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

Microsatellite markers for the onychophoran Euperipatoides rowelli.

Summary

Habitat loss and associated fragmentation are major drivers of biodiversity decline, and understanding how they affect population processes (e.g. dispersal) is an important conservation goal. In a large-scale test employing 10 × 10 km units of replication, three species of Australian birds, the fuscous honeyeater, yellow-tufted honeyeater and white-plumed honeyeater, responded differently to fragmentation. The fuscous and yellow-tufted honeyeaters are ‘decliners’ that disappeared from suitable habitat in landscapes where levels of tree-cover fell below critical thresholds of 17 and 8%, respectively. The white-plumed honeyeater is a ‘tolerant’ species whose likelihood of occurrence in suitable habitat was independent of landscape-level tree-cover.
To determine whether the absence of the two decliner species in low tree-cover landscapes can be explained by reduced genetic connectivity, we looked for signatures of reduced mobility and gene flow in response to fragmentation across agricultural landscapes in the Box-Ironbark region of north-central Victoria, Australia.
We compared patterns of genetic diversity and population structure at the regional scale and across twelve 100 km2 landscapes with different tree-cover extents. We used genetic data to test landscape models predicting reduced dispersal through the agricultural matrix. We tested for evidence of sex-biased dispersal and sex-specific responses to fragmentation.
Reduced connectivity may have contributed to the disappearance of the yellow-tufted honey-eater from low tree-cover landscapes, as evidenced by male bias and increased relatedness among males in low tree-cover landscapes and signals of reduced gene flow and mobility through the agricultural matrix. We found no evidence for negative effects of fragmentation on gene flow in the other decliner, the fuscous honeyeater, suggesting that undetected pressures act on this species. As expected, there was no evidence for decreased movement through fragmented landscapes for the tolerant white-plumed honeyeater.
We demonstrated effects of habitat loss and fragmentation (stronger patterns of genetic differentiation, increased relatedness among males) on the yellow-tufted honeyeater above the threshold at which probability of occurrence dropped. Increasing extent and structural connectivity of habitat should be an appropriate management action for this species and other relatively sedentary woodland specialist species for which it can be taken as representative.

https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2656.12172

Does reduced mobility through fragmented landscapes explain patch extinction patterns for three honeyeaters

Isotoma klovstadi Carpenter, 1902 was one of the first Collembola described from the Antarctic continent. It was first collected in November 1899 during the British Antarctic Expedition on the north coast of Victoria Land in the Ross Sea region. It is now known to occur in an extensive area of northern Victoria Land, including the offshore Possession, Coulman, and Foyn Islands. More recently, I. klovstadi was moved to the genus Gnathisotoma Cassagnau, 1957 and has been included in this genus in an unpublished checklist (online) of all described Collembola. Here, we redescribe the species and use morphological and molecular (COI and 18S genes) evidence to investigate its affinities within the Isotominae. We show that it does not belong to Gnathisotoma, or Isotoma
 s. str. (the viridis group) as currently conceived, but is likely to be part of the species complex of Isotoma s. lat. We discuss reasons for placing it in the genus Desoria Nicolet, 1841. Our results reinforce the already high level of endemicity in the Antarctic fauna and emphasise the value of both morphological and molecular studies in examining relict Gondwanan taxa and their evolutionary relationships with those of other Southern Hemisphere continents.

Redescription of the Antarctic springtail Desoria klovstadi using morphological and molecular evidence

Divorce can be an important behavioral strategy to improve fitness. This is particularly relevant for species that are territorial year-round with continuous partnerships, where individuals face constraints on partner choice due to limited vacancies and dispersal opportunities. We tested several hypotheses for divorce in such a species, the cooperatively breeding bird Malurus coronatus. Based on 9 years of detailed information on dispersal and survival of 317 breeding pairs, we tested whether divorce is driven by inbreeding avoidance, by a better partner or territory, or by social variables (number of subordinates and fidelity of partners). We found that divorce is important to escape incest: incestuous pairs were substantially more likely to divorce (64%) than non-incestuous pairs (14%). However, incestuous pair bonds lasted up to a year, highlighting constraints on breeder dispersal. Non-incestuous pairs also divorced, but here the only predictor for divorce was the presence of extrapair offspring in a previous brood. Although reproductive failure did not trigger divorce, and reproductive success did not improve in the year following divorce, females that dispersed after divorce obtained higher quality territories, unlike females that dispersed after their partner died. Thus, divorce may be a strategy to improve long-term benefits associated with better territories. Some divorces appeared to be forced evictions by older females, although direct evidence for this is limited. Taken together, our findings demonstrate the complexity of factors that affect the occurrence of divorce when partner choice is constrained.

Incest avoidance, extrapair paternity, and territory quality drive divorce in a year-round territorial bird

Onychophorans (peripatus or velvet worms) show extraordinarily high local endemism, and cryptic species are common. As part of a programme addressing issues of endemicity at hierarchical spatial scales, we investigated reproduction in Euperipatoides rowelli (Onychophora: Peripatopsidae) using microsatellite analysis. This species is ovoviviparous, and females have up to 70 embryos in their uteri simultaneously. Batches of undeveloped and well-developed embryos may be present in the uteri of a female. Paired ovaries lead via a common oviduct into paired uteri, each of which has a spermatheca (sperm storage organ). Insemination in E. rowelli is dermal-haemocoelic: spermatophores are placed on the skin of the female, the body wall is breeched, and sperm are released into the haemocoel through which they migrate to the spermathecae. There is no obvious mechanism to prevent sperm mixing, yet microsatellite analysis indicated that offspring in a female’s paired reproductive tracts can be sired by different males, and that the paired spermathecae can contain sperm from different males. More than 70% of females had broods with multiple paternity. The data are consistent with the potential for female postcopulatory influence over fertilizations: in particular, compartmentalization of sperm from different males into different spermathecae. Female control of fertilizations could lead to benefits including increased diversity of offspring, minimization of maternal‐paternal genetic incompatibility, and influence on offspring genotypes. Multiple mating alone may increase the genetic diversity of offspring: this could be of importance in E. rowelli , which has very small genetic neighbourhoods and low genetic marker diversity.

Paul Sunnucks

Papers

Microsatellite markers for the onychophoran Euperipatoides rowelli.

Does reduced mobility through fragmented landscapes explain patch extinction patterns for three honeyeaters

Redescription of the Antarctic springtail Desoria klovstadi using morphological and molecular evidence

Incest avoidance, extrapair paternity, and territory quality drive divorce in a year-round territorial bird

Molecular anatomy of an onychophoran: compartmentalized sperm storage and heterogeneous paternity