Nuclear mitochondrial pseudogenes as molecular outgroups for phylogenetically isolated taxa: a case study in Sphenodon

Hay, Jennifer M.; Sarre, Stephen D.; Daugherty, Charles H.

doi:10.1038/sj.hdy.6800525

Cited by 17 publications

(14 citation statements)

References 33 publications

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“…We genotyped seven tuatara from Stephens Island and 18 from the single natural population of S. guntheri on North Brother Island. We chose to sequence the mitochondrial DNA control region because it has more variation than the ND1 and cytochrome b genes sequenced previously by Hay et al (2003Hay et al ( , 2004. Amplification of the control region by PCR followed the protocols of Hay et al (2003) using the primers ProL and PheTH from Table 2 of that paper.…”

Section: Methodsmentioning

confidence: 99%

“…Support for nodes on branches are confidence probabilities/bootstrap confidence levels 9 1,000 replications, only values above 50% are shown. Root of tree is between northern and Cook Strait populations as identified in Hay et al (2004). Cook Strait populations are shaded, Brothers tuatara are additionally shadowed.…”

Section: Ruamahua-itimentioning

confidence: 99%

“…Kimura-2 distances were used to construct minimum evolution trees in MEGA 3.1 using the pairwise deletion option and the topology was tested with confidence probabilities (CP) and bootstrap confidence levels (BCL) with 1,000 replications. The root for the phylogenetic tree was set between northern and Cook Strait populations in accordance with the mitochondrial genome root position identified by Hay et al (2004) which used mitochondrial cytochrome b and an ancient nuclear copy of cytochrome b; there is no living animal related closely enough to act as an outgroup taxon. Parsimony trees of mtDNA haplotypes were found using PHYLIP ver.…”

Section: Mitochondrial Dna Analysesmentioning

confidence: 99%

“…More recently, Hay et al (2003Hay et al ( , 2004) examined mitochondrial DNA (mtDNA) sequence variation (ND1, partial control region and cytochrome b) among tuatara populations. They recovered the two previously identified groups of S. punctatus (northern islands and western Cook Strait islands) but did not find the deep split between S. guntheri and S. punctatus that was evident in the allozyme data.…”

Section: Introductionmentioning

confidence: 99%

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Genetic diversity and taxonomy: a reassessment of species designation in tuatara (Sphenodon: Reptilia)

et al. 2009

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The identification of species boundaries for allopatric populations is important for setting conservation priorities and can affect conservation management decisions. Tuatara (Sphenodon) are the only living members of the reptile order Sphenodontia and are restricted to islands around New Zealand that are free of introduced mammals. We present new data of microsatellite DNA diversity and substantially increased mtDNA sequence for all 26 sampled tuatara populations. We also re-evaluate existing allozyme data for those populations, and together use them to examine the taxonomic status of those populations. Although one could interpret the data to indicate different taxonomic designations, we conclude that, contrary to current taxonomy, Sphenodon is best described as a single species that contains distinctive and important geographic variants. We also examine amounts of genetic variation within populations and discuss the implications of these findings for the conservation management of this iconic taxon.

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Section: Methodsmentioning

confidence: 99%

Section: Ruamahua-itimentioning

confidence: 99%

Section: Mitochondrial Dna Analysesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genetic diversity and taxonomy: a reassessment of species designation in tuatara (Sphenodon: Reptilia)

et al. 2009

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“…The chromatograms were clean, lacking ambiguous base signals that might have otherwise indicated presence of both mitochondrial and nuclear paralogues in a single PCR product. The coding section of the ND4 sequences for the 7 taxa were checked for the presence of premature stop codons (Coin & Durbin 2004, Hay et al 2004, Lerat & Ochman 2005, and none was found. The amplified DNA of all 7 taxa were aligned to a known complete ND4 genome from a distantly related tortoise, Geochelone pardalis (GenBank accession number DQ080041; Parham et al 2006).…”

Section: Methodsmentioning

confidence: 99%

Mitochondrial variation among Australian freshwater turtles (genus Myuchelys), with special reference to the Endangered M. bellii

Fielder¹,

Vernes²,

Alacs³

et al. 2012

Endang. Species. Res.

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Identifying species and the relationships among them remains important for assessing biodiversity trends and is a critical focus for reversing global biodiversity loss. The saw-shelled turtles of Australia, in the genus Myuchelys, show cryptic diversity and include species that range from Endangered (M. bellii), through those that are locally abundant but extremely limited in distribution (M. georgesi and M. purvisi) to those that are common and widespread (M. latisternum). The Endangered M. bellii is restricted to 3 small isolated populations in the headwaters of the Murray-Darling basin, in the Border, Gwydir and Namoi tributaries. There is no evidence of strong differentiation among these 3 populations based on mitochondrial DNA (mtDNA) divergences; rather there is only a shallow genetic structure ranging from 0.1 to 0.3% divergence. The 3 restricted and small populations of the Endangered M. bellii face a number of threatening processes and require conservation management across state boundaries as a single biological species. The mtDNA phylogeny supports previous phylogenetic findings of a deep phylogenetic divergence between M. purvisi and M. georgesi (13.5% mtDNA) and the sister taxa relationship of M. latisternum and M. bellii. A notable exception was our finding that Emydura macquarii and M. georgesi are sister taxa inside the Myuchelys radiation.

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Skull shape and feeding strategy in Sphenodon and other Rhynchocephalia (Diapsida: Lepidosauria)

Jones

2008

Journal of Morphology

181

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The Rhynchocephalia are a group of small diapsid reptiles that were globally distributed during the early Mesozoic. By contrast, the only extant representatives, Sphenodon punctatus and S. guntheri (Tuatara), are restricted to New Zealand off-shore islands. The Rhynchocephalia are widely considered to be morphologically uniform but research over the past 30 years has revealed unexpected phenotypic and taxonomic diversity. Phylogenetically ''basal taxa'' generally possess relatively simple conical or columnar teeth whereas more derived taxa possessed stouter flanged teeth and sophisticated shearing mechanisms: orthal in some (e.g., Clevosaurus hudsoni) and propalinal in others (e.g., S. punctatus). This variation in feeding apparatus suggests a wide range of feeding niches were exploited by rhynchocephalians. The relationship of skull shape to skull length, phylogenetic grouping, habit, and characters relating to the feeding apparatus are explored here with geometric morphometric analysis on two-dimensional landmarks. Principle components analysis demonstrates that there are significant differences between phylogenetic groups. In particular, Sphenodon differs significantly from all well known fossil taxa including the most phylogenetically basal forms. Therefore, it is not justifiable to use Sphenodon as a solitary outgroup when studying skull shape and feeding strategy in squamates; rhynchocephalian fossil taxa also need to be considered. There are also significant differences between the skull shapes of aquatic taxa and those of terrestrial taxa. Of the observed variation in skull shape, most variation is subsumed by variation in dentary tooth base shape, the type of jaw movement employed (e.g., orthal vs. propalinal) and the number of palatal tooth rows. By comparison, the presence or absence of flanges, dentary tooth number and palatal tooth row orientation subsume much less. Skull length was also found to be a poor descriptor of overall skull shape. Compared to basal rhynchocephalians members of more derived terrestrial radiations possess an enlarged postorbital area, a high parietal, and a jaw joint positioned ventral to the tooth row. Modification of these features is closely associated with increased biting performance and thus access to novel food items. Some of these same trends are apparent during Sphenodon ontogeny where skull growth is allometric and there is evidence for ontogenetic variation in diet. J.

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Nuclear mitochondrial pseudogenes as molecular outgroups for phylogenetically isolated taxa: a case study in Sphenodon

Cited by 17 publications

References 33 publications

Genetic diversity and taxonomy: a reassessment of species designation in tuatara (Sphenodon: Reptilia)

Genetic diversity and taxonomy: a reassessment of species designation in tuatara (Sphenodon: Reptilia)

Mitochondrial variation among Australian freshwater turtles (genus Myuchelys), with special reference to the Endangered M. bellii

Skull shape and feeding strategy in Sphenodon and other Rhynchocephalia (Diapsida: Lepidosauria)

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