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

With regard to sexually-reproducing organisms, several “species concepts” have been advanced (Box 7.1). Most of these entail the perception of conspecific populations as a field for gene recombination—in other words, as an extended reproductive community within which genetic exchange potentially takes place. For example, under the popular “biological species concept” (BSC) championed by Dobzhansky (1937), species are characterized as “groups of actually or potentially interbreeding natural populations which are reproductively isolated from other such groups” (Mayr, 1963). Many authors have expressed sentiments on the BSC similar to those of Ayala (1976b): “among cladogenetic processes, the most decisive one is speciation—the process by which one species splits into two or more .. Species are, therefore, independent evolutionary units. Adaptive changes occurring in an individual or population may be extended to all members of the species by natural selection; they cannot, however, be passed on to different species.” Thus, under the BSC and related concepts, species are perceived as biological and evolutionary entities that are far more meaningful and less arbitrary than other taxonomic categories such as subspecies, genera, or orders (Dobzhansky, 1970). Nonetheless, several complications can attend the application of BSC principles.

Speciation and Hybridization

The musk turtle ( Sternotherus minor ) is common throughout the southeastern United States. In 1955 a morphologically atypical form confined to the Black Warrior River System in Alabama was discov- ered and accorded full species status as S. depressus , the "flattened musk turtle." Questions remain about the taxonomic status and evolutionary history of the flattened musk turtle because (1) the geographic distribu- tion of S. depressus is nested within the range of S. minor ; (2) the flattened shell might be a recently evolved anti-predator adaptation; and (3) reports exist of intergrades between S. depressus and S. minor . We gener- ated and employed sequence data from mitochondrial DNA to address the phylogenetic distinctiveness and phylogeographic position of S. depressus relative to all other musk and mud turtles (Kinosternidae) in North America. The flattened musk turtle forms a well-supported monophyletic group separate from S. minor . Ge- netic divergence observed between S. depressus and geographic populations of S. minor is no less than that distinguishing many kinosternid congeners from one another. These molecular genetic findings bolster ratio- nale for the taxonomic recognition of S. depressus and, hence, for special efforts to protect this federally threatened species.

/pdf/phylogenetic-distinctiveness-of-a-threatened-aquatic-turtle-5fqkq5xcfm.pdf

Phylogenetic Distinctiveness of a Threatened Aquatic Turtle (Ster nother us depressus)

Allelic heterogeneity within protein electromorphs at three loci was examined in populations of deer mice (Peromyscus maniculatus) collected from five localities across North America. We used a variety of electrophoretic techniques (including several starch and acrylamide conditions, gel-sieving, and isoelectric focusing) plus heat denaturation. Of particular interest was the supernatant glutamate oxalate transaminase system (GOT-1; aspartate aminotransferase-1 of some authors), which under standard electrophoretic conditions had been shown to exhibit basically a two-allele polymorphism throughout the range of maniculatus. The use of all of the above techniques failed to uncover any additional variation for GOT-1 in these populations. Similarly, no new scorable variation was resolved at the essentially monomorphic malate dehydrogenase-1 locus by additional conditions of electrophoresis. In marked contrast to the results for the above two enzymes, the use of multiple conditions of electrophoresis resolved the 8 standard-condition electromorphs of esterase-1 into a total of 23 variants showing strong geographic differentiation in frequency. These 23 electromorphs were further divided into a total of 35 variants by thermal stability studies. However, the allelic nature of all of the thermal stability esterase variants remains to be documented. The results of this study, taken together with the remarkable geographic heterogeneity for this species in ecology, morphology, karyotype and mitochondrial DNA sequence, suggest that some form of balancing selection may be acting to maintain the GOT-1 polymorphism.

https://www.genetics.org/content/genetics/102/2/269.full.pdf

An assessment of "hidden" heterogeneity within electromorphs at three enzyme loci in deer mice.

Although individuals in many fish species move to shallow waters to spawn, the California grunion (Leuresthes tenuis) is almost unique in its constitutive display of synchronous full-emergence beach spawning. During a spawning event, fish ride large waves onshore to spawn on beach land, where their eggs incubate terrestrially. Here, we employ molecular markers to ascertain how this unusual reproductive behavior impacts genetic parentage. We developed and utilized four highly polymorphic microsatellite markers to assess maternal and paternal contributions in a total of 682 progeny from 17 nests of a natural population of L. tenuis. Alleles deduced to be of paternal origin in progeny were used to determine the minimum number of sires per nest and to estimate the true number of sires per nest via Bayesian analysis. We document the following: (a) no instances of multiple maternity for progeny within a nest; (b) a high frequency of nests (88%) with multiple paternity; and (c) an appreciable fraction of nests (18%) in which the estimated number of genetic sires (as many as nine) proved to be greater than the observed number of male attendants, thus implicating occasional extra-group fertilization events. From these and other observations, we also conclude that spawning behavior in grunions may involve site choice but not explicit mate choice. In addition to providing the first analysis of molecular parentage in a beach-spawning fish, we compare our findings to those reported previously for a beach-spawning arthropod, and we discuss the forces that may be maintaining this peculiar reproductive behavior.

/pdf/multiple-paternity-and-extra-group-fertilizations-in-a-knu48yifqb.pdf

Multiple paternity and extra-group fertilizations in a natural population of California grunion (Leuresthes tenuis), a beach-spawning marine fish

Fertilization assurance (Baker's contention) and multilocus coadaptation (Allard's argument) are two distinct hypotheses for the adaptive significance of self-fertilization in hermaphroditic taxa, and both scenarios have been invoked to rationalize isogenicity via incest in various plants and invertebrate animals with predominant selfing. Here we contrast Allard's argument and Baker's contention as applied to the world's only known vertebrate that routinely self-fertilizes. We pay special attention to frequencies of locally most common multilocus genotypes in Floridian populations of the Mangrove Rivulus (Kryptolebias marmoratus). Isogenicity patterns in this fish appear inconsistent with Allard's argument, thus leaving Baker’s contention as the more plausible scenario (a result also supported by natural history information for this species). These results contrast with the isogenicity patterns and conclusions previously drawn from several self-fertilizing plants and invertebrate animal species. Thus, the adaptive significance of selfing apparently varies across hermaphroditic taxa.

/pdf/allard-s-argument-versus-baker-s-contention-for-the-adaptive-1iigpzyqka.pdf

John C. Avise

Papers

Speciation and Hybridization

Phylogenetic Distinctiveness of a Threatened Aquatic Turtle (Ster nother us depressus)

An assessment of "hidden" heterogeneity within electromorphs at three enzyme loci in deer mice.

Multiple paternity and extra-group fertilizations in a natural population of California grunion (Leuresthes tenuis), a beach-spawning marine fish

Allard's argument versus Baker's contention for the adaptive significance of selfing in a hermaphroditic fish