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

We screened 11 populations of American, European, and Icelandic eels (Anguillidae) for allelic variation and genetic divergence at six polymorphic microsatellite loci. Within either of the two recognized Anguilla species in the North Atlantic (rostrata in the Americas, anguilla in Europe), population genetic structure was statistically significant but weak; fully 95% of the total genetic variation was present within geographic locales rather than distributed among them. The two Anguilla species also overlap greatly in allelic frequencies, so the available data proved ineffective for addressing hypotheses about the possible hybrid origins of some Icelandic eels. The overlapping microsatellite profiles contrast with nearly diagnostic species differences documented previously in allozymes and mtDNA. This and similar empirical findings in several other species support theoretical concerns that homoplasy (convergent evolution) in allelic states can compromise the utility of rapidly mutating microsatellite loci for certain types of microevolutionary questions regarding gene flow and species differences.

/pdf/microsatellite-variation-and-differentiation-in-north-qrwdhcez46.pdf

Microsatellite Variation and Differentiation in North Atlantic Eels

The recent application of multilocus protein-electrophoretic techniques to avian taxa has led to a rather surprising generalization: genetic distances between lower taxa of birds are exceptionally small compared to those observed between many other vertebrates of equivalent levels of taxonomic distinction (Smith and Zimmerman, 1976; Barrowclough and Corbin, 1978; Avise et al., 1980a, 1980b, 1980c, 1982; Barrowclough et al., 1981; Yang and Patton, 1981; Patton and Avise, unpubl.; Avise and Aquadro, 1982). For example, species of amphibians currently placed within a given genus are, on average, 11-22 times more divergent than congeneric avian species when assayed by common gel electrophoretic conditions (for a comprehensive review of genetic distances in vertebrates, see Avise and Aquadro, 1982). Genetic distances among fish, mammal and reptile congeners typically fall intermediate to those exhibited by amphibians and birds. This "conservative" pattern of protein evolution is not restricted to passerine birds but has also been observed in anseriforms (waterfowl: Patton and Avise, unpubl.) and procellariiforms (tube-nosed birds: Barrowclough et al., 1981). Evidence also exists for a conservative level of immunological divergence in albumins and transferrins among avian orders (Prager et al., 1974; but see Wilson et al., 1977). Perhaps the most striking example of the apparent protein conservatism in birds involves

Evolutionary genetics of birds. vi. a reexamination of protein divergence using varied electrophoretic conditions.

I recently returned from a Conservation Genetics symposium at which one of the speakers claimed to have caught a speciation event in the act. Earlier in this century, tiger beetles (Cicindela dorsalis) were distributed more or less continuously along the eastern coast of the U.S., but shoreline development extirpated populations in the mid-Atlantic states, causing a range disjunction between still-extant populations in New England and the southern states. By analyzing DNA sequences in living and museum-preserved specimens, small but detectable nucleotide differences were uncovered between these two extant populations, a distinction not formerly possible because mid-Atlantic populations had been polymorphic for the sequences in question. Under one version of the phylogenetic species concept (PSC), a new species had arisen precisely when the polymorphism became a fixed difference (in this case, via the extinction of intermediate demes). If this speaker’s PSC-based conclusion about species formation is to be taken seriously, and generalized, conservation biologists might naively rejoice. In the coming decades, as natural populations of many species are extirpated or reduced to small inbred units, intraspecific polymorphisms increasingly will be converted to fixed allelic differences between allopatric demes. Under PSC logic, by definition this will result in a great proliferation of new species. Thus, we may look forward to a twenty-first century in which the rate of species origin (via fixation of genetic variants) may outpace the rate at which currently recognized taxonomic species are driven to extinction. What most biologists had feared as a deepening valley in species numbers may instead soon become a numerical peak in taxonomic species richness!

Cladists in wonderland1

Taxonomic assignments are grossly nonstandardized in current biological classifications. For example, some genera such as Drosophila are an order of magnitude older than others such as Pan or Gorilla; and, further more, because of an "apples-versus-oranges" problem, a genus-level (or any other) designation for particular assemblages of fruit flies and primates provides almost no information on whether such disparate groups en compass comparable amounts of phenotypic, genetic, or evolutionary variation. Another aspect of nonstandard ization is that some taxa (e.g., Reptilia) are paraphyletic as traditionally delimited, whereas others (e.g., Aves) are monophyletic. Although it is sometimes proclaimed that taxa afforded the same taxonomic rank should in prin ciple be more or less equivalent by some criterion (Van Valen, 1973; Minelli, 2000), what that universal criterion might be and how to implement it have received scant attention (Dubois, 2005). In principle, a "temporal-banding" strategy (Hennig, 1966; Avise and Johns, 1999) for classification could rem edy this situation by moving taxonomy closer to both of its two ideal functions (Mayr, 1982): to provide a univer sal system for information storage and retrieval and to encapsulate an evolutionary interpretation of biological (Jiversity. For any phylogenetic tree with internal nodes reliably dated (from molecular clocks, biogeographic data, fossils, or other evidence), extant species compris ing any clade would be assigned a taxonomic rank de termined by the temporal window (band) in which the basal node for that clade resides. (Although nodal dates can be notoriously difficult to estimate, rapid progress is being made for many clades thanks especially to the availability of extensive molecular sequence data; e.g., Springer et al, 2003; Moreau et al, 2006.) Because clades in any phylogeny are hierarchically arranged, each re sulting classification would also be hierarchical (as un der traditional Linnaean schemes) but with the added benefit of now being calibrated and standardized by a universal yardstick: evolutionary time. Temporal banding could provide a simple way to equilibrate taxonomic ranks across any extant forms of life. The boundaries of the temporal windows to be associated with each rank are inherently arbitrary. However, once formally ratified by a consensus among systematists, they would thereafter provide an objec tive and universal standard for classifying any group of extant organisms for which a well-dated phylogeny is available. A serious problem with the temporal-banding scheme (as formulated above) is that it would necessitate dra matic rank changes for many taxa. Taxonomic stabil ity is also important in biology (Godfray and Knapp, 2004), so any wholesale taxonomic revision would be counterproductive if it complicated more so than fa cilitated effective communication and information re trieval. Here we suggest a simple and straightforward taxonomic tactic by which the epistemological advan tages of temporal banding could be achieved without abandoning tried-and-comfortable Linnaean ranks and nomenclatures. Although we prefer the retention of rank ing hierarchies in biological classifications, our current proposal could also be implemented in rank-free sys tems such as PhyloCode (see de Queiroz and Gauthier, 1992).

/pdf/time-to-standardize-taxonomies-1jjhyrlugi.pdf

Time to Standardize Taxonomies

Computer simulations are developed and employed to examine the expected temporal distributions of nodes under a null model of stochastic lineage bifurcation and extinction. These Markovian models of phylogenetic process were constructed so as to permit direct comparisons against empirical phylogenetic trees generated from molecular or other information available solely from extant species. For replicate simulated phylads with n extant species, cumulative distribution functions (cdf's) of branching times were calculated, and compared (using the Kolmogorov-Smirnov test statistic D) to those from three published empirical trees. Molecular phylogenies for columbine plants and avian cranes showed statistically significant departures from the null expectations, in directions indicating recent and ancient species' radiations, respectively, whereas a molecular phylogeny for the Drosophila virilis species group showed no apparent historical clustering of branching events. Effects of outgroup choice and phylogenetic frame of reference were investigated for the columbines and found to have a predictable influence on the types of conclusions to be drawn from such analyses. To enable other investigators to statistically test for nonrandomness in temporal cladogenetic pattern in empirical trees generated from data on extant species, we present tables of mean cdf's and associated probabilities under the null model for expected branching times in phylads of varying size. The approaches developed in this report complement and extend those of other recent methods for employing null models to assess the statistical significance of pattern in evolutionary trees.

/pdf/recognizing-the-forest-for-the-trees-testing-temporal-3vrben0i6o.pdf

John C. Avise

Papers

Microsatellite Variation and Differentiation in North Atlantic Eels

Evolutionary genetics of birds. vi. a reexamination of protein divergence using varied electrophoretic conditions.

Cladists in wonderland1

Time to Standardize Taxonomies

Recognizing the forest for the trees: testing temporal patterns of cladogenesis using a null model of stochastic diversification.