The detection of deleterious selection using ancestors inferred from a phylogenetic history

Abstract

The widespread use of restriction endonucleases and DNA sequencing provides a wealth of data on the genetic structure of natural populations. From such data, detailed phylogenies can be constructed and qualitatively different kinds of mutational and substitutional processes can be studied. A neutral model can be constructed to describe the frequencies of sequence haplotypes according to the haplotypes from which they arose and the types of substitution that distinguish them. One feature of such a model is that it examines the ancestors of various sequences. Deleterious selection against a character has a distinct effect on descendant sequences. Individuals containing many deleterious characters leave few or no descendants because these individuals are quickly eliminated by selection. Hence, such a model lends itself to the study of deleterious selection. It is possible to determine if selection is required by searching for any set of mutation rates that can explain an observed set of data. Simulations of artificial populations without selection suggest that this method seldom indicates selection when none is present. Furthermore, recent recombination events between the sequences do not induce false indications of deleterious selection. The method may, however, require relatively large simple sizes in order to accurately reflect the true nature of populations. The method is often very conservative and may not indicate selection when it is, in fact, present.

A Coalescent Approach to Chloroplast Genome Relationships Within and Between Populations of Pinus Devoniana in Mexico

“…Additionally, Fig. 4 supports the propositions that: 1) the high frequency/older haplotypes will have more mutational connections, that is more low frequency/derived haplotypes associated with them, and 2) singletons, haplotypes represented by a single individual, will tend to be at the ends of mutational branches (Golding 1987;Excoffier and Langaney 1989;Crandall and Templeton 1993).…”

“…One outcome of their work was that the expected rank of alleles by age is equal to the rank by their frequency, or E (rank in age of allele i) = C(n/n) , where n i is the number of individuals of allele (i) in the sample of n individuals, and C is a normalizing constant depending on the number of alleles. Additionally, Golding (1987) observed that older alleles have more mutational connections than younger alleles; Crandall and Templeton (1993) have lent support to these ideas using empirical data from Drosophila and added that mutational connections increase with increasing frequency of haplotypes. Another prediction from coalescent theory supported by Crandall and Templeton (1993) is that the number of mutational connections to a haplotype is proportional to the frequency of the haplotype in the population.…”

“…Since the early 1980s Ewens et al (1981), Donnelly andTavare (1986, 1995), Golding (1987), Templeton et al (1987Templeton et al ( , 1993, Excoffier and Langaney (1989), Crandall and Templeton (1993), and Griffiths and Tavare (1998), among others have developed methodology, insights, and statistical methods that aid in the translation of molecular data into evolutionary insights. These methods allow interpretations of data beyond simple parsimony.…”

Bursts of nonsynonymous substitutions in HIV-1 evolution reveal instances of positive selection at conservative protein sites

“…5-9). Instead, when we approach the leaves of a tree, nonsynonymous substitutions tend to become relatively more common, which is consistent with weak negative selection against a large fraction of nonsynonymous substitutions (18).…”

Evidence on the origin of cassava: Phylogeography of Manihot esculenta

“…This haplotype is positioned as a tip on the gene tree and occurs at a very low frequency (Fig. 3, Table 2), characteristics consistent with a recent evolutionary origin (49,50). Alternatively, this haplotype may be as old as the other cassava haplotypes and may have either gone extinct in the wild subspecies or simply been missed during population sampling.…”