skip to main content


The NSF Public Access Repository (NSF-PAR) system and access will be unavailable from 5:00 PM ET until 11:00 PM ET on Friday, June 21 due to maintenance. We apologize for the inconvenience.

Title: Reappraising the evolutionary history of the largest known gecko, the presumably extinct Hoplodactylus delcourti, via high-throughput sequencing of archival DNA

Hoplodactylus delcourtiis a presumably extinct species of diplodactylid gecko known only from a single specimen of unknown provenance. It is by far the largest known gekkotan, approximately 50% longer than the next largest-known species. It has been considered a member of the New Zealand endemic genusHoplodactylusbased on external morphological features including shared toe pad structure. We obtained DNA from a bone sample of the only known specimen to generate high-throughput sequence data suitable for phylogenetic analysis of its evolutionary history. Complementary sequence data were obtained from a broad sample of diplodactylid geckos. Our results indicate that the species is not most closely related to extantHoplodactylusor any other New Zealand gecko. Instead, it is a member of a clade whose living species are endemic to New Caledonia. Phylogenetic comparative analyses indicate that the New Caledonian diplodactylid clade has evolved significantly more disparate body sizes than either the Australian or New Zealand clades. Toe pad structure has changed repeatedly across diplodactylids, including multiple times in the New Caledonia clade, partially explaining the convergence in form betweenH. delcourtiand New ZealandHoplodactylus. Based on the phylogenetic results, we placeH. delcourtiin a new genus.

more » « less
Award ID(s):
Author(s) / Creator(s):
; ; ; ; ; ; ;
Publisher / Repository:
Nature Publishing Group
Date Published:
Journal Name:
Scientific Reports
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract

    Armored skin resulting from the presence of bony dermal structures, osteoderms, is an exceptional phenotype in gekkotans (geckos and flap‐footed lizards) only known to occur in three genera:Geckolepis,Gekko, andTarentola. The Tokay gecko (Gekko geckoLINNAEUS 1758) is among the best‐studied geckos due to its large size and wide range of occurrence, and although cranial dermal bone development has previously been investigated, details of osteoderm development along a size gradient remain less well‐known. Likewise, a comparative survey of additional species within the broaderGekkoclade to determine the uniqueness of this trait has not yet been completed. Here, we studied a large sample of gekkotans (38 spp.), including 18 specimens ofG. gecko, using X‐rays and high‐resolution computed tomography for visualizing and quantifying the dermal armorin situ. Results from this survey confirm the presence of osteoderms in a second species within this genus,GekkoreevesiiGRAY 1831, which exhibits discordance in timing and pattern of osteoderm development when compared with its sister taxon,G. gecko. We discuss the developmental sequence of osteoderms in these two species and explore in detail the formation and functionality of these enigmatic dermal ossifications. Finally, we conducted a comparative analysis of endolymphatic sacs in a wide array of gekkotans to explore previous ideas regarding the role of osteoderms as calcium reservoirs. We found thatG. geckoand other gecko species with osteoderms have highly enlarged endolymphatic sacs relative to their body size, when compared to species without osteoderms, which implies that these membranous structures might fulfill a major role of calcium storage even in species with osteoderms.

    more » « less
  2. This paper aims to expand understanding of a poorly known group of cestodes that parasitize an intriguingly diverse suite of elasmobranchs. The group’s three currently described members (i.e., Pentaloculum macrocephalum, Pentaloculum hoi, and Zyxibothrium kamienae) parasitize an electric ray, a carpet shark, and a skate, respectively. Pentaloculum grahami n. sp. is described from a second genus of carpet shark, specifically Parascyllium collare, in Australia. Zyxibothrium duffyi n. sp. and Zyxibothrium healyae n. sp. are described from the deep-sea skates Brochiraja asperula and Brochiraja spinifera, respectively off New Zealand. The three new species share distinctive bothridia that bear a small number of large, circular, facial loculi and lateral bands of vitelline follicles that converge posterior to the ovary—features which are found in all other members of these genera. Zyxibothrium healyae n. sp. is unique in possessing three, rather than four or five, facial loculi. Zyxibothrium duffyi n. sp. possesses a combination of five facial loculi and vitelline follicles that stop short of the anterior margin of the proglottid. Pentaloculum grahami n. sp. is the largest member of the group with the greatest number of proglottids. Based on striking similarities in scolex morphology, Pentaloculum and Zyxibothrium have been hypothesized to belong to a distinct subgroup of “tetraphyllideans” provisionally designated as Clade 1. Based on sequence data for the D1–D3 region of the 28S rDNA gene generated for species of Zyxibothrium for the first time, we confirm the reciprocal monophyly of both genera as well as the monophyly of Clade 1 and its status as a distinct lineage among the “Tetraphyllidea”. This work also suggests that the presence of five facial loculi is homoplasious given this character state is found in members of both genera. The new species expand the host associations of Clade 1 to include additional skate and carpet shark genera. Moving forward we would expect to find additional members of this group parasitizing other species of parascyliid carpet sharks as well as other species of the rajid genus Malacoraja and the arhynchobatid genus Brochiraja. Here we have doubled the number of described species in the taxon referred to as Clade 1 while simultaneously expanding our understanding of the morphology and anatomy of its members. This additional information will help inform the ultimate revision of the ordinal classification of the cestodes to address the highly polyphyletic nature of the order “Tetraphyllidea” as it is currently configured. 
    more » « less
  3. The Opiliones family Neopilionidae is restricted to the terranes of the former temperate Gondwana: South America, Africa, Australia, New Caledonia and New Zealand. Despite decades of morphological study of this unique fauna, it has been difficult reconciling the classic species of the group (some described over a century ago) with recent cladistic morphological work and previous molecular work. Here we attempted to investigate the pattern and timing of diversification of Neopilionidae by sampling across the distribution range of the family and sequencing three markers commonly used in Sanger-based approaches (18S rRNA, 28S rRNA and cytochrome-c oxidase subunit I). We recovered a well-supported and stable clade including Ballarra (an Australian ballarrine) and the Enantiobuninae from South America, Australia, New Caledonia and New Zealand, but excluding Vibone (a ballarrine from South Africa). We further found a division between West and East Gondwana, with the South American Thrasychirus/Thrasychiroides always being sister group to an Australian–Zealandian (i.e. Australia + New Zealand + New Caledonia) clade. Resolution of the Australian–Zealandian taxa was analysis-dependent, but some analyses found Martensopsalis, from New Caledonia, as the sister group to an Australian–New Zealand clade. Likewise, the species from New Zealand formed a clade in some analyses, but Mangatangi often came out as a separate lineage from the remaining species. However, the Australian taxa never constituted a monophyletic group, with Ballarra always segregating from the remaining Australian species, which in turn constituted 1–3 clades, depending on the analysis. Our results identify several generic inconsistencies, including the possibility of Thrasychiroides nested within Thrasychirus, Forsteropsalis being paraphyletic with respect to Pantopsalis, and multiple lineages of Megalopsalis in Australia. In addition, the New Zealand Megalopsalis need generic reassignment: Megalopsalis triascuta will require its own genus and M. turneri is here transferred to Forsteropsalis, as Forsteropsalis turneri (Marples, 1944), comb. nov. 
    more » « less
  4. To address the taxonomic uncertainty of Sporolithon species named in the early to mid-20th century, targeted PCR sequencing was performed on eight historical type specimens and on recently collected specimens. Six type specimens amplified for the rbcL gene and were Sanger sequenced yielding sequences ranging in length from 118 to 280 base pairs (bp). One, S. australasicum, failed to amplify and another, S. howei, was amplified for the psbA gene yielding a sequence 544 bp in length. The 118 bp long rbcL sequence of the lectotype of S. crassiramosum showed that it is a later, heterotypic synonym of S. molle. The rbcL sequences of type specimens of S. episoredion, S. schmidtii, S. sibogae and S. timorense ranged from 118 to 228 bp, and each is a distinct species. The 544 bp long psbA sequence of S. howei is also unique. The 280 bp long rbcL sequence of the lectotype of S. durum did not match any sequence with that name in any public repository, including the previously published complete plastome and mitogenome sequences. However, it was identical in sequence to a specimen in GenBank from the southern coast of Western Australia as well as several other sequences generated from field-collected specimens from the states of South Australia and Western Australia. The rhodolith specimens from New Zealand previously called S. durum are S. nodosum sp. nov. The species is endemic to New Zealand. The epilithic specimens from New Zealand previously called S. durum are S. immotum sp. nov., which is also found along the southeastern coast of Australia. Sporolithon crypticum sp. nov. is described from the southern coast of Western Australia. RAxML and Bayesian phylogenetic analyses of Sporolithon psbA and rbcL sequences are congruent between the two plastid encoded genes. DNA sequencing of type specimens of species of corallines is demonstrated to be the only reliable method to correctly apply names. 
    more » « less
  5. Abstract Aim

    The “sexy shrimp”Thor amboinensisis currently considered a single circumtropical species. However, the tropical oceans are partitioned by hard and soft barriers to dispersal, providing ample opportunity for allopatric speciation. Herein, we test the null hypothesis thatT. amboinensisis a single global species, reconstruct its global biogeographical history, and comment on population‐level patterns throughout the Tropical Western Atlantic.


    Coral reefs in all tropical oceans.


    Specimens ofThor amboinensiswere obtained through field collection and museum holdings. We used one mitochondrial (COI) and two nuclear (NaK, enolase) gene fragments for global species delimitation and phylogenetic analyses (n = 83 individuals, 30 sample localities), while phylogeographical reconstruction in theTWAwas based onCOIonly (n = 303 individuals, 10 sample localities).


    We found evidence for at least five cryptic lineages (9%–22%COIpairwise sequence divergence): four in the Indo‐West Pacific and one in the Tropical Western Atlantic. Phylogenetic reconstruction revealed that endemic lineages from Japan and the South Central Pacific are more closely related to the Tropical Western Atlantic lineage than to a co‐occurring lineage that is widespread throughout the Indo‐West Pacific. Concatenated and species tree phylogenetic analyses differ in the placement of an endemic Red Sea lineage and suggest alternate dispersal pathways into the Atlantic. Phylogeographical reconstruction throughout the Tropical Western Atlantic reveals little genetic structure over more than 3,000 km.

    Main conclusions

    Thor amboinensisis a species complex that has undergone a series of allopatric speciation events and whose members are in secondary contact in the Indo‐West Pacific. Nuclear‐ and mitochondrial‐ gene phylogenies show evidence of introgression between lineages inferred to have been separated more than 20 Ma. Phylogenetic discordance between multi‐locus analyses suggest thatT. amboinensisoriginated in the Tethys sea and dispersed into the Atlantic and Indo‐West Pacific through the Tethys seaway or, alternatively, originated in the Indo‐West Pacific and dispersed into the Atlantic around South Africa. Population‐level patterns in the Caribbean indicate extensive gene flow across the region.

    more » « less