Resolution of the African hominoid trichotomy by use of a mitochondrial gene sequence.

Ruvolo, Maryellen; Disotell, Todd R.; Allard, Marc W.; Brown, Wesley M.; Honeycutt, Rodney L.

doi:10.1073/pnas.88.4.1570

Cited by 189 publications

(116 citation statements)

References 48 publications

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“…All the annealing temperature trials produced the same results; the best based on band brightness was recorded at 51°C. This finding supports a previous study (Table 5) on the same gene and same subfamily Cercopithecinae in the tribe Papionini (Disotell et al, 1992), whereas for the PCR conditions of gorilla, siamang and macaques, as described by Ruvolo et al (1991), the annealing process required 50-57°C for 1 min. A study by Ernie-Muneerah et al (2005) on leaf monkeys required an annealing temperature of 54-55°C (1 min).…”

Section: Discussionsupporting

confidence: 79%

“…However, in many phylogenetic relationship studies, other genes of mitochondrial DNA are still favored as gene candidates (Shahrom et al, 2005;Khan et al, 2008;Lim et al, 2010;Md-Zain et al, 2010). In primate evolutionary studies, several COII gene data analyses have focused on hominoids and the New World Monkeys (Ruvolo et al, 1991(Ruvolo et al, , 1993. For New World Monkeys, the sequence of the COII gene has been studied on Platyrrhini including both Atelidae and Cebidae families (Ascunce et al, 2002): owl monkeys, genus Aotus (Ashley and Vaughn, 1995); spider monkeys, genus Ateles (Collins and Dubach, 2000) and marmoset species group (Sena et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

“…For example, the phylogenetic studies of the tribe Papionini, composed of baboons, mandrills, drills, and mangabeys were conducted on the African continent (Ruvolo et al, 1991;Disotell et al, 1992;Harris, 2000). Phylogenetic inference using COII gene in the Asian region remains less pronounced than in the African region.…”

Section: Introductionmentioning

confidence: 99%

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Phylogenetic relationships of Malaysian monkeys, Cercopithecidae, based on mitochondrial cytochrome c sequences

Mohamad

et al. 2010

Genet. Mol. Res.

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ABSTRACT. Mitochondrial DNA cytochrome c oxidase II (COII) gene sequences of Malaysian Cercopithecidae were examined to ascertain their phylogenetic relationships. Colobinae were represented by the genera Presbytis, Trachypithecus and Nasalis, while the genus Macaca represented Cercopithecinae. DNA amplification and sequencing of the COII gene was performed on 16 samples. Symphalangus syndactylus (Hylobatidae) was used as the outgroup. Data were analyzed using both character (maximum parsimony) and distance (neighbor-joining) methods. Tree topologies indicated that Colobinae and Cercopithecinae have their own distinct monophyletic clade. This result was well supported by bootstrap values and genetic distances derived from the Kimura-2-parameter algorithm. Separation of Macaca nemestrina from M. fascicularis was also well supported by bootstrap values. In addition, tree topologies indicate a good resolution of the Colobinae phylogenetic relationships at the intergeneric level, but with low bootstrap support. The position of Nasalis remained problematic in both trees. Overall, COII is a good gene candidate for portraying the phylogenetic relationships of Malaysian primates at the inter-and intra-subfamily levels.

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Section: Discussionsupporting

confidence: 79%

Section: Introductionmentioning

confidence: 99%

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Phylogenetic relationships of Malaysian monkeys, Cercopithecidae, based on mitochondrial cytochrome c sequences

Mohamad

et al. 2010

Genet. Mol. Res.

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“…Tubes were flash frozen or placed on ice, then transferred to À 80 1C freezers on arrival in the United States, and stored there until sample processing. To verify host origin, we amplified and sequenced mitochondrial 12S rRNA genes from all species and the COXII gene from genomic DNA (gDNA) extracted from these samples, using previously published primers (Kocher et al, 1989;Ruvolo et al, 1991). Comparison of the 12S rRNA and COXII gene sequences with Genbank using nucleotide-nucleotide basic local alignment search tool confirmed that the samples collected were from the designated primate species.…”

Section: Sample Collection and Processingmentioning

confidence: 99%

Primate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance

et al. 2014

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Bacterial communities colonizing the reproductive tracts of primates (including humans) impact the health, survival and fitness of the host, and thereby the evolution of the host species. Despite their importance, we currently have a poor understanding of primate microbiomes. The composition and structure of microbial communities vary considerably depending on the host and environmental factors. We conducted comparative analyses of the primate vaginal microbiome using pyrosequencing of the 16S rRNA genes of a phylogenetically broad range of primates to test for factors affecting the diversity of primate vaginal ecosystems. The nine primate species included: humans (Homo sapiens), yellow baboons (Papio cynocephalus), olive baboons (Papio anubis), lemurs (Propithecus diadema), howler monkeys (Alouatta pigra), red colobus (Piliocolobus rufomitratus), vervets (Chlorocebus aethiops), mangabeys (Cercocebus atys) and chimpanzees (Pan troglodytes). Our results indicated that all primates exhibited host-specific vaginal microbiota and that humans were distinct from other primates in both microbiome composition and diversity. In contrast to the gut microbiome, the vaginal microbiome showed limited congruence with host phylogeny, and neither captivity nor diet elicited substantial effects on the vaginal microbiomes of primates. Permutational multivariate analysis of variance and Wilcoxon tests revealed correlations among vaginal microbiota and host species-specific socioecological factors, particularly related to sexuality, including: female promiscuity, baculum length, gestation time, mating group size and neonatal birth weight. The proportion of unclassified taxa observed in nonhuman primate samples increased with phylogenetic distance from humans, indicative of the existence of previously unrecognized microbial taxa. These findings contribute to our understanding of host-microbe variation and coevolution, microbial biogeography, and disease risk, and have important implications for the use of animal models in studies of human sexual and reproductive diseases.

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“…Of the several genes exploited for this purpose, the mitochondrial cytochrome c oxidase subunit II (COII) is perhaps the most frequently used. A considerable amount of information concerning its evolution is now available for various groups, including rodents (Brown and Simpson 1982), primates (Disotell et al 1992;Adkins and Honeycutt 1994), hominoids (Ruvolo et al 1991), and several orders of pterygote (winged) insects (Liu and Beckenbach 1992;Beckenbach et al 1993;Willis et al 1992;Brower 1994;Brown et al 1994;. Prior to our study, no basal insect orders had been examined.…”

Section: Introductionmentioning

confidence: 99%

Evolution of the Mitochondrial Cytochrome Oxidase II Gene in Collembola

et al. 1997

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Abstract. The sequence of the mitochondrial COII gene has been widely used to estimate phylogenetic relationships at different taxomonic levels across insects. We investigated the molecular evolution of the COII gene and its usefulness for reconstructing phylogenetic relationships within and among four collembolan families. The collembolan COII gene showed the lowest A + T content of all insects so far examined, confirming that the well-known A + T bias in insect mitochondrial genes tends to increase from the basal to apical orders. Fiftyseven percent of all nucleotide positions were variable and most of the third codon positions appeared free to vary. Values of genetic distance between congeneric species and between families were remarkably high; in some cases the latter were higher than divergence values between other orders of insects. The remarkably high divergence levels observed here provide evidence that collembolan taxa are quite old; divergence levels among collembolan families equaled or exceeded divergences among pterygote insect orders. Once the saturated thirdcodon positions (which violated stationarity of base frequencies) were removed, the COII sequences contained phylogenetic information, but the extent of that information was overestimated by parsimony methods relative to likelihood methods. In the phylogenetic analysis, consistent statistical support was obtained for the monophyly of all four genera examined, but relationships among genera/families were not well supported. Within the genus Orchesella, relationships were well resolved and agreed with allozyme data. Within the genus Isotomurus, although three pairs of populations were consistently identified, these appeared to have arisen in a burst of evolution from an earlier ancestor. Isotomurus italicus always appeared as basal and I. palustris appeared to harbor a cryptic species, corroborating allozyme data.

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Resolution of the African hominoid trichotomy by use of a mitochondrial gene sequence.

Cited by 189 publications

References 48 publications

Phylogenetic relationships of Malaysian monkeys, Cercopithecidae, based on mitochondrial cytochrome c sequences

Phylogenetic relationships of Malaysian monkeys, Cercopithecidae, based on mitochondrial cytochrome c sequences

Primate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance

Evolution of the Mitochondrial Cytochrome Oxidase II Gene in Collembola

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