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J Felsenstein

Publications and source records attributed to J Felsenstein.

At least 37 records · Page 2Linked to original sources
PubMed1990

A maximum likelihood approach to the detection of selection from a phylogeny.

A large amount of information is contained within the phylogenetic relationships between species. In addition to their branching patterns it is also possible to examine other aspects of the biology of the species. The influence that deleterious selection might have is determined here. The likelihood of different phylogenies in the presence of selection is explored to determine the properties of such a likelihood surface. The calculation of likelihoods for a phylogeny in the presence and absence of selection, permits the application of a likelihood ratio test to search for selection. It is shown that even a single selected site can have a strong effect on the likelihood. The method is illustrated with an example from Drosophila melanogaster and suggests that deleterious selection may be acting on transposable elements.

Animals↗
PubMed1987

Estimation of hominoid phylogeny from a DNA hybridization data set.

Analysis of the expanded data set of Sibley and Ahlquist (1987) on primate phylogeny using a maximum likelihood mixed model analysis of variance method shows that there is significant evidence for resolving the Homo-Pan-Gorilla trifurcation in favor of a Homo-Pan clade. The resulting tree is close to that estimated by Sibley and Ahlquist (1984). The mixed model can be used to test a number of hypotheses about the existence of components of variance and the linearity of the relationship between branch length and expected distance. No evidence is found that there is a variance component for extract, or for the individual from which the extract was taken. A variance component for experiment does seem to exist, presumably arising as a result of error of measurement of the common standard from which all values in the same experiment were subtracted. There is significant evidence that the relationship between total branch length between species and their expected distances is nonlinear, or else that the measurement error on larger distances is greater than on smaller ones. Allowing for the nonlinearity might cause one to infer the time of distant common ancestors as less remote than the measured hybridization values would imply if used directly.

Analysis of Variance↗
PubMed1982

An efficient method for matching nucleic acid sequences.

A method of computing the fraction of matches between two nucleic acid sequences at all possible alignments is described. It makes use of the Fast Fourier Transform. It should be particularly efficient for very long sequences, achieving its result in a number of operations proportional to n ln n, where n is the length of the longer of the two sequences. Though the objective achieved is of limited interest, this method will complement algorithms for efficiently finding the longest matching parts of two sequences, and is faster than existing algorithms for finding matches allowing deletions and insertions. A variety of economies can be achieved by this Fast Fourier Transform technique in matching multiple sequences, looking for complementarity rather than identity, and matching the same sequences both in forward and reversed orientations.

Base Sequence↗
PubMed1981

A continuous migration model with stable demography.

A probability model of a population undergoing migration, mutation, and mating in a geographic continuum R is constructed, and an integro-differential equation is derived for the probability of genetic identity. The equation is solved in one case, and asymptotic analysis done in others. Individuals at x, y epsilon R in the model mate with probability V(x, y) dt in any time interval (t, t + dt). In two dimensions, if V(x, y) = V(x - y) where V(x) approximately V(x/beta)/beta2 approaches a delta function, the equilibrium probability of identity vanishes as beta Leads to 0. The asymptotic rate at which this occurs is discussed for mutation rates u = u0 Greater than 0 and for beta approximately cua, alpha Greater than 0, and u Leads to 0.

Animals↗
PubMed1981

Evolutionary trees from DNA sequences: a maximum likelihood approach.

The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests, and gives rough indication of the error of ;the estimate of the tree.

Base Sequence↗
PubMed1979

Isolation by distance: reply to Lalouel and Morton.

Lalouel's assertion that I misinterpreted Malécot's work on isolation by distance may or may not be correct. If so, my assertions of error in Malécot's derivation are wrong, although they do apply to others who have used models involving a spatial continuum. Lalouel's other claims of error in my derivations of the consequences of a spatially continuous model of population reproduction and migration are incorrect, with the exception of one isolated misprint.

Genetics, Population↗
PubMed1978

A model of kin selection for an altruistic trait considered as a quantitative character.

Conditions for natural selection to favor increase of a quantitative character are derived for a model in which individuals associate in groups of size n. It is assumed that the logarithm of the fitness of an individual is the sum of two parts, one proportional to the individual's own phenotype, and the other to the mean phenotype in its group. The resulting conditions for the trait to increase under natural selection are analogous to the results found previously in single-locus kin selection models.

Altruism↗
PubMed1976

The evolutionary advantage of recombination. II. Individual selection for recombination.

Based on the FISHER-MULLER theory of the evolution of recombination, an argument can be constructed predicting that a recessive allele favoring recombination will be favored, if there are either favorable or deleterious mutants occurring at other loci. In this case there is no clear distinction between individual and group selection. Computer simulation of populations segregating for recessive or dominant recombination alleles showed selection favoring recombination, except in the case of a dominant recombination allele with deleterious background mutants. The relationship of this work to parallel investigations by WILLIAMS and by STROBECK, MAYNARD SMITH, and CHARLESWORTH is explored. All seem to rely on the same phenomenon. There seems no reason to assume that the evolution of recombination must have occurred by group selection.

Alleles↗
PubMed1976

The occurrence of new mutants in the X-linked recessive Lesch-Nyhan disease.

In a population at equilibrium for a sex-linked lethal, one-third of the genes for that lethal must arise anew each generation. Therefore, one-third of all cases of Lesch-Nyhan disease, a severe X-linked recessive lethal disorder, should be new mutants. To test this hypothesis, we have collected 47 families, 20 with a single proband and 27 with multiple affected males in which the patients' mothers and other female relatives had been studied for heterozygosity. Available carrier detection tests identify heterozygous for HPRT deficiency in hair roots and skin fibroblasts. Only four mothers were found not to be carriers. This result deviates significantly from expected (P less than .001). Statistical tests for ascertainment effects indicated absence of bias for multiple proband families but strong bias in favor of families with many heterozygous females. When the analysis was limited to single proband families, the deviation from expected was still significant (P less than .01). The incidence of new mutants among the heterozygous mothers, as determined by the ratio of +/+ to +/- maternal grandmothers, should be one-half (see Appendix). Of all 20 maternal grandmothers studied, five were +/+ and 15 were +/- (P less than .05). Considering only the single proband families, the ratio of 5 +/+ to 8 +/- was not significantly different from expected. In four of the five cases in which the heterozygous mother of an affected individual was a new mutation, the age of her parents was considerably higher than the mean parental age in the population. This raises the possibility of a paternal age effect on X-linked mutations. There appears to be a true deficiency of new mutatnts among males but not among females. Data on additional Lesch-Nyhan families are needed before conclusions regarding a possible higher mutation rate in males can be drawn.

Female↗
PubMed1975

Genetic drift in clines which are maintained by migration and natural selection.

Genetic drift will cause a migration-selection cline to wobble about its expected position. A rough linear approximation is developed, valid when local populations are large. This is used to calculate effects of genetic drift on clines in a stepping-stone model with abrupt and with gradual changes of selection coefficients at a single haploid locus. Among the quantities calculated are measures of slope, standardized variation of gene frequencies around their expected values, and correlation among neighboring populations with respect to deviations from the expected gene frequencies. These quantities appear to be primarily functions of Ns and Nm for a given pattern of selection. Computer simulation gives rough confirmation of these results. Standardized variances of gene frequencies and correlation of neighbors differ along the cline in the case of smooth changes in selection. In no case is pathological behavior of gene frequency deviations found near the boundaries of selective regions. Local behavior of gene frequences of nearby colonies is approximately predicted by a simple adaptation of the stepping-stone theory of Kimura and Weiss. Approximate measures of the lateral variation of the midpoint of a cline and the probability of non-monotonicity are also calculated and discussed.

Gene Frequency↗
PubMed1974

The evolutionary advantage of recombination.

The controversy over the evolutionary advantage of recombination initially discovered by Fisher and by Muller is reviewed. Those authors whose models had finite-population effects found an advantage of recombination, and those whose models had infinite populations found none. The advantage of recombination is that it breaks down random linkage disequilibrium generated by genetic drift. Hill and Robertson found that the average effect of this randomly-generated linkage disequilibrium was to cause linked loci to interfere with each other's response to selection, even where there was no gene interaction between the loci. This effect is shown to be identical to the original argument of Fisher and Muller. It also predicts the "ratchet mechanism" discovered by Muller, who pointed out that deleterious mutants would more readily increase in a population without recombination. Computer simulations of substitution of favorable mutants and of the long-term increase of deleterious mutants verified the essential correctness of the original Fisher-Muller argument and the reality of the Muller ratchet mechanism. It is argued that these constitute an intrinsic advantage of recombination capable of accounting for its persistence in the face of selection for tighter linkage between interacting polymorphisms, and possibly capable of accounting for its origin.

Animals↗