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

A literature review is conducted on the phy- logenetic discontinuities in mtDNA sequences of 252 taxo- nomic species of vertebrates. About 140 of these species (56%) were subdivided clearly into two or more highly distinctive matrilineal phylogroups, the vast majority of which were localized geographically. However, only a small number (two to six) of salient phylogeographic subdivisions (those that stand out against mean within-group divergences) character- ized individual species. A previous literature summary showed that vertebrate sister species and other congeners also usually have pronounced phylogenetic distinctions in mtDNA se- quence. These observations, taken together, suggest that current taxonomic species often agree reasonably well in number (certainly within an order-of-magnitude) and com- position with biotic entities registered in mtDNA genealogies alone. In other words, mtDNA data and traditional taxonomic assignments tend to converge on what therefore may be ''real'' biotic units in nature. All branches in mtDNA phylogenies are nonanastomose, connected strictly via historical genealogy. Thus, patterns of historical phylogenetic connection may be at least as important as contemporary reproductive relation- ships per se in accounting for microevolutionary unities and discontinuities in sexually reproducing vertebrates. Findings are discussed in the context of the biological and phylogenetic species concepts.

Species realities and numbers in sexual vertebrates: Perspectives from an asexually transmitted genome (speciationyphylogenyysister speciesycomparative molecular evolutionyphylogeography)

Species Invasions and Extinction: The Future of Native Biodiversity on Islands

▪ Abstract Geographic patterns in mtDNA variation are compiled for 22 species of freshwater and terrestrial turtles in the southeastern United States, and the results are employed to evaluate phylogeographic hypotheses and principles of genealogical concordance derived previously from similar analyses of other vertebrates in the region. The comparative molecular findings are interpreted in the context of intraspecific systematics for these taxa, the historical geology of the area, traditional nonmolecular zoogeographic information, and conservation significance. A considerable degree of phylogeographic concordance is registered with respect to (a) the configuration of intraspecific mtDNA subdivisions across turtle species, (b) the principal molecular partitions and traditional morphology-based taxonomic boundaries, (c) genetic patterns in turtles versus those described previously for freshwater fishes and terrestrial vertebrates in the region, and (d) intraspecific molecular subdivisions versus the bounda...

/pdf/principles-of-phylogeography-as-illustrated-by-freshwater-2yc9p4ghmy.pdf

Principles of phylogeography as illustrated by freshwater and terrestrial turtles in the southeastern united states

With respect to conveying useful comparative information, current biological classifications are seriously flawed because they fail to (i) standardize criteria for taxonomic ranking and (ii) equilibrate assignments of taxonomic rank across disparate kinds of organisms. In principle, these problems could be rectified by adopting a universal taxonomic yardstick based on absolute dates of the nodes in evolutionary trees. By using procedures of temporal banding described herein, a simple philosophy of biological classification is proposed that would retain a manageable number of categorical ranks yet apply them in standardized fashion to time-dated phylogenies. The phylogenetic knowledge required for a time-standardized nomenclature arguably may emerge in the foreseeable future from vast increases in multilocus DNA sequence information (coupled with continued attention to phylogeny estimation from traditional systematic data). By someday encapsulating time-dated phylogenies in a familiar yet modified hierarchical ranking scheme, a temporal-banding approach would improve the comparative information content of biological classifications.

/pdf/proposal-for-a-standardized-temporal-scheme-of-biological-4z12p6u95v.pdf

Proposal for a standardized temporal scheme of biological classification for extant species

To assess population genetic structure and evolutionary relationships among nesting populations of loggerhead turtles (Caretta caretta), we analyzed mitochondrial (mt) DNA variation in 113 samples from four nesting beaches in the northwestern Atlantic Ocean and from one nesting beach in the Mediterranean Sea Significant differences in haplotype frequency between nesting populations in Florida and in Georgia/South Carolina, and between both of these assemblages and the Mediterranean nesting colony, indicate substantial restrictions on contemporary gene flow between regional populations, and therefore a strong tendency for natal homing by females Nonetheless, this regional genetic structure appears shallow, indicating recent evolutionary connections among rookeries Data from tag returns and mtDNA, as well as geological considerations, suggest that over short evolutionary time scales (perhaps a few thousand years), dispersal by female loggerheads is sufficient to allow colonization of appropriate habitat in proximity to established rookeries but is too low to significantly affect the population dynamics of rookeries on a contemporary time scale These data indicate that nesting populations of the loggerhead turtle must be managed as demographically independent units The population subdivisions based on mtDNA analyses are concordant with previously reported distinctions between Florida and Georgia/South Carolina nesting populations based on environmental markers, tag recaptures, and morphology



Resumen: Con el proposito de evaluar la estructura genetica de las poblaciones y las relaciones evolutivas entre poblaciones anidadoras de la tortuga caguama (Caretta caretta), analizamos la variacion en el ADN mitocondrial (ADNmt) de 113 muestras provenientes de cuatro playas de anidacion en el Oceano Atlantico noroccidental y de una en el Mar Mediterraneo Las diferencias significativas en la frecuencia de haplotipos entre poblaciones anidadoras en Florida y en Georgia/Carolina del Sur, y entre estos dos grupos y la colonia anidadora en el Mediterraneo, indican limitaciones substanciales en el flujo genetico contemporaneo entre poblaciones regionales y, por lo tanto una tendencia de las hembras a anidar en sus playas de nacimiento (“natal homing”) A pesar de lo anterior, dado que las distancias geneticas son pequenas se deducen conecciones evolutivas recientes entre colonias anidadoras Los resultados de marcaje y del ADNmt, ademas de consideraciones geologicas, sugieren que a lo largo de escalas evolutivas pequenas (quiza unos cuantos miles de anos), la dispersion de caguamas hembras es suficiente para permitir la colonizacion de habitats apropiados en la proximidad de playas de anida cion establecidas pero es demasiado leve para afectar significativamente la dinamica de poblaciones de las colonias anidadoras en una escala de tiempo contemporanea Nuestra informacion indica que las poblaciones anidadoras de la tortuga coguama deben ser manejadas como unidades demograficas independientes La subdivision poblacional basada en los analisis del ADNmt concuerdan con las distinciones ya reportadas entre las poblaciones anidadoras en Florida y Georgia/Carolina del Sur basadas en marcadores ambientales recapturas de tortugas marcadas y morfologa

http://obpa-nc.org/DOI-AdminRecord/0046600-0046610.pdf

John C. Avise

Papers

Species realities and numbers in sexual vertebrates: Perspectives from an asexually transmitted genome (speciationyphylogenyysister speciesycomparative molecular evolutionyphylogeography)

Species Invasions and Extinction: The Future of Native Biodiversity on Islands

Principles of phylogeography as illustrated by freshwater and terrestrial turtles in the southeastern united states

Proposal for a standardized temporal scheme of biological classification for extant species

Population Structure of Loggerhead Turtles (Caretta caretta) in the Northwestern Atlantic Ocean and Mediterranean Sea