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

Evolution. Matriarchal liberation.

/pdf/stability-equilibrium-and-molecular-aspects-of-conservation-4qnyto25co.pdf

Stability, equilibrium and molecular aspects of conservation in marine species

The year 2009 marked the 200th anniversary of Charles Darwin’s birth and the 150th anniversary of his most influential publication. Darwin transformed the biological sciences in much the same way that Nicolaus Copernicus, Galileo Galilei, and Isaac Newton, centuries earlier, transformed the physical sciences—by demonstrating that the universe operates according to natural laws that fall within the purview of rational scientific inquiry. In 1543, Copernicus published De Revolutionibus Orbium Celestium (“ On the Revolutions of the Celestial Spheres ”) that challenged conventional wisdom that the Earth was the center of creation and instead promoted the idea that natural laws govern the motion of physical objects in the universe. In 1859, in On the Origin of Species (4), Darwin developed the equally revolutionary concept that a natural but nonrandom process—natural selection—yields biological adaptations that otherwise can give the superficial impression of direct intelligent craftsmanship.

Actually, Darwin barely mentioned Homo sapiens in On the Origin of Species, cautiously stating only that “much light will be thrown on the origin of man and his history.” More than a decade later, however, Darwin addressed human evolution at considerable length in The Descent of Man and Selection in Relation to Sex (5) wherein can be found many thoughtful passages, such as, “Man may be excused for feeling some pride at having risen, though not through his own exertions, to the very summit of the organic scale; and the fact of his having thus risen, instead of having been aboriginally placed there, may give him hope for a still higher destiny in the distant future.”

Of course, much has been learned about humanity’s evolutionary origins and biological conditions since Darwin’s time, not least from the evidence of paleontology, comparative vertebrate biology, and genomics. An emerging field known as “anthropogeny” (6) seeks to understand the evolutionary origins … 

[↵][1]1To whom correspondence should be addressed. E-mail: javise{at}uci.edu.

 [1]: #xref-corresp-1-1

/pdf/in-the-light-of-evolution-iv-the-human-condition-544ook6sjg.pdf

In the Light of Evolution IV: The Human Condition

We describe for the first time reproductive behaviors in the Pirate Perch (Aphredoderus sayanus), a secretive nocturnal fish whose urogenital opening is positioned far anteriorally, under its throat. Some naturalists had speculated that this peculiar morphological condition might serve to promote egg transfer to the fish's branchial chamber for gill-brooding; others hypothesized that Pirate Perch spawn in the substrate of streams but offered no adaptive rationale for the odd placement of the fish's urogenital pore. Here we solve the conundrum through a combination of intensive field investigations, underwater filming, and molecular parentage analyses. We show that Pirate Perch spawn in underwater root masses, the first documentation of such nesting behavior in any species of North American fish. Female Pirate Perch thrust their heads and release their eggs into sheltered canals of these masses. Males congregate at these sites and likewise enter the narrow canals headfirst, to release sperm. Thus,...

Spawning Behavior and Genetic Parentage in the Pirate Perch (Aphredoderus sayanus), a Fish with an Enigmatic Reproductive Morphology

We developed ten microsatellite loci for the elegant sea snake, Hydrophis elegans, from partial genomic DNA libraries using a repeat enrichment protocol. Eight loci had nine or more alleles per locus (maximum 20), while the other two had three and seven. All ten loci amplified successfully in 11 of the 15 additional hydrophiine sea snake species screened. Nine loci amplified successfully for three species and eight amplified successfully for the remaining species. Based on this highly successful cross-amplification we expect these ten loci to be useful markers for investigating population genetic structure, gene flow and parentage for all sea snake species from the Hydrophis group.

/pdf/development-of-ten-polymorphic-microsatellite-loci-for-the-1zkyqwewb1.pdf

Development of ten polymorphic microsatellite loci for the sea snake Hydrophis elegans (Elapidae: Hydrophiinae) and cross-species amplification for fifteen marine hydrophiine species

John C. Avise

Papers

Evolution. Matriarchal liberation.

Stability, equilibrium and molecular aspects of conservation in marine species

In the Light of Evolution IV: The Human Condition

Spawning Behavior and Genetic Parentage in the Pirate Perch (Aphredoderus sayanus), a Fish with an Enigmatic Reproductive Morphology

Development of ten polymorphic microsatellite loci for the sea snake Hydrophis elegans (Elapidae: Hydrophiinae) and cross-species amplification for fifteen marine hydrophiine species