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

Inversions often underlie complex adaptive traits, but the genic targets inside them are largely unknown. Gene expression profiling provides a powerful way to link inversions with their phenotypic consequences. We examined the effects of the Cf-Inv(1) inversion in the seaweed fly Coelopa frigida on gene expression variation across sexes and life stages. Our analyses revealed that Cf-Inv(1) shapes global expression patterns but the extent of this effect is variable with much stronger effects in adults than larvae. Furthermore, within adults, both common as well as sex specific patterns were found. The vast majority of these differentially expressed genes mapped to Cf-Inv(1). However, genes that were differentially expressed in a single context (i.e. in males, females or larvae) were more likely to be located outside of Cf-Inv(1). By combining our findings with genomic scans for environmentally associated SNPs, we were able to pinpoint candidate variants in the inversion that may underlie mechanistic pathways that determine phenotypes. Together the results in this study, combined with previous findings, support the notion that the polymorphic Cf-Inv(1) inversion in this species is a major factor shaping both coding and regulatory variation resulting in highly complex adaptive effects.

https://biorxiv.org/content/10.1101/2021.06.03.446913v1.full.pdf

A large chromosomal inversion shapes gene expression in seaweed flies (Coelopa frigida)

Good communication needs a common language. As Harrison (2012) pointed out, the ‘language of speciation’ has a complex evolutionary history, sometimes resulting in both modification and diversification in the use of terms. There is a risk that this erodes the effective exchange of ideas. It is surprising that Harrison did not discuss the meaning of ‘reproductive isolation’. He seems to have assumed, along with many others, that there is a common understanding of this term. In fact, it is not an easy term to define and the conversation started here by Westram et al. (2022) is both valuable and timely. Multiple terms are in use to describe the extent to which populations are connected by interbreeding and gene flow: ‘reproductive isolation’ itself, various terms for ‘components of reproductive isolation’ in a temporal sequence derived from Dobzhansky's seminal table (Dobzhansky, 1937, pp. 231– 232; prezygotic isolation, postzygotic isolation and a series of finer divisions), a partly independent categorization into ‘intrinsic’ vs ‘extrinsic’ components and a set of terms related to ‘barriers to gene flow’, such as ‘barrier traits’, ‘barrier loci’ and ‘barrier effects’. Having multiple terms is potentially confusing, but it can also be very helpful: if these terms have clear and distinct meanings, they can be used to make descriptions more precise and so to communicate more reliably. They can also guide decisions about what to measure empirically and help to show how different types of empirical information fit together. Westram et al. (2022) define ‘reproductive isolation’ as a quantitative measure of the effect that genetic differences between populations have on gene flow, specifically aiming to bring together what they describe as the ‘organismal focus’ and the ‘genetic focus’ revealed in their survey of practitioners. Here, I argue that better communication can be achieved by using the available terminology to describe different aspects of the evolutionary independence of populations rather than finding a single definition of reproductive isolation that incorporates all aspects. The issue of interest is the evolutionary independence of populations. This depends on gene flow, which tends to homogenize neutral variation, restrict responses to divergent selection and facilitate shared responses to common selection pressures. Populations of the same species have high levels of interdependence, whereas populations of different species can evolve independently (in a genetic sense: their evolutionary trajectories may well be constrained by ecological factors, but that is not the point at issue here). At this conceptual level, there is broad agreement and ‘reproductive isolation’ is used in a general sense to describe a continuum of relationships (Stankowski & Ravinet, 2021). The problems arise when trying to be more precise, especially when looking for quantitative comparisons. One key distinction to consider lies in the entities for which a quantitative measure is required. Reproductive isolation is generally considered a property of a pair of populations, but gene flow is only meaningful at the level of genes. In a theoretical construct of two populations connected by gene flow but experiencing no selection, it might be true that all loci have the same expected gene flow. However, such pairs of populations do not exist in nature. Habitat variation is ubiquitous, leading to divergent selection on a subset of loci and so lower gene flow for these loci. Even in the absence of divergent selection, gene flow would be expected to vary due to beneficial and deleterious mutations appearing independently in the two populations. Gene flow at neutral loci is influenced by linkage to

https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/jeb.14029

The language of isolation: a commentary on Westram et al., 2022

Next-generation sequencing of pooled samples (Pool-seq) is a popular method to assess genome-wide diversity patterns in natural and experimental populations. However, Pool-seq is associated with specific sources of noise, such as unequal individual contributions. Consequently, using Pool-seq for the reconstruction of evolutionary history has remained underexplored. Here we describe a novel Approximate Bayesian Computation (ABC) method to infer demographic history, explicitly modelling Pool-seq sources of error. By jointly modelling Pool-seq data, demographic history and the effects of selection due to barrier loci, we obtain estimates of demographic history parameters accounting for technical errors associated with Pool-seq. Our ABC approach is computationally efficient as it relies on simulating subsets of loci (rather than the whole-genome) and on using relative summary statistics and relative model parameters. Our simulation study results indicate Pool-seq data allows distinction between general scenarios of ecotype formation (single versus parallel origin) and to infer relevant demographic parameters (e.g. effective sizes and split times). We exemplify the application of our method to Pool-seq data from the rocky-shore gastropod Littorina saxatilis, sampled on a narrow geographical scale at two Swedish locations where two ecotypes (Wave and Crab) are found. Our model choice and parameter estimates show that ecotypes formed before colonization of the two locations (i.e. single origin) and are maintained despite gene flow. These results indicate that demographic modelling and inference can be successful based on pool-sequencing using ABC, contributing to the development of suitable null models that allow for a better understanding of the genetic basis of divergent adaptation.

Integrating Pool-seq uncertainties into demographic inference.

The application of molecular techniques to the study of ostracods

Sandy beaches are biogeochemical hotspots that bridge marine and terrestrial ecosystems via the transfer of marine organic matter, such as seaweed (termed wrack). A keystone of this unique ecosystem is the microbial community, which helps to degrade wrack and re-mineralize nutrients. However, little is known about the wrackbed microbiome, its composition, trophic ecology, or how it varies over time and space. Here we characterize the wrackbed microbiome as well as the microbiome of a primary consumer, the seaweed fly Coelopa frigida, and examine how they change along one of the most studied ecological gradients in the world, the transition from the marine North Sea to the brackish Baltic Sea. We found that polysaccharide degraders dominated both the wrackbed and seaweed fly microbiomes but there were still consistent differences between wrackbed and fly samples. Furthermore, we observed a shift in both microbial communities and functionality between the North and Baltic Sea. These shifts were mostly due to changes in the frequency of different groups of known polysaccharide degraders (Proteobacteria and Bacteroidota). We hypothesize that microbes were selected for their abilities to degrade different polysaccharides corresponding to a shift in polysaccharide content in the seaweed communities of the North vs. Baltic Sea. Our results reveal the complexities of both the wracked microbial community, with different groups specialized to different roles, and the cascading trophic consequences of shifts in the near shore algal community.

https://www.biorxiv.org/content/biorxiv/early/2021/11/01/2021.11.01.466799.full.pdf

Roger K. Butlin

Papers

A large chromosomal inversion shapes gene expression in seaweed flies (Coelopa frigida)

The language of isolation: a commentary on Westram et al., 2022

Integrating Pool-seq uncertainties into demographic inference.

The application of molecular techniques to the study of ostracods

A metagenomic analysis of the wrackbed microbiome indicates a phylogeographic break along the North Sea - Baltic Sea transition zone