Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution

Willerslev, Eske; Gilbert, M. Thomas P.; Binladen, Jonas; Ho, Simon Y. W.; Campos, Paula F.; Ratan, Aakrosh; Tomsho, Lynn P.; Fonseca, Rute R. da; Sher, Andrei; Кузнецова, Т. В.; Nowak-Kemp, Małgosia; Roth, Terri L.; Miller, Webb; Schuster, Stephan C.

doi:10.1186/1471-2148-9-95

Cited by 95 publications

(86 citation statements)

References 51 publications

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“…The white rhinoceros sequencing results using complete mitochondrial genomes confirmed the results of Tougard et al (2001), which were based on mitochondrial Cytochrome B and 12S rRNA Genes, and those of Willerslev et al (2009) from whole mitochondrial genomes. Our results, like Tougard et al (2001) and Willerslev et al (2009), show a lack of resolution for the placement of the Sumatran Rhinoceros (Dicerorhinus sumatrensis), which in some analyses clustered with the African genera but at others with the other Asian genera.…”

Section: Discussionsupporting

confidence: 74%

“…Our results, like Tougard et al (2001) and Willerslev et al (2009), show a lack of resolution for the placement of the Sumatran Rhinoceros (Dicerorhinus sumatrensis), which in some analyses clustered with the African genera but at others with the other Asian genera. On the question as to the time of divergence of NWR and SWR, our data imply that the mtDNA genomes of NWR and SWR diverged somewhere between 0.46 and 0.97 million years ago.…”

Section: Discussioncontrasting

confidence: 53%

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Comparison of whole mitochondrial genome sequences of northern and southern white rhinoceroses (Ceratotherium simum): the conservation consequences of species definitions

et al. 2016

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The probable extinction of the last confirmed population of northern white rhinoceros (Ceratotherium simum cottoni) in the world has ignited debate regarding its species status compared to the southern white rhinoceros (Ceratotherium simum simum). Previous studies, based on partial mitochondrial sequences, have reported conflicting results regarding the species status of the northern white rhinoceros. We use whole mitochondrial genomes obtained using Next Generation Sequencing of four northern white rhinoceros and three southern white rhinoceros using novel primers in three overlapping fragments. Phylogenetic relationships were constructed, using Maximum Likelihood, and recovered monophyletic clades for northern white rhinoceros and southern white rhinoceros. The divergence time between the two mitochondrial DNA lineages was estimated to be between 0.46 and 0.97 million years ago using Bayesian inferences. Since there are currently only three surviving northern white rhinoceros individuals these results put into sharp focus the ongoing debate regarding the methods of species definition, and in particular the consequences of such definitions in conservation management of endangered species and subspecies. We conclude that the designation of sub-species status is more applicable to northern and southern white rhinoceros.

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Section: Discussionsupporting

confidence: 74%

Section: Discussioncontrasting

confidence: 53%

Comparison of whole mitochondrial genome sequences of northern and southern white rhinoceroses (Ceratotherium simum): the conservation consequences of species definitions

et al. 2016

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“…4) in all phylogenetic analyses, but not with the Javan rhinoceros R. sondaicus instead, as the label and documents from the museum's archives would suggest. A comparison of sequences showed a 100% identity with all available sequences of the Sumatran rhinoceros from GenBank with respect to the trimmed alignment and also with the untrimmed sequence of the Sumatran rhinoceros from the study of Willerslev et al (2009) leaving no doubt on the correct molecular identification of the ZMH specimen. Pairwise genetic p-distances within the African white rhinoceros and black rhinoceros ranged from 0 to 1.8% between specimens, while the p-distances between Javan rhinoceros specimens were less than 0.9%.…”

Section: Molecular Resultsmentioning

confidence: 82%

“…In addition to the newly generated data, all available 12S rDNA sequences for Rhinocerotidae from the previously published studies of Douzery and Catzeflis (1995), Xu et al (1996), Xu and Árnason (1997), Tougard et al (2001), Fernando et al (2006), Willerslev et al (2009) and Groves et al (2010), in total 21 sequences, were downloaded from GenBank (www.ncbi. nlm.nih.gov/Genbank).…”

Section: Sampling Dna Isolation and Amplificationmentioning

confidence: 99%

“…Surprisingly, it was noticed that the sequences from the study of Fernando et al (2006) lacked data in five variable regions of the aligned 12S rDNA fragment, i.e. between positions 155 and 164, 193 and 198, 290 and 294, 375 and 388 and 538 and 545 of the complete mitochondrial genome of D. sumatrensis (GenBank accession number FJ_905816; Willerslev et al 2009). Since all other Rhinocerotidae possess a variable number of bases in these regions, it is assumed here that Fernando et al (2006) erroneously uploaded trimmed sequences to the GenBank database.…”

Section: Sampling Dna Isolation and Amplificationmentioning

confidence: 99%

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Museum specimens as Noah’s Arc of lost genes. The case of a rhinoceros from Sumatra in the Zoological Museum Hamburg

Glaubrecht¹,

Neiber²

2017

EvolSyst

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Understanding past and present genetic diversity, in particular in endangered species such as the rhinoceroses, is of paramount importance for a series of aspects in natural history, evolutionary systematics and conservation. As it turned out from several recent studies even in eminent museum specimens the historical context including its provenance often remains unresolved. At the same time modern molecular genetic techniques make this material more and more available also for integrative studies. With probably less than fifty extant specimens, among the Asian rhinoceroses the Javan rhinoceros, Rhinoceros sondaicus, is one of the most critically endangered mammal species, rendering also each of its rare museum specimens of great significance. We here apply available DNA isolation and sequencing techniques to a horn of a specimen housed at the Zoological Museum in Hamburg with indication as to derive from the extinct conspecific Sumatra population. In comparison with already existing mitochondrial gene fragment sequence data of Asian rhino populations, we were able to verify the identification of this particular museum specimen as of the nearly equally rare Sumatran rhinoceros, Dicerorhinus sumatrensis, instead as of the extremely rare R. sondaicus.

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Mitogenomic phylogenetic analyses of Leptogorgia virgulata and Leptogorgia hebes (Anthozoa: Octocorallia) from the Gulf of Mexico provides insight on Gorgoniidae divergence between Pacific and Atlantic lineages

Silvestri

Figueroa

Hicks

et al. 2019

Ecology and Evolution

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The use of genetics in recent years has brought to light the need to reevaluate the classification of many gorgonian octocorals. This study focuses on two Leptogorgia species—Leptogorgia virgulata and Leptogorgia hebes—from the northwestern Gulf of Mexico (GOM). We target complete mitochondrial genomes and mtMutS sequences, and integrate this data with previous genetic research of gorgonian corals to resolve phylogenetic relationships and estimate divergence times. This study contributes the first complete mitochondrial genomes for L. ptogorgia virgulata and L. hebes. Our resulting phylogenies stress the need to redefine the taxonomy of the genus Leptogorgia in its entirety. The fossil‐calibrated divergence times for Eastern Pacific and Western Atlantic Leptogorgia species based on complete mitochondrial genomes shows that the use of multiple genes results in estimates of more recent speciation events than previous research based on single genes. These more recent divergence times are in agreement with geologic data pertaining to the formation of the Isthmus of Panama.

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Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution

Cited by 95 publications

References 51 publications

Comparison of whole mitochondrial genome sequences of northern and southern white rhinoceroses (Ceratotherium simum): the conservation consequences of species definitions

Comparison of whole mitochondrial genome sequences of northern and southern white rhinoceroses (Ceratotherium simum): the conservation consequences of species definitions

Museum specimens as Noah’s Arc of lost genes. The case of a rhinoceros from Sumatra in the Zoological Museum Hamburg

Mitogenomic phylogenetic analyses of Leptogorgia virgulata and Leptogorgia hebes (Anthozoa: Octocorallia) from the Gulf of Mexico provides insight on Gorgoniidae divergence between Pacific and Atlantic lineages

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