Phylogenetic Uncertainty and Taxonomic Re-revisions: An Example from the Australian Short-necked Turtles (Testudines: Chelidae)

Spinks, Phillip Q.; Georges, Arthur; Shaffer, H. Bradley

doi:10.1643/ch-14-147

Cited by 10 publications

(12 citation statements)

References 26 publications

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“…The relationships among the species of Elseya is not yet clear. The new species Elseya flaviventralis has Elseya dentata or E. branderhorsti as its sister taxon (Georges & Adams 1992;Todd et al 2014;Spinks et al 2015). The subgenus Hanwarachelys (Thomson et al 2015) appears to lie phylogenetically between the subgenera Elseya and Pelocomastes, as sister taxon to subgenus Elseya (Georges & Adams 1992;Georges et al 1998;Le et al 2013;Spinks et al 2015).…”

Section: Discussionmentioning

confidence: 94%

“…Three major clades are recognized: the northern Elseya (nominal subgenus Elseya, two species) with type species Elseya dentata, the Queensland Elseya (subgenus Pelocomastes, three living and two fossil species) with type species Elseya uberrima, and the New Guinea stream Elseya (subgenus Hanwarachelys, three species) with type species Elseya novaeguineae, and two other taxa E. schultzii and E. rhodini (Thomson et al 2015). The genus Myuchelys (three or four species depending upon usage/ acceptance of the genus Flaviemys, Le et al 2013;Spinks et al 2015) is similar to Elseya but lacks the alveolar ridge. The final three genera are monotypic, if extant forms only are considered, represented by Pseudemydura umbrina, Elusor macrurus and Rheodytes leukops (Georges & Thomson 2010;Rhodin et al 2015).…”

Section: Introductionmentioning

confidence: 99%

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A new species of freshwater turtle of the genus Elseya (Testudinata: Pleurodira: Chelidae) from the Northern Territory of Australia

Thomson¹,

Georges²

2016

Zootaxa

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The genus Elseya has had a checkered taxonomic history, but is now restricted to species characterized by an alveolar ridge on the triturating surfaces of the jaw. The Australian forms were once regarded as a single widespread species extending from the Mary River of south-eastern Queensland to the Fitzroy River of north Western Australia, but a number of Australian species have now been identified based on a combination of molecular and morphological data-Elseya dentata, E. irwini, E. lavarackorum and E. albagula. The genus is represented in New Guinea by E. branderhorsti, E. novaeguineae, E. schultzii, and E. rhodini. One additional Australian taxon first identified in 1981 and subsequently established as a distinct taxon by molecular studies, is described here. It is a large chelid turtle that can be distinguished from all other Australian members of the genus Elseya by the distinctive cream or yellow plastron, free of the dark streaking, blotches or suffusing present in other species; an extensive bridge with little or no abrupt angle between the bridge and the ventral surface of the plastron; a head shield broken into a series of small plates rather than a single unit; flat uncornified temporal scales; and a narrower, less robust skull. Osteologically, it can be distinguished from Elseya dentata by the contact of the vomer and the pterygoids. The carapace is typically a light to medium brown in color whereas the carapace of Elseya dentata is typically dark brown to almost black in color. Distribution is the Mary, South Alligator, East Alligator, Goyder and Mann River drainages of the north east of the Northern Territory, Australia. It does not appear to be in sympatry with any other member of Elseya. It is, however, in sympatry with three species of Chelodina, at least two species of Emydura, Myuchelys latisternum and Carettochelys insculpta.

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Section: Discussionmentioning

confidence: 94%

Section: Introductionmentioning

confidence: 99%

A new species of freshwater turtle of the genus Elseya (Testudinata: Pleurodira: Chelidae) from the Northern Territory of Australia

Thomson¹,

Georges²

2016

Zootaxa

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“…We used the implementation of SVDquartets in PAUP* (version 4.0a162; Swofford, ) with parameters evalQuartets = random, bootstrap = standard, nreps = 10,000 and ambigs = distribute. Trees were rooted with E. victoriae and E. subglobossa worrelli (Supporting Information Table ; Spinks, Georges, & Shaffer, ). Instances of historical migration were identified by treemix version 1.13 (Pickrell & Pritchard, ).…”

Section: Methodsmentioning

confidence: 99%

“…For bootstrapping, we ran 1,000 replicates with the previous settings with the following changes: genthreshfortopoterm = 10,000; significanttopochange = 0.01; treerejectionthreshold = 20 as suggested in the GARLI manual to speed up bootstrapping. Trees were rooted with E. victoriae and E. tanybaraga (Supporting Information Table ; Spinks et al., ).…”

Section: Methodsmentioning

confidence: 99%

Genomewide SNP markers breathe new life into phylogeography and species delimitation for the problematic short‐necked turtles (Chelidae: Emydura) of eastern Australia

et al. 2018

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Understanding the evolutionary history of diversifying lineages and the delineation of evolutionarily significant units and species remains major challenges for evolutionary biology. Low-cost representational sampling of the genome for single nucleotide polymorphisms shows great potential at the temporal scales that are typically the focus of species delimitation and phylogeography. We apply these markers to a case study of a freshwater turtle, Emydura macquarii, whose systematics has so far defied resolution, to bring to light a dynamic system of substantive allopatric lineages diverging on independent evolutionary trajectories, but held back in the process of speciation by low level and episodic exchange of alleles across drainage divides on various timescales. In the context of low-level episodic gene flow, speciation is often reticulate, rather than a bifurcating process. We argue that species delimitation needs to take into account the pattern of ancestry and descent of diverging lineages in allopatry together with the recent and contemporary processes of dispersal and gene flow that retard and obscure that divergence. Underpinned by a strong focus on lineage diagnosability, this combined approach provides a means for addressing the challenges of incompletely isolated populations with uncommon, but recurrent gene flow in studies of species delimitation, a situation likely to be frequently encountered. Taxonomic decisions in cases of allopatry often require subjective judgements.Our strategy, which adds an additional level of objectivity before that subjectivity is applied, reduces the risk of taxonomic inflation that can accompany lineage approaches to species delimitation. K E Y W O R D S ddRAD-seq, hybridization, introgression, landscape genomics, Murray-Darling Basin, species boundaries S U PP O RTI N G I N FO R M ATI O N Additional supporting information may be found online in the Supporting Information section at the end of the article. How to cite this article: Georges A, Gruber B, Pauly GB, et al. Genomewide SNP markers breathe new life into phylogeography and species delimitation for the problematic short-necked turtles (Chelidae: Emydura) of eastern Australia.

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“…Mitochondrial sequence evidence and limited nuclear sequence evidence suggest that M. latisternum, M. bellii, and species of the genus Emydura have arisen from a common ancestor with M. georgesi after their divergence from M. purvisi, an arrangement at odds with the multiple nuclear gene data (n = 54) of Georges and Adams (1992). An attempt to resolve this paraphyly was proposed through the erection of a monophyletic genus for M. purvisi (Flaviemys, Le et al 2013), but this action has been questioned following the generation of additional nuclear sequence data (Spinks et al 2015).…”

Section: 3mentioning

confidence: 99%

Myuchelys georgesi (Cann 1997) – Bellinger River Turtle.

Cann¹,

Spencer²,

Welsh³

et al. 2015

Chelonian Research Monographs

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The Bellinger River Turtle, Myuchelys georgesi (Family Chelidae), is a turtle of moderate size (carapace length to 240 mm in females, 185 mm in males) with a distribution restricted to the small coastal drainage of Bellinger River in New South Wales, Australia. The species is widely distributed within the drainage basin and has been locally abundant, but with a very restricted range. Its preferred habitat is the deeper pools of the clear-water upstream reaches of the river, where water flows continuously in most months over a bedrock basement and a streambed of boulders, pebbles, and gravel. The species takes advantage of the highly oxygenated water with low particulate load by supplementing its oxygen uptake through cloacal breathing, reducing its obligation to come to the surface to breathe. Myuchelys georgesi is essentially an omnivore, with tendencies leaning toward carnivory. A high proportion of its diet comes from benthic macroinvertebrate communities that are relatively sedentary and live in immediate association with the substratum, but with some terrestrial fruit and aquatic vegetation also eaten. Breeding occurs in the austral spring and early summer. Current threats to its persistence include habitat modification and loss of native riparian vegetation, associated turbidification and sedimentation, predation by the introduced European fox, competition with the recently introduced Emydura macquarii, and a severe recent die-off caused by unknown factors, possibly viral disease, leading to greatly heightened sudden risk of extinction. diStRibution.-Australia. Restricted to the small Bellinger River drainage of northeastern coastal New South Wales. SynonyMy.-Elseya georgesi Cann 1997, Wollumbinia georgesi 1 , Elseya latisternum georgesi, Myuchelys georgesi. SubSpeCieS.-None currently recognized. StatuS.

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Phylogenetic Uncertainty and Taxonomic Re-revisions: An Example from the Australian Short-necked Turtles (Testudines: Chelidae)

Cited by 10 publications

References 26 publications

A new species of freshwater turtle of the genus Elseya (Testudinata: Pleurodira: Chelidae) from the Northern Territory of Australia

A new species of freshwater turtle of the genus Elseya (Testudinata: Pleurodira: Chelidae) from the Northern Territory of Australia

Genomewide SNP markers breathe new life into phylogeography and species delimitation for the problematic short‐necked turtles (Chelidae: Emydura) of eastern Australia

Myuchelys georgesi (Cann 1997) – Bellinger River Turtle.

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