Rapid divergent evolution of internal female genitalia and the coevolution of male genital morphology revealed by micro-computed tomography.

Animal genitalia are thought to evolve rapidly and divergently in response to sexual selection. Studies of genital evolution have focused largely on male genitalia. The paucity of work on female genital morphology is probably due to problems faced in quantifying shape variation, due to their composition and accessibility. Here we use a combination of micro-computed tomography, landmark free shape quantification and phylogenetic analysis to quantify the rate of female genital shape evolution among 29 species of Antichiropus millipedes, and their coevolution with male genitalia. We found significant variation in female and male genital shape among species. Male genital shape showed a stronger phylogenetic signal than female genital shape, although the phylogenetic signal effect sizes did not differ significantly. Male genital shape was found to be evolving 1.2 times faster than female genital shape. Female and male genital shape exhibited strong correlated evolution, indicating that genital shape changes in one sex are associated with corresponding changes in the genital shape of the other sex. This study adds novel insight into our growing understanding of how female genitalia can evolve rapidly and divergently, and highlights the advantages of three-dimensional techniques and multivariate analyses in studies of female genital evolution.

The systematics of the pseudoscorpion genus Indohya (Pseudoscorpiones: Hyidae) in Australia.

The pseudoscorpion genus Indohya Beier, 1974 is known to occur in three Gondwanan fragments around the Indian Oceansouthern India, Madagascar and north-western Australiasuggesting that the genus had evolved prior to the breakup of Gondwana and was present on each landmass as they rifted apart during the Mesozoic. The Australian fauna is the most diverse, with nine species previously described from Cape Range and the Kimberley region of north-western Australia. The present study documents the genus Indohya in Australia using a combination of morphology and DNA sequence data. We found a total of 36 species, including 27 new species. The majority of the Pilbara fauna consist of blind troglobites collected from subterranean ecosystems, with an additional three eyed species from epigean habitats. The new species consist of one from Cape Range (I. anastomosa Harvey & Burger, n. sp.), 21 from the Pilbara (I. adlardi Harvey & Burger, n. sp., I. alexanderi Harvey & Burger, n. sp., I. aphana Harvey & Burger, n. sp., I. aquila Harvey & Burger, n. sp., I. arcana Harvey & Burger, n. sp., I. arnoldstrongi Harvey & Burger, n. sp., I. boltoni Harvey & Burger, n. sp., I. cardo Harvey & Burger, n. sp., I. catherineae Harvey & Burger, n. sp., I. cockingi Harvey & Burger, n. sp., I. cribbi Harvey & Burger, n. sp., I. draconis Harvey & Burger, n. sp., I. furtiva Harvey & Burger, n. sp., I. incomperta Harvey & Burger, n. sp., I. jessicae Harvey & Burger, n. sp., I. lynbeazlyeae Harvey & Burger, n. sp., I. morganstrongi Harvey & Burger, n. sp., I. rixi Harvey & Burger, n. sp., I. sagmata Harvey & Burger, n. sp., I. scanloni Harvey & Burger, n. sp. and I. silenda Harvey & Burger, n. sp.) and five from the Kimberley (I. currani Harvey & Burger, n. sp., I. finitima Harvey & Burger, n. sp., I. julianneae Harvey & Burger, n. sp., I. karenae Harvey & Burger, n. sp. and I. sachsei Harvey & Burger, n. sp.). The study is augmented with sequence data from 29 species of Indohya, including all of the 24 species recorded from the Pilbara and Cape Range, and five of the 12 known Kimberley species. Seven clades recovered during the molecular analysis are only represented by nymphs, but we used COI sequence data to diagnose these species in the absence of adult morphological data.

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.

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.

Multi-Species Phylogeography of Arid-Zone Sminthopsinae (Marsupialia: Dasyuridae) Reveals Evidence of Refugia and Population Expansion in Response to Quaternary Change.

Historical population contraction and expansion events associated with Pleistocene climate change are important drivers of intraspecific population structure in Australian arid-zone species. We compared phylogeographic patterns among arid-adapted Dasyuridae (Sminthopsis and Planigale) with close phylogenetic relationships and similar ecological roles to investigate the drivers of phylogeographic structuring and the importance of historical refugia. We generated haplotype networks for two mitochondrial (control region and cytochrome b) and one nuclear (omega-globin) gene from samples distributed across each species range. We used ΦST to test for a genetic population structure associated with the four Pilbara subregions, and we used expansion statistics and Bayesian coalescent skyline analysis to test for signals of historical population expansion and the timing of such events. Significant population structure associated with the Pilbara and subregions was detected in the mitochondrial data for most species, but not with the nuclear data. Evidence of population expansion was detected for all species, and it likely began during the mid-late Pleistocene. The timing of population expansion suggests that these species responded favorably to the increased availability of arid habitats during the mid-late Pleistocene, which is when previously patchy habitats became more widespread. We interpret our results to indicate that the Pilbara region could have acted as a refugium for small dasyurids.

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.

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.

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.

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.

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.

Conservation systematics of the shield-backed trapdoor spiders of the nigrum-group (Mygalomorphae, Idiopidae, Idiosoma): integrative taxonomy reveals a diverse and threatened fauna from south-western Australia.

The aganippine shield-backed trapdoor spiders of the monophyletic nigrum-group of Idiosoma Ausserer s. l. are revised, and 15 new species are described from Western Australia and the Eyre Peninsula of South Australia: I. arenaceum Rix & Harvey, sp. n., I. corrugatum Rix & Harvey, sp. n., I. clypeatum Rix & Harvey, sp. n., I. dandaragan Rix & Harvey, sp. n., I. formosum Rix & Harvey, sp. n., I. gardneri Rix & Harvey, sp. n., I. gutharuka Rix & Harvey, sp. n., I. incomptum Rix & Harvey, sp. n., I. intermedium Rix & Harvey, sp. n., I. jarrah Rix & Harvey, sp. n., I. kopejtkaorum Rix & Harvey, sp. n., I. kwongan Rix & Harvey, sp. n., I. mcclementsorum Rix & Harvey, sp. n., I. mcnamarai Rix & Harvey, sp. n., and I. schoknechtorum Rix & Harvey, sp. n. Two previously described species from south-western Western Australia, I. nigrum Main, 1952 and I. sigillatum (O. P.-Cambridge, 1870), are re-illustrated and re-diagnosed, and complementary molecular data for 14 species and seven genes are analysed with Bayesian methods. Members of the nigrum-group are of long-standing conservation significance, and I. nigrum is the only spider in Australia to be afforded threatened species status under both State and Commonwealth legislation. Two other species, I. formosum Rix & Harvey, sp. n. and I. kopejtkaorum Rix & Harvey, sp. n., are also formally listed as Endangered under Western Australian State legislation. Here we significantly relimit I. nigrum to include only those populations from the central and central-western Wheatbelt bioregion, and further document the known diversity and conservation status of all known species.

Genome-Wide SNPs Identify Limits to Connectivity in the Extreme Freshwater Disperser, Spangled Perch Leiopotherapon unicolor (Terapontidae).

The utility of restriction-site associated DNA sequencing (RADseq) to resolve fine-scale population structure was tested on an abundant and vagile fish species in a tropical river. Australia's most widespread freshwater fish, the "extreme disperser" Leiopotherapon unicolor was sampled from 6 locations in an unregulated system, the Daly River in Australia's Northern Territory. Despite an expectation of high connectivity based on life history knowledge of this species derived from arid zone habitats, L. unicolor was not a panmictic population in the tropical lower Daly. Using ~14000 polymorphic RADseq loci, we found a pattern of upstream versus downstream population subdivision and evidence for differentiation among tributary populations. The magnitude of population structure was low with narrow confidence intervals (global FST = 0.014; 95% CI = 0.012-0.016). Confidence intervals around pairwise FST estimates were all nonzero and consistent with the results of clustering analyses. This population structure was not explained by spatially heterogeneous selection acting on a subset of loci, or by sampling groups of closely related individuals (average within-site relatedness ≈ 0). One implication of the low but significant structure observed in the tropics is the possibility that L. unicolor may exhibit contrasting patterns of migratory biology in tropical versus arid zone habitats. We conclude that the RADseq revolution holds promise for delineating subtle patterns of population subdivision in species characterized by high within-population variation and low among-population differentiation.

Extremely low microsatellite diversity but distinct population structure in a long-lived threatened species, the Australian lungfish Neoceratodus forsteri (Dipnoi).

The Australian lungfish is a unique living representative of an ancient dipnoan lineage, listed as 'vulnerable' to extinction under Australia's Environment Protection and Biodiversity Conservation Act 1999. Historical accounts indicate this species occurred naturally in two adjacent river systems in Australia, the Burnett and Mary. Current day populations in other rivers are thought to have arisen by translocation from these source populations. Early genetic work detected very little variation and so had limited power to answer questions relevant for management including how genetic variation is partitioned within and among sub-populations. In this study, we use newly developed microsatellite markers to examine samples from the Burnett and Mary Rivers, as well as from two populations thought to be of translocated origin, Brisbane and North Pine. We test whether there is significant genetic structure among and within river drainages; assign putatively translocated populations to potential source populations; and estimate effective population sizes. Eleven polymorphic microsatellite loci genotyped in 218 individuals gave an average within-population heterozygosity of 0.39 which is low relative to other threatened taxa and for freshwater fishes in general. Based on FST values (average over loci = 0.11) and STRUCTURE analyses, we identify three distinct populations in the natural range, one in the Burnett and two distinct populations in the Mary. These analyses also support the hypothesis that the Mary River is the likely source of translocated populations in the Brisbane and North Pine rivers, which agrees with historical published records of a translocation event giving rise to these populations. We were unable to obtain bounded estimates of effective population size, as we have too few genotype combinations, although point estimates were low, ranging from 29 - 129. We recommend that, in order to preserve any local adaptation in the three distinct populations that they be managed separately.

Low interbasin connectivity in a facultatively diadromous fish: evidence from genetics and otolith chemistry.

Southern smelts (Retropinna spp.) in coastal rivers of Australia are facultatively diadromous, with populations potentially containing individuals with diadromous or wholly freshwater life histories. The presence of diadromous individuals is expected to reduce genetic structuring between river basins due to larval dispersal via the sea. We use otolith chemistry to distinguish between diadromous and nondiadromous life histories and population genetics to examine interbasin connectivity resulting from diadromy. Otolith strontium isotope ((87) Sr:(86) Sr) transects identified three main life history patterns: amphidromy, freshwater residency and estuarine/marine residency. Despite the potential for interbasin connectivity via larval mixing in the marine environment, we found unprecedented levels of genetic structure for an amphidromous species. Strong hierarchical structure along putative taxonomic boundaries was detected, along with highly structured populations within groups using microsatellites (FST  = 0.046-0.181), and mtDNA (ΦST  = 0.498-0.816). The presence of strong genetic subdivision, despite the fact that many individuals reside in saline water during their early life history, appears incongruous. However, analysis of multielemental signatures in the otolith cores of diadromous fish revealed strong discrimination between river basins, suggesting that diadromous fish spend their early lives within chemically distinct estuaries rather than the more homogenous marine environment, thus avoiding dispersal and maintaining genetic structure.

Aquatic Insects in Eastern Australia: A Window on Ecology and Evolution of Dispersal in Streams.

Studies of connectivity of natural populations are often conducted at different timescales. Studies that focus on contemporary timescales ask questions about dispersal abilities and dispersal behavior of their study species. In contrast, studies conducted at historical timescales are usually more focused on evolutionary or biogeographic questions. In this paper we present a synthesis of connectivity studies that have addressed both these timescales in Australian Trichoptera and Ephemeroptera. We conclude that: (1) For both groups, the major mechanism of dispersal is by adult flight, with larval drift playing a very minor role and with unusual patterns of genetic structure at fine scales explained by the "patchy recruitment hypothesis"; (2) There is some evidence presented to suggest that at slightly larger spatial scales (~100 km) caddisflies may be slightly more connected than mayflies; (3) Examinations of three species at historical timescales showed that, in southeast Queensland Australia, despite there being no significant glaciation during the Pleistocene, there are clear impacts of Pleistocene climate changes on their genetic structure; and (4) The use of mitochondrial DNA sequence data has uncovered a number of cryptic species complexes in both trichopterans and ephemeropterans. We conclude with a number of suggestions for further work.