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 Queensland M. antilopinus populations. In contrast, the continuously distributed M. 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.     

Genetic population structure of grey mackerel Scomberomorus semifasciatus in northern Australia

This study used mtDNA sequence and microsatellite markers to elucidate the population structure of Scomberomorus semifasciatus collected from 12 widespread sampling locations in Australia. Samples (n = 544) were genotyped with nine microsatellite loci, and 353 were sequenced for the control (384 bp) and ATPase (800 bp) mtDNA gene regions. Combined interpretation of microsatellite and mtDNA data identified four genetic stocks of S. semifasciatus: Western Australia, north-west coast of the Northern Territory, Gulf of Carpentaria and the eastern coast of Queensland. Connectivity among stocks across northern Australia from the Northern Territory to the eastern coast of Queensland was high (mean F(ST) = 0·003 for the microsatellite data and Φ(ST) = 0·033 and 0·009 for control region and ATPase, respectively) leading to some uncertainty about stock boundaries. In contrast, there was a clear genetic break between the stock in Western Australia compared to the rest of northern Australia (mean F(ST) = 0·132 for the microsatellite data and Φ(ST) = 0·135 and 0·188 for control region and ATPase, respectively). This indicates a restriction to gene flow possibly associated with suboptimal habitat along the Kimberley coast (north Western Australia). The appropriate scale of management for this species corresponds to the jurisdictions of the three Australian states, except that authorities in Queensland and Northern Territory should co-ordinate the management of the Gulf of Carpentaria stock.     

Extensive intraspecific genetic diversity of a freshwater crayfish in a biodiversity hotspot

1. The freshwater crayfish Cherax dispar (Decapoda: Parastacidae) inhabits coastal regions and islands of South East Queensland, Australia. We hypothesised that populations of C. dispar on different islands would be more genetically divergent from each other than populations from different drainages within the same island or on the mainland. 2. Phylogenetic and phylogeographic analyses were conducted on two mitochondrial genes (cytochrome oxidase subunit I & 16S ribosomal DNA) and one nuclear gene (Internal Transcribed Spacer region 2). Phylogeographic patterns were compared with those for other freshwater organisms in the area. 3. Deep genetic divergences were found within C. dispar, including four highly divergent (up to 20%) clades. The geographic distribution of each of the clades revealed strong latitudinal structuring along the coast rather than structuring among the islands. The high genetic divergence observed among the C. dispar clades was estimated to have pre‐dated island formation and may represent ancient river drainage patterns. 4. A restricted distribution was observed for the most divergent clade, which was discovered only on two of the sand islands (North Stradbroke Island and Moreton Island). Furthermore, strong phylogeographic structuring was observed within this clade on North Stradbroke Island, where no haplotypes were shared between samples from opposite sides of the island. This low connectivity within the island supports the idea that C. dispar rarely disperse terrestrially (i.e. across watersheds).     

Seascape genomics reveals fine‐scale patterns of dispersal for a reef fish along the ecologically divergent coast of Northwestern Australia

Understanding the drivers of dispersal among populations is a central topic in marine ecology and fundamental for spatially explicit management of marine resources. The extensive coast of Northwestern Australia provides an emerging frontier for implementing new genomic tools to comparatively identify patterns of dispersal across diverse and extreme environmental conditions. Here, we focused on the stripey snapper (Lutjanus carponotatus), which is important to recreational, charter‐based and customary fishers throughout the Indo‐West Pacific. We collected 1,016 L. carponotatus samples at 51 locations in the coastal waters of Northwestern Australia ranging from the Northern Territory to Shark Bay and adopted a genotype‐by‐sequencing approach to test whether realized connectivity (via larval dispersal) was related to extreme gradients in coastal hydrodynamics. Hydrodynamic simulations using CONNIE and a more detailed treatment in the Kimberley Bioregion provided null models for comparison. Based on 4,402 polymorphic single nucleotide polymorphism loci shared across all individuals, we demonstrated significant genetic subdivision between the Shark Bay Bioregion in the south and all locations within the remaining, more northern bioregions. More importantly, we identified a zone of admixture spanning a distance of 180 km at the border of the Kimberley and Canning bioregions, including the Buccaneer Archipelago and adjacent waters, which collectively experiences the largest tropical tidal range and some of the fastest tidal currents in the world. Further testing of the generality of this admixture zone in other shallow water species across broader geographic ranges will be critical for our understanding of the population dynamics and genetic structure of marine taxa in our tropical oceans.     

Phylogeography of the widespread African puff adder (Bitis arietans) reveals multiple Pleistocene refugia in southern Africa

Evidence from numerous Pan‐African savannah mammals indicates that open‐habitat refugia existed in Africa during the Pleistocene, isolated by expanding tropical forests during warm and humid interglacial periods. However, comparative data from other taxonomic groups are currently lacking. We present a phylogeographic investigation of the African puff adder (Bitis arietans), a snake that occurs in open‐habitat formations throughout sub‐Saharan Africa. Multiple parapatric mitochondrial clades occur across the current distribution of B. arietans, including a widespread southern African clade that is subdivided into four separate clades. We investigated the historical processes responsible for generating these phylogeographic patterns in southern Africa using species distribution modelling and genetic approaches. Our results show that interior regions of South Africa became largely inhospitable for B. arietans during glacial maxima, whereas coastal and more northerly areas remained habitable. This corresponds well with the locations of refugia inferred from mitochondrial data using a continuous phylogeographic diffusion model. Analysis of data from five anonymous nuclear loci revealed broadly similar patterns to mtDNA. Secondary admixture was detected between previously isolated refugial populations. In some cases, this is limited to individuals occurring near mitochondrial clade contact zones, but in other cases, more extensive admixture is evident. Overall, our study reveals a complex history of refugial isolation and secondary expansion for puff adders and a mosaic of isolated refugia in southern Africa. We also identify key differences between the processes that drove isolation in B. arietans and those hypothesized for sympatric savannah mammals.     

Global mitochondrial DNA phylogeography and biogeographic history of the antitropically and longitudinally disjunct marine bryozoan Membranipora membranacea L. (Cheilostomata): another cryptic marine sibling species complex?

The origin of disjunct distributions in high dispersal marine taxa remains an important evolutionary question as it relates to the formation of new species in an environment where barriers to gene flow are not always obvious. To reconstruct the relationships and phylogeographic history of the antitropically and longitudinally disjunct bryozoan Membranipora membranacea populations were surveyed with mtDNA cytochrome oxidase 1 (COI) sequences across its cosmopolitan range. Maximum parsimony, maximum likelihood and Bayesian genealogies revealed three deep clades in the North Pacific and one monophyletic clade each in the southeast Pacific (Chile), southwest Pacific (Australia/New Zealand), North Atlantic and southeast Atlantic (South Africa). Human-mediated dispersal has not impacted M. membranacea’s large-scale genetic structure. M. membranacea did not participate in the trans-arctic interchange. Episodic long-distance dispersal, combined with climatic vicariance can explain the disjunct distribution. Dispersal led southward across the tropics perhaps 13 mya in the East Pacific and again northwards perhaps 6 mya in the Eastern Atlantic to colonize the North Atlantic from the south, and along the West Wind Drift to colonize Australia. The clades differentiated over evolutionary time in their respective ocean region, potentially forming a sibling species complex. The taxonomic status of the clades is discussed.     

Comparative phylogeography of two co‐distributed but ecologically distinct rainbowfishes of far‐northern Australia

Aim

To test the influence of historical and contemporary environment in shaping the genetic diversity of freshwater fauna we contrast genetic structure in two co‐distributed, but ecologically distinct, rainbowfish; a habitat generalist (Melanotaenia splendida) and a habitat specialist (M. trifasciata).

Location

Fishes were sampled from far northern Australia (Queensland and Northern Territory).

Methods

We used sequence data from one mitochondrial gene and one nuclear gene to investigate patterns of genetic diversity in M. splendida and M. trifasciata to determine how differences in habitat preference and historical changes in drainage boundaries affected patterns of connectivity.

Results

Melanotaenia splendida showed high levels of genetic diversity and little population structure across its range. In contrast, M. trifasciata showed high levels of population structure. Whereas phylogeographic patterns differed, both species showed a strong relationship between geographical distance and genetic differentiation between populations. Melanotaenia splendida showed a shallower relationship with geographical distance, and genetic differentiation was best explained by stream length and a lower scaled ocean distance (11.98 times coast length). For M. trifasciata, genetic differentiation was best explained by overwater distance between catchments and ocean distance scaled at 1.16 × 10⁶ times coast length.

Main conclusions

Connectivity of freshwater populations inhabiting regions periodically interconnected during glacial periods appears to have been affected by ecological differences between species. Species‐specific differences are epitomized here by the contrast between co‐distributed congeners with different habitat requirements: for the habitat generalist, M. splendida, there was evidence for greater historical genetic connectivity with oceans as a weaker barrier to gene exchange in contrast with the habitat specialist, M. trifasciata.     

Cryptic lineage diversity,body size divergence,and sympatry in a species complex of Australian lizards (Gehyra)

Understanding the joint evolutionary and ecological underpinnings of sympatry among close relatives remains a key challenge in biology. This problem can be addressed through joint phylogenomic and phenotypic analysis of complexes of closely related lineages within, and across, species and hence representing the speciation continuum. For a complex of tropical geckos from northern Australia—Gehyra nana and close relatives—we combine mtDNA phylogeography, exon‐capture sequencing, and morphological data to resolve independently evolving lineages and infer their divergence history and patterns of morphological evolution. Gehyra nana is found to include nine divergent lineages and is paraphyletic with four other species from the Kimberley region of north‐west Australia. Across these 13 taxa, 12 of which are restricted to rocky habitats, several lineages overlap geographically, including on the diverse Kimberley islands. Morphological evolution is dominated by body size shifts, and both body size and shape have evolved gradually across the group. However, larger body size shifts are observed among overlapping taxa than among closely related parapatric lineages of G. nana, and sympatric lineages are more divergent than expected at random. Whether elevated body size differences among sympatric lineages are due to ecological sorting or character displacement remains to be determined.     

Phylogeographic analysis detects congruent biogeographic patterns between a woodland agamid and Australian wet tropics taxa despite disparate evolutionary trajectories

Aim To test the congruence of phylogeographic patterns and processes between a woodland agamid lizard (Diporiphora australis) and well‐studied Australian wet tropics fauna. Specifically, to determine whether the biogeographic history of D. australis is more consistent with a history of vicariance, which is common in wet tropics fauna, or with a history of dispersal with expansion, which would be expected for species occupying woodland habitats that expanded with the increasingly drier conditions in eastern Australia during the Miocene–Pleistocene. Location North‐eastern Australia. Methods Field‐collected and museum tissue samples from across the entire distribution of D. australis were used to compile a comprehensive phylo‐geographic dataset based on c. 1400 bp of mitochondrial DNA (mtDNA), incorporating the ND2 protein‐coding gene. We used phylogenetic methods to assess biogeographic patterns within D. australis and relaxed molecular clock analyses were conducted to estimate divergence times. Hierarchical Shimodaira–Hasegawa tests were used to test alternative topologies representing vicariant, dispersal and mixed dispersal/vicariant biogeographic hypotheses. Phylogenetic analyses were combined with phylogeographic analyses to gain an insight into the evolutionary processes operating within D. australis. Results Phylogenetic analyses identified six major mtDNA clades within D. australis, with phylogeographic patterns closely matching those seen in many wet tropics taxa. Congruent phylogeographic breaks were observed across the Black Mountain Corridor, Burdekin and St Lawrence Gaps. Divergence amongst clades was found to decrease in a north–south direction, with a trend of increasing population expansion in the south. Main conclusions While phylogeographic patterns in D australis reflect those seen in many rain forest fauna of the wet tropics, the evolutionary processes underlying these patterns appear to be very different. Our results support a history of sequential colonization of D. australis from north to south across major biogeographic barriers from the late Miocene–Pleistocene. These patterns are most likely in response to expanding woodland habitats. Our results strengthen the data available for this iconic region in Australia by exploring the understudied woodland habitats. In addition, our study shows the importance of thorough investigations of not only the biogeographic patterns displayed by species but also the evolutionary processes underlying such patterns.     

Phylogenomics at the tips: inferring lineages and their demographic history in a tropical lizard,Carlia amax

High‐throughput sequencing approaches offer opportunities to better understand the evolutionary processes driving diversification, particularly in nonmodel organisms. In particular, the 100–1000's of loci that can now be sequenced are providing unprecedented power in population, speciation and phylogenetic studies. Here, we apply an exon capture approach to generate >99% complete sequence and SNP data across >2000 loci from a tropical skink, Carlia amax, and exploit these data to identify divergent lineages and infer their relationships and demographic histories. This is especially relevant to low‐dispersal tropical taxa that often have cryptic diversity and spatially dynamic histories. For C. amax, clustering of nuclear SNPs and coalescent‐based species delimitation analyses identify four divergent lineages, one fewer than predicted based on geographically coherent mtDNA clades (>9.4% sequence divergence). Three of these lineages are widespread and parapatric on the mainland, whereas the most divergent is restricted to islands off the northeast Northern Territory. Tests for population expansion reject an equilibrium isolation‐by‐distance model for two of the three widespread lineages and infer refugial expansion sources in the relatively mesic northeast Top End and northwest Kimberley. The latter is already recognized as a hotspot of endemism, but our results also suggest that a stronger focus on the northeast Top End, and adjacent islands is warranted. More generally, our results show how genome‐reduction methods such as exon capture can yield insights into the pattern and dynamics of biodiversity across complex landscapes with as yet poorly understood biogeographic history and how exon data can link between population and phylogenetic questions.     

Landscape genetic analysis of the tropical freshwater fish Mogurnda mogurnda (Eleotridae) in a monsoonal river basin: importance of hydrographic factors and population history

1. We performed spatial genetic analyses, incorporating landscape genetic methods using microsatellite data and phylogeographic analyses using mtDNA data, to identify the principal factors that determine population heterogeneity of the tropical freshwater fish, Mogurnda mogurnda, in the Daly River, northern Australia. We tested the individual and interactive effects of several environmental variables on spatial genetic patterns, including metrics relating to connectivity (i.e. stream distance, maximum stream gradient and elevation), habitat size (i.e. mean annual discharge) and a categorical variable relating to population history, as determined by mtDNA phylogeographic analyses. The Daly River is geomorphologically and hydrologically complex, and M. mogurnda has life history traits that limit its dispersal potential at river basin scales. Thus, we predicted that variables relating to connectivity would be the most important landscape factors driving population structure of the species. 2. Tree‐based phylogeographic analyses indicated four divergent mtDNA lineages within M. mogurnda in the Daly River, although three of the lineages were sympatric in various combinations and did not correspond with microsatellite groups identified by assignment tests. The allopatric mtDNA lineage detected in the uppermost part of the catchment was also identified as being highly differentiated by the microsatellite data, strongly suggesting that it may be a cryptic species. This site was therefore excluded from subsequent landscape genetic analyses. 3. Analyses of Molecular Variance indicated that M. mogurnda has a hierarchical population structure in the Daly River, thus supporting theoretical expectations that hierarchically arranged river habitats in dendritic systems impose hierarchal population structures on lotic species. 4. All landscape genetic analyses rejected stream distance, and supported stream gradient, as the major determinant of spatial genetic variation in M. mogurnda in the Daly River. Support for elevation as a determinant of spatial genetic patterns differed among the landscape genetic methods. Several of the landscape genetic methods also indicate that population history, including secondary contact between divergent and formerly allopatric genetic lineages, has a strong influence on spatial genetic patterns within M. mogurnda in the Daly River. 5. This study demonstrates the need to consider multiple environmental factors, especially factors relating to connectivity, and their interactions in spatial genetic analysis, rather than just geographic distance. Importantly, it demonstrates the need to account for population history and evolutionary divergences in landscape genetic analyses.     

Origins and patterns of endemic diversity in two specialized lizard lineages from the Australian Monsoonal Tropics (Oedura spp.)

Aim

Savanna biomes cover around 20% of land surfaces, yet the origins and processes that have shaped their biodiversity remain understudied. Here, we assess the timing of diversification and how patterns of genetic diversity vary along an aridity gradient in specialized saxicoline gecko clades (Oedura spp.) from the tropical savannas of northern Australia.

Location

Australian Monsoonal Tropics (AMT), Kimberley region (Western Australia).

Methods

We compiled mitochondrial and nuclear data for two Kimberley endemic lizard clades (Oedura filicipoda/murrumanu and O. gracilis), and allied non‐Kimberley taxa (O. marmorata complex). Species delimitation methods were used to identify evolutionary lineages, Maximum‐likelihood and Bayesian phylogenetic methods were employed to assess relationships and diversification timeframes, and rainfall data and range sizes were tested for correlations.

Results

Phylogenetic analyses of cryptic or recently discovered lineage diversity revealed late‐Miocene to early‐Pliocene crown ages. Microendemism and diversity were highest in high‐rainfall regions, while the most widespread lineages occurred in the central and south‐east Kimberley, and showed evidence of introgression with parapatric lineages.

Main conclusions

The initial diversification in both clades was broadly concordant with global climatic events linked to the expansion of savanna biomes in the lateMiocene. Higher endemism in mesic and refugial areas suggests long histories of localized persistence, while wider distributions and evidence of introgression suggest a dynamic history at the arid‐monsoonal interface.     

Phylogeographic patterns and conservation implications of the endangered Chinese giant salamander

Understanding genetic diversity patterns of endangered species is an important premise for biodiversity conservation. The critically endangered salamander Andrias davidianus, endemic to central and southern mainland in China, has suffered from sharp range and population size declines over the past three decades. However, the levels and patterns of genetic diversity of A. davidianus populations in wild remain poorly understood. Herein, we explore the levels and phylogeographic patterns of genetic diversity of wild‐caught A. davidianus using larvae and adult collection with the aid of sequence variation in (a) the mitochondrial DNA (mtDNA) fragments (n = 320 individuals; 33 localities), (b) 19 whole mtDNA genomes, and (c) nuclear recombinase activating gene 2 (RAG2; n = 88 individuals; 19 localities). Phylogenetic analyses based on mtDNA datasets uncovered seven divergent mitochondrial clades (A–G), which likely originated in association with the uplifting of mountains during the Late Miocene, specific habitat requirements, barriers including mountains and drainages and lower dispersal ability. The distributions of clades were geographic partitioned and confined in neighboring regions. Furthermore, we discovered some mountains, rivers, and provinces harbored more than one clades. RAG2 analyses revealed no obvious geographic patterns among the five alleles detected. Our study depicts a relatively intact distribution map of A. davidianus clades in natural species range and provides important knowledge that can be used to improve monitoring programs and develop a conservation strategy for this critically endangered organism.     

GENETIC STRUCTURE AND MALE-MEDIATED GENE FLOW IN THE GHOST BAT (MACRODERMA GIGAS)

The Australian ghost bat is a large, opportunistic carnivorous species that has undergone a marked range contraction toward more mesic, tropical sites over the past century. Comparison of mitochondrial DNA (mtDNA) control region sequences and six nuclear microsatellite loci in 217 ghost bats from nine populations across subtropical and tropical Australia revealed strong population subdivision (mtDNA φ_ST = 0.80; microsatellites UR_ST = 0.337). Low-latitude (tropical) populations had higher heterozygosity and less marked phylogeographic structure and lower subdivision among sites within regions (within Northern Territory [NT] and within North Queensland [NQ]) than did populations at higher latitudes (subtropical sites; central Queensland [CQ]), although sampling of geographically proximal breeding sites is unavoidably restricted for the latter. Gene flow among populations within each of the northern regions appears to be male biased in that the difference in population subdivision for mtDNA and microsatellites (NT φ_ST = 0.39, UR_ST = 0.02; NQ φ_ST = 0.60, UR_ST = ?0.03) is greater than expected from differences in the effective population size of haploid versus diploid loci. The high level of population subdivision across the range of the ghost bat contrasts with evidence for high gene flow in other chiropteran species and may be due to narrow physiological tolerances and consequent limited availability of roosts for ghost bats, particularly across the subtropical and relatively arid regions. This observation is consistent with the hypothesis that the contraction of the species' range is associated with late Holocene climate change. The extreme isolation among higher-latitude populations may predispose them to additional local extinctions if the processes responsible for the range contraction continue to operate.     

Fat frogs,mobile genes: unexpected phylogeographic patterns for the ornate chorus frog (Pseudacris ornata)

The southeastern coastal plain of the United States is a region marked by extraordinary phylogeographic congruence that is frequently attributed to the changing sea levels that occurred during the glacial‐interglacial cycles of the Pleistocene epoch. A phylogeographic break corresponding to the Apalachicola River has been suggested for many species studied to date that are endemic to this region. Here, we used this pattern of phylogeographic congruence to develop and test explicit hypotheses about the genetic structure in the ornate chorus frog (Pseudacris ornata). Using 1299 bp of mtDNA sequence and seven nuclear microsatellite markers in 13 natural populations of P. ornata, we found three clades corresponding to geographically distinct regions; one spans the Apalachicola River (Southern Clade), one encompasses Georgia and South Carolina (Central Clade) and a third comprises more northerly individuals (Northern Clade). However, it does not appear that typical phylogeographic barriers demarcate these clades. Instead, isolation by distance across the range of the entire species explained the pattern of genetic variation that we observed. We propose that P. ornata was historically widespread in the southeastern United States, and that a balance between genetic drift and migration was the root of the genetic divergence among populations. Additionally, we investigated fine‐scale patterns of genetic structure and found the spatial scale at which there was significant genetic structure varied among the regions studied. Furthermore, we discuss our results in light of other phylogeographic studies of southeastern coastal plain organisms and in relation to amphibian conservation and management.     

Tropical specialist vs. climate generalist: Diversification and demographic history of sister species of Carlia skinks from northwestern Australia

Species endemic to the tropical regions are expected to be vulnerable to future climate change due in part to their relatively narrow climatic niches. In addition, these species are more likely to have responded strongly to past climatic change, and this can be explored through phylogeographic analyses. To test the hypothesis that tropical specialists are more sensitive to climate change than climate generalists, we generated and analyse sequence data from mtDNA and ~2500 exons to compare scales of historical persistence and population fluctuation in two sister species of Australian rainbow skinks: the tropical specialist Carlia johnstonei and the climate generalist C. triacantha. We expect the tropical specialist species to have deeper and finer‐scale phylogeographic structure and stronger demographic fluctuations relative to the closely related climate generalist species, which should have had more stable populations through periods of harsh climate in the late Quaternary. Within C. johnstonei, we find that some populations from the northern Kimberley islands are highly divergent from mainland populations. In C. triacantha, one major clade occurs across the deserts and into the mesic Top End, and another occurs primarily in the Kimberley with scattered records eastwards. Where their ranges overlap in the Kimberley, both mitochondrial DNA and nuclear DNA suggest stronger phylogeographic structure and range expansion within the tropical specialist, whereas the climate generalist has minimal structuring and no evidence of recent past range expansion. These results are consistent with the hypothesis that tropical specialists are more sensitive to past climatic change.     

Effects of historical forest contraction on the phylogeographic structure of Australo‐Papuan populations of the red‐legged pademelon (Macropodidae: Thylogale stigmatica)

Geographic patterns of genetic variation are strongly influenced by historical changes in species habitats. Whether such patterns are common to co‐distributed taxa may depend on the extent to which species vary in ecology and vagility. We investigated whether broad‐scale phylogeographic patterns common to a number of small‐bodied vertebrate and invertebrate species in eastern Australian forests were reflected in the population genetic structure of an Australo‐Papuan forest marsupial, the red‐legged pademelon (Macropodidae: Thylogale stigmatica). Strong genetic structuring of mtDNA haplotypes indicated the persistence of T. stigmatica populations across eastern Australia and southern New Guinea in Pleistocene refugial areas consistent with those inferred from studies of smaller, poorly dispersing species. However, there was limited divergence of haplotypes across two known historical barriers in the northeastern Wet Tropics (Black Mountain Barrier) and coastal mideastern Queensland (Burdekin Gap) regions. Lack of divergence across these barriers may reflect post‐glacial recolonization of forests from a large, central refugium in the Wet Tropics. Additionally, genetic structure is not consistent with the present delimitation of subspecies T. s. wilcoxi and T. s. stigmatica across the Burdekin Gap. Instead, the genetic division occurs further to the south in mideastern Queensland. Thus, while larger‐bodied marsupials such as T. stigmatica did persist in Pleistocene refugia common to a number of other forest‐restricted species, species‐specific local extinction and recolonization events have resulted in cryptic patterns of genetic variation. Our study demonstrates the importance of understanding individualistic responses to historical climate change in order to adequately conserve genetic diversity and the evolutionary potential of species.     

Genetic differentiation in the Trinidad endemic Mannophryne trinitatis (Anura: Aromobatidae): Miocene vicariance,in situ diversification and lack of geographical structuring across the island

Trinidad offers a unique study system within the Caribbean to assess the processes and patterns of amphibian speciation. We used mitochondrial DNA sequences to investigate the phylogenetic relationships and patterns of intraspecific genetic variation of Mannophryne trinitatis from Trinidad. Molecular clock estimates point to a genetic split between M. trinitatis and its sister species, M. venezuelensis, dating to the Late Miocene (c. 7–8 Mya), suggesting vicariance as a means of speciation when Trinidad pulled apart from northern Venezuela. M. trinitatis phylogenetic population analyses from ten Northern Range and four Central Range localities recovered three well‐resolved clades: a larger clade formed by haplotypes from Northern Range localities and two additional clades, one formed by haplotypes from the Central Range and another including haplotypes from Northern Range localities and one haplotype from the Central Range. Overall, our results show that the genetic diversity in M. trinitatis is not geographically structured but it is distributed among the various Northern and Central Range localities. In congruence with the vicariance speciation hypothesis, we attribute M. trinitatis present distribution and lack of genetic structure to multiple admixture events caused by climate changes that severely affected the topology of Trinidad throughout the Pliocene/Pleistocene periods.     

Comparative phylogeographies of six species of hinged terrapins (Pelusios spp.) reveal discordant patterns and unexpected differentiation in the P. castaneus/P. chapini complex and P. rhodesianus

Using up to 2117 bp of mitochondrial DNA and up to 2012 bp of nuclear DNA, we analysed phylogeographic differentiation of six widely distributed species of African hinged terrapins (Pelusios spp.) representing different habitat types. Two taxa each live in savannahs or in forests and mesic savannahs, respectively, and the remaining two species occur in intermediate habitats. The species living in forests and mesic savannahs do not enter dry savannahs, whereas the savannah species may occur in dry and wet savannahs and even in semi‐arid steppe regions. We found no obvious correlation between habitat type and phylogeographic pattern: one savannah species (P. rhodesianus) shows phylogeographic structure, i.e. pronounced genetic differences among geographically distinct populations, and the other (P. nanus) not. One species inhabiting forests and mesic savannahs (P. carinatus) has phylogeographic structure, the other (P. gabonensis) not. The same pattern is true for the two ecologically intermediate species, with phylogeographic structure present in P. castaneus and absent in P. chapini. Nuclear evidence suggests that the latter two taxa with abutting and partially overlapping ranges are distinct, while mtDNA is only weakly differentiated. Pelusios castaneus shows pronounced phylogeographic structure, which could reflect Pleistocene range interruptions correlated with the fluctuating forest cover in West and Central Africa. Our results do not support the recognition of an extinct subspecies of P. castaneus for the Seychelles. Pelusios carinatus contains two well supported clades, which are separated by the Congo River. This species is closely related to P. rhodesianus, a taxon consisting of two deeply divergent mitochondrial clades. One of these clades is paraphyletic with respect to P. carinatus, but the two clades of P. rhodesianus are not differentiated in the studied nuclear markers and, again, paraphyletic with respect to P. carinatus. Using mtDNA sequences from the type material of P. rhodesianus, we were able to allocate this name to one of the two clades. However, owing to the confusing relationships of P. rhodesianus and P. carinatus, we refrain from taxonomic decisions.     

Major genomic mitochondrial lineages delineate early human expansions

Background  

The phylogeographic distribution of human mitochondrial DNA variations allows a genetic approach to the study of modern Homo sapiens dispersals throughout the world from a female perspective. As a new contribution to this study we have phylogenetically analysed complete mitochondrial DNA(mtDNA) sequences from 42 human lineages, representing major clades with known geographic assignation.