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.

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

计量经济分析 = Econometric analysis

The genetic effects of pleistocene ice ages are approached by deduction from paleoenvironmental information, by induction from the genetic structure of populations and species, and by their combination to infer likely consequences. (1) Recent palaeoclimatic information indicate rapid global reversals and changes in ranges of species which would involve elimination with spreading from the edge. Leading edge colonization during a rapid expansion would be leptokurtic and lead to homozygosity and spatial assortment of genomes. In Europe and North America, ice age contractions were into southern refugia, which would promote genome reorganization. (2) The present day genetic structure of species shows frequent geographic subdivision, with parapatric genomes, hybrid zones and suture zones. A survey of recent DNA phylogeographic information supports and extends earlier work. (3) The grasshopperChorthippus parallelusis used to illustrate such data and processes. Its range in Europe is divided on DNA sequences into five parapatric races, with southern genomes showing greater haplotype diversity — probably due to southern mountain blocks acting as refugia and northern expansion reducing diversity. (4) Comparison with other recent studies shows a concordance of such phylogeographic data over pleistocene time scales. (5) The role that ice age range changes may have played in changing adaptations is explored, including the limits of range, rapid change in new invasions and refugial differentiation in a variety of organisms. (6) The effects of these events in causing divergence and speciation are explored usingChorthippusas a paradigm. Repeated contraction and expansion would accumulate genome differences and adaptations, protected from mixing by hybrid zones, and such a composite mode of speciation could apply to many organisms.

https://www.fc.up.pt/mestr_biodiv/aulas/hewitt_1996.pdf

Some genetic consequences of ice ages, and their role in divergence and speciation

All species are restricted in their distribution. Currently, ecological models can only explain such limits if patches vary in quality, leading to asymmetrical dispersal, or if genetic variation is too low at the margins for adaptation. However, population genetic models suggest that the increase in genetic variance resulting from dispersal should allow adaptation to almost any ecological gradient. Clearly therefore, these models miss something that prevents evolution in natural populations. We developed an individual-based simulation to explore stochastic effects in these models. At high carrying capacities, our simulations largely agree with deterministic predictions. However, when carrying capacity is low, the population fails to establish for a wide range of parameter values where adaptation was expected from previous models. Stochastic or transient effects appear critical around the boundaries in parameter space between simulation behaviours. Dispersal, gradient steepness, and population density emerge as key factors determining adaptation on an ecological gradient.

Why is adaptation prevented at ecological margins? New insights from individual-based simulations.

1. Introduction: Speciation and patterns of diversity Roger K. Butlin, Jon R. Bridle and Dolph Schluter 2. On the arbitrary identification of real species Jody Hey 3. The evolutionary nature of diversification in sexuals and asexuals Timothy G. Barraclough, Diego Fontaneto, Elisabeth A. Herniou and Claudia Ricci 4. The poverty of the protists Graham Bell 5. Theory, community assembly, diversity and evolution in the microbial world Thomas P. Curtis, Nigel C. Wallbridge and William T. Sloan 6. Patterns of biodiversity and limits to adaptation in time and space Jon R. Bridle, Jitka Polechova and Timothy H. Vines 7. Dynamic patterns of adaptive radiation: evolution of mating preferences Sergey Gavrilets and Aaron Vose 8. Niche dimensionality and ecological speciation Patrik Nosil and Luke Harmon 9. Progressive levels of trait divergence along a 'speciation transect' in the Lake Victoria cichlid fish Pundamilia Ole Seehausen 10. Rapid speciation, hybridization and adaptive radiation in the Heliconius melpomene group James Mallet 11. Investigating ecological speciation Daniel J. Funk 12. Biotic interactions and speciation in the tropics Douglas W. Schemske 13. Ecological influences on the temporal pattern of speciation Albert B. Phillimore and Trevor D. Price 14. Speciation, extinction, and diversity Robert E. Ricklefs 15. Temporal patterns in diversification rates Andy Purvis, C. David L. Orme, Nicola H. Toomey and Paul N. Pearson 16. Speciation and extinction in the fossil record of North American mammals John Alroy.

https://assets.cambridge.org/97805218/83184/frontmatter/9780521883184_frontmatter.pdf

Speciation and patterns of biodiversity

Genetic variability of the nonmarine ostracod speciesDarwinula stevensoni was estimated by sequencing part of the nuclear and the mitochondrial genome. As Darwinulidae are believed to be ancient as...

/pdf/slow-molecular-evolution-in-an-ancient-asexual-ostracod-5au1mfsllp.pdf

Slow molecular evolution in an ancient asexual ostracod

Genome scans using large numbers of randomly selected markers have revealed a small proportion of loci that deviate from neutral expectations and so may mark genomic regions that contribute to local adaptation. Measurements of sequence differentiation and identification of genes in these regions is important but difficult, especially in organisms with limited genetic information available. We have followed up a genome scan in the marine gastropod, Littorina saxatilis, by searching a bacterial artificial chromosome library with differentiated and undifferentiated markers, sequencing four bacterial artificial chromosomes and then analysing sequence variation in population samples for fragments at, and close to the original marker polymorphisms. We show that sequence differentiation follows the patterns expected from the original marker frequencies, that differentiated markers identify independent and highly localized sites and that these sites fall outside coding regions. Two differentiated loci are characterized by insertions of putative transposable elements that appear to have increased in frequency recently and which might influence expression of downstream genes. These results provide strong candidate loci for the study of local adaptation in Littorina. They demonstrate an approach that can be applied to follow up genome scans in other taxa and they show that the genome scan approach can lead rapidly to candidate genes in nonmodel organisms.

Sequence differentiation in regions identified by a genome scan for local adaptation.

The process of speciation begins with genomically-localised barriers to gene exchange associated with loci for local adaptation, intrinsic incompatibility or assortative mating. The barrier then spreads until reproductive isolation influences the whole genome. The population genomics approach can be used to identify regions of reduced gene flow by detecting loci with greater differentiation than expected from the average across many loci. Recently, this approach has been used in several systems. I review these studies, concentrating on the robustness of the approach and the methods available to go beyond the simple identification of differentiated markers. Population genomics has already contributed significantly to understanding the balance between gene flow and selection during the evolution of reproductive isolation and has great future potential both in genome species and in non-model organisms.

https://www3.nd.edu/~mpfrende/Ecological%20Genomics/Papers/butlin,_pop_genomics%5b1%5d.pdf

Roger K. Butlin

Papers

Why is adaptation prevented at ecological margins? New insights from individual-based simulations.

Speciation and patterns of biodiversity

Slow molecular evolution in an ancient asexual ostracod

Sequence differentiation in regions identified by a genome scan for local adaptation.

Population genomics and speciation.