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

By Masami Hasegawa, Hirohisa Kishino, T. Yano. Journal of Molecular Evolution, 2005

7,433 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/27e5725be7e538f2329011e44481b68f4315f39e

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

1. Ziheng Yang
2. Alexei J. Drummond
3. Remco R. Bouckaert
4. Andrew Rambaut
5. Marc A. Suchard
6. John P. Huelsenbeck
7. Sudhir Kumar
8. Koichiro Tamura

In Molecular Biology

1. Ziheng Yang
2. Alexei J. Drummond
3. Remco R. Bouckaert
4. John P. Huelsenbeck
5. Sudhir Kumar
6. Alexandros Stamatakis
7. Koichiro Tamura
8. David Posada

In Paleontology

1. Alexei J. Drummond
2. Ziheng Yang
3. John P. Huelsenbeck
4. Remco R. Bouckaert
5. Andrew Rambaut
6. John J. Wiens
7. Marc A. Suchard
8. David Posada

Citations in the corpus

• Bayesian Phylogeography Finds Its Roots (2009, methodology): “explore these genes individually, as well as concatenated together, through a strictly parsimony-based ancestral reconstruction method. Our Bayesian approach builds upon stochastic models and naturally affords quantification of uncertainty in both the ancestral state reconstructions and the underlyi”
• Distribution and intensity of constraint in mammalian genomic sequence. (2005, methodology): “We used the HKY85 (Hasegawa et al. 1985) model of nucleotide evolution (alternative realistic models have negligible impacts on the results) and the topology described in Figure 1B.”
• Molecular Phylogeny of Aristolochia sensu lato (Aristolochiaceae) based on Sequences of rbcL, matK, and phyA Genes, with Special Reference to Differentiation of Chromosome Numbers (2006, methodology): “In the ML analysis, the Hasegawa-Kishino-Yano model (Hasegawa et al. 1985) with a gamma distribution (the HKY G model) was selected as the best fitting model for the phyA sequence data, and the best likelihood score for the obtained ML tree was ln 4226.05120.”
• Molecular Evidence for the Major Clades of Placental Mammals (2001, methodology): “Seq-Gen settings corresponding to the above were as follows (where −mhky specifies the HKY85 model of sequence evolution, − t refers to the transition/ transversion ratio, −n equals the number of simulated data sets, − l is the length setting for each simulated data set, and − f is the specified nuc”
• Bayesian analysis of elapsed times in continuous‐time Markov chains (2008, background): “For richer infinitesimal rate matrix parameterization, the most popular CTMC for nucleotides is arguably the HKY85 (Hasegawa et al., 1985) model.”
• ACARYOCHLORIS MARINA GEN. ET SP. NOV. (CYANOBACTERIA), AN OXYGENIC PHOTOSYNTHETIC PROKARYOTE CONTAINING CHL D AS A MAJOR PIGMENT 1 (2003, background): “Unicellular cyanobacteria dispersed independently at least into five subgroups, Gloeobacter, thermo-philic Synechococcus, Phormidium 2, Synechococcus, and Synechocystis/Pleurocapsa/Microcystis (Honda et al. 1999).”
• Efficient approximations for learning phylogenetic HMM models from data (2004, methodology): “2% shorter than those estimated using PAML (Yang, 1997) with single-site models HKY (Hasegawa et al., 1985) and UNR (Yang, 1994) on the whole dataset.”
• Molecular phylogenetic analyses of the Japanese Ulva and Enteromorpha (Ulvales, Ulvophyceae), with special reference to the free‐floating Ulva (2003, methodology): “The models used were JC (Jukes & Cantor 1969), F81 (Felsenstein 1981), KP2 Kimura-2-parameter (Kimura 1980), HKY (Hasegawa et al. 1985), and GTR general time reversible model (Lanave et al. 1984).”
• mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters (2013, neutral): “We make the simplifying assumption that mutations*To whom correspondence should be addressed.”
• A random effects branch-site model for detecting episodic diversifying selection. (2011, methodology): “1A ) using the codon substitutionmodel definedabove, withequal codon equilibriumfrequencies (π = 1/61) and the HKY85 (Hasegawa et al. 1985) nucleotide substitution biases (i.”
• Genetic conspecificity of the worldwide populations of Didemnum vexillum Kott, 2002. (2009, methodology): “Two nucleotide substitution models were used based on the results of modeltest (Posada and Crandall 1998): HKY85 (Hasegawa et al. 1985) and GTR (e.g. Lanave et al. 1984).”
• Isolation and introgression in the Intermountain West: contrasting gene genealogies reveal the complex biogeographic history of the American pika (Ochotona princeps) (2010, methodology): “The final MGF and PRKCI datasets included two sequences per individual, whether they were heterozygous or homozygous, to allow for proper estimates of allele frequencies.”
• Real-time, portable genome sequencing for Ebola surveillance (2016, background): “England, Porton Down, Wiltshire SP4 0JG, UK (12)Friedrich-Loeffler-Institute, Greifswald, Germany (13)Spiez Laboratory, Spiez, Switzerland (14)Janssen-Cilag, Stockholm, Sweden (15)Public Health Agency of Canada, Winnipeg, Canada (16)Institut Pasteur Dakar, Dakar, Senegal (17)Laboratoire de Fièvres H”
• Phylogeny of subtribe Pyrinae (formerly the Maloideae, Rosaceae): Limited resolution of a complex evolutionary history (2007, neutral): “The ‘‘HKY’’ ( Hasegawa et al. 1985 ) model calls for different rates of transitions and transversions.”
• Inferring Evolutionary Trees with PAUP* (2003, methodology): “Further refine the model. lscores 1/nst=2 tratio=estimate basefreq=estimate rates=gamma shape=estimate; The model specified in this iteration of the lscores command is generally referred to as the HKY + Γ model (Hasegawa et al., 1985; Yang, 1994b).”