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.

Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Integrative Genomics Viewer

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

As debate continues over how courts should handle expert testimony, judges might do well to consider what makes science scientific

Sequence variation among 10 alleles of the alcohol dehydrogenase (Adh) gene of the Hawaiian drosophilid D. mimica was analyzed with reference to the evolutionary history of the Hawaiian subgroup as well as to levels and patterns of polymorphism of the Adh gene in continental drosophilid species. The Adh gene of D. mimica is less polymorphic than that of other drosophilid species, and no replacement substitutions were found. Statistical analyses of the Adh alleles suggested the action of balancing selection and revealed significant linkage disequilibrium among three of the variable sites. The effective population size was estimated to be only slightly smaller than that of continental species and, surprisingly, on the same order of magnitude as the actual size.

Molecular Population Genetics of the Alcohol Hawaiian Drosophilid D. mimica

Sexual Selection and Mating Systems

The theory of biological evolution is the central organizing principle of modern biology. In 1973, the eminent evolutionist Theodosius Dobzhansky famously asserted that “Nothing in biology makes sense except in the light of evolution.” Evolution provides a scientific explanation for why there are so many different kinds of organisms on Earth and gives an account of their similarities and differences (morphological, physiological, and genetic). Science has demonstrated again and again, beyond reasonable doubt, that living organisms evolve and diversify over time, and that their features have come about by natural selection, a process that accounts for their design. Yet, there are many people of faith in the United States and elsewhere who think that science, particularly the theory of evolution, is contrary to the teachings of the Bible and to religious beliefs, such as creation by God. Well before the formulation of the theory of evolution, religious authors over the centuries used the “argument-from-design” to demonstrate rationally, without reference to faith or divine revelation, the existence of God, as the author of the design of organisms. The argument from design has two parts. In one familiar form it asserts, first, that organisms evince to have been designed; second, that only God could account for the design. The argument from design was advanced, in a variety of forms, in Classical Greece and early Christianity. Its most extensive formulation is due to William Paley in his Natural Theology (Natural theology, or evidences of the existence and attributes of the deity collected from the appearances of nature. American Tract Society, New York, 1802). The eye—as well as all sorts of organs, organisms, and their interactions—manifests to be the outcome of design and not of chance, thus it shows to have been created by God. In the 1990s, the design argument was revived in the United States by several authors. The flagellum used by bacteria for swimming and the immune system of mammals, as well as some improbability calculations, were advanced as evidence of “intelligent design,” on the grounds that chance processes could not account for the phenomena to be explained. In The Origin of Species, Darwin (On the origin of species by means of natural selection. John Murray, London, 1859) advanced a scientific explanation of the design of organisms. The adaptations of organisms are outcomes not of chance, but of a process that, over time, causes the gradual accumulation of features beneficial to organisms, whenever these features increase the organisms’ chances of surviving and reproducing. There is design in the living world: eyes are designed for seeing, wings for flying, and kidneys for regulating the composition of the blood. The design of organisms comes about not by intelligent design, but by a natural process, which is creative through the interaction of chance and necessity. Organisms are pervaded by imperfections, dysfunctions, cruelties, and even sadism. The theory of evolution accounts for these mishaps by natural selection, as outcomes of natural processes, so that they need not be attributed to God’s explicit design. The theory of evolution perceived by some people of faith as contrary to religion, may thus be acknowledged as their “disguised friend.” The theory of evolution accounts for the design of organisms, but also for the dysfunctions, oddities, cruelty, and sadism that pervade the world of life, so that these deficiencies need not be attributed to specific agency by the Creator, which might implicitly amount to blasphemy. The foregoing considerations are important both for understanding and for accepting evolution as a fact of life, and should be taken into account by science educators and teachers.

Biology and Religion: The Case for Evolution

The complete mitochondrial genomes were sequenced in two individuals of blunt-snouted lenok Brachymystax tumensis. The sizes of the genomes in the two isolates were 16,754 and 16,836; the difference was due to variable number of repeat sequences within the control region. The gene arrangement, base composition, and size of the two sequenced genomes are very similar to the B. lenok and B. lenok tsinlingensis genomes previously published (JQ686730 and JQ686731). However, the level of divergence inferred from 12 protein-coding genes (3.48%) indicated clear species boundaries between the lenok species.

/pdf/complete-mitochondrial-genome-of-blunt-snouted-lenok-ckygpyk0m8.pdf

Complete mitochondrial genome of blunt-snouted lenok Brachymystax tumensis (Salmoniformes, Salmonidae)

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