Multiple biogeographical barriers identified across the monsoon tropics of northern Australia: phylogeographic analysis of the brachyotis group of rock-wallabies

Dragons in the tropics - Phylogeography and speciation in Diporiphora lizards and common geographic breaks in co-distributed taxa

Co-distributed taxa can respond both similarly or differently to the same climatic and geological events, resulting in a range of phylogeographic patterns across the region. Using a nested approach on a taxonomically diverse yet morphologically conservative group of agamid lizards, we first aimed to evaluate more precisely the extent of phylogeographic structuring within the genus. Then, focusing on four lineages within the more widespread species, we assessed the impact of biogeographic barriers on phylogeographic structuring and demographic history of species, comparing to patterns previously observed in co-distributed taxa. These species occur in the Australian Monsoonal Tropics, a vast tropical savanna system with high richness and endemism associated with environmental heterogeneity and past climate fluctuations. The employment of genomic data helped to determine the relationships between specific taxa that were previously difficult to place. We found a local influence of biogeographic and climatic breaks on population dynamics, analogous to other species. We detected high levels of population structure in the West Kimberley and Arnhem Plateau, which are already known for high endemism. However, we also highlighted unique lineages in areas that have been overlooked until recently, in the South Kimberley and West Top End. Climatic and geographical features in the Arnhem Plateau act as a soft barrier between populations in the east and west regions of the Top End. These observations reflect patterns observed for other vertebrates across this rich biome, indicating how climatic variation, species' ecology, and landscape features interact to shape regional diversity and endemism.

Revision of Litoria rothii (Anura: Pelodryadidae) from northern Australia

Litoria rothii is a widespread pelodryadid frog with a charismatic laughing advertisement call, distributed across the Australian Monsoon Tropics and southern New Guinea. Given its large distribution spanning well-known biogeographic barriers, variation in male advertisement calls and the prevalence of unresolved species complexes in the Australian frog fauna, we examine the genetic, morphological and acoustic diversity in the species from across its range. Our analyses reveal the presence of a previously unrecognised species in western parts of the range of L. rothii sensu lato, which we describe herein as a new species. Litoria ridibunda sp. nov. is distinguished from L. rothii on the basis of paraphyly of nuclear gene trees with L. everetti from Indonesia, colour patterns on the posterior thigh and male advertisement calls. Compared to L. rothii, the new species has a less contrasting pattern on the posterior thigh and a male advertisement call with a greater number of notes per call and a greater call duration. In particular, the magnitude of call differences between the species is highest where the ranges of the two species are in proximity in north-western Queensland. Our study further emphasises the undiagnosed diversity that remains in Australian frogs, even in relatively large, charismatic, frequently encountered species that often share human dwellings.

Multilocus phylogeography, population genetics and niche evolution of Australian brown and black-tailed treecreepers (Aves: Climacteris)

The Carpentarian barrier across north-eastern Australia is a major biogeographic barrier and a generator of biodiversity within the Australian Monsoonal Tropics. Here we present a continent-wide analysis of mitochondrial (control region) and autosomal (14 anonymous loci) sequence and indel variation and niche modelling of brown and black-tailed treecreepers (Climacteris picumnus and Climacteris melanurus), a clade with a classic distribution on either side of the Carpentarian barrier. mtDNA control region sequences exhibited reciprocal monophyly and strong differentiation (Fst = 0.91), and revealed a signature of a recent selective sweep in C. picumnus. A variety of tests support an isolation-with-migration model of divergence, albeit with low levels of gene flow across the Carpentarian barrier and a divergence time between species of ~1.7–2.8 Mya. Palaeoecological niche models show that both range size as measured by available habitat and estimated historical population sizes of both species declined in the past ~600 kyr and that the area of interspecific range overlap was never historically large, perhaps decreasing opportunities for extensive gene flow. The relatively long divergence time and low opportunity for gene flow may have facilitated speciation more so than in other co-distributed bird taxa across the Australian Monsoonal Tropics.

Initiation of speciation across multiple dimensions in a rock-restricted, tropical lizard

Population isolation and concomitant genetic divergence, resulting in strong phylogeographical structure, is a core aspect of speciation initiation. If and how speciation then proceeds and ultimately completes depends on multiple factors that mediate reproductive isolation, including divergence in genomes, ecology and mating traits. Here we explored these multiple dimensions in two young (Plio-Pleistocene) species complexes of gekkonid lizards (Heteronotia) from the Kimberley-Victoria River regions of tropical Australia. Using mitochondrial DNA screening and exon capture phylogenomics, we show that the rock-restricted Heteronotia planiceps exhibits exceptional fine-scale phylogeographical structure compared to the codistributed habitat generalist Heteronotia binoei. This indicates pervasive population isolation and persistence in the rock-specialist, and thus a high rate of speciation initiation across this geographically complex region, with levels of genomic divergence spanning the "grey zone" of speciation. Proximal lineages of H. planiceps were often separated by different rock substrates, suggesting a potential role for ecological isolation; however, phylogenetic incongruence and historical introgression were inferred between one such pair. Ecomorphological divergence among lineages within both H. planiceps and H. binoei was limited, except that limestone-restricted lineages of H. planiceps tended to be larger than rock-generalists. By contrast, among-lineage divergence in the chemical composition of epidermal pore secretions (putative mating trait) exceeded ecomorphology in both complexes, but with less trait overlap among lineages in H. planiceps. This system-particularly the rock-specialist H. planiceps-highlights the role of multidimensional divergence during incipient speciation, with divergence in genomes, ecomorphology and chemical signals all at play at very fine spatial scales.

Sequence Capture From Historical Museum Specimens: Maximizing Value for Population and Phylogenomic Studies

The application of high-throughput, short-read sequencing to degraded DNA has greatly increased the feasibility of generating genomic data from historical museum specimens. While many published studies report successful sequencing results from historical specimens; in reality, success and quality of sequence data can be highly variable. To examine predictors of sequencing quality, and methodological approaches to improving data accuracy, we generated and analyzed genomic sequence data from 115 historically collected museum specimens up to 180 years old. Data span both population genomic and phylogenomic scales, including historically collected specimens from 34 specimens of four species of Australian rock-wallabies (genus Petrogale) and 92 samples from 79 specimens of Australo-Papuan murine rodents (subfamily Murinae). For historical rodent specimens, where the focus was sampling for phylogenomics, we found that regardless of specimen age, DNA sequence libraries prepared from toe pad or bone subsamples performed significantly better than those taken from the skin (in terms of proportion of reads on target, number of loci captured, and data accuracy). In total, 93% of DNA libraries from toe pad or bone subsamples resulted in reliable data for phylogenetic inference, compared to 63% of skin subsamples. For skin subsamples, proportion of reads on target weakly correlated with collection year. Then using population genomic data from rock-wallaby skins as a test case, we found substantial improvement in final data quality by mapping to a high-quality “closest sister” de novo assembly from fresh tissues, compared to mapping to a sample-specific historical de novo assembly. Choice of mapping approach also affected final estimates of the number of segregating sites and Watterson's θ, both important parameters for population genomic inference. The incorporation of accurate and reliable sequence data from historical specimens has important outcomes for evolutionary studies at both population and phylogenomic scales. By assessing the outcomes of different approaches to specimen subsampling, library preparation and bioinformatic processing, our results provide a framework for increasing sequencing success for irreplaceable historical specimens.

Identification of a novel hybrid zone within the black-footed rock-wallaby (Petrogale lateralis) in Western Australia

It is increasingly recognised that intertaxon hybridisation is more common in vertebrates than previously thought. However, recent hybridisation has rarely been reported from wild marsupials, with only three instances of first generation (F1) hybrids reported, all in macropodids. In the 1990s a chromosomally anomalous population of black-footed rock-wallaby (Petrogale lateralis) was identified in the Townsend Ridges in central eastern Western Australia. Individuals from this population had chromosomes characteristic of two P. lateralis subspecies (P. l. centralis and P. l. kimberleyensis). This unusual mixture is suggestive of a novel hybrid zone between subspecies, but it could also represent a P. l. centralis population in which a 9–10 chromosome fusion has independently arisen. To test between these hypotheses, we compared mitochondrial DNA Control Region (CR) sequence data from Townsend Ridges individuals to published data for all P. lateralis subspecies. Two divergent lineages of CR haplotypes were identified at Townsend Ridges, suggesting that it represents a novel rock-wallaby hybrid zone, the third reported in the genus. While one CR haplotype clustered with those typical of P. l. centralis, the other Townsend Ridges haplotypes clustered with those from three different P. lateralis subspecies but not with P. l. kimberleyensis. Additional studies with multiple nuclear genes will be necessary to fully understand the nature of this novel hybrid zone.

A revision of the bioregionalisation of freshwater fish communities in the Australian Monsoonal Tropics

The Australian freshwater fish fauna is very unique, but poorly understood. In the Australian Monsoonal Tropics (AMT) biome of northern Australia, the number of described and candidate species has nearly doubled since the last attempt to analyse freshwater fish species composition patterns and determine a bioregionalisation scheme. Here, we utilise the most complete database of catchment-scale freshwater fish distributions from the AMT to date to: (a) reanalyze spatial patterns of species richness, endemism and turnover of freshwater fishes; (b) propose a biogeographic regionalisation based on species turnover; (c) assess the relationship between species turnover and patterns of environmental change and historic drainage connectivity; and (d) identify sampling gaps. Biogeographic provinces were identified using an agglomerative cluster analysis of a Simpson's beta (β sim) dissimilarity matrix. A generalised dissimilarity model incorporating eighteen environmental variables was used to investigate the environmental correlates of species turnover. Observed and estimated species richness and endemism were calculated and inventory completeness was estimated based on the ratio of observed to estimated species richness. Three major freshwater fish biogeographic provinces and 14 subprovinces are proposed. These differ substantially from the current bioregionalisation scheme. Species turnover was most strongly influenced by environmental variables that are interpreted to reflect changes in terrain (catchment relief and confinement), geology and climate (runoff perenniality, stream density), and biotic responses to climate (net primary productivity). Past connectivity between rivers during low sea-level events is also influential highlighting the importance of historical processes in explaining contemporary patterns of biodiversity in the AMT. The inclusion of 49 newly discovered species and candidate species only reinforced known focal points of species richness and endemism in the AMT. However, a number of key sampling gaps remain that need to be filled to fully characterise the proposed bioregionalisation.

On and off the rocks: persistence and ecological diversification in a tropical Australian lizard radiation

Background

Congruent patterns in the distribution of biodiversity between regions or habitats suggest that key factors such as climatic and topographic variation may predictably shape evolutionary processes. In a number of tropical and arid biomes, genetic analyses are revealing deeper and more localised lineage diversity in rocky ranges than surrounding habitats. Two potential drivers of localised endemism in rocky areas are refugial persistence through climatic change, or ecological diversification and specialisation. Here we examine how patterns of lineage and phenotypic diversity differ across two broad habitat types (rocky ranges and open woodlands) in a small radiation of gecko lizards in the genus Gehyra (the australis group) from the Australian Monsoonal Tropics biome.

Results

Using a suite of approaches for delineating evolutionarily independent lineages, we find between 26 and 41 putative evolutionary units in the australis group (versus eight species currently recognised). Rocky ranges are home to a greater number of lineages that are also relatively more restricted in distribution, while lineages in open woodland habitats are fewer, more widely distributed, and, in one case, show evidence of range expansion. We infer at least two shifts out of rocky ranges and into surrounding woodlands. Phenotypic divergence between rocky ranges specialist and more generalist taxa is detected, but no convergent evolutionary regimes linked to ecology are inferred.

Conclusions

In climatically unstable biomes such as savannahs, rocky ranges have functioned as zones of persistence, generators of diversity and a source of colonists for surrounding areas. Phenotypic divergence can also be linked to the use of differing habitat types, however, the extent to which ecological specialisation is a primary driver or secondary outcome of localised diversification remains uncertain.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1408-1) contains supplementary material, which is available to authorized users.

Pleistocene-dated biogeographic barriers drove divergence within the Australo-Papuan region in a sex-specific manner: an example in a widespread Australian songbird

Understanding how environmental change has shaped species evolution can inform predictions of how future climate change might continue to do so. Research of widespread biological systems spanning multiple climates that have been subject to environmental change can yield generalizable inferences about the neutral and adaptive processes driving lineage divergence during periods of environmental change. We contribute to the growing body of multi-locus phylogeographic studies investigating the effect of Pleistocene climate change on species evolution by focusing on a widespread Australo-Papuan songbird with several mitochondrial lineages that diverged during the Pleistocene, the grey shrike-thrush (Colluricincla harmonica). We employed multi-locus phylogenetic, population genetic and coalescent analyses to (1) assess whether nuclear genetic diversity suggests a history congruent with that based on phenotypically defined subspecies ranges, mitochondrial clade boundaries and putative biogeographical barriers, (2) estimate genetic diversity within and genetic differentiation and gene flow among regional populations and (3) estimate population divergence times. The five currently recognized subspecies of grey shrike-thrush are genetically differentiated in nuclear and mitochondrial genomes, but connected by low levels of gene flow. Divergences among these populations are concordant with recognized historical biogeographical barriers and date to the Pleistocene. Discordance in the order of population divergence events based on mitochondrial and nuclear genomes suggests a history of sex-biased gene flow and/or mitochondrial introgression at secondary contacts. This study demonstrates that climate change can impact sexes with different dispersal biology in different ways. Incongruence between population and mitochondrial trees calls for a genome-wide investigation into dispersal, mitochondrial introgression and mitonuclear evolution.

Identification of a remnant population of the black-flanked rock-wallaby (Petrogale lateralis lateralis) in Kalbarri National Park, Western Australia, and implications for its management

Black-flanked rock-wallabies (Petrogale lateralis lateralis) were thought to be locally extinct in Kalbarri National Park, Western Australia, until 2015 when a pair were photographed in the Murchison River gorge. Subsequent searches failed to locate any other populations and, in combination with previous surveys, suggest that these animals were the sole survivors of a formerly abundant population. Efforts to capture the rock-wallabies to obtain tissue samples and ascertain their genetic affinities were unsuccessful. However, fresh faecal material was collected and a ~600-bp fragment of DNA sequence data was obtained from a mitochondrial DNA gene. The Kalbarri rock-wallabies were found to be genetically distinct from all other sampled populations of P. l. lateralis. They were genetically most similar to rock-wallabies in the Calvert Range, 950km to the north-east in the Little Sandy Desert. Nearer populations in Cape Range (600km north) and the Western Australian Wheatbelt (500km south-east) were less closely related. Following evaluation of a variety of factors, including population size, genetics, demography, ecology, environment and logistics, a decision was made to supplement the Kalbarri National Park population with females sourced from the Western Australian Wheatbelt. In May 2016 three females were released at the same site as the Kalbarri pair to try to ensure the survival of the population whilst still preserving unique Kalbarri alleles.

Chromosome Evolution in Marsupials

Marsupials typically possess very large, distinctive chromosomes that make them excellent subjects for cytogenetic analysis, and the high level of conservation makes it relatively easy to track chromosome evolution. There are two speciose marsupial families with contrasting rates of karyotypic evolution that could provide insight into the mechanisms driving genome reshuffling and speciation. The family Dasyuridae displays exceptional karyotype conservation with all karyotyped species possessing a 2n = 14 karyotype similar to that predicted for the ancestral marsupial. In contrast, the family Macropodidae has experienced a higher rate of genomic rearrangement and one genus of macropods, the rock-wallabies (Petrogale), has experienced extensive reshuffling. For at least some recently diverged Petrogale species, there is still gene flow despite hybrid fertility issues, making this species group an exceptional model for studying speciation. This review highlights the unique chromosome features of marsupial chromosomes, particularly for these two contrasting families, and the value that a combined cytogenetics, genomics, and epigenomics approach will have for testing models of genome evolution and speciation.

Reticulation, divergence, and the phylogeography-phylogenetics continuum

Phylogeography, and its extensions into comparative phylogeography, have their roots in the layering of gene trees across geography, a paradigm that was greatly facilitated by the nonrecombining, fast evolution provided by animal mtDNA. As phylogeography moves into the era of next-generation sequencing, the specter of reticulation at several levels-within loci and genomes in the form of recombination and across populations and species in the form of introgression-has raised its head with a prominence even greater than glimpsed during the nuclear gene PCR era. Here we explore the theme of reticulation in comparative phylogeography, speciation analysis, and phylogenomics, and ask how the centrality of gene trees has fared in the next-generation era. To frame these issues, we first provide a snapshot of multilocus phylogeographic studies across the Carpentarian Barrier, a prominent biogeographic barrier dividing faunas spanning the monsoon tropics in northern Australia. We find that divergence across this barrier is evident in most species, but is heterogeneous in time and demographic history, often reflecting the taxonomic distinctness of lineages spanning it. We then discuss a variety of forces generating reticulate patterns in phylogeography, including introgression, contact zones, and the potential selection-driven outliers on next-generation molecular markers. We emphasize the continued need for demographic models incorporating reticulation at the level of genomes and populations, and conclude that gene trees, whether explicit or implicit, should continue to play a role in the future of phylogeography.

Congruent biogeographical disjunctions at a continent-wide scale: Quantifying and clarifying the role of biogeographic barriers in the Australian tropics

AIM

To test whether novel and previously hypothesized biogeogaphic barriers in the Australian Tropics represent significant disjunction points or hard barriers, or both, to the distribution of plants.

LOCATION

Australian tropics: Australian Monsoon Tropics and Australian Wet Tropics.

METHODS

The presence or absence of 6,861 plant species was scored across 13 putative biogeographic barriers in the Australian Tropics, including two that have not previously been recognised. Randomizations of these data were used to test whether more species showed disjunctions (gaps in distribution) or likely barriers (range limits) at these points than expected by chance.

RESULTS

Two novel disjunctions in the Australian Tropics flora are identified in addition to eleven putative barriers previously recognized for animals. Of these, eleven disjunction points (all within the Australian Monsoon Tropics) were found to correspond to range-ending barriers to a significant number of species, while neither of the two disjunctions found within the Australian Wet Tropics limited a significant number of species' ranges.

MAIN CONCLUSIONS

Biogeographic barriers present significant distributional limits to native plant species in the Australian Monsoon Tropics but not in the Australian Wet Tropics.

Chromosomal Speciation in the Genomics Era: Disentangling Phylogenetic Evolution of Rock-wallabies

The association of chromosome rearrangements (CRs) with speciation is well established, and there is a long history of theory and evidence relating to "chromosomal speciation." Genomic sequencing has the potential to provide new insights into how reorganization of genome structure promotes divergence, and in model systems has demonstrated reduced gene flow in rearranged segments. However, there are limits to what we can understand from a small number of model systems, which each only tell us about one episode of chromosomal speciation. Progressing from patterns of association between chromosome (and genic) change, to understanding processes of speciation requires both comparative studies across diverse systems and integration of genome-scale sequence comparisons with other lines of evidence. Here, we showcase a promising example of chromosomal speciation in a non-model organism, the endemic Australian marsupial genus Petrogale. We present initial phylogenetic results from exon-capture that resolve a history of divergence associated with extensive and repeated CRs. Yet it remains challenging to disentangle gene tree heterogeneity caused by recent divergence and gene flow in this and other such recent radiations. We outline a way forward for better integration of comparative genomic sequence data with evidence from molecular cytogenetics, and analyses of shifts in the recombination landscape and potential disruption of meiotic segregation and epigenetic programming. In all likelihood, CRs impact multiple cellular processes and these effects need to be considered together, along with effects of genic divergence. Understanding the effects of CRs together with genic divergence will require development of more integrative theory and inference methods. Together, new data and analysis tools will combine to shed light on long standing questions of how chromosome and genic divergence promote speciation.

Phylogeographic evidence for evolutionary refugia in the Gulf sandstone ranges of northern Australia

Locating and protecting climate change refugia is important to conserving biodiversity with accelerating climate change. Comparative phylogeographic analysis provides an effective tool for locating such refugia, as long-term retention of one or more populations within a refugial landscape will generate unique genetic lineages. The ranges of the western Gulf region of northern Australia are thought to represent a significant arid-zone refugium, in which case low-dispersal organisms should have strong phylogeographic structure across the region. To test for this, we conducted extensive sampling of three species of Gehyra geckos and analysed diversity for mitochondrial DNA and eight nuclear loci. These analyses revealed congruent and high phylogeographic diversity, especially, but not exclusively, in rock-restricted species. This finding, and other recent phylogeographic evidence, demonstrates that these topographically variable landforms have enabled persistence of ecologically diverse vertebrate species through the climate changes of the late Pleistocene. Identification of this relatively under-protected region as a significant climate change refugium points to the need to expand protected areas in this region and to invest in ecological management across existing National Parks and Indigenous Protected Areas.

Three Molecular Markers Show No Evidence of Population Genetic Structure in the Gouldian Finch (Erythrura gouldiae)

Assessment of genetic diversity and connectivity between regions can inform conservation managers about risk of inbreeding, potential for adaptation and where population boundaries lie. The Gouldian finch (Erythrura gouldiae) is a threatened species in northern Australia, occupying the savannah woodlands of the biogeographically complex monsoon tropics. We present the most comprehensive population genetic analysis of diversity and structure the Gouldian finch using 16 microsatellite markers, mitochondrial control region and 3,389 SNPs from genotyping-by-sequencing. Mitochondrial diversity is compared across three related, co-distributed finches with different conservation threat-statuses. There was no evidence of genetic differentiation across the western part of the range in any of the molecular markers, and haplotype diversity but not richness was lower than a common co-distributed species. Individuals within the panmictic population in the west may be highly dispersive within this wide area, and we urge caution when interpreting anecdotal observations of changes to the distribution and/or flock sizes of Gouldian finch populations as evidence of overall changes to the population size of this species.

Phylogeography of the antilopine wallaroo (Macropus antilopinus) across tropical northern Australia

The distribution of antilopine wallaroo, Macropus antilopinus, is marked by a break in the species’ range between Queensland and the Northern Territory, coinciding with the Carpentarian barrier. Previous work on M. antilopinus revealed limited genetic differentiation between the Northern Territory and Queensland M. antilopinus populations across this barrier. The study also identified a number of divergent lineages in the Northern Territory, but was unable to elucidate any geographic structure. Here, we re‐examine these results to (1) determine phylogeographic patterns across the range of M. antilopinus and (2) infer the biogeographic barriers associated with these patterns. The tropical savannahs of northern Australia: from the Cape York Peninsula in the east, to the Kimberley in the west. We examined phylogeographic patterns in M. antilopinus using a larger number of samples and three mtDNA genes: NADH dehydrogenase subunit 2, cytochrome b, and the control region. Two datasets were generated and analyzed: (1) a subset of samples with all three mtDNA regions concatenated together and (2) all samples for just control region sequences that included samples from the previous study. Analysis included generating phylogenetic trees based on Bayesian analysis and intraspecific median‐joining networks. The contemporary spatial structure of M. antilopinus mtDNA lineages revealed five shallow clades and a sixth, divergent lineage. The genetic differences that we found between Queensland and Northern Territory M. antilopinus samples confirmed the split in the geographic distribution of the species. We also found weak genetic differentiation between Northern Territory samples and those from the Kimberley region of Western Australia, possibly due to the Kimberley Plateau–Arnhem Land barrier. Within the Northern Territory, two clades appear to be parapatric in the west, while another two clades are broadly sympatric across the Northern Territory. MtDNA diversity of M. antilopinus revealed an unexpectedly complex evolutionary history involving multiple sympatric and parapatric mtDNA clades across northern Australia. These phylogeographic patterns highlight the importance of investigating genetic variation across distributions of species and integrating this information into biodiversity conservation.

Alpha taxonomy of Dromiciops (Microbiotheriidae) with the description of 2 new species of monito del monte

A previous study showed that Dromiciops gliroides has deep phylogeographic structure, with 3 allopatric and highly differentiated groups. Here, we constructed on that study by assessing the morphologic variation of D. gliroides. Our results show that along its distribution Dromiciops is morphologically highly variable and that the geographic pattern of morphologic variation matches the phylogeographic pattern. Taken together, morphological and molecular data indicate the existence of 2 unrecognized and unnamed species of monito del monte, which are here named and described. Cranial and dental features can easily distinguish species of Dromiciops. One of the new species is endemic of Chile, and the other new species occurs in Argentina and Chile. D. gliroides s.s. is restricted to the southern part of the genus distribution including Chiloé Island. We comment on the conservation significance of our findings and on the need of continuing with field- and collection-based research in order to characterize the richness of the Chilean mammal assemblage.

Un estudio previo mostró que Dromiciops gliroides tiene una marcada estructura filogeográfica con 3 grupos alopátridos bien diferenciados. Dado esos resultados, en el presente estudio analizamos la variación morfológica de D. gliroides. Nuestros resultados indican que D. gliroides es, a través de su distribución, altamente variable y que el patrón geográfico de la variación morfológica es congruente con el patrón filogeografico. Considerada en conjunto, la evidencia morfológica y molecular indica la existencia de dos especies de monito del monte que no han sido reconocidas, las que son aca descritas y nominadas. Las tres especies de Dromiciops se pueden distinguir fácilmente por características craneales y dentales. Una de las nuevas especies es endémica de Chile y la otra se distribuye en Argentina y Chile. D. gliroides s.s. se restringe a la porción sur del área distribucional del género, incluyendo la Isla de Chiloé. Cerramos el trabajo comentado sobre la necesidad de continuar realizando colectas y trabajo basado en colecciones con el fin de caracterizar la diversidad del ensamble de mamíferos de Chile.

A plethora of planigales: genetic variability and cryptic species in a genus of dasyurid marsupials from northern Australia

Multiple mitochondrial and nuclear gene sequences reveal substantial genetic variation within the dasyurid marsupial genus Planigale, suggesting greater taxonomic diversity than is currently recognised. To further investigate planigale relationships 116 new mitochondrial and nuclear gene sequences, including 16 new specimens, were added to our database. We confirm the presence of an unrecognised species (Planigale ‘species 1’) limited to the Pilbara region of Western Australia and suggest that the ‘Mt Tom Price’ animals may be closely related to Planigale ingrami subtilissima. We also confirm that at least four distinct genetic lineages make up what is currently recognised as P. maculata. This complex of closely related taxa represents a radiation of sibling species rather than a single, genetically diverse one. Three of these lineages (M1 + M2, M3 and M4) are distributed sympatrically across the Top End of Australia and one (M5 = P. maculata sensu stricto) is localised to the eastern coast of Australia. Within the Planigale ingrami complex, Planigale ‘Mt Tom Price’ (lineage Ing. 1) occurs in the Pilbara in sympatry with Planigale ‘species 1’ and lineage Ing. 2 is found in the Northern Territory in sympatry with species of the P. maculata complex. There is thus a plethora of northern Australian planigales, many of which are formally undescribed and whose geographic ranges require careful re-evaluation.

New genetic and linguistic analyses show ancient human influence on baobab evolution and distribution in Australia

This study investigates the role of human agency in the gene flow and geographical distribution of the Australian baobab, Adansonia gregorii. The genus Adansonia is a charismatic tree endemic to Africa, Madagascar, and northwest Australia that has long been valued by humans for its multiple uses. The distribution of genetic variation in baobabs in Africa has been partially attributed to human-mediated dispersal over millennia, but this relationship has never been investigated for the Australian species. We combined genetic and linguistic data to analyse geographic patterns of gene flow and movement of word-forms for A. gregorii in the Aboriginal languages of northwest Australia. Comprehensive assessment of genetic diversity showed weak geographic structure and high gene flow. Of potential dispersal vectors, humans were identified as most likely to have enabled gene flow across biogeographic barriers in northwest Australia. Genetic-linguistic analysis demonstrated congruence of gene flow patterns and directional movement of Aboriginal loanwords for A. gregorii. These findings, along with previous archaeobotanical evidence from the Late Pleistocene and Holocene, suggest that ancient humans significantly influenced the geographic distribution of Adansonia in northwest Australia.

Australia's arid-adapted butcherbirds experienced range expansions during Pleistocene glacial maxima

A model of range expansions during glacial maxima (GM) for cold-adapted species is generally accepted for the Northern Hemisphere. Given that GM in Australia largely resulted in the expansion of arid zones, rather than glaciation, it could be expected that arid-adapted species might have had expanded ranges at GM, as cold-adapted species did in the Northern Hemisphere. For Australian biota, however, it remains paradigmatic that arid-adapted species contracted to refugia at GM. Here we use multilocus data and ecological niche models (ENMs) to test alternative GM models for butcherbirds. ENMs, mtDNA and estimates of nuclear introgression and past population sizes support a model of GM expansion in the arid-tolerant Grey Butcherbird that resulted in secondary contact with its close relative--the savanna-inhabiting Silver-backed Butcherbird--whose contemporary distribution is widely separated. Together, these data reject the universal use of a GM contraction model for Australia's dry woodland and arid biota.

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.

Differing impact of a major biogeographic barrier on genetic structure in two large kangaroos from the monsoon tropics of Northern Australia

Tropical savannas cover 20-30% of the world's land surface and exhibit high levels of regional endemism, but the evolutionary histories of their biota remain poorly studied. The most extensive and unmodified tropical savannas occur in Northern Australia, and recent studies suggest this region supports high levels of previously undetected genetic diversity. To examine the importance of barriers to gene flow and the environmental history of Northern Australia in influencing patterns of diversity, we investigated the phylogeography of two closely related, large, vagile macropodid marsupials, the antilopine wallaroo (Macropus antilopinus; n = 78), and the common wallaroo (Macropus robustus; n = 21). Both species are widespread across the tropical savannas of Australia except across the Carpentarian Barrier (CB) where there is a break in the distribution of M. antilopinus. We determined sequence variation in the hypervariable Domain I of the mitochondrial DNA control region and genotyped individuals at 12 polymorphic microsatellite loci to assess the historical and contemporary influence of the CB on these species. Surprisingly, we detected only limited differentiation between the disjunct Northern Territory and QueenslandM. antilopinus populations. In contrast, the continuously distributedM. robustus was highly divergent across the CB. Although unexpected, these contrasting responses appear related to minor differences in species biology. Our results suggest that vicariance may not explain well the phylogeographic patterns in Australia's dynamic monsoonal environments. This is because Quaternary environmental changes in this region have been complex, and diverse individual species' biologies have resulted in less predictable and idiosyncratic responses.

Taxonomy of rock-wallabies, Petrogale (Marsupialia: Macropodidae). IV. Multifaceted study of the brachyotis group identifies additional taxa

Defining taxonomic units is an important component of understanding how biodiversity has formed, and in guiding efforts to sustain it. Understanding patterns of biodiversity across the monsoonal tropics of northern Australia is limited, with molecular technology revealing deep phylogenetic structure and complex evolutionary histories. The brachyotis group of rock-wallabies (Petrogale spp.), which currently consists of three species (Petrogale brachyotis, P. burbidgei and P. concinna) distributed across north-western Australia, provides an example where current taxonomy does not reflect the true diversity or phylogenetic relationships within the group. We have used an integrative approach, combining morphological data, together with DNA sequences (~1000 bp mitochondrial DNA; ~3000 bp nuclear DNA) to resolve relationships within P. brachyotis. Phylogenetic and morphological analyses indicated that P. brachyotis (sensu lato) represents at least two separate species: P. brachyotis (sensu stricto) from the Kimberley and western Northern Territory, and P. wilkinsi from the northern and eastern Northern Territory. Petrogale brachyotis (sensu stricto) can be separated on genetic and morphological evidence into two subspecies: P. b. brachyotis and P. b. victoriae (subsp. nov.). Distinct genetic lineages have also been identified within both P. brachyotis and P. wilkinsi, as well as within P. burbidgei and P. concinna.

Long-term persistence and vicariance within the Australian Monsoonal Tropics: the case of the giant cave and tree geckos (Pseudothecadactylus)

The Australian Monsoonal Tropics (AMT) are one of the largest unbroken areas of savannah woodland in the world. The history of the biota of this region is poorly understood; however, data from fossil deposits indicate that the climate was more mesic in the past, and that biodiversity has been shaped by attenuation and turnover as arid conditions expanded and intensified through the Miocene and Plio-Pleistocene. The giant cave and tree geckos (Pseudothecadactylus) are distributed across three disjunct regions of relatively high rainfall in the AMT (the north-west Kimberley, the ‘Top End’, and Cape York). We present an analysis of the diversity and biogeography of this genus based on mitochondrial (ND2) and nuclear (RAG-1) loci. These data indicate that the three widely allopatric lineages of Pseudothecadactylus diverged around the mid-Miocene, a novel pattern of relatively long-term persistence that has not previously been documented within the AMT. Two Pseudothecadactylus species endemic to sandstone scarps in the west Kimberley Region and ‘Top End’ also include divergent mitochondrial lineages, indicative of deep intraspecific coalescence times within these regions. Pseudothecadactylus is a highly relictual lineage with an extant distribution that has been shaped by a history of attenuation, isolation and persistence in the face of increasingly arid conditions. The low ecological and morphological diversity of Pseudothecadactylus also contrasts with its diverse sister lineage of geckos in New Caledonia, further underlining the relictual nature of standing diversity in the former.

Inferring population connectivity across the range of the purple-crowned fairy-wren (Malurus coronatus) from mitochondrial DNA and morphology: implications for conservation management

Knowledge of population structure and patterns of connectivity is required to implement effective conservation measures for the purple-crowned fairy-wren (Malurus coronatus), a threatened endemic of northern Australia. This study aimed to identify barriers to dispersal across the distribution of M. coronatus, investigate the impact that the recent declines may have on population connectivity, and propose conservation actions to maintain natural patterns of gene flow. Analysis of mitochondrial DNA sequences from 87 M. coronatus identified two phylogenetic clusters that corresponded with the phenotypically defined western (M. c. coronatus) and eastern (M. c. macgillivrayi) subspecies. The genetic divergence between these subspecies was consistent with isolation by a natural barrier to gene flow, and supports their separate conservation management. Within the declining M. c. coronatus, the lack of genetic divergence and only slight morphological difference between remnant populations indicates that populations were recently linked by gene flow. It is likely that widespread habitat degradation and the recent extirpation of M. c. coronatus from the Ord River will disrupt connectivity between, and dynamics within, remnant populations. To prevent further declines, conservation of M. coronatus must preserve areas of quality habitat and restore connectivity between isolated populations.