This journal frequently contains papers that report values of F-statistics estimated from genetic data collected from several populations. These parameters, FST, FIT, and FIS, were introduced by Wright (1951), and offer a convenient means of summarizing population structure. While there is some disagreement about the interpretation of the quantities, there is considerably more disagreement on the method of evaluating them. Different authors make different assumptions about sample sizes or numbers of populations and handle the difficulties of multiple alleles and unequal sample sizes in different ways. Wright himself, for example, did not consider the effects of finite sample size. The purpose of this discussion is to offer some unity to various estimation formulae and to point out that correlations of genes in structured populations, with which F-statistics are concerned, are expressed very conveniently with a set of parameters treated by Cockerham (1 969, 1973). We start with the parameters and construct appropriate estimators for them, rather than beginning the discussion with various data functions. The extension of Cockerham's work to multiple alleles and loci will be made explicit, and the use of jackknife procedures for estimating variances will be advocated. All of this may be regarded as an extension of a recent treatment of estimating the coancestry coefficient to serve as a mea-

https://www.jstor.org/stable/pdfplus/2408641.pdf

Estimating F-statistics for the analysis of population structure.

Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

The Theory of Island Biogeography

Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fortunately, intermediate models employing relaxed molecular clocks have been described. These models open the gate to a new field of “relaxed phylogenetics.” Here we introduce a new approach to performing relaxed phylogenetic analysis. We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times. Our approach also provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies. We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data. In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme. Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments. From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution.

/pdf/relaxed-phylogenetics-and-dating-with-confidence-5ez5tgzy1b.pdf

Relaxed Phylogenetics and Dating with Confidence

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

/pdf/identification-and-analysis-of-functional-elements-in-1-of-2o640l8ikl.pdf

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

George Gaylord Simpson said in his classic Tempo and Mode in Evolution (1) that paleontologists enjoy special advantages over geneticists on two evolutionary topics. One general topic, suggested by the word "tempo," has to do with "evolutionary rates. . ., their acceleration and deceleration, the conditions of exceptionally slow or rapid evolutions, and phenomena suggestive of inertia and momentum." A group of related problems, implied by the word "mode," involves "the study of the way, manner, or pattern of evolution, a study in which tempo is a basic factor, but which embraces considerably more than tempo" (pp. xvii-xviii). Simpson's book was self-consciously written in the wake of Theodosius Dobzhansky's Genetics and the Origin of Species (2). The title of Dobzhansky's book suggested its theme: the role of genetics in explaining "the origin of species"-i.e., a synthesis of Darwin's theory of evolution by natural selection and the maturing science of genetics. In the introduction to his book, Simpson averred that an essential part of his study was an "attempted synthesis of paleontology and genetics," an effort that pervaded the whole book, but was particularly the subject of the first two chapters, which accounted for nearly half the book's pages. Darwin believed that evolutionary change occurs by natural selection of small individual differences appearing every generation within any species. Singly the changes effected by selection are small but, given enough time, great changes can take place. Two of Darwin's most dedicated supporters, Thomas Huxley and Francis Galton, argued instead that evolution occurs by selection of discontinuous variations, or sports; evolution proceeds rapidly by discrete leaps. According to Huxley, if natural selection operates only upon gradual differences among individuals, the gaps between existing species and in the paleontological record could not be explained. For Galton, evolution was not a smooth and uniform process, but proceeded by "jerks," some of which imply considerable organic change. This controversy was continued in the latter part of the nineteenth century by the biometricians Karl Pearson and W. F. R. Weldon, who believed, like Darwin, in the primary importance of common individual differences, and by the geneticist William Bateson, who maintained the primary importance of discontinuous variations. The rediscovery of Mendelian inheritance in 1900 provided what might have been common grounds to resolve the conflict. Instead, the dispute between biometricians and geneticists extended to continental Europe and to the United States. Bateson was the champion of the Mendelians, many of whom accepted the mutation theory proposed by De Vries, and denied that natural selection played a major role in evolution. The biometricians for their part argued that Mendelian characters were sports of little importance to the evolutionary process.

/pdf/tempo-and-mode-in-evolution-4vmduy3ymm.pdf

Tempo and mode in evolution.

We describe allelic variation at 28 gene loci in natural populations of D. willistoni. Seventy samples were studied from localities extending from Mexico and Florida, through Central America, the West Indies, and tropical South America, down to South Brazil. At least several hundred, and often several thousand, genomes were sampled for each locus. We have discovered a great deal of genetic variation. On the average, 58% loci are polymorphic in a given population. (A locus is considered polymorphic when the frequency of the most common allele is no greater than 0.95). An individual fly is heterozygous, on the average, at 18.4% loci.—Concerning the pattern of the variation, the most remarkable finding is the similarity of the configuration of allelic frequencies from locality to locality throughout the distribution of the species. Our observations support the conclusion that balancing natural selection is the major factor responsible for the considerable genetic variation observed in D. willistoni.

/pdf/enzyme-variability-in-the-drosophila-willistoni-group-iv-1lt5ngx0z9.pdf

Enzyme variability in the drosophila willistoni group. iv. genic variation in natural populations of drosophila willistoni

We propose a general theory of clonal reproduction for parasitic protozoa, which has important medical and biological consequences. Many parasitic protozoa have been assumed to reproduce sexually, because of diploidy and occasional sexuality in the laboratory. However, a population genetic analysis of extensive data on biochemical polymorphisms indicates that the two fundamental consequences of sexual reproduction (i.e., segregation and recombination) are apparently rare or absent in natural populations of the parasitic protozoa. Moreover, the clones recorded appear to be stable over large geographical areas and long periods of time. A clonal population structure demands that the medical attributes of clones be separately characterized; ubiquitous clones call for priority characterization. Uniparental reproduction renders unsatisfactory Linnean taxonomy; this needs to be supplemented by the "natural clone" as an additional taxonomic unit, which is best defined by means of genetic markers.

/pdf/a-clonal-theory-of-parasitic-protozoa-the-population-1wtyzmucnb.pdf

A clonal theory of parasitic protozoa: the population structures of Entamoeba, Giardia, Leishmania, Naegleria, Plasmodium, Trichomonas, and Trypanosoma and their medical and taxonomical consequences

Very precise data on the dynamics of a competitive system of two species of Drosophila have been obtained. By a curvilinear regression approach, analytical models of competition have been fitted. By statistical and biological criteria of simplicity, reality, generality, and accuracy, the best of these models has been chosen. This model represents an extension of the Lotka-Volterra model of competition; it adds a fourth parameter that controls the degree of nonlinearity in intraspecific growth regulation. It represents a similar extension of the logistic model of population growth.

https://www.pnas.org/content/pnas/70/12/3590.full.pdf

Global Models of Growth and Competition

▪ Abstract Pseudogenes have been defined as nonfunctional sequences of genomic DNA originally derived from functional genes. It is therefore assumed that all pseudogene mutations are selectively neutral and have equal probability to become fixed in the population. Rather, pseudogenes that have been suitably investigated often exhibit functional roles, such as gene expression, gene regulation, generation of genetic (antibody, antigenic, and other) diversity. Pseudogenes are involved in gene conversion or recombination with functional genes. Pseudogenes exhibit evolutionary conservation of gene sequence, reduced nucleotide variability, excess synonymous over nonsynonymous nucleotide polymorphism, and other features that are expected in genes or DNA sequences that have functional roles. We first review the Drosophila literature and then extend the discussion to the various functional features identified in the pseudogenes of other organisms. A pseudogene that has arisen by duplication or retroposition may, a...

https://apologetyka.com/ptkr/groups/ptkrmember/inne/2003/Pseudogenes%20Are%20they%20junk...,%20caly%20tekst%20Balakirev.pdf

Francisco J. Ayala

Papers

Tempo and mode in evolution.

Enzyme variability in the drosophila willistoni group. iv. genic variation in natural populations of drosophila willistoni

A clonal theory of parasitic protozoa: the population structures of Entamoeba, Giardia, Leishmania, Naegleria, Plasmodium, Trichomonas, and Trypanosoma and their medical and taxonomical consequences

Global Models of Growth and Competition

Pseudogenes: are they "junk" or functional DNA?