Mutations as missing data: Inferences on the ages and distributions of nonsynonymous and synonymous mutations

Genetics

Volumn 159, Issue 1, 2001, Pages 401-411

  Nielsen, Rasmus ^a  

^a Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

AGE; ANALYTIC METHOD; ARTICLE; DATA ANALYSIS; DNA SEQUENCE; GENE MAPPING; GENE MUTATION; NONHUMAN; PHYLOGENY; POPULATION GENETICS; PRIORITY JOURNAL; RAT; SYSTEM ANALYSIS;

ALGORITHMS; ANIMALS; DNA MUTATIONAL ANALYSIS; EVOLUTION, MOLECULAR; GENES, VIRAL; GENETICS, POPULATION; MARKOV CHAINS; MODELS, GENETIC; MODELS, STATISTICAL; MONTE CARLO METHOD; MUTATION; PHYLOGENY; RATS; SOFTWARE; TIME FACTORS;

EID: 0034804321     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (52)

1. Inference from gene trees in a subdivided population
2. Detecting population expansion and decline using microsatellites
3. Maximum likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach
4. Positive selection on the H3 hemagglutinin gene of human influenza virus A
5. Amazonian phylogeography: mtDNA sequence variation in arboreal echimyid rodents (Caviomorpha)
6. Estimation of branch points from a branching diffusion process
7. Evolutionary trees from DNA sequences: A maximum likelihood approach
8. Estimating effective population size from samples of sequences: A bootstrap Monte Carlo integration method
9. A hidden Markov model approach to variation among sites in rate of evolution
10. Long term trends in the evolution of H(3) HA1 human influenza type A
11. Efficient Metropolis jumping rules
12. Markov chain Monte Carlo likelihood
13. A codon-based model of nucleotide substitution for protein-coding DNA sequences
14. Simulating probability distributions in the coalescent
15. Ancestral inference in population genetics
16. The age of a mutation in a general coalescent tree
17. The ages of mutations in gene trees
18. Monte Carlo sampling methods using Markov chains and their applications
19. A Bayesian framework for the analysis of cospeciation
20. The coalescent
21. On the genealogy of large populations
22. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order of Hominoidea
23. Estimating effective population size and mutation rate from sequence data using METROPOLIS-HASTINGS sampling
24. Maximum likelihood estimation of population growth rates based on the coalescent
25. The simultaneous diversification of South American echimyid rodents (Hystricognathi) based on complete cytochrome b sequences
26. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees
27. The age of a unique event polymorphism
28. Bayesian phylogenetic inference via Markov Chain Monte Carlo methods
29. Equations of state calculations by fast computing machines
30. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to chloroplast genome
31. Estimation of population parameters and recombination rates from single nucleotide polymorphisms (SNPs)
32. The age of nonsynonymous and synonymous mutations in animal mtDNA and implications for the mildly deleterious theory
33. Likelihood analysis of disequilibrium mapping, and related problems
34. Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference
35. Estimating the age of alleles by use of intraallelic variability
36. Reconstructing ancestral character states under Wagner parsimony
37. Some probabilistic and statistical problems on the analysis of DNA sequences
38. Contingency tests of neutrality using intra/interspecific gene trees: The rejection of neutrality for the evolution of the mitochondrial cytochrome oxidase II gene in the hominoid primates
39. Substitution rate variation among sites in hypervariable region-1 of human mitochondrial DNA
40. Substitution-rate variation among sites and the estimation of transition bias
41. Extensive mitochondrial diversity within a single Amerindian tribe
42. On the number of segregating sites in genetical models without recombination
43. Genealogical inference from microsatellite data
44. Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites
45. Likelihood ratio tests for detecting positive selection and application to primate lyzosyme evolution
46. Synonymous and nonsynonymous rate variation is nuclear genes of mammals
47. Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method
48. Codon-substitution models for variable selection pressure at amino acid sites