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

Paternity inference using highly polymorphic codominant markers is becoming common in the study of natural populations. However, multiple males are often found to be genetically compatible with each offspring tested, even when the probability of excluding an unrelated male is high. While various methods exist for evaluating the likelihood of paternity of each nonexcluded male, interpreting these likelihoods has hitherto been difficult, and no method takes account of the incomplete sampling and error-prone genetic data typical of large-scale studies of natural systems. We derive likelihood ratios for paternity inference with codominant markers taking account of typing error, and define a statistic delta for resolving paternity. Using allele frequencies from the study population in question, a simulation program generates criteria for delta that permit assignment of paternity to the most likely male with a known level of statistical confidence. The simulation takes account of the number of candidate males, the proportion of males that are sampled and gaps and errors in genetic data. We explore the potentially confounding effect of relatives and show that the method is robust to their presence under commonly encountered conditions. The method is demonstrated using genetic data from the intensively studied red deer (Cervus elaphus) population on the island of Rum, Scotland. The Windows-based computer program, CERVUS, described in this study is available from the authors. CERVUS can be used to calculate allele frequencies, run simulations and perform parentage analysis using data from all types of codominant markers.

Statistical confidence for likelihood-based paternity inference in natural populations

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

Neophobia (fear of new stimuli) is an important component of mammalian behavioural ecology. In addition, information on neophobia in pest species could be of great significance in targetting control measures and predicting changes in responses to them. Novel objects and an auditory stimulus were presented to individually marked wild rabbits living socially in clumped warrens in southern British farmland. Avoidance of stimuli was measured by scan sampling of rabbits’ locations, in replicated experiments. Rabbits avoided a variety of novel objects by staying below ground, and by changing their activity ranges. Responses to different stimuli were correlated within individuals. There were non-significant differences in the degree of avoidance elicited by novel visual stimuli. The most important factors in avoidance were distance from the stimulus, number of previous presentations, and rabbit identity. Individual characteristics, including sex, social rank, and trappability, were less important determinants of neophobia, although dominant females were significantly more neophobic than were non-dominant ones. Only one or two presentations were required for attenuation of avoidance, so novel objects would be of limited application to crop protection. However, equipment used for delivering control measures should also quickly become accepted by rabbits. The measured avoidance and its attenuation indicate that rabbits assessed and responded to their surroundings with high precision, with significant individual variation consistent over stimuli.

Avoidance of novel objects by rabbits (oryctolagus cuniculus l.)

The typical life cycle of an aphid is cyclical parthenogenesis which involves the alternation of sexual and asexual reproduction. However, aphid life cycles, even within a species, can encompass everything on a continuum from obligate sexuality, through facultative sexuality to obligate asexuality. Loss of the sexual cycle in aphids is frequently associated with the introduction of a new pest and can occur for a number of environmental and genetic reasons. Here we investigate loss of sexual function in Sitobion aphids in Australia. Specifically, we aimed to determine whether an absence of sexual reproduction in Australian Sitobion results from genetic loss of sexual function or environmental constraints in the introduced range. We addressed our aims by performing a series of breeding experiments. We found that some lineages have genetically lost sexual function while others retain sexual function and appear environmentally constrained to asexuality. Further, in our crosses, using autosomal and X-linked microsatellite markers, we identified processes deviating from normal Mendelian segregation. We observed strong deviations in X chromosome transmission through the sexual cycle. Additionally, when progeny genotypes were examined across multiple loci simultaneously we found that some multilocus genotypes are significantly over-represented in the sample and that levels of heterozygosity were much higher than expected at almost all loci. This study demonstrates that strong biases in the transmission of X chromosomes through the sexual cycle are likely to be widespread in aphids. The mechanisms underlying these patterns are not clear. We discuss several possible alternatives, including mutation accumulation during periods of functional asexuality and genetic imprinting.

The genetic outcomes of sex and recombination in long-term functionally parthenogenetic lineages of Australian Sitobion aphids.

Human impacts on natural systems can cause local population extinctions, which may promote redistribution of taxa and secondary contact between divergent lineages. In mammalian populations that have mating systems shaped by polygyny and sexual selection, the potential for hybridization to ensue and persist depends on individual and demographic factors. At Macquarie Island, a recently formed fur seal population is comprised of both sexes of breeding Antarctic (Arctocephalus gazella) and subantarctic (A. tropicalis) fur seals, and an itinerant collection of male New Zealand fur seals (A. forsteri), presumed to be non-breeders due to their absence from principle breeding areas. The mating system of the three species is described as resource-defence polygyny: males defend beach territories containing breeding females for exclusive mating rights. A recent genetic study identified a high level of hybridization in the population (17-30%), unexpectedly involving all three species. This study examined the source of involvement in breeding by A. forsteri with respect to mating strategies operating in the population. Ninety-five (10%) pups born from 1992 to 2003 were genetically identified as New Zealand hybrids. Most resulted from reproduction within territories by New Zealand hybrids of both sexes, although some were conceived extra-territorially, indicating that males successfully utilize strategies other than territory holding to achieve paternities. Female reproductive status influenced mating partner and mating location, and females without pups were more likely to conceive extra-territorially and with A. forsteri males. This study illustrates an important consequence of low heterospecific discrimination in a sympatric population of long-lived mammals.

Multiple mating strategies explain unexpected genetic mixing of New Zealand fur seals with two congenerics in a recently recolonized population.

Climatic differences across a taxon's range may be associated with specific bioenergetic demands and may result in genetics-based metabolic adaptation, particularly in aquatic ectothermic organisms that rely on heat exchange with the environment to regulate key physiological processes. Extending down the east coast of Australia, the Great Dividing Range (GDR) has a strong influence on climate and the evolutionary history of freshwater fish species. Despite the GDR acting as a strong contemporary barrier to fish movement, many species, and species with shared ancestries, are found on both sides of the GDR, indicative of historical dispersal events. We sequenced complete mitogenomes from the four extant species of the freshwater cod genus Maccullochella, two of which occur on the semi-arid, inland side of the GDR, and two on the mesic coastal side. We constructed a dated phylogeny and explored the relative influences of purifying and positive selection in the evolution of mitogenome divergence among species. Results supported mid- to late-Pleistocene divergence of Maccullochella across the GDR (220-710 thousand years ago), bringing forward previously reported dates. Against a background of pervasive purifying selection, we detected potentially functionally relevant fixed amino acid differences across the GDR. Although many amino acid differences between inland and coastal species may have become fixed under relaxed purifying selection in coastal environments rather than positive selection, there was evidence of episodic positive selection acting on specific codons in the Mary River coastal lineage, which has consistently experienced the warmest and least extreme climate in the genus.

/pdf/pleistocene-divergence-across-a-mountain-range-and-the-3iqkziz9hg.pdf

Paul Sunnucks

Papers

Avoidance of novel objects by rabbits (oryctolagus cuniculus l.)

The genetic outcomes of sex and recombination in long-term functionally parthenogenetic lineages of Australian Sitobion aphids.

Multiple mating strategies explain unexpected genetic mixing of New Zealand fur seals with two congenerics in a recently recolonized population.

Pleistocene divergence across a mountain range and the influence of selection on mitogenome evolution in threatened Australian freshwater cod species.

Incorporating landscape genetics into road ecology