Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity

Anthropogenic trade and development have broken down dispersal barriers, facilitating the spread of diseases that threaten Earth's biodiversity. We present a global, quantitative assessment of the amphibian chytridiomycosis panzootic, one of the most impactful examples of disease spread, and demonstrate its role in the decline of at least 501 amphibian species over the past half-century, including 90 presumed extinctions. The effects of chytridiomycosis have been greatest in large-bodied, range-restricted anurans in wet climates in the Americas and Australia. Declines peaked in the 1980s, and only 12% of declined species show signs of recovery, whereas 39% are experiencing ongoing decline. There is risk of further chytridiomycosis outbreaks in new areas. The chytridiomycosis panzootic represents the greatest recorded loss of biodiversity attributable to a disease.

Three divergent lineages within an Australian marsupial (Petrogale penicillata) suggest multiple major refugia for mesic taxa in southeast Australia

Mesic southeastern Australia represents the continent's ancestral biome and is highly biodiverse, yet its phylogeographic history remains poorly understood. Here, we examine mitochondrial DNA (mtDNA) control region and microsatellite diversity in the brush-tailed rock-wallaby (Petrogale penicillata;n = 279 from 31 sites), to assess historic evolutionary and biogeographic processes in southeastern Australia. Our results (mtDNA, microsatellites) confirmed three geographically discrete and genetically divergent lineages within brush-tailed rock-wallabies, whose divergence appears to date to the mid-Pleistocene. These three lineages had been hypothesized previously but data were limited. While the Northern and Central lineages were separated by a known biogeographic barrier (Hunter Valley), the boundary between the Central and Southern lineages was not. We propose that during particularly cool glacial cycles, the high peaks of the Great Dividing Range and the narrow adjacent coastal plain resulted in a more significant north-south barrier for mesic taxa in southeastern Australia than has been previously appreciated. Similarly, located phylogeographic breaks in codistributed species highlight the importance of these regions in shaping the distribution of biodiversity in southeastern Australia and suggest the existence of three major refuge areas during the Pleistocene. Substructuring within the northern lineage also suggests the occurrence of multiple local refugia during some glacial cycles. Within the three major lineages, most brush-tailed rock-wallaby populations were locally highly structured, indicating limited dispersal by both sexes. The three identified lineages represent evolutionarily significant units and should be managed to maximize the retention of genetic diversity within this threatened species.

The impact of multiple biogeographic barriers and hybridization on species-level differentiation

PREMISE OF THE STUDY

The glacial cycles of the Quaternary did not impact Australia in the same way as Europe and North America. Here we investigate the history of population isolation, species differentiation, and hybridization in the southeastern Australian landscape, using five species of Lomatia (Proteaceae). We use a chloroplast DNA phylogeography to assess chloroplast haplotype (chlorotype) sharing among these species and whether species with shared distributions have been affected by shared biogeographic barriers. •

METHODS

We used six chloroplast DNA simple sequence repeats (cpSSR) across five species of Lomatia, sampled across their entire distributional range in southeastern Australia. Resulting size data were combined, presented as a network, and visualized on a map. Biogeographical barriers were tested using AMOVA. To explore hypotheses of chlorotype origin, we converted the network into a cladogram and reconciled with all possible species trees using parsimony-based tree mapping. •

KEY RESULTS

Some chlorotypes were shared across multiple species of Lomatia in the study, including between morphologically differentiated species. Chlorotypes were either widespread in distribution or geographically restricted to specific regions. Biogeographical structure was identified across the range of Lomatia. The most parsimonious reconciled tree incorporated horizontal transfer of chlorotypes. •

CONCLUSIONS

Lomatia shows evidence of both incomplete lineage sorting and extensive hybridization between co-occurring species. Although the species in the study appear to have responded to a number of biogeographic barriers to varying degrees, our findings identified the Hunter River Valley as the most important long-term biogeographic barrier for the genus in southeastern Australia.

Phylogeographic divergence in the widespread delicate skink (Lampropholis delicata) corresponds to dry habitat barriers in eastern Australia

BACKGROUND

The mesic habitats of eastern Australia harbour a highly diverse fauna. We examined the impact of climatic oscillations and recognised biogeographic barriers on the evolutionary history of the delicate skink (Lampropholis delicata), a species that occurs in moist habitats throughout eastern Australia. The delicate skink is a common and widespread species whose distribution spans 26° of latitude and nine major biogeographic barriers in eastern Australia. Sequence data were obtained from four mitochondrial genes (ND2, ND4, 12SrRNA, 16SrRNA) for 238 individuals from 120 populations across the entire native distribution of the species. The evolutionary history and diversification of the delicate skink was investigated using a range of phylogenetic (Maximum Likelihood, Bayesian) and phylogeographic analyses (genetic diversity, ΦST, AMOVA, Tajima's D, Fu's F statistic).

RESULTS

Nine geographically structured, genetically divergent clades were identified within the delicate skink. The main clades diverged during the late Miocene-Pliocene, coinciding with the decline and fragmentation of rainforest and other wet forest habitats in eastern Australia. Most of the phylogeographic breaks within the delicate skink were concordant with dry habitat or high elevation barriers, including several recognised biogeographic barriers in eastern Australia (Burdekin Gap, St Lawrence Gap, McPherson Range, Hunter Valley, southern New South Wales). Genetically divergent populations were also located in high elevation topographic isolates inland from the main range of L. delicata (Kroombit Tops, Blackdown Tablelands, Coolah Tops). The species colonised South Australia from southern New South Wales via an inland route, possibly along the Murray River system. There is evidence for recent expansion of the species range across eastern Victoria and into Tasmania, via the Bassian Isthmus, during the late Pleistocene.

CONCLUSIONS

The delicate skink is a single widespread, but genetically variable, species. This study provides the first detailed phylogeographic investigation of a widespread species whose distribution spans virtually all of the major biogeographic barriers in eastern Australia.

Population structure, timing of divergence and contact between lineages in the endangered Hastings River mouse (Pseudomys oralis)

Management of threatened species requires understanding their genetic structure, particularly when the potential for cryptic lineages exists for species with a broad geographic range. The Hastings River mouse (Pseudomys oralis) is an endangered species found along the eastern coast of Australia. Previous genetic investigation revealed two mitochondrial lineages, separated by an unsampled gap in northern New South Wales. Using new samples from within this gap and from throughout the species’ range, we recovered two evolutionary lineages in agreement with previous studies. Importantly, we identified Washpool National Park as the area of lineage overlap, located at the northern limit of the Macleay–McPherson Overlap Zone. We confirmed limited haplotype sharing between localities, suggesting low levels of gene flow. Historical demography suggested recent population expansion and decline for Lineages I and II, respectively. Our dating estimates placed lineage divergence at 300 000–900 000 years ago, at the lower limit of percentage divergence between other sister species in Pseudomys. While these results support separate management consideration for each lineage, nuclear markers are needed to evaluate whether these lineages represent separate species. In addition, comparative phylogeographic analyses of divergence times among lineages of other species distributed across the Macleay–McPherson Overlap Zone are needed to determine the significance of this biogeographic contact zone for ecological communities in the region generally.

Plio-pleistocene diversification and connectivity between mainland and Tasmanian populations of Australian snakes (Drysdalia, Elapidae, Serpentes)

The genus Drysdalia contains three recognised species of elapid (front-fanged) snakes, distributed across south-eastern Australia (including Tasmania). Here we aim to clarify the biogeography and phylogeographical relationships of this poorly documented region. We conducted molecular phylogenetic and dating analyses, using mitochondrial genes (ND4 and cyt-b). Our analyses suggest that divergence events among the three extant species, and among major lineages within those species, are congruent with Plio-pleistocene climatic variations. Two highly divergent genetic lineages within Drysdalia coronoides occur in Tasmania. Molecular dating suggests that these lineages were isolated from the mainland in the Pleistocene.

Phylogeography of the Australian sugar glider (Petaurus breviceps): evidence for a new divergent lineage in eastern Australia

The sugar glider (Petaurus breviceps) shows considerable variation in external morphology and mitochondrial DNA (mtDNA) diversity across its distribution in New Guinea and Australia. Here we investigate the phylogeography of P. breviceps in Australia using data from two mitochondrial genes (ND2 and ND4) and a nuclear gene (ω-globin). Phylogenetic analyses revealed the existence of two divergent mtDNA clades that are distributed over distinct geographical regions, one from coastal New South Wales and south-eastern Queensland and a second over the remaining distributional range of the species in Australia. The two groups generally had distinct ω-globin haplotypes that differed by one or two mutational steps. Analyses of Molecular Variation further supported the presence of at least two populations, accounting for 84.8% of the total mtDNA variation and 44% of the ω-globin variation. The general concordance of phylogeographic and population analyses suggests that population subdivision, possibly resulting from the combined influences of aridification after the Pliocene and uplift of the Great Dividing Range has impacted the evolution of P. breviceps. Our results also show that the geographical distribution of the two evolutionary lineages does not correspond with the distribution of the current morphological subspecies and we further propose that they be considered as separate Evolutionarily Significant Units for the purposes of conservation management.

Phylogeographic patterns in reptiles on the New England Tablelands at the south-western boundary of the McPherson Macleay Overlap

Phylogeographic studies of eastern Australia have generally supported earlier biogeographical studies based on taxon distributions by concurring in the placement of significant intraspecific boundaries. Such studies may potentially clarify biogeographic boundaries that are presently unclear, such as the poorly defined southern edges of the McPherson Macleay Overlap. Here we investigate reptile phylogeography in the northern tablelands of New South Wales to study the south-western boundaries of the Overlap as these are especially uncertain. Cytochrome b sequences from Ctenotus robustus, C. taeniolatus and Oedura lesueurii, three lizard species widespread across the New England Tablelands, were analysed by examining single-strand conformational polymorphism and DNA sequencing. In both O. lesueurii and C. taeniolatus most deeper nodes within species define geographically localised clades. This was not the case for C. robustus. Boundaries between sister-group clades were discovered in multiple locations in the region – between Glen Innes and Armidale, between Armidale and Tamworth and to the south of the Liverpool Plains. The boundaries in C. taeniolatus and O. lesueurii were probably formed in at least two different periods. The phylogeographic patterns may be partly explained by glacially induced aridity cycles in the early Pleistocene or before.

Ancient phylogeographic divergence in southeastern Australia among populations of the widespread common froglet, Crinia signifera

Geographic patterns of species diversity in southeast Australia have been attributed to changes in Pleistocene climate, but related phylogeographic patterns and processes are relatively understudied. 12S and 16S mitochondrial DNA sequences in Crinia signifera populations were used to infer historical patterns and processes in southeast Australia. Phylogenetic analysis identified three geographically restricted ancient lineages and several geographically restricted sub-clades. Present-day features that may prevent gene flow are absent between these geographic regions. Divergence among the three lineages corresponds to a late Miocene origin, approximately 9 million years ago (mya). The geographic breaks among the lineages are consistent with Miocene-Pliocene uplift in the Great Dividing Range and elevated sea levels in East Gippsland. Divergence among sub-clades in Victoria and South Australia is estimated to be within the early Pliocene, whereas sub-clades in New South Wales are estimated to have diverged near the Plio-Pleistocene boundary, approximately 2 mya. Geographic limits of sub-clades are consistent with geographic variation in advertisement calls, but are inconsistent with phylogeographic limits previously identified in other southeastern species.

Substantial genetic substructuring in southeastern and alpine Australia revealed by molecular phylogeography of the Egernia whitii (Lacertilia: Scincidae) species group

Palaeoclimatic events and biogeographical processes since the mid-Tertiary are believed to have strongly influenced the evolution and distribution of the terrestrial vertebrate fauna of southeastern Australia. We examined the phylogeography of the temperate-adapted members of the Egernia whitii species group, a group of skinks that comprise both widespread low- to mid-elevation (E. whitii) and montane-restricted species (Egernia guthega, Egernia montana), in order to obtain important insights into the influence of past biogeographical processes on the herpetofauna of southeastern Australia. Sequence data were obtained from all six temperate-adapted species within the E. whitii species group, and specifically from across the distributional ranges of E. whitii, E. guthega and E. montana. We targeted a fragment of the ND4 mitochondrial gene (696 bp) and analysed the data using maximum likelihood and Bayesian methods. Our data reveal a deep phylogeographical break in the east Gippsland region of Victoria between 'northern' (Queensland, New South Wales, Australian Capital Territory) and 'southern' (Victoria, Tasmania, South Australia) populations of E. whitii. This divergence appears to have occurred during the late Miocene-Pliocene, with the Gippsland basin possibly forming a geographical barrier to dispersal. Substantial structuring within both the 'northern' and the 'southern' clades is consistent with the effects of Plio-Pleistocene glacial-interglacial cycles. Pleistocene glacial cycles also appear to have shaped the phylogeographical patterns observed in the alpine species, E. guthega and E. montana. We used our results to examine the biogeographical process that led to the origin and subsequent diversification of the lowland and alpine herpetofauna of southeastern Australia.

Phylogeography of an east Australian wet-forest bird, the satin bowerbird (Ptilonorhynchus violaceus), derived from mtDNA, and its relationship to morphology

Australian wet forests have undergone a contraction in range since the mid-Tertiary, resulting in a fragmented distribution along the east Australian coast incorporating several biogeographical barriers. Variation in mitochondrial DNA and morphology within the satin bowerbird was used to examine biogeographical structure throughout almost the entire geographical extent of these wet forest fragments. We used several genetic analysis techniques, nested clade and barrier analyses, that use patterns inherent in the data to describe the spatial structuring. We also examined the validity of the two previously described satin bowerbird subspecies that are separated by well-defined biogeographical barriers and tested existing hypotheses that propose divergence occurs within each subspecies across two other barriers, the Black Mountain corridor and the Hunter Valley. Our data showed that the two subspecies were genetically and morphologically divergent. The northern subspecies, found in the Wet Tropics region of Queensland, showed little divergence across the Black Mountain corridor, a barrier found to be significant in other Wet Tropics species. Biogeographical structure was found through southeastern Australia; three geographically isolated populations showed genetic differentiation, although minimal divergence was found across the proposed Hunter Valley barrier. A novel barrier was found separating inland and coastal populations in southern New South Wales. Little morphological divergence was observed within subspecies, bar a trend for birds to be larger in the more southerly parts of the species' range. The results from both novel and well-established genetic analyses were similar, providing greater confidence in the conclusions about spatial divergence and supporting the validity of these new techniques.

Intraspecific phylogeography in the sedge frog Litoria fallax (Hylidae) indicates pre-Pleistocene vicariance of an open forest species from eastern Australia

The eastern sedge frog Litoria fallax (Anura: Hylidae) is common throughout the open forests and coastal wetlands along the eastern coast of Australia. Its range spans four biogeographical zones from northern Queensland to central New South Wales. Phylogenetic analysis of mitochondrial DNA (mtDNA) haplotypes of 87 L. fallax individuals from 22 populations identified two major mtDNA lineages, differing by 11-12% sequence divergence. The two clades of haplotypes were separated by the McPherson Range, indicating that this mesic upland area has acted as a major long-term barrier to gene flow for this open forest species. Slight isolation by distance was observed within both the northern and southern lineages but was insufficient to explain the large sequence divergence between lineages. Within the northern lineage, additional phylogeographical structure was observed across the relatively dry Burdekin Gap which separates Atherton populations from all populations in the central and eastern Queensland biogeographical zones. There was less phylogeographical structure in the southern lineage suggesting historical gene flow across the drier portions of the Great Dividing Range. These data, together with recent observations of deep phylogeographical divergences in rainforest-restricted Litoria suggest that the east coast hylids of Australia represent an old (Tertiary) radiation. Individual species of Litoria have been strongly affected by climatic and ecological barriers to gene flow during the Quaternary.