Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

Hasegawa, Masami; Kishino, Hirohisa; Yano, Taka-aki

doi:10.1007/bf02101694

Cited by 7,946 publications

(5,678 citation statements)

References 81 publications

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“…The best substitution model achieved by jModelTest2 was HKY + invariable sites. The HKY is a nucleotide substitution model that assumes every base has a different equilibrium base frequency and that transitions and transversions evolve at different rates (Hasegawa, Kishino, & Yano, 1985). We then reconstructed historical population‐size dynamics using the Bayesian coalescent skyline plot method (Drummond, Rambaut, Shapiro, & Pybus, 2005) as implemented in Beast v.1.8.2 (Drummond, Suchard, Xie, & Rambaut, 2012).…”

Section: Methodsmentioning

confidence: 99%

Genetic diversity and spatial structure of the Rufous‐throated Antbird (Gymnopithys rufigula), an Amazonian obligate army‐ant follower

Menger

Henle

Magnusson

et al. 2017

Ecology and Evolution

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Amazonian understory antbirds are thought to be relatively sedentary and to have limited dispersal ability; they avoid crossing forest gaps, and even narrow roads through a forest may limit their territories. However, most evidence for sedentariness in antbirds comes from field observations and plot‐based recapture of adult individuals, which do not provide evidence for lack of genetic dispersal, as this often occurs through juveniles. In this study, we used microsatellite markers and mitochondrial control‐region sequences to investigate contemporary and infer historical patterns of genetic diversity and structure of the Rufous‐throated Antbird (Gymnopithys rufigula) within and between two large reserves in central Amazonia. Analyses based on microsatellites suggested two genetically distinct populations and asymmetrical gene flow between them. Within a population, we found a lack of genetic spatial autocorrelation, suggesting that genotypes are randomly distributed and that G. rufigula may disperse longer distances than expected for antbirds. Analyses based on mitochondrial sequences did not recover two clear genetic clusters corresponding to the two reserves and indicated the whole population of the Rufous‐throated Antbird in the region has been expanding over the last 50,000 years. Historical migration rates were low and symmetrical between the two reserves, but we found evidence for a recent unilateral increase in gene flow. Recent differentiation between individuals of the two reserves and a unilateral increase in gene flow suggest that recent urban expansion and habitat loss may be driving changes and threatening populations of Rufous‐throated Antbird in central Amazonia. As ecological traits and behavioral characteristics affect patterns of gene flow, comparative studies of other species with different behavior and ecological requirements will be necessary to better understand patterns of genetic dispersal and effects of urban expansion on Amazonian understory antbirds.

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Section: Methodsmentioning

confidence: 99%

Genetic diversity and spatial structure of the Rufous‐throated Antbird (Gymnopithys rufigula), an Amazonian obligate army‐ant follower

Menger

Henle

Magnusson

et al. 2017

Ecology and Evolution

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“…Conditions under which recoding of nucleotides are possible for the K2P [45] and HKY [46] models are given in Table 3.2 of [32]. …”

Section: Methodsmentioning

confidence: 99%

Statistical tests to identify appropriate types of nucleotide sequence recoding in molecular phylogenetics

et al. 2014

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BackgroundUnder a Markov model of evolution, recoding, or lumping, of the four nucleotides into fewer groups may permit analysis under simpler conditions but may unfortunately yield misleading results unless the evolutionary process of the recoded groups remains Markovian. If a Markov process is lumpable, then the evolutionary process of the recoded groups is Markovian.ResultsWe consider stationary, reversible, and homogeneous Markov processes on two taxa and compare three tests for lumpability: one using an ad hoc test statistic, which is based on an index that is evaluated using a bootstrap approximation of its distribution; one that is based on a test proposed specifically for Markov chains; and one using a likelihood-ratio test. We show that the likelihood-ratio test is more powerful than the index test, which is more powerful than that based on the Markov chain test statistic. We also show that for stationary processes on binary trees with more than two taxa, the tests can be applied to all pairs. Finally, we show that if the process is lumpable, then estimates obtained under the recoded model agree with estimates obtained under the original model, whereas, if the process is not lumpable, then these estimates can differ substantially. We apply the new likelihood-ratio test for lumpability to two primate data sets, one with a mitochondrial origin and one with a nuclear origin.ConclusionsRecoding may result in biased phylogenetic estimates because the original evolutionary process is not lumpable. Accordingly, testing for lumpability should be done prior to phylogenetic analysis of recoded data.

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“…The Bayesian inference utilized Markov Chain Monte Carlo (MCMC) simulations in combination with the best Model (HKY+G) [38] in MODELTEST 3.7 [39]). Four chains were set to run simultaneously for 1,000,000 generations during the MCMC process, with trees being sampled every 100 generations.…”

Section: Methodsmentioning

confidence: 99%

Analysis of vkorc1 polymorphisms in Norway rats using the roof rat as outgroup

et al. 2010

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BackgroundCertain mutations in the vitamin K epoxide reductase subcomponent 1 gene (vkorc1) mediate rodent resistance to warfarin and other anticoagulants. Testing for resistance often involves analysis of the vkorc1. However, a genetic test for the roof rat (Rattus rattus) has yet to be developed. Moreover, an available roof rat vkorc1 sequence would enable species identification based on vkorc1 sequence and the evaluation of natural selection on particular vkorc1 polymorphisms in the Norway rat (R. norvegicus).ResultsWe report the coding sequence, introns and 5' and 3' termini for the vkorc1 gene of roof rats (R. r. alexandrinus and R. r. frugivorus) from Uganda, Africa. Newly designed PCR primers now enable genetic testing of the roof rat and Norway rat. Only synonymous and noncoding polymorphisms were found in roof rats from Uganda. Both nominal subspecies of roof rats were indistinguishable from each other but were distinct from R. losea and R. flavipectus; however, the roof rat also shares at least three coding sequence polymorphisms with R. losea and R. flavipectus. Many of recently published vkorc1 synonymous and non-synonymous single nucleotide polymorphisms (SNPs) in Norway rats are likely SNPs from roof rats and/or other Rattus species. Tests applied to presumably genuine Norway rat vkorc1 SNPs are consistent with a role for selection in two populations carrying the derived Phe63Cys and Tyr139Cys mutations.ConclusionGeographic mapping of vkorc1 SNPs in roof rats should be facilitated by our report. Our assay should be applicable to most species of Rattus, which are intermediate in genetic distance from roof and Norway rats. Vkorc1-mediated resistance due to non-synonymous coding SNPs is not segregating in roof rats from Uganda. By using the roof rat sequence as a reference vkorc1, SNPs now can be assigned to the correct rat species with more confidence. Sampling designs and genotyping strategies employed so far have helped detect candidate mutations underlying vkorc1-mediated resistance, but generally provided unsuitable data to test for selection. We propose that our understanding of vkorc1-mediated evolution of resistance in rodents would benefit from the adoption of sampling and genotyping designs that enable tests for selection on vkorc1.

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Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

Cited by 7,946 publications

References 81 publications

Genetic diversity and spatial structure of the Rufous‐throated Antbird (Gymnopithys rufigula), an Amazonian obligate army‐ant follower

Genetic diversity and spatial structure of the Rufous‐throated Antbird (Gymnopithys rufigula), an Amazonian obligate army‐ant follower

Statistical tests to identify appropriate types of nucleotide sequence recoding in molecular phylogenetics

Analysis of vkorc1 polymorphisms in Norway rats using the roof rat as outgroup

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