Comparative and population mitogenomic analyses of Madagascar's extinct, giant ‘subfossil’ lemurs

Kistler, Logan; Ratan, Aakrosh; Godfrey, Laurie R.; Crowley, Brooke E.; Hughes, Cris E.; Lei, Runhua; Cui, Yinqiu; Wood, Mindy L.; Muldoon, Kathleen M.; Andriamialison, Haingoson; McGraw, John J.; Tomsho, Lynn P.; Schuster, Stephan C.; Miller, Webb; Louis, Edward E.; Yoder, Anne D.; Malhi, Ripan S.; Perry, George H.

doi:10.1016/j.jhevol.2014.06.016

Cited by 93 publications

(107 citation statements)

References 67 publications

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“…It is 17 106 bp long and includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a non-coding region. The arrangement of the multiple genes is in line with other lemur species (Finstermeier et al, 2013;Kistler et al, 2015;Matsui et al, 2007) and most primates (Lei et al, 2010;Wang et al, 2014). With the exception of NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes, all the other genes are encoded on the heavy strand.…”

supporting

confidence: 52%

Sequence characterization and phylogeny analysis of the complete mitochondrial genome of verreaux's sifaka, Propithecus verreauxi (primates: indriidae)

Yao

Gao²,

Liu

et al. 2015

Mitochondrial DNA Part A

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The Verreaux's sifaka, Propithecus verreauxi, is a medium-sized lemur that inhabits in tropical dry lowland and montane forest. Here, we reported the complete mitochondrial genome sequence of this species. The mitogenome of P. verreauxi is 17 106 bp in length and composed of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes and a control region. The structure about gene order and composition is identical to that of the other lemur species and related genera. The overall base composition of the heavy strand in descending order is A (32.84%), T (27.13%), C (26.95%), and G (13.08%). Most of the genes are encoded on the heavy strand except for the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes. With the exception of COX3, which terminates with an incomplete stop codon (T-), all the other PCGs initiates with a traditional ATN start codon and ends with the typical mitochondrial stop codon (TAG/TAA/AGA). The phylogenetic tree constructed using the complete mitochondrial genome sequences of P. verreauxi together with 15 other closely related species with Neighbor-Joining (NJ) method shows that P. verreauxi is closer to P. coquereli in the phylogenetic relationship.

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supporting

confidence: 52%

Sequence characterization and phylogeny analysis of the complete mitochondrial genome of verreaux's sifaka, Propithecus verreauxi (primates: indriidae)

Yao

Gao²,

Liu

et al. 2015

Mitochondrial DNA Part A

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“…When full mitochondrial genome data were unavailable, we used all publicly available data for mitochondrial coding regions (Dataset S5). Our sampling included representatives of all major lineages and was based on a recently published phylogeny (11), as well as those species studied by Perry and Hartstone-Rose (24). For those extinct taxa lacking any genetic data, we conditioned the placement of the taxa For all DNA sequence data, we aligned the mitochondrial coding regions to a complete mtDNA reference sequence (V. variegata, GI:671760213), using MUSCLE v3.7 (38) implemented in Geneious v7.1.2 (39) with alignments checked by eye.…”

Section: Methodsmentioning

confidence: 99%

“…To time-calibrate the phylogeny, we used two fossil-based prior age calibrations following the methodology of Kistler et al (11). Briefly, we dated the split between the Lorisiformes and Lemuriformes as being between 52 and 66 Ma (Fig.…”

Section: Methodsmentioning

confidence: 99%

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Implications of lemuriform extinctions for the Malagasy flora

Federman

Dornburg

Daly

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Madagascar's lemurs display a diverse array of feeding strategies with complex relationships to seed dispersal mechanisms in Malagasy plants. Although these relationships have been explored previously on a case-by-case basis, we present here the first comprehensive analysis of lemuriform feeding, to our knowledge, and its hypothesized effects on seed dispersal and the long-term survival of Malagasy plant lineages. We used a molecular phylogenetic framework to examine the mode and tempo of diet evolution, and to quantify the associated morphological space occupied by Madagascar's lemurs, both extinct and extant. Using statistical models and morphometric analyses, we demonstrate that the extinction of large-bodied lemurs resulted in a significant reduction in functional morphological space associated with seed dispersal ability. These reductions carry potentially far-reaching consequences for Malagasy ecosystems, and we highlight large-seeded Malagasy plants that appear to be without extant animal dispersers. We also identify living lemurs that are endangered yet occupy unique and essential dispersal niches defined by our morphometric analyses.anachronism | extinction | lemurs | Madagascar | seed dispersal

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“…The differing positioning of Dicerorhinus in these two studies might simply be due to differences in the mitochondrial genes included in each analysis, as discussed above (Willerslev et al, 2009). Molecular sequences of additional, now extinct, species of rhinoceros have the potential to contribute to our understanding of the relationships among these mammals, as it has done in the past for other mammals by utilising ancient DNA or ancient protein sequences (Der Sarkissian et al, 2015; Kistler et al, 2015; Lister et al, 2005; Welker et al, 2015a). …”

Section: Introductionmentioning

confidence: 99%

Middle Pleistocene protein sequences from the rhinoceros genusStephanorhinusand the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae

Welker

Smith

Hutson

et al. 2017

PeerJ

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BackgroundAncient protein sequences are increasingly used to elucidate the phylogenetic relationships between extinct and extant mammalian taxa. Here, we apply these recent developments to Middle Pleistocene bone specimens of the rhinoceros genus Stephanorhinus. No biomolecular sequence data is currently available for this genus, leaving phylogenetic hypotheses on its evolutionary relationships to extant and extinct rhinoceroses untested. Furthermore, recent phylogenies based on Rhinocerotidae (partial or complete) mitochondrial DNA sequences differ in the placement of the Sumatran rhinoceros (Dicerorhinus sumatrensis). Therefore, studies utilising ancient protein sequences from Middle Pleistocene contexts have the potential to provide further insights into the phylogenetic relationships between extant and extinct species, including Stephanorhinus and Dicerorhinus.MethodsZooMS screening (zooarchaeology by mass spectrometry) was performed on several Late and Middle Pleistocene specimens from the genus Stephanorhinus, subsequently followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) to obtain ancient protein sequences from a Middle Pleistocene Stephanorhinus specimen. We performed parallel analysis on a Late Pleistocene woolly rhinoceros specimen and extant species of rhinoceroses, resulting in the availability of protein sequence data for five extant species and two extinct genera. Phylogenetic analysis additionally included all extant Perissodactyla genera (Equus, Tapirus), and was conducted using Bayesian (MrBayes) and maximum-likelihood (RAxML) methods.ResultsVarious ancient proteins were identified in both the Middle and Late Pleistocene rhinoceros samples. Protein degradation and proteome complexity are consistent with an endogenous origin of the identified proteins. Phylogenetic analysis of informative proteins resolved the Perissodactyla phylogeny in agreement with previous studies in regards to the placement of the families Equidae, Tapiridae, and Rhinocerotidae. Stephanorhinus is shown to be most closely related to the genera Coelodonta and Dicerorhinus. The protein sequence data further places the Sumatran rhino in a clade together with the genus Rhinoceros, opposed to forming a clade with the black and white rhinoceros species.DiscussionThe first biomolecular dataset available for Stephanorhinus places this genus together with the extinct genus Coelodonta and the extant genus Dicerorhinus. This is in agreement with morphological studies, although we are unable to resolve the order of divergence between these genera based on the protein sequences available. Our data supports the placement of the genus Dicerorhinus in a clade together with extant Rhinoceros species. Finally, the availability of protein sequence data for both extinct European rhinoceros genera allows future investigations into their geographic distribution and extinction chronologies.

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Comparative and population mitogenomic analyses of Madagascar's extinct, giant ‘subfossil’ lemurs

Cited by 93 publications

References 67 publications

Sequence characterization and phylogeny analysis of the complete mitochondrial genome of verreaux's sifaka, Propithecus verreauxi (primates: indriidae)

Sequence characterization and phylogeny analysis of the complete mitochondrial genome of verreaux's sifaka, Propithecus verreauxi (primates: indriidae)

Implications of lemuriform extinctions for the Malagasy flora

Middle Pleistocene protein sequences from the rhinoceros genusStephanorhinusand the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae

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