26 research outputs found
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The Phylogenomics and Macroevolutionary Dynamics of Australasian Diplodactyloid Geckos
Our planet supports a staggering array of biodiversity. A firm understanding of the species with which we share this planet requires researchers to develop a solid basis on which pertinent questions about biodiversity can addressed. My dissertation uses one group of speciose and ecologically diverse geckos to ask questions regarding evolutionary relationships, macroevolutionary patterns, adaptive radiation, and processes at the species level responsible for generating this diversity. I implement a number of cutting edge molecular and computational methods to demonstrate the importance of taking an integrative approach by incorporating both molecules and morphology.Chapter 1: Molecular data has vast applications in exploring the evolutionary histories of organisms. Some groups, however, continually confound attempts at elucidating their relationships with conventional molecular methods. The advent of genomic sequencing has allowed researchers to gather vast amounts of sequence data to tackle troublesome phylogenetic questions. The diplodactyloid geckos endemic to Australasia are an extremely diverse of clade squamates with an array of ecologies and phenotypes. However, there exist a number of poorly resolved relationships and some studies recover well-supported groups which disagree across datasets. Here, we implement 4,268 ultraconserved element loci (UCEs) to address the phylogeny of the diplodactyloids. In comparison to previous studies, the UCEs resolved nearly every node, the exceptions being some at the base of the New Caledonian and core Australian diplodactylid clades. Our concatenated and coalescent phylogenies directly conflict with those from four previous studies, sometimes by as much as 45% of nodes, and received much higher support. Divergence time estimates were largely congruent previous estimates, though slightly older for some deeper nodes. Our findings demonstrate the importance of incorporating numerous independent loci in phylogenetic estimates.Chapter 2: Adaptive radiations are notoriously difficult to define, particularly across broad taxonomic and temporal scales. However, most examples can be characterized by ecological differentiation. The diplodactyloid geckos exhibit a staggering array of ecologies accompanied by a morphological diversity that vastly exceeds that seen elsewhere in Gekkota. Using ecological data and ecomorphological measurements, we address how ecological differentiation has progressed in this clade as well as the prevalence of convergent evolution due to similar selective pressures. Ancestral trait reconstruction methods find that diplodactyloids were ancestrally rupicolous. Hansen models find that arboreal forms have higher rates body size evolution than all other ecological categories. We also find that convergence is widespread within the diplodactyloids, though intraclade convergence was more common that interclade convergence. Furthermore, tests of phenotypic convergence reveal that convergence is most widespread in the insular diplodactylids. The phenomenon of adaptive radiation has been most well documented in groups like Anolis lizards and cichlid fishes, but diplodactyloids likely represent another example of exceptional morphological diversification in novel habitats.Chapter 3: The generation of biodiversity has fascinated researchers for decades, particularly in the case of putative adaptive radiations. Speciation and extinction rates are subject to both biotic and abiotic forces, and both are notoriously difficult to estimate from molecular data without fossils. However, many methods have limited power to inform us of diversification trajectories. The diplodactyloids represent a unique opportunity to investigate rates of diversification and trait evolution. Examination of branch lengths and divergence times indicated that the insular forms, which were recent arrivals, had experienced bursts of diversification over the background rate for the whole clade. We used likelihood and Bayesian-based methods to infer diversification trajectories of diplodactyloids, implementing a phylogenomic estimate of more the 4,200 independent loci. Remarkably, most methods find that there is no rate heterogeneity in the diplodactyloid tree, but that the background rate of speciation is relatively high. In contrast to previous studies that have suggested a mass extinction event around the Eocene-Oligocene boundary (EOb), we find very little support for any such event. The weak signature of mass extinction we find vastly predates the EOb, dating back to the Campanian. Diplodactyloids demonstrate a complex pattern of trait evolution, with signatures of modularity in the rate of phenotypic diversification. Using Bayesian methods, we found that not all traits are evolving at the same rate for all clades. Rather, certain traits, namely those tied to substrate and diet experienced higher rates of diversification than others. While the insular clades possessed similar net diversification patterns to the rest of the diplodactyloids, they exhibited higher rates of trait evolution. A similar pattern is evident in clades that have transitioned to new substrates. These findings suggest that high rates of background diversification coupled with dispersal and environmental instability have facilitated phenotypic and ecological diversification in this clade.Chapter 4: Australia has acted as an engine of biodiversity for a number of disparate clades, producing a wide diversity of species and ecologies seen nowhere else in the world. While the continent is typified by arid environs, a major epicenter of biodiversity is located in the ancient monsoonal tropics of the north. In this study, we investigate the phylogeographic patterns of the marbled velvet gecko (Oedura marmorata) in the Top End. Using mitochondrial (mtDNA) data and 4,268 UCEs, we find that there are eight well supported clades in this species complex. However, the UCEs vastly outperform the mtDNA in resolving the phylogenetic relationships between them as well provide context as to the geographic features that led to this diversity. Furthermore, we find signatures of potential hybrid speciation and Dobzhansky-Muller incompatibilities. From clustering analyses, it appears that several major rivers have played a large role in isolating lineages in the Top End. In conjunction with ancient formations such as the Arnhem Plateau and Carpentarian Gap, these rivers have allowed for the formation and maintenance of these lineages
Recommended from our members
The Phylogenomics and Macroevolutionary Dynamics of Australasian Diplodactyloid Geckos
Our planet supports a staggering array of biodiversity. A firm understanding of the species with which we share this planet requires researchers to develop a solid basis on which pertinent questions about biodiversity can addressed. My dissertation uses one group of speciose and ecologically diverse geckos to ask questions regarding evolutionary relationships, macroevolutionary patterns, adaptive radiation, and processes at the species level responsible for generating this diversity. I implement a number of cutting edge molecular and computational methods to demonstrate the importance of taking an integrative approach by incorporating both molecules and morphology.Chapter 1: Molecular data has vast applications in exploring the evolutionary histories of organisms. Some groups, however, continually confound attempts at elucidating their relationships with conventional molecular methods. The advent of genomic sequencing has allowed researchers to gather vast amounts of sequence data to tackle troublesome phylogenetic questions. The diplodactyloid geckos endemic to Australasia are an extremely diverse of clade squamates with an array of ecologies and phenotypes. However, there exist a number of poorly resolved relationships and some studies recover well-supported groups which disagree across datasets. Here, we implement 4,268 ultraconserved element loci (UCEs) to address the phylogeny of the diplodactyloids. In comparison to previous studies, the UCEs resolved nearly every node, the exceptions being some at the base of the New Caledonian and core Australian diplodactylid clades. Our concatenated and coalescent phylogenies directly conflict with those from four previous studies, sometimes by as much as 45% of nodes, and received much higher support. Divergence time estimates were largely congruent previous estimates, though slightly older for some deeper nodes. Our findings demonstrate the importance of incorporating numerous independent loci in phylogenetic estimates.Chapter 2: Adaptive radiations are notoriously difficult to define, particularly across broad taxonomic and temporal scales. However, most examples can be characterized by ecological differentiation. The diplodactyloid geckos exhibit a staggering array of ecologies accompanied by a morphological diversity that vastly exceeds that seen elsewhere in Gekkota. Using ecological data and ecomorphological measurements, we address how ecological differentiation has progressed in this clade as well as the prevalence of convergent evolution due to similar selective pressures. Ancestral trait reconstruction methods find that diplodactyloids were ancestrally rupicolous. Hansen models find that arboreal forms have higher rates body size evolution than all other ecological categories. We also find that convergence is widespread within the diplodactyloids, though intraclade convergence was more common that interclade convergence. Furthermore, tests of phenotypic convergence reveal that convergence is most widespread in the insular diplodactylids. The phenomenon of adaptive radiation has been most well documented in groups like Anolis lizards and cichlid fishes, but diplodactyloids likely represent another example of exceptional morphological diversification in novel habitats.Chapter 3: The generation of biodiversity has fascinated researchers for decades, particularly in the case of putative adaptive radiations. Speciation and extinction rates are subject to both biotic and abiotic forces, and both are notoriously difficult to estimate from molecular data without fossils. However, many methods have limited power to inform us of diversification trajectories. The diplodactyloids represent a unique opportunity to investigate rates of diversification and trait evolution. Examination of branch lengths and divergence times indicated that the insular forms, which were recent arrivals, had experienced bursts of diversification over the background rate for the whole clade. We used likelihood and Bayesian-based methods to infer diversification trajectories of diplodactyloids, implementing a phylogenomic estimate of more the 4,200 independent loci. Remarkably, most methods find that there is no rate heterogeneity in the diplodactyloid tree, but that the background rate of speciation is relatively high. In contrast to previous studies that have suggested a mass extinction event around the Eocene-Oligocene boundary (EOb), we find very little support for any such event. The weak signature of mass extinction we find vastly predates the EOb, dating back to the Campanian. Diplodactyloids demonstrate a complex pattern of trait evolution, with signatures of modularity in the rate of phenotypic diversification. Using Bayesian methods, we found that not all traits are evolving at the same rate for all clades. Rather, certain traits, namely those tied to substrate and diet experienced higher rates of diversification than others. While the insular clades possessed similar net diversification patterns to the rest of the diplodactyloids, they exhibited higher rates of trait evolution. A similar pattern is evident in clades that have transitioned to new substrates. These findings suggest that high rates of background diversification coupled with dispersal and environmental instability have facilitated phenotypic and ecological diversification in this clade.Chapter 4: Australia has acted as an engine of biodiversity for a number of disparate clades, producing a wide diversity of species and ecologies seen nowhere else in the world. While the continent is typified by arid environs, a major epicenter of biodiversity is located in the ancient monsoonal tropics of the north. In this study, we investigate the phylogeographic patterns of the marbled velvet gecko (Oedura marmorata) in the Top End. Using mitochondrial (mtDNA) data and 4,268 UCEs, we find that there are eight well supported clades in this species complex. However, the UCEs vastly outperform the mtDNA in resolving the phylogenetic relationships between them as well provide context as to the geographic features that led to this diversity. Furthermore, we find signatures of potential hybrid speciation and Dobzhansky-Muller incompatibilities. From clustering analyses, it appears that several major rivers have played a large role in isolating lineages in the Top End. In conjunction with ancient formations such as the Arnhem Plateau and Carpentarian Gap, these rivers have allowed for the formation and maintenance of these lineages
Gehyra serraticauda Skipwith & Oliver, 2014, sp. nov.
Gehyra serraticauda sp. nov. (Figs 1–3) Holotype. MCZ R 7314, adult male, purchased from Antwerp Edgar Pratt and with collection locality recorded as Fakfak, Onin Peninsula (~ 2 ° 55 '"S, 132 ° 18 'E), West Papua Province, Indonesia. Date of original collection unknown, but lodged in the MCZ collection in 1909. Additional material. Uncollected specimen, from near Kamaka (formerly Warika) Village, 45 km SSE of Kaimana, Triton Bay, (03° 46 ’ 14 ”S, 134 ° 10 ’ 14 ”E), West Papua Province, Indonesia, 150–160 m a.s.l., collected, photographed and released by Dmitry Telnov, 10 September 2010. Diagnosis. Gehyra serraticauda is distinguished from other Gehyra species by the following suite of characters: moderately large size (91 mm SVL), prominent popliteal fold on the hindlimbs, high number of digital lamellae (finger IV = 16, toe IV = 17), distal lamellae deeply notched, rostral concave, supranasals small and widely separated by numerous small internasals, preanal pores arranged in a long single continuous chevron (36), and original tail strongly compressed dorsoventrally and adorned with a continuous series of acuminate scales on the lateral edges. Comparisons. A summary of comparative data for Melanesian Gehyra is given in Table 1. The combination of moderately large body size (> 90 mm) and distinctive acuminate lateral scales on the tail distinguish this species from all other Gehyra. Gehyra serraticauda sp. nov. specifically differs from Gehyra mutilata, G. papuana and the types of G. lampei and G. interstitialis in having very distinct lateral caudal serrations (versus minute or none), a much larger adult size (> 90 mm versus 9 (exceptions being finger I and toe I)), and presence of only a single internasal in a dorsal concavity of the rostral. Gehyra serraticauda sp. nov. is similar in size to G. baliola, G. barea and G. oceanica, but again differs in having well developed tail serrations. It is further differentiated from G. oceanica by having deeply notched lamellae (versus shallowly notched and undivided), the presence of numerous small internasal scales (versus absent), enlarged subcaudals (versus small), and the presence of a prominent popliteal skinfold (versus absent). Gehyra serraticauda sp. nov. can be distinguished from a final large species of Papuan Gehyra, G. membranacrularis by its deeply notched subdigital lamellae (versus shallowly notched and undivided) and smaller and more numerous internasals (~ 10 versus 1–4). Gehyra serraticauda sp. nov. differs from Gehyra marginata Boulenger from the Maluku Islands of Indonesia (just west of New Guinea) in its smaller adult size ( 130 mm), divided digital lamellae (versus undivided), lower number of lamellae (digit IV manus = 17 versus 20–25, digit IV pes = 17 versus 20–23), by the presence of many small internasals (versus a single large internasal), well developed popliteal skin folds only (versus well developed lateral skin folds on the trunk and both antecubital and popliteal skin folds), and having enlarged polygonal subcaudals (versus small and relatively uniform). Two other gekkonid genera occuring in the Pacific region may also have flattened tails with lateral serrations. The three species of Perochirus from Micronesia and Vanuatu have dorso-ventrally flattened tails with very distinct lateral spines; but differ from all Gehyra in the presence of a well developed claw and free phalanx on the inner toe (versus vestigal or absent), and further differ from G. serraticauda sp. nov. specifically in lacking popliteal folds and having much more widely spaced lateral spines (one per tail segment) (Zug 2013). Hemidactylus includes a number of species that have tail serrations and expanded digital pads, but can again be readily distinguished by the presence of a distinct claw on all digits (greatly reduced on the inner toe in Gehyra serraticauda sp. nov.), and are also generally somewhat smaller than G.serraticauda sp. nov. Description of holotype.– Adult male with expressed postcloacal pores and large flap of loosely attached skin on the right side of the head (Figs. 1 a–b): SVL 91.0 mm; TrK 46.3 mm; HW 17.1 mm; HL 21.8 mm; HD 10.8 mm; EN 7.6; IORB 8.6 mm; POM 2.9 mm; FA 12.3 mm; CS 13.3 mm; EYE 5.8 mm; EAR 2.1 mm; TL(total) 83.0; TL(original) 65.0; IN 10; INT 5; SUPR 13; INFR 11; LAMF 4 17; LAMT 4 17. Head triangular, longer than wide (HW/HL= 0.78) moderately large (HL/SVL = 0.24) and deep (HD/HL = 0.50); anterior left dentary fractured, posterior corner of jaw upturned. Rostrum long and robust (EN/HL = 0.35) with distinct dorsal concavity, transverse fold of skin extends across tip of rostrum. Rostral with deep dorsal notch, in contact with two supranasals and five small internasals along dorsal edge (Fig. 2 c). Supranasals separated by a high number of small internasals (n = 10) and up to five in transverse series. Nares contacting one supralabial, rostral, one large supranasal and one large postnasal; supralabials 11–12; infralabials 12. Mental U-shaped, bordered by oblong post-mentals. Pupil partially dilated, somewhat elliptical with smooth margins and limited crenulations (Fig. 2 d). Body long and robust (TrK /SVL = 0.40), thorax flexed prominently to the left. Skin on dorsum and venter smooth and composed entirely of small, flat, granular scales. Limbs relatively short and stout. Digits on both the fore and hind limbs with prominent and expanded pads (finger pads 1.1–1.6 times minimum width of finger, toe pads 1.2–1.5 minimum width of toe) (Fig. 2 a–b); penultimate phalanx free and well developed on all digits except finger I and toe I. The scansorial pad of digit I of both manus and pes is narrower relative to length than the other digits. Distal lamallae (excluding penultimate lamallae) deeply notched on fingers and toes, lamellar counts for all digits (total/deeply notched) as follows: fingers I = 11 / 4, II = 12 / 5, III = 16 / 6, IV = 17 / 7, V = 16 / 7; toes I = 14 / 6, II = 16 / 7, III = 17 / 8, IV = 17 / 8, V = 16 / 7. Basal webbing between digits limited, never reaches first phalangeal joint. Precloacal and femoral pores (n = 36) arranged in a single curved row terminating halfway along the femur (Fig. 2 f). Hemipenal bulge present but not pronounced, single row of three short cloacal spurs angled posteriorly on each bulge. Tail strongly compressed dorsoventrally, approximately 1.5 times wider than high, 83.0 mm in total length (65.0 mm original, 18.0 mm regenerated). Original portion partially autotomised 24.0 mm from the vent, with a distinct medial groove on the ventral surface, a single row of greatly enlarged pentagonal subcaudals extending its full length, and a continuous lateral fringe of densely packed acuminate scales extending from just posterior to the hindlimbs to the end of the original tail (Fig. 2 e). Scalation on the regenerated section of the tail is substantially smaller and more irregular and heterogeneous than that of the original, although the subcaudals are still relatively enlarged. In preservative, dorsum beige with irregular dark grey patches on the left shoulder, lateral regions of torso, pelvic area, and distal portion of the tail. Dorsal surface of the hands and feet beige like the dorsum of the body but with a slight reddish tinge, giving an overall darker appearance; lamellae of all digits beige becoming slightly darker distally. Colouration on the regenerated tail light reddish-grey. Variation. Photographs of the uncollected specimen from near Kamaka Village kindly provided to us by Dmitry Telnov (Fig. 3 a–c), specimen details above) show that it has a deeply divided rostral, prominent popliteal folds and acuminate scales on the lateral edges of the original tail. It is on the basis of these characters and its large size (field measured SVL ~ 120mm) that we assign this individual to the G. serraticauda sp. nov. When originally captured the colouration of this specimen was as follows; dorsum silvery grey with very extensive terracotta mottling and numerous indistinctly edged transverse bands along the dorsum; fore and hindlimbs predominently terracotta with no clear pattern but some silvery flecking; head with similar mottled colouration to the body and distinct silvery loreal and postorbital stripes; regrown tail silvery brown with no clear pattern; supralabials, infralabials and region of venter visible in photographs yellow; iris light olive green and pupil ellipitical with scalloped edges. In photos taken at a later time prior to release the dorsal colouration is greatly faded and mostly silvery grey with a brownish tinge towards the anterior regions and the only clear patterning being a small number of silvery spots and stripes on the head and neck. Distribution and ecology. Presuming the collection data for the holotype is accurate; this distribution of this species extends from Fakfak on the Onin Peninsula east as far as the Triton Bay region. Collection information for the holotype indicates that it was purchased from local people, and it thus seems likely that it is from a locality that is within walking distance of Fakfak. However, more fieldwork is required to confirm that this species occurs in this area. The Triton Bay specimen was collected in primary lowland rainforest on limestone in the environs of Kamaka Village. It was found during the day while hiding under bark on a dead standing tree. Like many Gehyra the strong dorsal patterning on this specimen varied over short periods of time (King & Horner 1989). Nothing is known about the collection locality and habitat of the holotype. Eytmology. The specific epithet is a feminine combination of the Latin adjective ‘serratus’ (notched like a saw) and the noun “cauda” (tail), and refers to the distinctive enlarged lateral scales on the tail of this species. Remarks. The taxonomic status and distribution of many Papuan Gehyra remains unclear (a situation exacerbated by low samples sizes for non-human commensal species and the loss and destruction of key types). New material and a proper phylogenetic analysis is required before G. serraticauda sp. nov. can be confidently placed in the phylogeny of Gehyra. However, it is superficially most similar to G. baliola and G. b a re a in overall size and proportions, the presence of a high number of scales between the nasals, and deeply notched lamellae. The distribution of this species also sits between the known range of G. baliola (southern New Guinea) and G. barea (probably widespread over islands just to the west of New Guinea), suggesting possible geographic turnover of ecologically similar and related taxa. Gehyra, for the most part, is a morphologically conserved taxon and the prominent lateral fringe of acuminate scales on the tail of G. serraticauda sp. nov. is quite unique (although Gehyra mutilata does have a similar, but much less prominent fringe). Many other gekkonids have flattened and or ornamented tails; ranging from prominent lappets (e.g., Ptyhcozoon sp.) to spiniform scales (e.g., Kolekanos plumicaudus and Phelsuma serraticauda). These structures may serve an array of functions, but are most frequently and most easily correlated with outline disruption and camouflage (Young et al. 2002; Heinicke et al. 2012).Published as part of Skipwith, Phillip L. & Oliver, Paul M., 2014, A new Gehyra (Gekkonidae: Reptilia) from New Guinea with unique caudal scalation, pp. 57-66 in Zootaxa 3827 (1) on pages 58-63, DOI: 10.11646/zootaxa.3827.1.5, http://zenodo.org/record/28648
A new Gehyra (Gekkonidae: Reptilia) from New Guinea with unique caudal scalation
Skipwith, Phillip L., Oliver, Paul M. (2014): A new Gehyra (Gekkonidae: Reptilia) from New Guinea with unique caudal scalation. Zootaxa 3827 (1): 57-66, DOI: 10.11646/zootaxa.3827.1.
Data from: Crossing the line: increasing body size in a trans-Wallacean lizard radiation (Cyrtodactylus, Gekkota)
The region between the Asian and Australian continental plates (Wallacea) demarcates the transition between two differentiated regional biotas. Despite this striking pattern, some terrestrial lineages have successfully traversed the marine barriers of Wallacea and subsequently diversified in newly colonized regions. The hypothesis that these dispersals between biogeographic realms are correlated with detectable shifts in evolutionary trajectory has however rarely been tested. Here, we analyse the evolution of body size in a widespread and exceptionally diverse group of gekkotan lizards (Cyrtodactylus), and show that a clade that has dispersed eastwards and radiated in the Australopapuan region appears to have significantly expanded its body size ‘envelope’ and repeatedly evolved gigantism. This pattern suggests that the biotic composition of the proto-Papuan Archipelago provided a permissive environment in which new colonists were released from evolutionary constraints operating to the west of Wallacea
A new velvet gecko (Oedura: Diplodactylidae) from Groote Eylandt, Northern Territory
Over the last decade, the combination of biological surveys, genetic diversity assessments and systematic research has revealed a growing number of previously unrecognised vertebrate species endemic to the Australian Monsoonal Tropics. Here we describe a new species of saxicoline velvet gecko in the Oedura marmorata complex from Groote Eylandt, a large island off the eastern edge of the Top End region of the Northern Territory.Oedura nesos sp. nov. differs from all congeners in combination of moderate size, and aspects of tail morphology and colouration. It has not been reported from the nearby mainland regions (eastern Arnhem Land) suggesting it may be an insular endemic, although further survey work is required to confirm this. While Groote Eylandt is recognised as a contemporary ecological refuge for declining mammal species of northern Australia, newly detected endemic species suggest it may also be of significance as an evolutionary refuge for many taxa, especially those associated with sandstone escarpmentsRevisionary and survey work
on the Oedura marmorata complex has been funded by a McKenzie Postdoctoral Fellowship from the University
of Melbourne to PMO, an Australian Research Council Discovery early career researcher fellowship to PMO, an
Australian Research Council linkage grant to PMO, P. Doughty, and M. Lee, an Australian Biological Resources
Survey Grant to M. Adams, PMO, P. Doughty, and M. Lee, and an ARC Laureate Fellowship to C. Moritz