Mitochondrial 16S rRNA Sequence Diversity of Hominoids

Noda, Reiko; Kim, C. G.; Takenaka, Osamu; Ferrell, Robert E.; Tanoue, Tetsuya; Hayasaka, Ichirô; Ueda, Shigenori; Ishida, Takafumi; Saitou, Naruya

doi:10.1093/jhered/92.6.490

Cited by 24 publications

(16 citation statements)

References 32 publications

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“…They would occasionally substitute to G, as they did in the human lineage, and transiently become G→A hypermutable until state A fixes again. This simple process might partly explain the decrease of polymorphism co-occurrence with species divergence: The mutation rate of a site simply varies when it substitutes from a mu- Noda et al (2001). This site might correspond to a unidirectional G→A hot spot, hypermutable only when in state G. Site 3010, finally, shows state G in four of the five species surveyed by Noda et al (2001) but appears monomorphic in these species.…”

Section: Discussionmentioning

confidence: 99%

Mutation hot spots in mammalian mitochondrial DNA

et al. 2005

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Animal mitochondrial DNA is characterized by a remarkably high level of within-species homoplasy, that is, phylogenetic incongruence between sites of the molecule. Several investigators have invoked recombination to explain it, challenging the dogma of maternal, clonal mitochondrial inheritance in animals. Alternatively, a high level of homoplasy could be explained by the existence of mutation hot spots. By using an exhaustive mammalian data set, we test the hot spot hypothesis by comparing patterns of site-specific polymorphism and divergence in several groups of closely related species, including hominids. We detect significant co-occurrence of synonymous polymorphisms among closely related species in various mammalian groups, and a correlation between the site-specific levels of variability within humans (on one hand) and between Hominoidea species (on the other hand), indicating that mutation hot spots actually exist in mammalian mitochondrial coding regions. The whole data, however, cannot be explained by a simple mutation hot spots model. Rather, we show that the site-specific mutation rate quickly varies in time, so that the same sites are not hypermutable in distinct lineages. This study provides a plausible mutation model that potentially accounts for the peculiar distribution of mitochondrial sequence variation in mammals without the need for invoking recombination. It also gives hints about the proximal causes of mitochondrial site-specific hypermutability in humans.

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Section: Discussionmentioning

confidence: 99%

Mutation hot spots in mammalian mitochondrial DNA

et al. 2005

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“…''There are several competing hypotheses on the phylogenetic relationships of species within subgenus Hylobates y these gibbon species are closely related, hybridization is possible, and this may be the source of incongruent phylogenetic relationships y'' (Noda et al, 2001). Indeed, the expectation of a close evolutionary and genetic relationship between species of Hylobates (i.e.…”

Section: Hominoids/gibbonsmentioning

confidence: 99%

“…For example, an analysis of sequence variation in the mitochondrial 16S rRNA gene resulted in the paraphyletic placement of one individual of H. pileatus, of the subgenus Hylobates, with H. concolor, subgenus Nomascus (Noda et al, 2001). In addition, within the ''monophyletic'' subgenus Hylobates clade, individuals of H. klossii were more closely related to individuals of H. agilis or H. lar than to other gibbons that morphologically resemble H. klossii (Noda et al, 2001). In contrast, Hayashi et al (1995) had previously found a monophyletic relationship of individuals of H. lar and H. klossii.…”

Section: Hominoids/gibbonsmentioning

confidence: 99%

“…In contrast, Hayashi et al (1995) had previously found a monophyletic relationship of individuals of H. lar and H. klossii. This led Noda et al (2001) to the conclusion that hybridization ''y may be the source of incongruent phylogenetic relationships, depending on the individuals used from the same species''.…”

Section: Hominoids/gibbonsmentioning

confidence: 99%

“…In particular, which Hylobates taxa are defined as basal varies between studies (Noda et al, 2001;Roos and Geissmann, 2001), though if the basal lineage divergences were temporally closely associated the genetic signal could be small. In any case, it seems likely that evolution within the gibbons has been profoundly affected by natural hybridization.…”

Section: Hominoids/gibbonsmentioning

confidence: 99%

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Natural hybridization in primates: One evolutionary mechanism

Arnold

Meyer

2006

Zoology

154

138

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The role and importance of natural hybridization in the evolutionary histories of animal taxa is still debated. This results largely from a history of zoological investigations that assumed, rather than documented, a limited evolutionary role for this process. However, it is now becoming apparent that, just as for plants, the creative effects of reticulate evolution are widespread in animal taxa as well. This conclusion is supported by the documentation of numerous instances of the formation of new taxa and the genetic enrichment through introgressive hybridization. In the present review, we use primates as a paradigm for how natural hybridization can affect the evolution of species complexes and remains a footprint on genomes. Findings for a number of groups, including basal (e.g. lemurs) and derived (e.g. Old World apes) lineages, demonstrate that introgression and hybrid speciation have caused a reticulate pattern that is still detectable in the, often mosaic, genomes of primates. For example, results from genetic analyses of our own species demonstrate the process of past introgressive hybridization with the progenitors of our sister taxa (i.e. chimpanzees and gorillas) and most likely also our extinct, close relatives in the hominid lineage.

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Reduced Polymorphism in the Chimpanzee Semen Coagulating Protein, Semenogelin I

Kingan

Tatar

Rand

2003

Journal of Molecular Evolution

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The semen of many primate species coagulates into a mating plug believed to prevent the sperm of subsequent mating events from accessing the ova. The texture of the coagulum varies among species: from a semisoft mass in humans to a firm plug in chimpanzees. In humans, a component of the coagulum, semenogelin I, also inhibits sperm motility. We tested the hypothesis that polymorphism and divergence at semenogelin I differ among hominoid species with different mating systems. Sequence data for the semenogelin I locus were obtained from 12 humans, 10 chimpanzees, 7 gorillas, and 1 bonobo. Mitochondrial D-loop data were collected from a subset of individuals to assess levels of variation at an unlinked locus. HKA tests using D-loop sequence data revealed a significant reduction of polymorphism at semenogelin I in chimpanzees, consistent with predictions of a selective sweep at this locus. This result was supported by independent HKA tests using polymorphism data from a putatively neutral locus from the literature. Humans show a similar trend toward reduced polymorphism, although HKA tests were only marginally significant. Gorilla sequence data show evidence of functional loss at the semenogelin I locus, indicated by stop codons within the putative open reading frame as well as high levels of polymorphism. Elevated Ka/Ks ratios within the Pan-Homo clade suggest a history of positive selection at semenogelin I. Our results suggest that there is a positive relationship between the intensity of sperm competition in a species and the strength of positive Darwinian selection on the seminal protein semenogelin I.

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Mitochondrial 16S rRNA Sequence Diversity of Hominoids

Cited by 24 publications

References 32 publications

Mutation hot spots in mammalian mitochondrial DNA

Mutation hot spots in mammalian mitochondrial DNA

Natural hybridization in primates: One evolutionary mechanism

Reduced Polymorphism in the Chimpanzee Semen Coagulating Protein, Semenogelin I

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