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Spots before the eyes: revision of the saxicoline geckos of the Gehyra punctata (Squamata: Gekkonidae) species complex in the Pilbara region of Western Australia
... The genus has long been recognised as taxonomically difficult (King 1979(King , 1983. Recent phylogeographic studies have revealed extraordinary levels of undescribed cryptic diversity within many nominal species of Australian Gehyra (Sistrom et al. 2013;Moritz et al. 2018;Ashman et al. 2018;Noble et al. 2018;Oliver et al. 2019), and more than 20 new species have been described or elevated from synonymy in the last decade (Sistrom et al. 2009;Doughty et al. 2012Doughty et al. , 2018aDoughty et al. , 2018bHutchinson et al. 2014;Oliver et al. 2016;Bourke et al. 2017;Kealley et al. 2018). As a result of these considerable efforts there are now 42 species of Gehyra recognised in Australia, making it the most speciose genus of gekkotan lizards in Australia, with the rocky Pilbara and Kimberley regions of north-western Australia being centres of diversity and endemism (Ashman et al. 2018;Doughty et al. 2018aDoughty et al. , 2018bKealley et al. 2018). ...
... Recent phylogeographic studies have revealed extraordinary levels of undescribed cryptic diversity within many nominal species of Australian Gehyra (Sistrom et al. 2013;Moritz et al. 2018;Ashman et al. 2018;Noble et al. 2018;Oliver et al. 2019), and more than 20 new species have been described or elevated from synonymy in the last decade (Sistrom et al. 2009;Doughty et al. 2012Doughty et al. , 2018aDoughty et al. , 2018bHutchinson et al. 2014;Oliver et al. 2016;Bourke et al. 2017;Kealley et al. 2018). As a result of these considerable efforts there are now 42 species of Gehyra recognised in Australia, making it the most speciose genus of gekkotan lizards in Australia, with the rocky Pilbara and Kimberley regions of north-western Australia being centres of diversity and endemism (Ashman et al. 2018;Doughty et al. 2018aDoughty et al. , 2018bKealley et al. 2018). ...
... We recommend the common name 'Amber rock dtella' for this species. Recent taxonomic revisions of Gehyra have moved away from recommending 'dtella' in common names, instead favouring 'Gehyra' (Doughty 2018a;Kealley 2018) or simply 'gecko' (Oliver et al. 2016;Doughty 2018b). Kealley et al. (2018) provide justification for this: "We prefer to use 'Gehyra' as the common name over 'dtella' as the generic name is already available and just as easy or difficult to remember than an additional name fabricated for use as a common name." ...
We describe a new species of rock-dwelling Gehyra Gray, 1834 (Gekkonidae) from the Einasleigh Uplands of inland north Queensland, Australia. Morphological, ecological, and molecular data clearly support the new species as distinct and place it within the 'australis group'. Gehyra electrum sp. nov. is distinguished from congeners by a combination of medium adult size (SVL 46-50 mm), an orange-brown to pinkish-orange background colouration with a pattern of distinct whitish spots and irregular black to purple-brown blotches or bars, possessing 7-8 undivided subdigital lamellae on the expanded portion of the fourth toe, and a wedge-shaped mental scale that separates the inner-postmental scales along 40% or more of their length. Gehyra electrum sp. nov. is a rock specialist currently known only from granite outcrops of the Mt Surprise region, Queensland. This is the second recently described Gehyra from the Einasleigh Uplands and adds to the growing number of endemic reptiles recognised in the region.
... Storr (1982) synonymised G. fenestra with G. punctata Fry, 1914; however, it was recognised as a distinct taxon by Cogger et al. (1983), further supported by Bauer and Henle (1994) who stated, 'we tentatively recognise G. fenestra as distinct'. See Doughty et al. (2018a) for the decision to maintain synonmy of G. fenestra with G. punctata based on the rediscovery of the missing syntype of the latter. Paratypes (6) R113727, Cadjbut Mine, 90 km SE Fitzroy Crossing, WA; R175037 (field no. ...
... Scale bar = 10 mm. (Figures 2-3), see Doughty et al. (2018a) for lectotype designation. ...
... Although P. variegatus punctatus was considered a wider ranging species at the time of description, the species range is now known to be confined to Western Australia and the two syntypes represent different species. Despite the poor condition of the specimen, the WAM lectotype designated by Doughty et al. (2018a) is representative of what is commonly referred to as G. punctata. The syntype illustration from Lucas and Frost (1896), relegated to paralectotype status by inference of lectotype designation, most closely resembles what has since been described as Gehyra moritzi Hutchinson, Sistrom, Donnellan and Hutchinson, 2014. ...
... Rocky ranges and residuals (sensu Gardner 1957) within Australia's tropical savannas act as 'islands' of habitat in a 'sea' of open savanna woodland. This, in combination with taxa that are of relatively low mobility, has resulted in many significant radiations, especially among reptiles (e.g., Doughty et al. 2018;Oliver et al. 2019;Potter et al. 2019;Oliver et al. 2020). In recent years there has been a steady stream of reptile descriptions from all three northern Australian states and territories, concentrated on rocky ranges and residual ranges (Western Australia- Doughty et al. 2012Doughty et al. , 2016Doughty et al. , 2018Oliver et al. 2014b; the Northern Territory- Oliver & Parkin 2014;Queensland-Hoskin & Couper 2015;Vanderduys 2016Vanderduys , 2017Bourke et al. 2017;Hoskin et al. 2018;Hoskin 2019;Zozaya et al. 2019). ...
... This, in combination with taxa that are of relatively low mobility, has resulted in many significant radiations, especially among reptiles (e.g., Doughty et al. 2018;Oliver et al. 2019;Potter et al. 2019;Oliver et al. 2020). In recent years there has been a steady stream of reptile descriptions from all three northern Australian states and territories, concentrated on rocky ranges and residual ranges (Western Australia- Doughty et al. 2012Doughty et al. , 2016Doughty et al. , 2018Oliver et al. 2014b; the Northern Territory- Oliver & Parkin 2014;Queensland-Hoskin & Couper 2015;Vanderduys 2016Vanderduys , 2017Bourke et al. 2017;Hoskin et al. 2018;Hoskin 2019;Zozaya et al. 2019). ...
The Einasleigh Uplands bioregion of central north Queensland, Australia, harbours a unique suite of reptiles that have begun to receive significant attention in the last 20 years. This has resulted in a number of new reptile species being described, and recognition that others await description. We describe a new species of Lucasium Wermuth, 1965 from the western Einasleigh Uplands. Lucasium iris sp. nov. is genetically distinct and morphologically diagnosable from all congeners by its large size, long and narrow tail, nares in contact with rostral scale, homogeneous body scales, distinct vertebral stripe, and paired, enlarged, apical subdigital lamellae. It is known from low rocky hills in a localised area of the Gregory Range, has the most restricted known distribution of any Lucasium, and is the only Lucasium endemic to Queensland. The new species appears most closely related to L. steindachneri (Boulenger, 1885), based on mitochondrial DNA sequences, but has a colour-pattern more similar to L. immaculatum Storr, 1988. All three of these species occur in the Einasleigh Uplands, but only L. steindachneri is known to occur in sympatry with L. iris sp. nov. In addition to the description of the new species, we present records of Lucasium immaculatum from the Einasleigh Uplands, which represent a significant known range extension.
... The gekkonid lizards in the genus Gehyra from Australia show conservative body form, variable appearance and have been a test case for implementing new methods to document species diversity (King, 1979(King, , 1982Sistrom, Donnellan & Hutchinson, 2013;Sistrom et al., 2014;Ashman et al., 2018;Kealley et al., 2018;Moritz et al., 2018;summarised in Doughty et al., 2018a). The various genetic techniques have led to increasingly finer resolution of phylogenetic structure, and have recently resulted in major revisions of Gehyra species-groups from the Australian arid zone and the Australian Monsoonal Tropics (AMT) such that the number of recognised species has nearly doubled from 22 to 43 (Hutchinson et al., 2014;Doughty et al., 2018aDoughty et al., , 2018bKealley et al., 2018). ...
... nov. and G. australis group; Oliver et al., 2019), body size evolution associated with establishment of sympatric assemblages (Doughty et al., 2018a;Moritz et al., 2018) and the high prevalence of short-range taxa in complex rocky environments (Ashman et al., 2018), and association of chromosome change with few loci, have revealed deep and geographically fine-grained phylogeographic structure (Oliver, Doughty & Palmer, 2012;Moritz et al., 2016Moritz et al., , 2018Potter et al., 2016;Laver et al., 2017;. With a few exceptions (Doughty, Ellis & Oliver, 2016;Afonso Silva et al., 2017;Moritz et al., 2018), the taxonomic status of much of this diversity remains to be evaluated. ...
For over two decades, assessments of geographic variation in mtDNA and small numbers of nuclear loci have revealed morphologically similar, but genetically divergent, intraspecific lineages in lizards from around the world. Subsequent morphological analyses often find subtle corresponding diagnostic characters to support the distinctiveness of lineages, but occasionally do not. In recent years it has become increasingly possible to survey geographic variation by sequencing thousands of loci, enabling more rigorous assessment of species boundaries across morphologically similar lineages. Here we take this approach, adding new, geographically extensive SNP data to existing mtDNA and exon capture datasets for the Gehyra australis and G. koira species complexes of gecko from northern Australia. The combination of exon-based phylogenetics with dense spatial sampling of mitochondrial DNA sequencing, SNP-based tests for introgression at lineage boundaries and newly-collected morphological evidence supports the recognition of nine species, six of which are newly described here. Detection of discrete genetic clusters using new SNP data was especially convincing where candidate taxa were continuously sampled across their distributions up to and across geographic boundaries with analyses revealing no admixture. Some species defined herein appear to be truly cryptic, showing little, if any, diagnostic morphological variation. As these SNP-based approaches are progressively applied, and with all due conservatism, we can expect to see a substantial improvement in our ability to delineate and name cryptic species, especially in taxa for which previous approaches have struggled to resolve taxonomic boundaries.
... For low-dispersal species such as lizards ( Bragg, et al., 2017;Laver, Doughty, & Oliver, 2018;Oliver, Couper, & Pepper, 2014). The major exception in the AZ is for taxa occupying the major topographic refugia, in particular the Pilbara craton, which often shows complex and localized phylogeographic structure or in situ speciation (Ashman et al., 2018;Doughty, Bauer, Pepper, & Keogh, 2018;Keally et al., 2018;Pepper et al., 2013). Evidence of multiple refugia across the AZ is prevalent in broadly distributed species of geckos and agamids that are specialists of disjunct habitats, such as stony deserts or major rocky ranges (Table 1). ...
Aim
Focussing on pairs of sister species across three genera of scincid lizards, we use genomic evidence to test for larger‐scale, late‐Pleistocene changes in distributions of lizards in the Australian arid zone (AZ) than in the adjacent monsoonal tropics (MT).
Location
Northern and central Australia.
Taxon
Scincidae: Squamata.
Methods
We sequenced ~2000 nuclear exons and one mitochondrial gene across the distributions of species with primarily MT or AZ distributions from three genera of lizards. Using phylogenetic analysis and population structure analyses we identified major phylogeographic lineages and then compared the spatial scale of structuring and tested for recent demographic expansions.
Results
Two genera in particular, Proablepharus and Morethia, showed deeper and more geographically localized phylogeographic diversity in the MT than the AZ. In the MT, localized diversity was prevalent in the relatively mesic regions. By contrast, the AZ was characterized by widespread and often genetically uniform lineages and a higher proportion of these had signals of recent population expansion.
Main conclusions
Consistent with other recent, but mostly less genetically extensive studies, our results point to deeper and more localized diversity in MT compared to AZ. In turn, this suggests higher local persistence in more mesic and topographically diverse biome through the late Quaternary climate fluctuations. For the AZ, geographically extensive range expansions have likely contributed to the low spatial turnover of this exceptionally rich lizard fauna.
... In the absence of a type specimen, the inability to determine with certainty to which species the name applies and limited information in the description of Phyria and Phyria punctulata by Gray (1842) Doughty, Bauer, Pepper & Keogh, 2018. The species epithet finipunctata is derived from the Latin words finis (fine) and punctata (punctate or bearing small spots), as in bearing fine spots or finely spotted, in reference to the dorsal pattern which forms part of the species diagnosis, described by Doughty et al. (2018a) as 'background colour light reddish to greyish-brown with small dark and pale spots not in contact and evenly spaced ' (pp. 19-20). ...
... Gehyra lazelli (Wells & Wellington, 1985) Dactyloperus lazelli Wells & Wellington, 1985:11 Gehyra leopoldi Brongersma, 1930 Gehyra leopoldi Brongersma, 1930:1. Gehyra micra Doughty, Bauer, Pepper and Keogh, 2018 Gehyra micra Doughty, Bauer, Pepper and Keogh, 2018: 29 Gehyra montium Storr, 1982 Gehyra montium Storr, 1982: 56. Gehyra mutilata Hemidactylus mutilatus Wiegmann, 1834: 238. ...
See http://www.afriherp.org/gekkota-catalog/ for details
Aim
Climatic variation has long been regarded as a primary source of morphological variation. However, there is mixed support for the adherence of reptiles to ecogeographical hypotheses, such as Bergmann’s rule (body size decreases with temperature) and Allen’s rule (limb length increases with temperature). We quantified body and limb morphology among the diverse Australian gecko fauna (4 families, 30 genera, 226 of the 231 described species) to investigate environmental correlates of morphological variation in this radiation.
Location
Australia.
Major taxa studied
Geckos (Squamata: Gekkota; the families Gekkonidae, Carphodactylidae, Diplodactylidae and Pygopodidae).
Methods
We measured 20 external features of ethanol‐preserved museum specimens. We investigated whether principal component axes of morphology were correlated with three key environmental variables, and the microhabitat occupied by each species.
Results
Morphology varied greatly among Australian gecko families and genera, although there was a strong phylogenetic signal in morphology. After accounting for phylogeny, morphology was correlated with a species’ microhabitat use. Saxicolous species and species with variable microhabitat requirements (i.e., generalists) had larger body dimensions than terrestrial species. Saxicolous species also had longer proportional forelimbs and hindlimbs than terrestrial species.
Main conclusions
Our results highlight the importance of phylogeny and microhabitat use in shaping the morphology of Australian geckos. We find little evidence that Australian geckos adhere to Bergmann’s rule or Allen’s rule, suggesting that these ecogeographical hypotheses provide limited insight into the adaptive potential of lizard species to altered environmental conditions.
The methods used to detect and describe morphologically cryptic species have advanced in recent years, owing to the integrative nature of molecular and morphological techniques required to elucidate them. Here we integrate recent phylogenomic work that sequenced many genes but few individuals, with new data from mtDNA and morphology from hundreds of gecko specimens of the Gehyra variegata group from the Australian arid zone. To better understand morphological and geographical boundaries among cryptic forms, we generated new sequences from 656 Gehyra individuals, largely assigned to G. variegata group members over a wide area in Western Australia, with especially dense sampling in the Pilbara region, and combined them with 566 Gehyra sequences from GenBank, resulting in a dataset of 1,222 specimens. Results indicated the existence of several cryptic species, from new species with diagnostic morphological characters, to cases when there were no useful characters to discriminate among genetically distinctive species. In addition, the cryptic species often showed counter-intuitive distributions, including broad sympatry among some forms and short range endemism in other cases. Two new species were on long branches in the phylogram and restricted to the northern Pilbara region: most records of the moderately sized G. incognita sp. nov. are near the coast with isolated inland records, whereas the small-bodied saxicoline G. unguiculata sp. nov. is only known from a small area in the extreme north of the Pilbara. Three new species were on shorter branches in the phylogram and allied to G. montium . The moderately sized G. crypta sp. nov. occurs in the western and southern Pilbara and extends south through the Murchison region; this species was distinctive genetically, but with wide overlap of characters with its sister species, G. montium . Accordingly, we provide a table of diagnostic nucleotides for this species as well as for all other species treated here. Two small-bodied species occur in isolated coastal regions: G. capensis sp. nov. is restricted to the North West Cape and G. ocellata sp. nov. occurs on Barrow Island and other neighbouring islands. The latter species showed evidence of introgression with the mtDNA of G. crypta sp. nov., possibly due to recent connectivity with the mainland owing to fluctuating sea levels. However, G. ocellata sp. nov. was more closely related to G. capensis sp. nov. in the phylogenomic data and in morphology. Our study illustrates the benefits of combining phylogenomic data with extensive screens of mtDNA to identify large numbers of individuals to the correct cryptic species. This approach was able to provide sufficient samples with which to assess morphological variation. Furthermore, determination of geographic distributions of the new cryptic species should greatly assist with identification in the field, demonstrating the utility of sampling large numbers of specimens across wide areas.
Targeting phylogenetic diversity (PD) in systematic conservation planning is an efficient way to minimize losses across the Tree of Life. Considering representation of genetic diversity below and above species level, also allows robust analyses within systems where taxonomy is in flux. We use dense sampling of phylogeographic diversity for eleven lizard genera, to demonstrate how PD can be applied to a policy-ready conservation planning problem. Our analysis bypasses named taxa, using genetic data directly to inform conservation decisions. We highlight areas that should be prioritised for ecological management, and also areas that would provide the greatest benefit if added to the multi-sector conservation estate. We provide a rigorous and effective approach to represent the spectrum of genetic and species diversity in conservation planning.
The tropical savannah landscapes of Australia’s north, though previously overshadowed by the biodiverse rainforests of the Wet Tropics, are themselves now attracting interest for their biological significance and uniqueness. The Einasleigh Uplands region of north-east Queensland is home to a diverse group of mammals and reptiles and was previously recognised for its importance in shaping speciation in birds. Here we add a small saxicoline gecko to a growing list of recently described reptiles that are endemic to this region. Phylogenetic analyses including Gehyra species from the arid zone and the monsoonal tropics reveal that small Gehyra geckos in this area, while closely resembling Gehyra nana from the Top End and Kimberley, form a clade that is geographically isolated and phylogenetically distant from the G. nana complex. Instead, the Einasleigh Uplands taxon is sister to a large, arboreal species within the arid zone clade. It is readily distinguished from all lineages within the G. nana complex, its closest relative G. purpurascens, and all other rock-dwelling species from the arid zone by a combination of its very small body size, few subdigital lamellae, and mid tan to golden dorsal coloration with a pattern of scattered pale ocelli and irregular dark-brown blotches on a stippled background. We therefore describe this taxon as a new Australian species of Gehyra, Gehyra einasleighensis sp. nov., based on a combination of phylogenetic separation, morphological characters and discrete geographic distribution.
Ongoing fieldwork and molecular research continues to reveal that the monsoonal tropics of northern Australia contain more vertebrate species than currently recognised. Here we focus on two morphologically distinctive, yet unrecognised forms in the genus Gehyra from the southern Kimberley region and surrounding deserts. We base our descriptions on a combination of unpublished genetic data and a morphological examination of voucher specimens. We recognise and re-describe G. kimberleyi, a species with a broad distribution extending over most of the south-west Kimberley, across the Great Sandy Desert and into the far northern Pilbara. This species has been previously assigned to G. pilbara owing to its frequent occurrence on termite mounds and short snout, but can be distinguished from G. pilbara and other regionally sym-patric Gehyra by its moderate body size, moderate number of pre-cloacal pores in males (12-17) and aspects of dorsal colouration. We also describe G. girloorloo sp. nov., a small rock-dwelling species with a short snout, low number of pre-cloacal pores in males (8-11) and pinkish-grey dorsal colouration with alternating series of indistinct pale spots and irreg-ular transversely-aligned dark blotches. The new species appears to be restricted to a relatively small region of exposed limestone karst in the south-west Kimberley and is entirely circumscribed by morphologically similar congeners.
The Pilbara region has one of the most diverse reptile assemblages in the world and includes many typical arid zone species as well as many saxicoline endemics. We present the results of a four-year survey of the region during which pitfall trap lines were used to sample 297 quadrats for a total of two weeks in spring and in autumn. The quadrats were located across the region and were chosen to sample the main substrate types. Environmental variables were measured to characterise the soil as well as the geomorphic, vegetative and climatic setting of each quadrat. We used the program PATN to expose patterns in species composition among quadrats, and in relation to the environmental variables. A strong signal for community structure emerged that was linked to surface type. Broad rock, clay, sand and loam categorisations seemed to explain most assemblage composition, with climatic variables showing only weak influence. However, many taxa occurred across several surface types, reflecting the close juxtaposition of habitats within the region, wide dispersion of some taxa, and perhaps the influence of recent environmental history including anthropogenic changes. Examination of biogeographic characteristics of the species groups indicated strong endemism for taxa that preferred rocky substrates. In addition, many saxicoline Pilbara taxa have ranges that extend south into rocky areas of the Gascoyne, western Murchison and adjacent areas. Sandy habitats similar to those found in the Pilbara are widespread across Australia's arid zone, and accordingly few endemic taxa showed a preference for sandy surface types, and taxa with such preferences have distributions extending far beyond the Pilbara. The sandy areas of the coastal plain in the Roebourne subregion contained many taxa from Dampierland and the Great Sandy Desert to the north and north-east, as well as some taxa from the rich sand-adapted fauna of the Carnarvon region to the south. Some endemic taxa are associated with clay in the region, although clay surfaces were not as extensive as the rocky, loamy and sandy surfaces. Species associated with the fine-textured soils of the mulga woodlands in the southern part of the region appear to be an extension of herpetofaunal communities of regions to the south.
The taxonomy of central Australian populations of geckos of the genus Gehyra has been uncertain since chromosomal studies carried out in the 1970s and 1980s revealed considerable heterogeneity and apparently independent patterns of morphological and karyotypic diversity. Following detailed molecular genetic studies, species boundaries in this complex have become clearer and we here re-set the boundaries of the three named species involved, G. variegata (Duméril & Bibron, 1836), G. montium Storr, 1982, and G. nana King, 1982, and describe three new species. Two of the new species, G. moritzi and G. pulingka, include populations formerly assigned to either G. montium or G. nana Storr, 1982, while the third, G. versicolor, includes all of the eastern Australian populations formerly assigned to G. variegata.
Species tree methods have provided improvements for estimating species relationships and the timing of diversification in recent radiations by allowing for gene tree discordance. Although gene tree discordance is often observed, most discordance is attributed to incomplete lineage sorting rather than other biological phenomena, and the causes of discordance are rarely investigated. We use species trees from multi-locus data to estimate the species relationships, evolutionary history and timing of diversification among Australian Gehyra-a group renowned for taxonomic uncertainty and showing a large degree of gene tree discordance. We find support for a recent Asian origin and two major clades: a tropically adapted clade and an arid adapted clade, with some exceptions, but no support for allopatric speciation driven by chromosomal rearrangement in the group. Bayesian concordance analysis revealed high gene tree discordance and comparisons of Robinson-Foulds distances showed that discordance between gene trees was significantly higher than that generated by topological uncertainty within each gene. Analysis of gene tree discordance and incomplete taxon sampling revealed that gene tree discordance was high whether terminal taxon or gene sampling was maximized, indicating discordance is due to biological processes, which may be important in contributing to gene tree discordance in many recently diversified organisms.Heredity advance online publication, 19 March 2014; doi:10.1038/hdy.2014.6.
Stone geckos (Diplodactylus spp.) are a small group of moderately robust geckos that occur on hard soils in southern and arid regions of Australia. We present a morphological and molecular assessment of the systematics of D. g. granariensis, D. g. rex and D. mitchelli, including an isolated population of D. 'mitchelli' from the Northwest Cape. Genetic data from allozyme analysis and 757bp of the mitochondrial ND2 gene provided evidence for very recent divergence between the subspecies of D. granariensis, despite the morphological distinctiveness of D. g. rex from other stone geckos owing to large size, massive head, different pattern and scalation. In contrast, morphological and molecular data indicated that the isolated population of D. 'mitchelli' from the Northwest Cape was distinct at the species level and also more closely allied to D. granariensis. The new species differs from D. mitchelli in having smaller dorsal scales, fewer vertebrae and cloacal spurs, from D. g. granariensis in larger size, shorter tail and uncreased rostral scale, from D. g. rex by smaller body and head size and from both subspecies by fewer undivided subdigital lamellae, reddish colouration and distinctive dorsal stripe with transverse bands. The Northwest Cape has several other endemic species of reptiles indicating that this region is biogeographically significant and hence of special conservation value.
We provide the first phylogenetic hypothesis for the Australian species of the gekkonid genus Gehyra, based on 1044bp of the mitochondrial ND2 gene. Species representing the Asian, Melanesian and Australian radiations are resolved as separate clades, indicating relative isolation and independence of each of these evolutionary lines. Within the Australian radiation, the arid zone species form a monophyletic subgroup distinct from the remaining species found in tropical and warm mesic habitats. Extensive chromosome variation and highly variable external morphology have made species recognition difficult within Gehyra, exacerbated by the likely presence of numerous undescribed cryptic species. Three species of Gehyra are currently recognized in the southeastern inland of Australia, G. variegata, G. montium and G. purpurascens. We re-describe a fourth species, G. lazelli, to include those populations long referred to informally as the 2n=44 chromosome 'race' of Gehyra variegata. Gehyra lazelli widely overlaps the distribution of G. variegata in South Australia and the southern inland of New South Wales, with no suggestion of intergradation in morphology, mitochondrial DNA, allozyme variation or karyotype.
We describe the origins, relevance, aims, specifications and sampling strategy of a six-year biodiversity survey of Western Australia's Pilbara biogeographic region (179,000 km 2). During the project, 422 terrestrial sites were sampled for perennial and annual vascular plants, of which 304 were also sampled for small ground-dwelling mammals, birds, reptiles, frogs, ground-dwelling spiders, ants, beetles and scorpions. Ninety-eight sites on waterbodies were sampled for aquatic invertebrates, macro-and microphytes and the fringing riparian vegetation; 508 boreholes were sampled for stygofauna; 69 sites were sampled for microbats; and mammal bone material from 15 late Holocene deposits was identified. An introduction to literature on the region's physical environments and recent land-use history is provided, along with descriptions of the Pilbara's four sub-regions in terms of their different landforms and vegetations.
Species are routinely used as fundamental units of analysis in biogeography, ecology, macroevolution, and conservation biology. A large literature focuses on defining species conceptually, but until recently little attention has been given to the issue of empirically delimiting species. Researchers confronted with the task of delimiting species in nature are often unsure which method(s) is (are) most appropriate for their system and data type collected. Here, we review twelve of these methods organized into two general categories of tree- and nontree-based approaches. We also summarize the relevant biological properties of species amenable to empirical evaluation, the classes of data required, and some of the strengths and limitations of each method. We conclude that all methods will sometimes fail to delimit species boundaries properly or will give conflicting results, and that virtually all methods require researchers to make qualitative judgments. These facts, coupled with the fuzzy nature of species boundaries, require an eclectic approach to delimiting species and caution against the reliance on any single data set or method when delimiting species.
No one definition has as yet satisfied all naturalists; yet every naturalist knows vaguely what he means when he speaks of a species.
Darwin (1859/1964)
Geckos are well known for their extraordinary clinging abilities and many species easily scale vertical or even inverted surfaces. This ability is enabled by a complex digital adhesive mechanism (adhesive toepads) that employs van der Waals based adhesion, augmented by frictional forces. Numerous morphological traits and behaviors have evolved to facilitate deployment of the adhesive mechanism, maximize adhesive force and enable release from the substrate. The complex digital morphologies that result allow geckos to interact with their environment in a novel fashion quite differently from most other lizards. Details of toepad morphology suggest multiple gains and losses of the adhesive mechanism, but lack of a comprehensive phylogeny has hindered efforts to determine how frequently adhesive toepads have been gained and lost. Here we present a multigene phylogeny of geckos, including 107 of 118 recognized genera, and determine that adhesive toepads have been gained and lost multiple times, and remarkably, with approximately equal frequency. The most likely hypothesis suggests that adhesive toepads evolved 11 times and were lost nine times. The overall external morphology of the toepad is strikingly similar in many lineages in which it is independently derived, but lineage-specific differences are evident, particularly regarding internal anatomy, with unique morphological patterns defining each independent derivation.
The statistical rigor of species delimitation has increased dramatically over the past decade. Coalescent theory provides powerful models for population genetic inference, and is now increasingly important in phylogenetics and speciation research. By applying probabilistic models, coalescent-based species delimitation provides clear and objective testing of alternative hypotheses of evolutionary independence. As acquisition of multilocus data becomes increasingly automated, coalescent-based species delimitation will improve the discovery, resolution, consistency, and stability of the taxonomy of species. Along with other tools and data types, coalescent-based species delimitation will play an important role in an integrative taxonomy that emphasizes the identification of species limits and the processes that have promoted lineage diversification.
Body size affects life history, the ecological niche of an organism and its interactions with other organisms. Resultantly, marked differences in body size between related organisms are often an indication of a species boundary. This is particularly evident in the Gehyra variegata species complex of geckos, which displays differential body sizes between genetically divergent species, but high levels of intraspecific morphological conservatism. We report on a Gehyra population that displays extraordinary body size differentiation in comparison with other G. variegata species. We used morphological and environmental data to show this population is phenotypically and ecologically distinct from its parapatric congener Gehyra lazelli and that morphology and ecology are significantly correlated. Contrastingly, mtDNA analysis indicates paraphyly between the two groups, and allele frequencies at six microsatellite loci show no population structure concordant with morpho-/ecotype. These results suggest either ecological speciation or environmentally induced phenotypic polymorphism, in an otherwise morphologically conservative group.
Molecular studies have revealed that many putative 'species' are actually complexes of multiple morphologically conservative, but genetically divergent 'cryptic species'. In extreme cases processes such as non-adaptive diversification (speciation without divergent selection) could mask the existence of ancient lineages as divergent as ecologically and morphologically diverse radiations recognised as genera or even families in related groups. The identification of such ancient, but cryptic, lineages has important ramifications for conservation, biogeography and evolutionary biology. Herein, we use an integrated multilocus genetic dataset (allozymes, mtDNA and nuclear DNA) to test whether disjunct populations of the widespread nominal Australian gecko species Crenadactylus ocellatus include distinct evolutionary lineages (species), and to examine the timing of diversification among these populations.
We identify at least 10 deeply divergent lineages within the single recognised species Crenadactylus ocellatus, including a radiation of five endemic to the Kimberley region of north-west Australia, and at least four known from areas of less than 100 km2. Lineages restricted to geographically isolated ranges and semi-arid areas across central and western Australia are estimated to have began to diversify in the late Oligocene/early Miocence (~20-30 mya), concurrent with, or even pre-dating, radiations of many iconic, broadly sympatric and much more species-rich Australian vertebrate families (e.g. venomous snakes, dragon lizards and kangaroos).
Instead of a single species, Crenadactylus is a surprisingly speciose and ancient vertebrate radiation. Based on their deep divergence and no evidence of recent gene flow, we recognise each of the 10 main lineages as candidate species. Molecular dating indicates that the genus includes some of the oldest vertebrate lineages confounded within a single species yet identified by molecular assessments of diversity. Highly divergent allopatric lineages are restricted to putative refugia across arid and semi-arid Australia, and provide important evidence towards understanding the history and spread of the Australian arid zone, suggesting at a minimum that semi-arid conditions were present by the early Miocene, and that severe aridity was widespread by the mid to late Miocene. In addition to documenting a remarkable instance of underestimation of vertebrate species diversity in a developed country, these results suggest that increasing integration of molecular dating techniques into cryptic species delimitation will reveal further instances where taxonomic conservatism has led to profound underestimation of not only species numbers, but also highly significant phylogenetic diversity and evolutionary history.
Taxonomy is the biological discipline that identifies, describes, classifies and names extant and extinct species and other taxa. Nowadays, species taxonomy is confronted with the challenge to fully incorporate new theory, methods and data from disciplines that study the origin, limits and evolution of species.
Integrative taxonomy has been proposed as a framework to bring together these conceptual and methodological developments. Here we review perspectives for an integrative taxonomy that directly bear on what species are, how they can be discovered, and how much diversity is on Earth.
We conclude that taxonomy needs to be pluralistic to improve species discovery and description, and to develop novel protocols to produce the much-needed inventory of life in a reasonable time. To cope with the large number of candidate species revealed by molecular studies of eukaryotes, we propose a classification scheme for those units that will facilitate the subsequent assembly of data sets for the formal description of new species under the Linnaean system, and will ultimately integrate the activities of taxonomists and molecular biologists.
A major problem for biodiversity conservation and management is that a significant portion of species diversity remains undocumented (the 'taxonomic impediment'). This problem is widely acknowledged to be dire among invertebrates and in developing countries; here, we demonstrate that it can be acute even in conspicuous animals (reptiles) and in developed nations (Australia). A survey of mtDNA, allozyme and chromosomal variation in the Australian gecko, genus Diplodactylus, increases overall species diversity estimates from 13 to 29. Four nominal species each actually represent multi-species complexes; three of these species complexes are not even monophyletic. The high proportion of cryptic species discovered emphasizes the importance of continuing detailed assessments of species diversity, even in apparently well-known taxa from industrialized countries.
Haplotype phylogenies based on DNA sequence data are increasingly being used to test traditional species-level taxonomies
based on morphology. However, few studies have critically compared species limits based on morphological and DNA data, and
the methods used to delimit species using either type of data are only rarely explained. In this paper, we review three approaches
for species delimitation (tree-based with DNA data and tree-based and character-based with morphological data) and propose
explicit protocols for each. We then compare species limits inferred from these approaches, using morphological and mtDNA
data for the Yarrow's spiny lizard (Sceloporus jarrovii), a traditionally polytypic species from the southwestern United States and Mexico. All three approaches support division
of S. jarrovii into five species, but only two species are the same among the three approaches. We find the greatest support for the five
species that are delimited based on mtDNA data, and we argue that mtDNA data may have important (and previously unappreciated)
advantages for species delimitation. Because different data and approaches can disagree so extensively, our results demonstrate
that the methodology of species delimitation is a critical issue in systematics.
Recent advances in molecular genetic techniques and increased fine scale sampling in the Australian Monsoonal Tropics (AMT) have provided new impetus to reassess species boundaries in the Gehyra nana species complex, a clade of small-bodied, saxicolous geckos which are widely distributed across northern Australia. A recent phylogenomic analysis re-vealed eight deeply divergent lineages that occur as a series of overlapping distributions across the AMT and which, as a whole, are paraphyletic with four previously described species. Several of these lineages currently included in G. nana are phenotypically distinct, while others are highly conservative morphologically. Here we use an integrated approach to ex-plore species delimitation in this complex. We redefine G. nana as a widespread taxon with complex genetic structure across the Kimberley of Western Australia and Top End of the Northern Territory, including a lineage with mtDNA intro-gressed from the larger-bodied G. multiporosa. We describe four new species with more restricted distributions within the G. nana complex. The new species are phylogenetically divergent and morphologically diagnosable, and include the rel-atively cryptic G. paranana sp. nov. from the western Northern Territory, the large-bodied G. pseudopunctata sp. nov. from the southern Kimberley ranges, G. granulum sp. nov., a small-bodied form with granules on the proximal lamellae from the north-west and southern Kimberley ranges and the small-bodied G. pluraporosa sp. nov. restricted to the northern Kimberley. Our revision largely stabilises the taxonomy of the G. nana complex, although further analyses of species lim-its among the remaining mostly parapatric lineages of G. nana sensu stricto are warranted.
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. This article is protected by copyright. All rights reserved
Significance
Despite its widespread application to the species delimitation problem, our study demonstrates that what the multispecies coalescent actually delimits is structure. The current implementations of species delimitation under the multispecies coalescent do not provide any way for distinguishing between structure due to population-level processes and that due to species boundaries. The overinflation of species due to the misidentification of general genetic structure for species boundaries has profound implications for our understanding of the generation and dynamics of biodiversity, because any ecological or evolutionary studies that rely on species as their fundamental units will be impacted, as well as the very existence of this biodiversity, because conservation planning is undermined due to isolated populations incorrectly being treated as distinct species.
Background
Geckos of the genus Pachydactylus and their close relatives comprise the most species-rich clade of lizards in sub-Saharan Africa. Many explanations have been offered to explain species richness patterns of clades. In the Pachydactylus group, one possible explanation is a history of diversification via geographic isolation. If geographic isolation has played a key role in facilitating diversification, then we expect species in more species-rich subclades to have smaller ranges than species in less diverse subclades. We also expect traits promoting geographic isolation to be correlated with small geographic ranges. In order to test these expectations, we performed phylogenetic analyses and tested for correlations among body size, habitat choice, range sizes, and diversification rates in the Pachydactylus group.
Results
Both body size and habitat use are inferred to have shifted multiple times across the phylogeny of the Pachydactylus group, with large size and generalist habitat use being ancestral for the group. Geographic range size is correlated with both of these traits. Small-bodied species have more restricted ranges than large-bodied species, and rock-dwelling species have more restricted ranges than either terrestrial or generalist species. Rock-dwelling and small body size are also associated with higher rates of diversification, and subclades retaining ancestral conditions for these traits are less species rich than subclades in which shifts to small body size and rocky habitat use have occurred. The phylogeny also illustrates inadequacies of the current taxonomy of the group.
Conclusions
The results are consistent with a model in which lineages more likely to become geographically isolated diversify to a greater extent, although some patterns also resemble those expected of an adaptive radiation in which ecological divergence acts as a driver of speciation. Therefore, the Pachydactylus group may represent an intermediate between clades in which radiation is adaptive versus those in which it is non-adaptive.
We provide a taxonomic revision of the genus Crenadactylus, a group of very small clawless geckos from western and central Australia, with currently only one recognized species and four subspecies. Morphological comparisons were made on genotyped specimens from two recent genetic studies, then with an expanded sample to encompass all specimens to determine diagnostic characters in addition to morphological and geographic boundaries. Based on our findings, we elevate the subspecies Crenadactylus ocellatus ocellatus from south-Western Australia and C. o. horni from the Central Uplands to full species. Consultation of the types of Diplodactylus (= Crenadactylus) bilineatus indicate they are C. ocellatus based on a dorsal pattern with intermixing of dark and pale scales not shared with any other taxa; we therefore maintain synonymy of 'D.' bilineatus with 'D.' ocellatus. We describe three new Western Australian species formerly allocated to C. o. horni: C. occidentalis sp. nov. from the western coast, C. tuberculatus sp. nov. from the Cape Range and C. pilbarensis sp. nov. from the Pilbara region. To stabilize the Kimberley taxa, we also raise C. ocellatus rostralis and C. ocellatus naso, both monophyletic taxa from the monsoonal tropics, to full species, while acknowledging further work is required on the C. naso species complex. All new species treated here possess distinctive morphological characters to diagnose them, including enlarged dorsal tubercles in C. tuberculatus sp. nov., a single enlarged supranasal in C. horni and a single enlarged postmental in C. pilbarensis sp. nov. Pattern was relatively conserved among taxa, with highly contrasting dark and pale longitudinal lines, with the exception of the type species C. ocellatus that possesses intermixed dark and pale scales and ocelli. Crenadactylus species are separated by deep genetic divergences and are usually allopatrically distributed. This indicates that despite being Australia's smallest geckos, or possibly because of it, these diminutive lizards have a long history of localised persistence through major climatic changes over millions of years.
Chromosome banding techniques have been used in a large-scale survey of karyotypic variation within and between the chromosomal
races of the Gehyra variegata-punctata species group. A total of nine chromosome races are now known among these taxa. G-banding
confirms that the principal mode of chromosome change is centric fusion and, in most cases, allowed the specific chromosomes
involved to be identified. The location of C-band heterochromatin and the nucleolar organizing region varied within and between
the races. In two of the chromosome forms, heteromorphic sex chromosomes were observed in the early stages of evolution. The
cytogenetic characters were evaluated and then used to construct a phylogeny for these taxa. The types of chromosome change
between the races and their geographic relationships were then considered to examine the role of chromosomal mechanisms of
speciation in these gekkos. The previously suggested role of single centric fusions as initiators of speciation in Gehyra
requires further evaluation. In one case, an unusual form of tandem fusion has been established and this race is clearly reproductively
isolated from all others. The presence of monobrachial homology between the biarmed chromosomes of some taxa suggests that
a distinct mode of chromosomal speciation may also be important in Gehyra.
A karyotypic analysis of the widely distributed Australian gekko Gehyra australis has revealed a complex of chromosome races. Each of these is fixed for a particular karyomorph, and is found over a geographically delimited distribution. The seven chromosome races differ by number, or chromosome morphology, and are defined as: 2n=44,2n=42a, 2n=42b, 2n=42c, 2n=40a, 2n=40b, 2n=38. In addition, a series of animals from these races possess novel chromosome rearrangements. A model for the evolution of this complex of races is proposed, and the relationship ofthese forms to each other and to members of the Gehyra variegata-punctata complex is discussed.
A karyotypic analysis of populations of the gekkos Gehyra variegata and G. punctata reveals three chromosome races in G. variegata (2n = 44; 2n = 40a; 2n = 40b), and three in G. punctata (2n = 44; 2n = 42; 2n = 38). The chromosome races have differentiated by a series of chromosome fusions. The ordered nature of these changes suggests that the phylogenetic relationships of the races cut across the current taxonomy, and it is argued that there is but one 2n = 44 race, occurring as a number of morphologically distinct populations, two of which were erroneously described as the separate Gehyra species. Isolated populations within a number of the chromosome races show pronounced morphological differences. It is believed that these gekkos are an ancient Australian group which differentiated chromosomally during a number of colonizing radiations. Since then, populations within each race have been isolated by geographic barriers and have speciated allopatrically. This suggests that the chromosome races are at least good species and may be of a higher taxon.
We review the biogeography of the Pilbara, synthesize information on the geological and landscape history of this region and surrounds, and assess fine-scale genetic structure across multiple taxa to examine hypotheses concerning the distribution of genetic lineages. We use this to provide a baseline for future biological studies in an ancient area of endemism.
The Pilbara region, Western Australia.
Literature is summarized, including the history of Pilbara landscapes and climate, and previous biogeographical work. We used mitochondrial DNA phylogenetic datasets of seven co-distributed gecko (diplodactyline and gekkonine) lineages to assess the monophyly of Pilbara lineages, and concordance with geological and habitat divisions.
The Pilbara harbours taxa genetically distinct from their non-Pilbara relatives, despite close geographical proximity of populations. This is emphasized at the eastern and southern margins of the Pilbara, where habitat gradients are pronounced. In contrast, the northern margin, where sandy substrates of the Pilbara meet the dunes of the northern deserts, exhibits little genetic differentiation. Within the Pilbara, diversification patterns are idiosyncratic and may reflect species-specific ecological differences. However, a repeated north/south partitioning of genetic diversity is evident across taxa. An additional emerging pattern is an east/west genetic division in the northern Pilbara, which may relate to major drainage divides and geological discontinuities associated with east and west Pilbara terrains.
The Pilbara is an area of exceptionally high biotic diversity and endemism. The broader biogeographical patterns revealed in our molecular analyses are consistent with those recently identified using species richness patterns of invertebrates. Future studies of additional taxa using multiple molecular markers will provide the means to test and refine the biogeographical hypotheses presented here. Understanding the biogeography of the Pilbara and the partitioning of genetic diversity across the ancient and heterogeneous landscape is of paramount importance in the face of rapidly expanding economic and developmental pressures.
A new species of Gehyra Gray, 1834 (Reptilia: Gekkonidae) with two allopatric subspecies, G. koira koira ssp. nov. and G. koira ipsa ssp. nov., is described. A member of the G. australis species complex, G. koira sp. nov. is distinguished from congeners by a combination of morphometric and meristic characteristics. The two subspecies are allopatric in distribution and show morphological differentiation. The species is saxicoline and occurs on sandstone ranges and outliers in the Ord-Victoria region of north-western Australia. A key is provided to members of the G. australis species complex.
A chromosomal analysis of gekkos of the Gehyra australis complex from the Alligator Rivers region of the Northern Territory indicates that those animals living on trees or human habitation have 2n=40 chromosomes, whereas those living on the rock outliers and cliffs of the Arnhem Land escarpment have 2n=42. A morphological analysis of these specimens shows that two distinct species are present: Gehyra australis and a new species, which is described below as Gehyra pamela.
Recent conceptual and methodological advances have increased the ability to apply multifaceted approaches to species delimitation, which is particularly useful in delimiting recently diversified species where single lines of evidence lead to incorrect species delimitation or assignment of individuals to species (e.g. cryptic, morphological species and paraphyletic, hybridizing species). Species of the Australian Gehyra gecko radiation have historically proven difficult to delimit due the group's uniform, almost continent-wide geographic distribution and conservative morphology, contrasting high chromosomal and genetic diversity. Using an integrated approach to species delimitation taking advantage of morphological, geographic distributional and multi-locus genetic data, we investigate the diversity within three Gehyra species from the Australian arid zone. Our results show that these species represent eight distinct phylogenetic lineages, which display different patterns of morphological distinction and reproductive isolation. Using a recently developed Bayesian species delimitation method, we also find different levels of support for putative species dependent on priors for population size and timing of diversification assumed. Our results show that the current taxonomy does not adequately account for the diversity of the group. Discrepancies between lines of evidence indicate that diversification of the group is recent and ongoing, thus posing challenges for both species concepts and delimitation.
A chromosomal analysis of the gekko Gehyra australis (KING in press) revealed the presence of a series of genetically distinct chromosome races. Specimens from four of these chromosome races have been analysed morphologically. The present study indicates that each chromosome race can be specified in terms of pattern, colouration, scalation and morphometrics. The species Gehyra australis is therefore redefined, and a number of new species are described. Members of the Gehyra australis species group are listed, and a key to their diagnostic characteristics is provided.
The systematics of the widespread neotropical gekkonid genus Thecadactylus is investigated using a combination of morphological, morphometric and mtDNA (cytochrome b) sequence data, forming a total evidence dataset. The analysis tackles the common yet complex problem of a widespread taxon consisting of one or more cryptic species that are difficult to diagnose using morphology alone. The data are analysed using both maximum parsimony and Bayesian inference. Virtually all analyses resolve a well-supported south-western Amazonian clade distinct from the remainder of the recognized T. rapicauda. The south-western Amazonian clade is not only robustly supported, but also exclusive, geographically coherent and sufficiently distinct to warrant specific recognition. The new species is diagnosable on the basis of molecular sequences that are 23.0–26.9% divergent from those of T. rapicauda, and morphological evidence. Bayesian inference analysis robustly resolves meaningful and repeatable patterns of relationship. The biogeography of Thecadactylus is interpreted in the context of its two constituent species, and difficulties of resolving systematic and biogeographical patterns in widespread, cosmopolitan taxa are discussed. © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 339–370.
Aims (1) To map the species richness of Australian lizards and describe patterns of range size and species turnover that underlie them. (2) To assess the congruence in the species richness of lizards and other vertebrate groups. (3) To search for commonalities in the drivers of species richness in Australian vertebrates.
Location Australia.
Methods We digitized lizard distribution data to generate gridded maps of species richness and β-diversity. Using similar maps for amphibians, mammals and birds, we explored the relationship between species richness and temperature, actual evapotranspiration, elevation and local elevation range. We used spatial eigenvector filtering and geographically weighted regression to explore geographical patterns and take spatial autocorrelation into account. We explored congruence between the species richness of vertebrate groups whilst controlling for environmental effects.
Results Lizard richness peaks in the central deserts (where β-diversity is low) and tropical north-east (where β-diversity is high). The intervening lowlands have low species richness and β-diversity. Generally, lizard richness is uncorrelated with that of other vertebrates but this low congruence is strongly spatially structured. Environmental models for all groups also show strong spatial heterogeneity. Lizard richness is predicted by different environmental factors from other vertebrates, being highest in dry and hot regions. Accounting for environmental drivers, lizard richness is weakly positively related to richness of other vertebrates, both at global and local scales.
Main conclusions Lizard species richness differs from that of other vertebrates. This difference is probably caused by differential responses to environmental gradients and different centres of diversification; there is little evidence for inter-taxon competition limiting lizard richness. Local variation in habitat diversity or evolutionary radiations may explain weak associations between taxa, after controlling for environmental variables. We strongly recommend that studies of variation in species richness examine and account for non-stationarity.
Phylogenetic relationships within theLaudakia caucasiaspecies group on the Iranian Plateau were investigated using 1708 aligned bases of mitochondrial DNA sequence from the genes encoding ND1 (subunit one of NADH dehydrogenase), tRNAGln, tRNAIle, tRNAMet, ND2, tRNATrp, tRNAAla, tRNAAsn, tRNACys, tRNATyr, and COI (subunit I of cytochromecoxidase). The aligned sequences contain 207 phylogenetically informative characters. Three hypotheses for historical fragmentation ofLaudakiapopulations on the Iranian Plateau were tested. In two hypotheses, fragmentation of populations is suggested to have proceeded along continuous mountain belts that surround the Iranian Plateau. In another hypothesis, fragmentation is suggested to have resulted from a north–south split caused by uplifting of the Zagros Mountains in the late Miocene or early Pliocene [5–10 MYBP (million years before present)]. The shortest tree suggests the latter hypothesis, and statistical tests reject the other two hypotheses. The phylogenetic tree is exceptional in that every branch is well supported. Geologic history provides dates for most branches of the tree. A plot of DNA substitutions against dates from geologic history refines the date for the north–south split across the Iranian Plateau to 9 MYBP (late Miocene). The rate of evolution for this segment of mtDNA is 0.65% (0.61–0.70%) change per lineage per million years. A hypothesis of area relationships for the biota of the Iranian Plateau is generated from the phylogenetic tree.
Heinicke, M. P., Greenbaum, E., Jackman, T. R. & Bauer, A. M. Phylogeny of a trans‐Wallacean radiation (Squamata, Gekkonidae, Gehyra ) supports a single early colonization of Australia. — Zoologica Scripta, 40 , 584–602.
The genus Gehyra (34 species) is rare among squamate reptile radiations in spanning continents, extending from southeast Asia to Australia and Polynesia. Among the family Gekkonidae sensu stricto, Gehyra is the only genus that is species rich in Australia. We performed molecular phylogenetic, divergence timing, and ancestral area analyses to investigate the evolutionary and biogeographic history of Gehyra . Phylogenetic analyses resolve Hemiphyllodactylus as the closest relative of Gehyra . Some data also link Perochirus to this group, but previously suggested relationships with other morphologically similar genera of geckos are not supported. Within Gehyra , three geographically discrete clades are recovered, respectively, concentrated in Asia, the Pacific islands and Australia. Ancestral area analyses suggest that Gehyra originated in Asia, with a single colonization of Australia occurring in the mid‐Cenozoic. This date places the time of Gehyra colonization prior to those of other Australian gekkonid geckos, but after the near‐endemic pygopodoid geckos, a Gondwanan relictual group. Based on these dates, times of origin may best explain relative differences in species diversity among Australian gekkotans. In contrast, although originating earlier, Gehyra is less diverse in Asia than in Australia. This pattern may be explained by the long‐term presence of many competing, ecologically similar genera in Asia (e.g. Gekko , Hemidactylus , Lepidodactylus ), whereas nearly all pygopodoids in Australia (the only gekkotans present at the time of colonization of Australia by Gehyra ) are ecologically distinct.
The literature about species concepts might be larger than that about any other subject in evolutionary biology, but the issue of empirically testing species boundaries has been given little attention relative to seemingly endless debates over what species are. The practical issue of delimiting species boundaries is nevertheless of central importance to many areas of evolutionary biology. The number of recently described methods for delimiting species suggests renewed interest in the topic, and some methods are explicitly quantitative. Here, we review nine of these methods by summarizing the relevant biological properties of species amenable to empirical evaluation, the classes of data required and some of the strengths and limitations of each.
In phylogenetic analyses of molecular sequence data, partitioning involves estimating independent models of molecular evolution for different sets of sites in a sequence alignment. Choosing an appropriate partitioning scheme is an important step in most analyses because it can affect the accuracy of phylogenetic reconstruction. Despite this, partitioning schemes are often chosen without explicit statistical justification. Here, we describe two new objective methods for the combined selection of best-fit partitioning schemes and nucleotide substitution models. These methods allow millions of partitioning schemes to be compared in realistic time frames and so permit the objective selection of partitioning schemes even for large multilocus DNA data sets. We demonstrate that these methods significantly outperform previous approaches, including both the ad hoc selection of partitioning schemes (e.g., partitioning by gene or codon position) and a recently proposed hierarchical clustering method. We have implemented these methods in an open-source program, PartitionFinder. This program allows users to select partitioning schemes and substitution models using a range of information-theoretic metrics (e.g., the Bayesian information criterion, akaike information criterion [AIC], and corrected AIC). We hope that PartitionFinder will encourage the objective selection of partitioning schemes and thus lead to improvements in phylogenetic analyses. PartitionFinder is written in Python and runs under Mac OSX 10.4 and above. The program, source code, and a detailed manual are freely available from www.robertlanfear.com/partitionfinder.
DNA sequence evolution through nucleotide substitution may be assimilated to a stationary Markov process. The fundamental equations of the general model, with 12 independent substitution parameters, are used to obtain a formula which corrects the effect of multiple and parallel substitutions on the measure of evolutionary divergence between two homologous sequences. We show that only reversible models, with six independent parameters, allow the calculation of the substitution rates. Simulation experiments on DNA sequence evolution through nucleotide substitution call into question the effectiveness of the general model (and of any other more detailed description); nevertheless, the general model results are slightly superior to any of its particular cases.