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.

Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.

/pdf/biological-identifications-through-dna-barcodes-2m7h08avvi.pdf

Biological identifications through DNA barcodes

So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Human biochemical genetics

Hermaphroditism is a derived and polyphyletic condition in fishes, documented in about 2% of all extant teleost species scattered across more than 20 taxonomic families in 9 orders. It shows a variety of expressions that can be categorized into sequential and synchronous modes. Among the sequential hermaphrodites are protogynous species in which an individual begins reproductive life as a female and later may switch to male, protandrous species in which a fish starts as a male and later may switch to female, and serial bi-directional sex changers. Among the synchronous hermaphrodites (in which an individual can simultaneously produce eggs and sperm) are several outcrossing and one predominantly selfing species. A few species also consist of mixtures of hermaphroditic and single-sex individuals. All of these reproductive categories have been the subject of numerous theoretical and empirical treatments from an evolutionary perspective. Here we highlight some of the major conclusions from these studies, which collectively have been informative on a variety of biological topics related to reproductive modes, gender allocations, sexual conflict and gamesmanship, mating systems, and life-history tradeoffs.

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Evolutionary Perspectives on Hermaphroditism in Fishes

cations 25 . Of the approximately 120 species and 30 genera currently recognized' 3 - 2 5 , about 37 species and 12 genera regularly nest in eastern North America. This study describes electrophoretically assayed protein variation and differentiation in 28 species representing all of these eastern United States genera. One purpose of this study is to elucidate genetic and systematic relationships among wood warblers. However, the major motivation for this report derives from recent observations in several laboratories that protein evolution in birds appears conservative relative to that of many in

Evolutionary genetics of birdsComparative molecular evolution in New World warblers and rodents

Homage to Linnaeus: How Many Parasites? How Many Hosts?

Electrophoretic patterns of phosphoglucose isomerase (PGI) in bony fishes provide strong evidence for a model of genetic control by two independent structural gene loci, most likely resulting from a gene duplication. This model is confirmed by a comparison of certain kinetic and molecular properties of the PGI homodimers (PGI-1 and PGI-2) isolated from extracts of the teleost Astyanax mexicanus. In addition, in most higher teleosts examined, the PGI enzymes show a regular pattern of tissue distribution, with PGI-2 predominant in muscle, the heterodimer often strongest in the heart, and PGI-1 predominant in liver and other organs. An examination of 53 species of bony fishes belonging to 38 families indicates a widespread occurrence of duplicate PGI loci and an early origin of the gene duplication, perhaps in the Leptolepiformes. The apparent presence of three PGI loci in trout and goldfish exemplifies how new loci can be incorporated into the genome through polyploidization.

/pdf/phosphoglucose-isomerase-gene-duplication-in-the-bony-fishes-5dpcgaq974.pdf

Phosphoglucose isomerase gene duplication in the bony fishes: an evolutionary history.

-Surveys of electrophoretic variation in proteins, and restriction site variation in mitochondrial DNA (mtDNA), were conducted to assess the resolving power of these molecular genetic techniques to distinguish four pairs of avian sibling taxa. Samples of rails (Rallus elegans and R. longirostris), dowitchers (Limnodromus scolopaceus and L. griseus), grackles (Quiscalus major and Q. mexicanus), and titmice (Parus bicolor bicolor and P. b. atricristatus) were assayed for allozymes encoded by 34-37 nuclear loci, and for an average of 77 mtDNA restriction sites per individual by 19 endonucleases. MtDNA's of the two rail species showed large-scale size polymorphism and individual heteroplasmy, the first such findings of these molecular features in an avian species. Genetic distances based on allozyme comparisons were small for all assayed taxa (Nei's D c 0.063). The mtDNA assays offered consistently greater resolving power, providing at least five fixed restriction site differences for samples of any taxon pair. The Long-billed and Short-billed dowitchers were especially divergent, differing by at least 24 assayed mtDNA restriction sites and an estimated nucleotide sequence divergence of p = 0.082. We compared these results to previous reports of genetic distances within and among closely related bird species. The mtDNA divergence among dowitchers is near the high end of the scale of such estimates for avian congeners. The mtDNA distances between the pairs of rails (p = 0.006), titmice (p = 0.004), and grackles (p = 0.016) were typical for extremely closely related species, and overlap maximum values reported for some avian conspecifics. Received 13 November 1987, accepted 21 March 1988. VARIOUS laboratory techniques in molecular evolution offer differing resolution of genetic differentiation and phylogeny along a taxonomic hierarchy (Avise 1986a). For example, methods of nuclear DNA/DNA hybridization (Sibley and Ahlquist 1986) or of protein immunology such as microcomplement fixation (Wilson 1985) are usually best applied to higher taxonomic levels, because the observed genetic differences within and between closely related species are typically negligible. Conversely, multilocus protein electrophoresis (Ayala 1976) or restriction enzyme analysis of mitochondrial DNA (mtDNA; Avise 1986b) have proved best suited for phylogenetic comparisons within and among closely related species, because beyond the genus or family level, the maximum genetic distance observable by these techniques typically has been reached (see, however, Lanyon and Zink 1987). By the criterion of focus alone, it should not be claimed that any technique is necessarily "better" than another for systematics purposes. Rather, the situation can be likened to microscopy, where use of different lenses can bring into focus distinct and important aspects of structure at multiple tiers. As a general rule, birds at all taxonomic levels commonly exhibit less genetic divergence than do many of their counterparts in other vertebrate classes (Avise and Aquadro 1982; Barrowclough et al. 1985; Prager et al. 1974). Although this situation has facilitated molecular analysis of major groupings across the class Aves (Prager and Wilson 1980; Sibley and Ahlquist 1983), it has also exacerbated attempts genetically to differentiate and study entities at the lower end of the avian taxonomic scale. For example, many conspecific populations and congeneric avian species appear difficult to distinguish even when assayed by the sensitive and commonly employed protein electrophoretic methodology (e.g. Braun and Robbins 1986; Zink 1986). We characterized genetic divergence in each of 4 pairs of avian sibling "species" with two of the powerful molecular approaches of allozymes and mtDNA analysis. The taxa (Rallus 516 The Auk 105: 516-528. July 1988 This content downloaded from 207.46.13.21 on Tue, 27 Sep 2016 04:45:47 UTC All use subject to http://about.jstor.org/terms July 1988] Genetic Divergence Between Sibling Species 517 elegans and R. longirostris [Rallidae], Limnodromus scolopaceus and L. griseus [Scolopacidae], Quiscalus major and Q. mexicanus [Emberizidae], and Parus bicolor bicolor and P. b. atricristatus [Paridae]) include non passerines as well as passerines, and involve systematically controversial taxonomic pairs that have all been considered conspecific and specifically distinct at one time or another. We were interested in the relative sensitivities of allozyme and mtDNA assay techniques to disclose genetic markers that may distinguish avian sibling species, and what the genetic results reveal about the particular evolutionary histories of the taxa. MATERIALS AND METHODS Specimens were collected in Louisiana and Texas (precise locales available from RMZ on request) during the winter and spring of 1987. Voucher specimens are deposited in the Museum of Zoology, LSU. Allozyme data for titmice were obtained from Braun et al. (1984). For mtDNA analyses, samples of liver, heart, and kidney were immersed in MSB-Ca-EDTA buffer (Lansman et al. 1981), and transported on wet ice to the laboratory within 7 days. For protein electrophoresis, samples of liver and muscle were frozen until time of assay. Protein electrophoresis followed standard protocols (Selander et al. 1971, Johnson et al. 1984). Between 34 and 37 loci were scored for each species pair. Sixteen of these loci are listed in Table 1; the remainder (which proved monomorphic and incapable of discriminating members of any species pair in which they were assayed) are ethanol dehydrogenase (Enzyme Commission number 1.1.1.1), a-glycerophosphate dehydrogenase (1.1.1.8), lactate dehydrogenase-1 and 2 (1.1.1.27), malate dehydrogenases-1 and 2 (1.1.1.37), malic enzyme (1.1.1.40), isocitrate dehydrogenase-2 (1.1.1.42), glutamate dehydrogenase (1.1.1.47), glutathione reductase (1.6.4.2), superoxide dismutase (1.15.1.1), glutamic-pyruvic transaminase2 (2.6.1.2), creatine kinases-1 and 2 (2.7.3.2), acid phosphatases-1 and 2 (3.1.3.2), leucineamino peptidase (3.4.11), fumarate hydratase (4.2.1.2), aconitate hydratase (4.2.1.3), and non-enzymatic proteins-i and 2. Mean observed heterozygosity in each species was calculated from genotypic counts. These counts were also used to determine allele frequencies, from which genetic distances were computed by Nei's (1978) method. MtDNA in closed-circular form was isolated from pooled tissues of each specimen by ultracentrifugation in cesium chloride gradients. Following dialysis, the purified mtDNA was digested by each of 19 restriction endonucleases. Fifteen of these enzymes are listed in Table 2; the remaining 4 (which proved not to distinguish any of the sibling species assayed) are KpnI (recognition site GGTACC), PstI (CTGCAG), SstII (CCGCGG), and XbaI (TCTAGA). MtDNA fragments were end-labeled with 35S-radionuclides, separated by molecular weight through 1.0, 1.2, or 1.8% agarose gels, and revealed by autoradiography as bands in gel profiles (Brown 1980; Lansman et al. 1981; Maniatis et al. 1982). Fragment sizes were compared against a 1-kilobase ladder standard purchased from Bethesda Research Labs. MtDNA genetic distances in terms of estimated base substitutions per nucleotide were calculated by the fragment method of Nei and Li (1979), which involves appropriate weighting of distance estimates calculated separately for endonucleases recognizing 4-, 5-, and 6-base sites. Many of the mtDNA fragment profile differences between sibling taxa were attributable to gains (or losses, depending on which state was ancestral) of single restriction sites. Such instances are recognized when two digestion profiles (A and B) are identical at all except three fragments, and in which the sum of the molecular weights of the two unique fragments in A equals the weight of the third unique fragment in B (for a detailed description of the gel scoring procedure, see Fig. 2 in Avise et al. 1987). Thus, although sites were not formally mapped in this study, we were often able to interpret gel patterns with respect to restriction site as well as restriction fragment changes. We observed a total of more than 100 distinct fragment profiles. (Avise will gladly supply diagrams of any gel patterns upon request.)

Molecular Genetic Divergence between Avian Sibling Species: King and Clapper Rails, Long-Billed and Short-Billed Dowitchers, Boat-Tailed and Great-Tailed Grackles, and Tufted and Black-Crested Titmice

John C. Avise

Papers

Evolutionary Perspectives on Hermaphroditism in Fishes

Evolutionary genetics of birdsComparative molecular evolution in New World warblers and rodents

Homage to Linnaeus: How Many Parasites? How Many Hosts?

Phosphoglucose isomerase gene duplication in the bony fishes: an evolutionary history.

Molecular Genetic Divergence between Avian Sibling Species: King and Clapper Rails, Long-Billed and Short-Billed Dowitchers, Boat-Tailed and Great-Tailed Grackles, and Tufted and Black-Crested Titmice