Birth of a biome: insights into the assembly and maintenance of the Australian arid zone biota

The integration of phylogenetics, phylogeography and palaeoenvironmental studies is providing major insights into the historical forces that have shaped the Earth's biomes. Yet our present view is biased towards arctic and temperate/tropical forest regions, with very little focus on the extensive arid regions of the planet. The Australian arid zone is one of the largest desert landform systems in the world, with a unique, diverse and relatively well-studied biota. With foci on palaeoenvironmental and molecular data, we here review what is known about the assembly and maintenance of this biome in the context of its physical history, and in comparison with other mesic biomes. Aridification of Australia began in the Mid-Miocene, around 15 million years, but fully arid landforms in central Australia appeared much later, around 1-4 million years. Dated molecular phylogenies of diverse taxa show the deepest divergences of arid-adapted taxa from the Mid-Miocene, consistent with the onset of desiccation. There is evidence of arid-adapted taxa evolving from mesic-adapted ancestors, and also of speciation within the arid zone. There is no evidence for an increase in speciation rate during the Pleistocene, and most arid-zone species lineages date to the Pliocene or earlier. The last 0.8 million years have seen major fluctuations of the arid zone, with large areas covered by mobile sand dunes during glacial maxima. Some large, vagile taxa show patterns of recent expansion and migration throughout the arid zone, in parallel with the ice sheet-imposed range shifts in Northern Hemisphere taxa. Yet other taxa show high lineage diversity and strong phylogeographical structure, indicating persistence in multiple localised refugia over several glacial maxima. Similar to the Northern Hemisphere, Pleistocene range shifts have produced suture zones, creating the opportunity for diversification and speciation through hybridisation, polyploidy and parthenogenesis. This review highlights the opportunities that development of arid conditions provides for rapid and diverse evolutionary radiations, and re-enforces the emerging view that Pleistocene environmental change can have diverse impacts on genetic structure and diversity in different biomes. There is a clear need for more detailed and targeted phylogeographical studies of Australia's arid biota and we suggest a framework and a set of a priori hypotheses by which to proceed.     

Palaeoclimate change drove diversification among isolated mountain refugia in the Australian arid zone

Refugia featured prominently in shaping evolutionary trajectories during repeated cycles of glaciation in the Quaternary, particularly in the Northern Hemisphere. The Southern Hemisphere instead experienced cycles of severe aridification but little is known about the temporal presence and role of refugia for arid-adapted biota. Isolated mountain ranges located in the Australian arid zone likely provided refugia for many species following Mio/Pliocene (<15 Ma) aridification; however, the evolutionary consequences of the recent development of widespread sand deserts is largely unknown. To test alternative hypotheses of ancient vs. recent isolation, we generated a 10 gene data set to assess divergence history among saxicolous geckos in the genus Heteronotia that have distributions confined to major rocky ranges in the arid zone. Phylogenetic analyses show that each rocky range harbours a divergent lineage, and substantial intraspecific diversity is likely due to topographic complexity in these areas. Old divergences (~4 Ma) among lineages pre-date the formation of the geologically young sand deserts (<1 Ma), suggesting that Pliocene climate shifts fractured the distributions of biota long before the spread of the deserts.     

The evolution of sexual and parthenogenetic Warramaba: a window onto Plio–Pleistocene diversification processes in an arid biome

Environmental changes over the Plio‐Pleistocene have been key drivers of speciation patterns and genetic diversification in high‐latitude and mesic environments, yet comparatively little is known about the evolutionary history of species in arid environments. We applied phylogenetic and phylogeographic analyses to understand the evolutionary history of Warramaba grasshoppers from the Australian arid zone, a group including sexual and parthenogenetic lineages. Sequence data (mitochondrial COI) showed that the four major sexual lineages within Warramaba most likely diverged in the Pliocene, around 2–7 million years ago. All sexual lineages exhibited considerable phylogenetic structure. Detailed analyses of the hybrid parthenogenetic species W. virgo and its sexual progenitors showed a pattern of high phylogenetic diversity and phylogeographic structure in northern lineages, and low diversity and evidence for recent expansion in southern lineages. Northern sexual lineages persisted in localized refugia over the Pleistocene, with sustained barriers promoting divergence over this period. Southern parts of the present range became periodically unsuitable during the Pleistocene, and it is into this region that parthenogenetic lineages have expanded. Our results strongly parallel those for sexual and parthenogenetic lineages of the gecko Heteronotia from the same region, indicating a highly general effect of Plio‐Pleistocene environmental change on diversification processes in arid Australia.     

Out of Africa: biogeographic history of the open‐habitat chats (Aves,Muscicapidae: Saxicolinae) across arid areas of the old world

Arid and semi‐arid areas constitute a prominent feature of the earth today, especially in Asia and Africa. Their formation started in the middle Miocene with increased stepwise aridification since the Pliocene. This aridification had strong ecological and evolutionary consequences and not only led to fragmentation of moist‐adapted biota, but also fostered the evolution of arid‐adapted taxa from mesic ancestors and triggered speciation within arid areas. The open‐habitat chats, a clade within Saxicolinae (Aves, Muscicapidae), constitute one of the most significant arid‐adapted passerine groups of Africa and Eurasia. Here, we present a temporal and spatial framework for the diversification of open‐habitat chats, using probabilistic approaches for the reconstruction of their biogeographic history based on a time‐calibrated multilocus molecular phylogenetic hypothesis. The diversification of open‐habitat chats was initiated in the late Miocene at around 7.4 Ma, most likely in sub‐Saharan Africa. Southern Africa and the Horn of Africa acted as centres of diversification and biogeographic expansion. From the latter area, the Arabo‐Sindic region and subsequently further parts of Eurasia and North Africa were colonized. The colonization history out of sub‐Saharan Africa contrasts with that of several other songbird clades, where a biogeographic expansion from Eurasia or northern Africa to southern Africa was prevalent. Habitat fragmentation through forest expansions during intermittent wetter periods in Africa influenced diversification in several clades. However, phases of increased aridity, with hyperarid regions acting as drivers of vicariance, seem to have also been important in radiations of the Arabo‐Sindic region and the Horn of Africa during the Pleistocene. Different processes such as colonization of new areas followed by vicariance or speciation across ecotones might have played a role throughout the radiation of open‐habitat chats.     

High diversity Pleistocene rainforest Dasyurid assemblages with implications for the radiation of the dasyuridae

It is commonly accepted that dasyurids (Marsupialia: Dasyuridae) radiated in the late Miocene or early Pliocene in response to a drying trend in Australia's climate as evidenced from the high diversity of dasyurids from modern arid environments compared with Miocene rainforest assemblages. However, mid‐Pleistocene dasyurid assemblages from cave deposits at Mt Etna, Queensland are more diverse than any previously known from rainforest habitats. New taxa will be described elsewhere, but include three new genera as well as new species of Dasyurus, Antechinus and Phascogale. Comparison of dasyurids from Mt Etna sites that are interpreted as rainforest palaeoenvironments with fossil and extant assemblages indicate that they are at least as diverse as those from modern arid environments. Thus Neogene diversification of dasyurids occurred in both arid and rainforest habitats, but only the former survived continuing aridification. Hence, aridification cannot be invoked for the diversification of all dasyurid lineages.     

Mass turnover and recovery dynamics of a diverse Australian continental radiation

Trends in global and local climate history have been linked to observed macroevolutionary patterns across a variety of organisms. These climatic pressures may unilaterally or asymmetrically influence the evolutionary trajectory of clades. To test and compare signatures of changing global (Eocene‐Oligocene boundary cooling) and continental (Miocene aridification) environments on a continental fauna, we investigated the macroevolutionary dynamics of one of Australia's most diverse endemic radiations, pygopodoid geckos. We generated a time‐calibrated phylogeny (>90% taxon coverage) to test whether (i) asymmetrical pygopodoid tree shape may be the result of mass turnover deep in the group's history, and (ii) how Miocene aridification shaped trends in biome assemblages. We find evidence of mass turnover in pygopodoids following the isolation of the Australian continental plate ～30 million years ago, and in contrast, gradual aridification is linked to elevated speciation rates in the young arid zone. Surprisingly, our results suggest that invasion of arid habitats was not an evolutionary end point. Instead, arid Australia has acted as a source for diversity, with repeated outward dispersals having facilitated diversification of this group. This pattern contrasts trends in richness and distribution of other Australian vertebrates, illustrating the profound effects historical biome changes have on macroevolutionary patterns.     

Multiple periglacial refugia in the Patagonian steppe and post‐glacial colonization of the Andes: the phylogeography of Calceolaria polyrhiza

Aim We perform a phylogeographical study of an endemic Patagonian herbaceous plant to assess whether geographical patterns of genetic variation correspond to in situ Pleistocene survival or to glacial retreat and post‐glacial expansion. We also seek to determine the locations of potential glacial refugia and post‐glacial colonization routes. Location Southern Andes and Patagonian steppe. Methods We used Calceolaria polyrhiza, a widely distributed Patagonian herbaceous plant that occurs mainly in the understorey of Nothofagus rain forests and in the arid Patagonian steppe, as our model system. The chloroplast intergenic spacer trnH–psbA was sequenced for 590 individuals from 68 populations. Sequence data were analysed using phylogenetic (maximum parsimony, maximum likelihood and Bayesian inference) and population genetic (spatial analyses of molecular variance, mismatch distributions and neutrality tests) methods. Nested clade phylogeographic analyses, and divergence time estimates using a calibrated molecular clock, were also conducted. Results A total of 27 haplotypes identified in the present study clustered into four primary genealogical lineages, revealing three significant latitudinal phylogeographical breaks. The two high Andean lineages probably split first, during the late Miocene, and the Patagonian lineage split around 4 Ma, coincident with the establishment of the Patagonian steppe. Within each haplogroup, major diversification occurred in the Pleistocene. The Patagonian groups show a pattern consistent with a rapid post‐glacial expansion and colonization of the Andean flanks, achieved independently by four lineages. The highest haplotype diversity was found along a longitudinal transect that is remarkably congruent with the limit of the ice‐sheet extension during the Greatest Patagonian Glaciation. A north‐east expansion is evident, which is probably associated with the ‘Arid Diagonal’ fluctuations. Main conclusions Glacial climate fluctuations had a substantial impact on the diversification, distribution and demography of the study species. A scenario of multiple periglacial Pleistocene refugia and subsequent multiple recolonization routes, from eastern Patagonia to the Andean flanks, may explain the phylogeographical patterns observed. However, current genetic structure also preserves the imprints of older events that probably occurred in the Miocene and Pliocene, providing evidence that multiple processes, operating at different spatial and temporal scales, have moulded biodiversity in Patagonia.     

The genetic legacy of aridification: climate cycling fostered lizard diversification in Australian montane refugia and left low-lying deserts genetically depauperate

It is a widely held assumption that populations historically restricted to mountain refugia tend to exhibit high levels of genetic diversity and deep coalescent histories, whereas populations distributed in surrounding low-lying regions tend to be genetically depauperate following recent expansion from refugia. These predicted genetic patterns are based largely on our understanding of glaciation history in Northern Hemisphere systems, yet remain poorly tested in analogous Southern Hemisphere arid systems because few examples in the literature allow the comparison of widespread taxa distributed across mountain and desert biomes. We demonstrate with multiple datasets from Australian geckos that topographically complex mountain regions harbor high nucleotide diversity, up to 18 times higher than that of the surrounding desert lowlands. We further demonstrate that taxa in topographically complex areas have older coalescent histories than those in the geologically younger deserts, and that both ancient and more recent aridification events have contributed to these patterns. Our results show that, despite differences in the details of climate and landscape changes that occurred in the Northern and Southern hemispheres (ice-sheets versus aridification), similar patterns emerge that illustrate the profound influence of the Pleistocene on contemporary genetic structure.     

Evolutionary systematics and biogeography of the arid habitat‐adapted rodent genus Gerbillus (Rodentia,Muridae): a mostly Plio‐Pleistocene African history

The systematics of the arid‐adapted Old World Gerbillus rodent genus has always been challenging, with many different taxonomic arrangements proposed. Beyond such taxonomic aspects, the timing and geographical pattern of the evolutionary history of this group remains largely unknown. Based on mitochondrial (cytochrome b) and nuclear (interphotoreceptor retinoid‐binding protein) sequences obtained from the specimens of 21 species, we conducted a phylogenetic analysis of the group, estimated the ages and putative ancestral ranges of its major lineages. Four major clades were clearly retrieved within Gerbillus, for which we propose a subgenus rank. We showed that the emergence of the genus dates back to the end of the Miocene, which corresponds to a period of aridification and C4 vegetation expansion in open habitats, while the four sublineages originated at the end of the Pliocene. Most subsequent diversification events occurred during the Pleistocene, a period characterized by recurrent climatic/environmental shifts with increasing aridification during the last two millions of years. Finally, we suggested that most of the Gerbillus evolutionary history took place in Africa. Only in a few instances did dispersal events from Africa to Asia give birth to extant Asian lineages, a pattern that contrasts with what has been found in many animal groups.     

Evolution of Asian Interior Arid-Zone Biota: Evidence from the Diversification of Asian Zygophyllum (Zygophyllaceae)

The Asian interior arid zone is the largest desert landform system in the Northern Hemisphere, and has high biodiversity. Little is currently known about the evolutionary history of its biota. In this study, we used Zygophyllum, an important and characteristic component of the Asian interior arid zone, to provide new insights into the evolution of this biota. By greatly enlarged taxon sampling, we present the phylogenetic analysis of Asian Zygophyllum based on two plastid and one nuclear markers. Our phylogenetic analyses indicate that Asian Zygophyllum and Sarcozygium form a clade and Sarcozygium is further embedded within the shrub subclade. An integration of phylogenetic, biogeographic, and molecular dating methods indicates that Zygophyllum successfully colonized the Asian interior from Africa in the early Oligocene, and Asian Zygophyllum became differentiated in the early Miocene and underwent a burst of diversification in the late Miocene associated with the expansion of Asian interior arid lands due to orogenetic and climatic changes. Combining diversification patterns of other important components of the Asian interior arid zone, we propose a multi-stage evolution model for this biota: the late Eocene–early Oligocene origin, the early Miocene expansion, and the middle-late Miocene rapid expansion to the whole Asian interior arid zone. This study also demonstrates that, for Zygophyllum and perhaps other arid-adapted organisms, arid biomes are evolutionary cradles of diversity.     

Geographical variation in genetic structure of an Atlantic Coastal Forest frog reveals regional differences in habitat stability

Climatic oscillations throughout the Pleistocene combined with geological and topographic complexity resulted in extreme habitat heterogeneity along the Atlantic coast of Brazil. Inferring how these historic landscape patterns have structured the current diversity of the region's biota is important both for our understanding of the factors promoting diversification, as well as the conservation of this biodiversity hotspot. Here we evaluate potential historical scenarios of diversification in the Atlantic Coastal Forest of Brazil by investigating the population genetic structure of a frog endemic to the region. Using mitochondrial and nuclear sequences, we generated a Bayesian population-level phylogeny of the Thoropa miliaris species complex. We found deep genetic divergences among five geographically distinct clades. Southern clades were monophyletic and nested within paraphyletic northern clades. Analyses of historical demographic patterns suggest an overall north to south population expansion, likely associated with regional differences in habitat stability during the Pliocene and early Pleistocene. However, genetic structure among southern populations is less pronounced and likely represents more recent vicariant events resulting from Holocenic sea-level oscillations. Our analyses corroborate that the Atlantic Coastal Forest has been a biogeographically dynamic landscape and suggest that the high diversity of its fauna and flora resulted from a combination of climatic and geologic events from the Pliocene to the present.     

On the evolution of fish–coral interactions

The biodiversity of tropical reefs is typified by the interaction between fishes and corals. Despite the importance of this ecological association, coevolutionary patterns between these two animal groups have yet to be critically evaluated. After compiling a large dataset on the prevalence of fish–coral interactions, we found that only a minority of fish species associate strongly with live corals (~5%). Furthermore, we reveal an evolutionary decoupling between fish and coral lineage trajectories. While fish lineages expanded in the Miocene, the bulk of coral diversification occurred in the Pliocene/Pleistocene. Most importantly, we found that coral association did not drive major differences in fish diversification. These results suggest that the Miocene fish diversification is more likely related to the development of novel, wave-resistant reef structures and their associated ecological opportunities. Macroevolutionary patterns in reef fishes are thus more strongly correlated with the expansion of reefs than with the corals themselves.     

Multiple Pleistocene refugia and Holocene range expansion of an abundant southwestern American desert plant species (Melampodium leucanthum,Asteraceae)

Pleistocene climatic fluctuations had major impacts on desert biota in southwestern North America. During cooler and wetter periods, drought‐adapted species were isolated into refugia, in contrast to expansion of their ranges during the massive aridification in the Holocene. Here, we use Melampodium leucanthum (Asteraceae), a species of the North American desert and semi‐desert regions, to investigate the impact of major aridification in southwestern North America on phylogeography and evolution in a widespread and abundant drought‐adapted plant species. The evidence for three separate Pleistocene refugia at different time levels suggests that this species responded to the Quaternary climatic oscillations in a cyclic manner. In the Holocene, once differentiated lineages came into secondary contact and intermixed, but these range expansions did not follow the eastwardly progressing aridification, but instead occurred independently out of separate Pleistocene refugia. As found in other desert biota, the Continental Divide has acted as a major migration barrier for M. leucanthum since the Pleistocene. Despite being geographically restricted to the eastern part of the species’ distribution, autotetraploids in M. leucanthum originated multiple times and do not form a genetically cohesive group.     

Miocene and Pliocene dominated diversification of the lichen-forming fungal genus Melanohalea (Parmeliaceae, Ascomycota) and Pleistocene population expansions

ABSTRACT: BACKGROUND: Factors promoting diversification in lichen symbioses remain largely unexplored. While Pleistocene events have been important for driving diversification and affecting distributions in many groups, recent estimates suggest that major radiations within some genera in the largest clade of macrolichens (Parmeliaceae, Ascomycota) vastly predate the Pleistocene. To better understand the temporal placement and sequence of diversification events in lichens, we estimated divergence times in a common lichen-forming fungal genus, Melanohalea, in the Northern Hemisphere. Divergence times were estimated using both concatenated gene tree and coalescence-based multilocus species tree approaches to assess the temporal context of major radiation events within Melanohalea. In order to complement our understanding of processes impacting genetic differentiation, we also evaluated the effects of Pleistocene glacial cycles on population demographics of distinct Melanohalea lineages, differing in reproductive strategies. RESULTS: We found that divergence estimates, from both concatenated gene tree and coalescence-based multilocus species tree approaches, suggest that diversification within Melanohalea occurred predominantly during the Miocene and Pliocene, although estimated of divergence times differed by up to 8.3 million years between the two methods. These results indicate that, in some cases, taxonomically diagnostic characters may be maintained among divergent lineages for millions of years. In other cases, similar phenotypic characters among non-sister taxa, including reproductive strategies, suggest the potential for convergent evolution due to similar selective pressures among distinct lineages. Our analyses provide evidence of population expansions predating the last glacial maximum in the sampled lineages. These results suggest that Pleistocene glaciations were not inherently unfavorable or restrictive for some Melanohalea species, albeit with apparently different demographic histories between sexually and vegetatively reproducing lineages. CONCLUSIONS: Our results contribute to the understanding of how major changes during the Miocene and Pliocene have been important in promoting diversification within common lichen-forming fungi in the northern Hemisphere. Additionally, we provide evidence that glacial oscillations have influenced current population structure of broadly distributed lichenized fungal species throughout the Holarctic.     

Impact of Pleistocene aridity oscillations on the population history of a widespread,vagile Australian mammal,Macropus fuliginosus

Aim Climatic fluctuations during the Pleistocene have shaped the population structure of many extant taxa. However, few studies have examined widespread species inhabiting the Australian continent, where periods of increased aridity characterized the Pleistocene. Here we investigate the phylogeography and population history of a widespread and vagile southern Australian marsupial, the western grey kangaroo (Macropus fuliginosus). Location Southern Australia. Methods We examined the variation of the mitochondrial DNA (mtDNA) control region from 511 individuals of M. fuliginosus sampled throughout their transcontinental distribution. Maximum likelihood and Bayesian analyses were used to investigate the phylogeography and coalescence analyses were then used to test hypothesized biogeographical scenarios. Results The combined results of the phylogeographical and coalescence analyses revealed a complex evolutionary history. Macropus fuliginosus originated in the south‐west of the continent, with north‐western and south‐western populations subsequently diverging as a result of vicariance events during the mid‐Pleistocene. Subsequent arid phases affected these populations differently. In the north‐west, the expansion and contraction of the arid zone resulted in repeated vicariance events and multiple divergent north‐western mtDNA subclades. In contrast, the south‐western population was less impacted by climatic oscillations but gave rise to a major transcontinental eastward expansion. Main conclusions Macropus fuliginosus exhibits the genetic signature of divergence due to unidentified barriers in south‐western Western Australia, while previously identified barriers across southern Australia appear to have had little impact despite evidence of a broad‐scale range expansion prior to the Last Glacial Maximum (LGM). This pattern of localized expansion and contraction is comparable to unglaciated regions in both the Northern and Southern Hemispheres. Furthermore, this study indicates that despite the potential similarities between Northern Hemisphere glaciation and the activation of dune systems in the Australian arid zone, both of which rendered large areas inhospitable, the biotic responses and resultant phylogeographical signatures are dissimilar. Whereas a limited number of major geographically concordant refugia are observed in glaciated areas, the Southern Hemisphere arid zone appears to be associated with multiple species‐specific idiosyncratic refugia.     

The anatomy of a ‘suture zone’ in Amazonian butterflies: a coalescent‐based test for vicariant geographic divergence and speciation

Attempts by biogeographers to understand biotic diversification in the Amazon have often employed contemporary species distribution patterns to support particular theories, such as Pleistocene rainforest refugia, rather than to test among alternative hypotheses. Suture zones, narrow regions where multiple contact zones and hybrid zones between taxa cluster, have been seen as evidence for past expansion of whole biotas that have undergone allopatric divergence in vicariant refuges. We used coalescent analysis of mutilocus sequence data to examine population split times in 22 pairs of geminate taxa in ithomiine and heliconiine butterflies. We test a hypothesis of simultaneous divergence across a suture zone in NE Peru. Our results reveal a scattered time course of diversification in this suture zone, rather than a tight cluster of split times. Additionally, we find rapid diversification within some lineages such as Melinaea contrasting with older divergence within lineages such as the Oleriina (Hyposcada and Oleria). These results strongly reject simple vicariance as a cause of the suture zone. At the same time, observed lineage effects are incompatible with a series of geographically coincident vicariant events which should affect all lineages similarly. Our results suggest that Pleistocene climatic forcing cannot readily explain this Peruvian suture zone. Lineage‐specific biological traits, such as characteristic distances of gene flow or varying rates of parapatric divergence, may be of greater importance.     

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.     

Phylogeographical patterns shed light on evolutionary process in South America

The South American continent is composed of several biogeographical regions harbouring the highest biodiversity on the globe, encompassing five of the world's biodiversity ‘hot spots’. Nonetheless, the patterns and processes responsible for shaping its astonishing species diversity are largely unknown. Here, we present a review of current South American phylogeographical knowledge based on published articles on this topic. An appraisal of the literature reveals emerging phylogeographical patterns in the biota of South America. The striking phylogeographical divergence observed among organism lineages in South American studies is suggestive of high levels of undocumented species diversity. The interplay between Pleistocene climatic oscillations and Pliocene/Miocene orogenic events has contributed to shaping the current diversity and distribution of modern lineages in both the tropical and temperate regions of South America. Although older divergence times were observed for a range of species, most herpetofauna underwent an intraspecific lineage split much earlier than other organisms. The geographical ranges of species associated with forest habitats were reduced mainly during glacial cycles, whereas species associated with open vegetation domains have shown variable responses to climatic oscillations. The results suggest a highly complex mosaic of phylogeographical patterns in South America. We suggest future research directions to promote a better understanding of the origin and maintenance of the South American biota.     

Phylogeography of sexual Heteronotia binoei (Gekkonidae) in the Australian arid zone: climatic cycling and repetitive hybridization

The biota of much of continental Australia have evolved within the context of gradual aridification of the region over several million years, and more recently of climatic cycling between relatively dry and humid conditions. We performed a phylogeographical study of three sexual chromosome races of the Heteronotia binoei complex of geckos found throughout the Australian arid zone. Two of these three races were involved in two separate hybridization events leading to parthenogenetic lineages (also H. binoei), and the third is widespread and broadly sympatric with the parthenogens. Based on our analyses, the three sexual races diversified approximately 6 million years ago in eastern Australia, during a period of aridification, then each moved west through northern, southern, and central dispersal corridors to occupy their current ranges. In each case, the timing of major phylogeographical inferences corresponds to inferred palaeoclimatic changes in continental Australia. This scenario provides a simple explanation for diversification, secondary contact, and hybridization between the races. However, data presented elsewhere indicate that formation of the parthenogens was considerably more recent than the westward expansion of the hybridizing races, and that multiple hybridization events were geographically and temporally distinct. We suggest that cyclical climate changes may have led to regional range changes that facilitated hybridization between the races, which are not currently known to be in sympatry.     

Independent Transitions between Monsoonal and Arid Biomes Revealed by Systematic Revison of a Complex of Australian Geckos (Diplodactylus; Diplodactylidae)

How the widespread expansion and intensification of aridity through the Neogene has shaped the Austral biota is a major question in Antipodean biogeography. Lineages distributed across wide aridity gradients provide opportunities to examine the timing, frequency, and direction of transitions between arid and mesic regions. Here, we use molecular genetics and morphological data to investigate the systematics and biogeography of a nominal Australian gecko species (Diplodactylus conspicillatus sensu lato) with a wide distribution spanning most of the Australian Arid Zone (AAZ) and Monsoonal Tropics (AMT). Our data support a minimum of seven genetically distinct and morphologically diagnosable taxa; we thus redefine the type species, ressurrect three names from synonymy, and describe three new species. Our inferred phylogeny suggests the history and diversification of lineages in the AAZ and AMT are intimately linked, with evidence of multiple independent interchanges since the late Miocene. However, despite this shared history, related lineages in these two regions also show evidence of broadly contrasting intra-regional responses to aridification; vicarance and speciation in older and increasingly attenuated mesic regions, versus a more dynamic history including independent colonisations and recent range expansions in the younger AAZ.