Diversification of the mygalomorph spider genus Aname (Araneae: Anamidae) across the Australian arid zone: Tracing the evolution and biogeography of a continent-wide radiation.

The assembly of the Australian arid zone biota has long fascinated biogeographers. Covering over two-thirds of the continent, Australia's vast arid zone biome is home to a distinctive fauna and flora, including numerous lineages which have diversified since the Eocene. Tracing the origins and speciation history of these arid zone taxa has been an ongoing endeavour since the advent of molecular phylogenetics, and an increasing number of studies on invertebrate animals are beginning to complement a rich history of research on vertebrate and plant taxa. In this study, we apply continent-wide genetic sampling and one of the largest phylogenetic data matrices yet assembled for a genus of Australian spiders, to reconstruct the phylogeny and biogeographic history of the open-holed trapdoor spider genus Aname L. Koch, 1873. This highly diverse lineage of Australian mygalomorph spiders has a distribution covering the majority of Australia west of the Great Dividing Range, but apparently excluding the high rainfall zones of eastern Australia and Tasmania. Original and legacy sequences were obtained for three mtDNA and four nuDNA markers from 174 taxa in seven genera, including 150 Aname specimen terminals belonging to 102 species-level operational taxonomic units, sampled from 32 bioregions across Australia. Reconstruction of the phylogeny and biogeographic history of Aname revealed three radiations (Tropical, Temperate-Eastern and Continental), which could be further broken into eight major inclusive clades. Ancestral area reconstruction revealed the Pilbara, Monsoon Tropics and Mid-West to be important ancestral areas for the genus Aname and its closest relatives, with the origin of Aname itself inferred in the Pilbara bioregion. From these origins in the arid north-west of Australia, our study found evidence for a series of subsequent biome transitions in separate lineages, with at least eight tertiary incursions back into the arid zone from more mesic tropical, temperate or eastern biomes, and only two major clades which experienced widespread (primary) in situ diversification within the arid zone. Based on our phylogenetic results, and results from independent legacy divergence dating studies, we further reveal the importance of climate-driven biotic change in the Miocene and Pliocene in shaping the distribution and composition of the Australian arid zone biota, and the value of continent-wide studies in revealing potentially complex patterns of arid zone diversification in dispersal-limited invertebrate taxa.

Scratching the surface of subterranean biodiversity: Molecular analysis reveals a diverse and previously unknown fauna of Parabathynellidae (Crustacea: Bathynellacea) from the Pilbara, Western Australia.

Like other crustacean families, the Parabathynellidae is a poorly studied subterranean and aquatic (stygobiontic) group in Australia, with many regions of available habitat having not yet been surveyed. Here we used a combined approach of molecular species delimitation methods, applied to mitochondrial and nuclear genetic data, to identify putative new species from material obtained from remote subterranean habitats in the Pilbara region of Western Australia. Based on collections from these new localities, we delineated a minimum of eight and up to 24 putative new species using a consensus from a range of molecular delineation methods and additional evidence. When we placed our new putative species into the broader phylogenetic framework of Australian Parabathynellidae, they grouped with two known genera and also within one new and distinct Pilbara-only clade. These new species significantly expand the known diversity of Parabathynellidae in that they represent a 22% increase to the 109 currently recognised species globally. Our investigations showed that sampling at new localities can yield extraordinary levels of new species diversity, with the majority of species showing likely restricted endemic geographical ranges. These findings represent only a small sample from a region comprising less than 2.5% of the Australian continent.

Too hot to handle: Cenozoic aridification drives multiple independent incursions of Schizomida (Hubbardiidae) into hypogean environments.

The formation of the Australian arid zone, Australia's largest and youngest major biome, has been recognized as a major driver of rapid evolutionary radiations in terrestrial plants and animals. Here, we investigate the phylogenetic diversity and evolutionary history of subterranean short-tailed whip scorpions (Schizomida: Hubbardiidae), which are a significant faunal component of Western Australian hypogean ecosystems. We sequenced two mitochondrial (12S, COI) and three nuclear DNA markers (18S, 28S, ITS2) from ∼600 specimens, largely from the genera Draculoides and Paradraculoides, including 20 previously named species and an additional 56 newly identified operational taxonomic units (OTUs). Phylogenetic analyses revealed a large and rapid species radiation congruent with Cenozoic aridification of the continent, in addition to the identification of a new genus in Western Australia and the first epigean schizomid from the Pilbara. Here, we also synonymise Paradraculoides with Draculoides (new synonymy), due to paraphyly and a lack of reliable characters to define the two genera. Our results are consistent with multiple colonisations of the subterranean realm from epigean ancestors as their forest habitat fragmented and retracted, with ongoing fragmentation and diversification of lineages underground. These findings illustrate the remarkable diversity and high incidence of short-range endemism of Western Australia's subterranean fauna, which has important implications for identifying and managing short-range endemic subterranean fauna. They also highlight the advantages of including molecular data in subterranean fauna surveys as all specimens can be utilized, regardless of sex and life stage. Additionally, we have provided the first multi-gene phylogenetic framework for Australian schizomids, which will enable researchers and environmental consultants to identify new taxa or align them to existing lineages.

Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events.

The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back to 40 Ma. Recent studies, however, suggest that much of Sulawesi's fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric datasets derived from Sulawesi's three largest mammals: the babirusa, anoa and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Ma to 2-3 Ma), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that emergence of land on Sulawesi (approx. 1-2 Myr) may have allowed species to expand synchronously. Altogether, our results indicate that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years.

A systematic revision of Draculoides (Schizomida: Hubbardiidae) of the Pilbara, Western Australia, Part I: the Western Pilbara.

The schizomid fauna of mainland Australia currently comprises 60 species within seven named genera, of which five are endemic to the continent: Attenuizomus Harvey, 2000, Brignolizomus Harvey, 2000, Draculoides Harvey, 1992, Julattenius Harvey, 1992, Notozomus Harvey, 2000. Most Australian schizomids have been described from eastern and northern Australia, but there is also a significant subterranean fauna that has been found in hypogean habitats in the semi-arid Pilbara region of Western Australia. The vast majority of these species can be assigned to the genus Draculoides and this study is the first in a proposed series to revise this highly diverse genus. We treat the species found in the western Pilbara region, which includes 13 new species and 13 previously named species, using morphological characters and multi-locus sequence data. We also incorporate a molecular "mini-barcode" approach for COI, 12S and ITS2 to diagnose the new species. The new species are named: Draculoides akashae Abrams and Harvey, n. sp., D. belalugosii Abrams and Harvey, n. sp., D. carmillae Abrams and Harvey, n. sp., D. christopherleei Abrams and Harvey, n. sp., D. claudiae Abrams and Harvey, n. sp., D. immortalis Abrams and Harvey, n. sp., D. karenbassettae Abrams and Harvey, n. sp., D. mckechnieorum Abrams and Harvey, n. sp., D. minae Abrams and Harvey, n. sp., D. noctigrassator Abrams and Harvey, n. sp., D. nosferatu Abrams and Harvey, n. sp., D. piscivultus Abrams and Harvey, n. sp. and D. warramboo Abrams and Harvey, n. sp. We also provide the first descriptions of males of D. anachoretus (Harvey, Berry, Edward and Humphreys, 2008) and D. gnophicola (Harvey, Berry, Edward and Humphreys, 2008). All of the new species are subterranean-dwelling, short-range endemic species that occur in regions subject to mining activities, rendering them of high conservation significance.

The millipede genus Antichiropus (Diplopoda: Polydesmida: Paradoxosomatidae), part 3: species of the Pilbara bioregion of Western Australia.

The species of the millipede genus Antichiropus Attems, 1911 found in the Pilbara region of Western Australia are reviewed, and 33 new species are described. The new species are: A. anguinus Car, n. sp., A. antius Car, n. sp., A. apricus Car, n. sp., A. cirratus Car, n. sp., A. confragus Car, n. sp., A. cristatus Car, n. sp., A. cucumeraceous Car, n. sp., A. cunicularis Car, n. sp, A. echinus Car, n. sp., A. filiolus Car, n. sp., A. forcipatus Car, n. sp., A. georginae Car, n. sp., A. gibbus Car, n. sp., A. hystricosus Car, n. sp., A. julianneae Car, n. sp., A. literulus Car, n. sp., A. lucyae Car, n. sp., A. nicholasi Car, n. sp., A. nimbus Car, n. sp., A. patriciae Car, n. sp., A. pendiculus Car, n. sp., A. picus Car, n. sp., A. procerus Car, n. sp., A. quaestionis Car, n. sp., A. rupinus Car, n. sp., A. salutus Car, n. sp., A. servulus Car, n. sp., A. simmonsi Car, n. sp., A. sloanae Car, n. sp., A. spathion Car, n. sp., A. uvulus Car, n. sp., A. verutus Car, n. sp. and A. vindicatus Car, n. sp.. The number of described Antichiropus species now stands at 72. Two species (A. julianneae Car, n. sp. and A. pendiculus Car, n. sp.) lack one diagnostic feature of the genus, namely a solenomere process, but are included here because they conform to the genus definition in all other characters. We also obtained sequence data from four mitochondrial genes (cytochrome c oxidase subunit 1 [COI], cytochrome c oxidase subunit 3 [COIII], cytochrome B [CytB], and 12S rRNA [12S]), and one nuclear gene (28S rRNA [28S]) for 19 species. Three main clades were recovered: one in the northern Pilbara, one in the southern Pilbara, and one just outside the south-western margin of the Pilbara.

Open-holed trapdoor spiders of the genus Teyl (Mygalomorphae: Nemesiidae: Anamini) from Western Australia's Pilbara bioregion: a new species and expanded phylogenetic assessment.

The open-holed trapdoor spiders of the genus Teyl Main, 1975 from the Pilbara bioregion of Western Australia are investigated. A single endemic species from the southern Pilbara, T. heuretes sp. nov., is newly described, representing the northern-most occurrence of the genus in Australia. Legacy molecular data for Australian Nemesiidae, along with newly generated sequences for all described species of Teyl known from Western Australia, are analysed using Maximum Likelihood methods, providing molecular data for T. heuretes and an expanded phylogenetic assessment of the genus.

Conspicuously concealed: revision of the arid clade of the Gehyra variegata (Gekkonidae) group in Western Australia using an integrative molecular and morphological approach, with the description of five cryptic species.

The methods used to detect and describe morphologically cryptic species have advanced in recent years, owing to the integrative nature of molecular and morphological techniques required to elucidate them. Here we integrate recent phylogenomic work that sequenced many genes but few individuals, with new data from mtDNA and morphology from hundreds of gecko specimens of the Gehyra variegata group from the Australian arid zone. To better understand morphological and geographical boundaries among cryptic forms, we generated new sequences from 656 Gehyra individuals, largely assigned to G. variegata group members over a wide area in Western Australia, with especially dense sampling in the Pilbara region, and combined them with 566 Gehyra sequences from GenBank, resulting in a dataset of 1,222 specimens. Results indicated the existence of several cryptic species, from new species with diagnostic morphological characters, to cases when there were no useful characters to discriminate among genetically distinctive species. In addition, the cryptic species often showed counter-intuitive distributions, including broad sympatry among some forms and short range endemism in other cases. Two new species were on long branches in the phylogram and restricted to the northern Pilbara region: most records of the moderately sized G. incognita sp. nov. are near the coast with isolated inland records, whereas the small-bodied saxicoline G. unguiculata sp. nov. is only known from a small area in the extreme north of the Pilbara. Three new species were on shorter branches in the phylogram and allied to G. montium. The moderately sized G. crypta sp. nov. occurs in the western and southern Pilbara and extends south through the Murchison region; this species was distinctive genetically, but with wide overlap of characters with its sister species, G. montium. Accordingly, we provide a table of diagnostic nucleotides for this species as well as for all other species treated here. Two small-bodied species occur in isolated coastal regions: G. capensis sp. nov. is restricted to the North West Cape and G. ocellata sp. nov. occurs on Barrow Island and other neighbouring islands. The latter species showed evidence of introgression with the mtDNA of G. crypta sp. nov., possibly due to recent connectivity with the mainland owing to fluctuating sea levels. However, G. ocellata sp. nov. was more closely related to G. capensis sp. nov. in the phylogenomic data and in morphology. Our study illustrates the benefits of combining phylogenomic data with extensive screens of mtDNA to identify large numbers of individuals to the correct cryptic species. This approach was able to provide sufficient samples with which to assess morphological variation. Furthermore, determination of geographic distributions of the new cryptic species should greatly assist with identification in the field, demonstrating the utility of sampling large numbers of specimens across wide areas.

Oxytocin and vasopressin receptor gene variation as a proximate base for inter- and intraspecific behavioral differences in bonobos and chimpanzees.

Recent literature has revealed the importance of variation in neuropeptide receptor gene sequences in the regulation of behavioral phenotypic variation. Here we focus on polymorphisms in the oxytocin receptor gene (OXTR) and vasopressin receptor gene 1a (Avpr1a) in chimpanzees and bonobos. In humans, a single nucleotide polymorphism (SNP) in the third intron of OXTR (rs53576 SNP (A/G)) is linked with social behavior, with the risk allele (A) carriers showing reduced levels of empathy and prosociality. Bonobos and chimpanzees differ in these same traits, therefore we hypothesized that these differences might be reflected in variation at the rs53576 position. We sequenced a 320 bp region surrounding rs53576 but found no indications of this SNP in the genus Pan. However, we identified previously unreported SNP variation in the chimpanzee OXTR sequence that differs from both humans and bonobos. Humans and bonobos have previously been shown to have a more similar 5' promoter region of Avpr1a when compared to chimpanzees, who are polymorphic for the deletion of ∼ 360 bp in this region (+/- DupB) which includes a microsatellite (RS3). RS3 has been linked with variation in levels of social bonding, potentially explaining part of the interspecies behavioral differences found in bonobos, chimpanzees and humans. To date, results for bonobos have been based on small sample sizes. Our results confirmed that there is no DupB deletion in bonobos with a sample size comprising approximately 90% of the captive founder population, whereas in chimpanzees the deletion of DupB had the highest frequency. Because of the higher frequency of DupB alleles in our bonobo population, we suggest that the presence of this microsatellite may partly reflect documented differences in levels of sociability found in bonobos and chimpanzees.

Molecular systematics of the Kakaducarididae (Crustacea: Decapoda: Caridea).

The systematic relationships of the freshwater shrimp family, Kakaducarididae, were examined using mitochondrial and nuclear DNA sequences. Combined nuclear (18S rDNA, 28S rDNA, Histone) and mitochondrial (16S rDNA) analyses placed the kakaducaridid genera, Kakaducaris and Leptopalaemon, as a strongly supported clade within the Palaemonidae, in a close relationship with the genus Macrobrachium. Monophyly of the Australian Kakaducarididae was strongly supported by the molecular data. Estimated net divergence times between Kakaducaris and Leptopalaemon using mitochondrial 16S rDNA equate to a late Miocene/Pliocene split. Within Leptopalaemon, each locality was distinct for mitochondrial COI haplotypes, suggesting long-term isolation or recent genetic bottlenecks, a lack of contemporary gene flow amongst sites and a small Ne. Mitochondrial groupings within Leptopalaemon were largely congruent with several previously recognised morphotypes. Estimated net divergence times between L. gagadjui and the new Leptopalaemon morphotypes equate to a split in the late Pliocene/early Pleistocene. The hypothesis that the Kakaducarididae is comprised of relict species in specialised ecological niches is not supported by the molecular data, which instead suggest a relatively recent origin for the group in northern Australia, sometime in the late Miocene or Pliocene.