimates with the nDNA species tree, estimate phyloendemism across the region. Highest levels of phyloendemism occur in northern Top End, especially on islands, across the topographically complex Arnhem escarpment, and across the sandstone ranges of the western Gulf region. These results drive home that deep phylogeographic structure is prevalent in tropical low‐dispersal taxa, even ones that are ubiquitous across geography and habitats.

Inferring Kangaroo Phylogeny from Incongruent Nuclear and Mitochondrial Genes

The marsupial genus Macropus includes three subgenera, the familiar large grazing kangaroos and wallaroos of M. (Macropus) and M. (Osphranter), as well as the smaller mixed grazing/browsing wallabies of M. (Notamacropus). A recent study of five concatenated nuclear genes recommended subsuming the predominantly browsing Wallabia bicolor (swamp wallaby) into Macropus. To further examine this proposal we sequenced partial mitochondrial genomes for kangaroos and wallabies. These sequences strongly favour the morphological placement of W. bicolor as sister to Macropus, although place M. irma (black-gloved wallaby) within M. (Osphranter) rather than as expected, with M. (Notamacropus). Species tree estimation from separately analysed mitochondrial and nuclear genes favours retaining Macropus and Wallabia as separate genera. A simulation study finds that incomplete lineage sorting among nuclear genes is a plausible explanation for incongruence with the mitochondrial placement of W. bicolor, while mitochondrial introgression from a wallaroo into M. irma is the deepest such event identified in marsupials. Similar such coalescent simulations for interpreting gene tree conflicts will increase in both relevance and statistical power as species-level phylogenetics enters the genomic age. Ecological considerations in turn, hint at a role for selection in accelerating the fixation of introgressed or incompletely sorted loci. More generally the inclusion of the mitochondrial sequences substantially enhanced phylogenetic resolution. However, we caution that the evolutionary dynamics that enhance mitochondria as speciation indicators in the presence of incomplete lineage sorting may also render them especially susceptible to introgression.

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.

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.

Systematics of a small Gehyra (Squamata: Gekkonidae) from the Einasleigh Uplands, Queensland: description of a new range restricted species

The tropical savannah landscapes of Australias north, though previously overshadowed by the biodiverse rainforests of the Wet Tropics, are themselves now attracting interest for their biological significance and uniqueness. The Einasleigh Uplands region of north-east Queensland is home to a diverse group of mammals and reptiles and was previously recognised for its importance in shaping speciation in birds. Here we add a small saxicoline gecko to a growing list of recently described reptiles that are endemic to this region. Phylogenetic analyses including Gehyra species from the arid zone and the monsoonal tropics reveal that small Gehyra geckos in this area, while closely resembling Gehyra nana from the Top End and Kimberley, form a clade that is geographically isolated and phylogenetically distant from the G. nana complex. Instead, the Einasleigh Uplands taxon is sister to a large, arboreal species within the arid zone clade. It is readily distinguished from all lineages within the G. nana complex, its closest relative G. purpurascens, and all other rock-dwelling species from the arid zone by a combination of its very small body size, few subdigital lamellae, and mid tan to golden dorsal coloration with a pattern of scattered pale ocelli and irregular dark-brown blotches on a stippled background. We therefore describe this taxon as a new Australian species of Gehyra, Gehyra einasleighensis sp. nov., based on a combination of phylogenetic separation, morphological characters and discrete geographic distribution.