Sean Nee

Imperfect vaccines and the evolution of pathogen virulence

Vaccines rarely provide full protection from disease. Nevertheless, partially effective (imperfect) vaccines may be used to protect both individuals and whole populations. We studied the potential impact of different types of imperfect vaccines on the evolution of pathogen virulence (induced host mortality) and the consequences for public health. Here we show that vaccines designed to reduce pathogen growth rate and/or toxicity diminish selection against virulent pathogens. The subsequent evolution leads to higher levels of intrinsic virulence and hence to more severe disease in unvaccinated individuals. This evolution can erode any population-wide benefits such that overall mortality rates are unaffected, or even increase, with the level of vaccination coverage. In contrast, infection-blocking vaccines induce no such effects, and can even select for lower virulence. These findings have policy implications for the development and use of vaccines that are not expected to provide full immunity, such as candidate vaccines for malaria.

Phylogenetics and speciation

Species-level phylogenies derived from molecular data provide an indirect record of the speciation events that have led to extant species. This offers enormous potential for investigating the general causes and rates of speciation within clades. To make the most of this potential, we should ideally sample all the species in a higher group, such as a genus, ensure that those species reflect evolutionary entities within the group, and rule out the effects of other processes, such as extinction, as explanations for observed patterns. We discuss recent practical and theoretical advances in this area and outline how future work should benefit from incorporating data from genealogical and phylogeographical scales.

Sexual Selection and Taxonomic Diversity in Passerine Birds

Many authors have suggested that sexual selection by female choice may increase the speciation rate and hence generate taxonomic diversity. Using sister taxa comparisons, we find a significant positive correlation between the proportion of sexually dichromatic species within taxa of passerine birds, and the number of species in those taxa. Theory predicts this result if sexual dichromatism in passerines has evolved through the action of female choice.

New uses for new phylogenies

What this book is about new phylogenies - an introductory look at the coalescent genealogies and geography the coalescent process and background selection inferring population history from molecular phylogenies applications of intraspecific phylogenetics inferring phylogenies from DNA sequence data - the effects of sampling uses for evolutionary trees cross-species transmission and recombination of AIDS viruses using interspecies phylogenies to test macroevolutionary hypotheses using phylogenetic trees to reconstruct the history of infectious disease epidemics relating geographic patterns to phylogenetic processes uses of molecular phylogenies for conservation testing the time axis of phylogenies comparative evolution of larval and adult life-history stages and small subunit ribosomal RNA amongst post-Palaeozoic echinoids molecular phylogenies and host-parasite cospeciation - gophers and lice as a model system a microevolutionary link, between phylogenies and comparative data comparative test of evolutionary lability and rats using molecular phylogenies community evolution in Greater Antilean anolis lizards - phylogenetic patterns and experimental tests the evolution of body plans: HOM/HOX cluster evolution, model systems, and the importance of phylogeny.

Transient cross-reactive immune responses can orchestrate antigenic variation in malaria

The malaria parasite Plasmodium falciparum has evolved to prolong its duration of infection by antigenic variation of a major immune target on the surface of the infected red blood cell. This immune evasion strategy depends on the sequential, rather than simultaneous, appearance of immunologically distinct variants. Although the molecular mechanisms by which a single organism switches between variants are known in part, it remains unclear how an entire population of parasites within the host can synchronize expression to avoid rapidly exhausting the variant repertoire. Here we show that short-lived, partially cross-reactive immune responses to parasite-infected erythrocyte surface antigens can produce a cascade of sequentially dominant antigenic variants, each of which is the most immunologically distinct from its preceding types. This model reconciles several previously unexplained and apparently conflicting epidemiological observations by demonstrating that individuals with stronger cross-reactive immune responses can, paradoxically, be more likely to sustain chronic infections. Antigenic variation has always been seen as an adaptation of the parasite to evade host defence: we show that the coordination necessary for the success of this strategy might be provided by the host.

Macroevolutionary Inferences from Primate Phylogeny

We apply new statistical methods to a recent estimate of the phylogeny of all living primate species to test a range of models of cladogenesis. Null models in which probabilities of speciation and extinction do not differ among contemporaneous lineages are not consistent with the phylogeny. We present evidence that the net rate of cladogenesis (speciation rate minus extinction rate) increased in the lineage leading to the Cercopithecidae (Old World monkeys), and that there have been further increases in some lineages within that family. Such increases suggest the occurrence of clade selection, although we have not identified the selected trait or traits. There is no evidence that the net rate of cladogenesis is a function either of how many primate lineages are already present or of time. Intriguingly, three other major clades — Strepsirhini, Platyrrhini and Hominoidea — appear to have had very similar rates of clade growth, in spite of their great biological differences.

Lifting the veil on abundance patterns

The distribution of species abundances in samples from large species assemblages appears to follow a lognormal distribution truncated on the left at what Preston called the ‘veil line’. MacArthur suggested that if we could see the entire, unveiled distribution of abundances in the assemblage, we would discover that the distribution is left-skewed. This suggestion takes on a particular interest because, as we will show, Sugihara’s so-far successful model of abundance patterns predicts that abundance distributions are more likely to be left- than right-skewed. Recently published estimates of the population sizes of British bird species allow us to observe the completely unveiled distribution of a natural assemblage. This data set is, perhaps, uniquely informative because of the accuracy of the population size estimates of rare British bird species. The distribution is indeed left-skewed and the degree of left-skewness is quantitatively compatible with Sugihara’s model.

Two-Species Metapopulation Models

Publisher Summary This chapter discusses two-species metapopulation models. Results for single-species models and models with more than two species are also referred to for some topics discussed in the chapter. Theoretical studies of spatially distributed populations with restricted migration between patches have revealed a fundamental tendency for populations to become spatially organized into spiral or chaotic patterns of local abundance. A necessary condition for these patterns are unstable local dynamics, but the results persist with very low host rates of increase, very low migration rates, even if a small minority of adults disperse much more widely. This chapter generalizes the single-species Levins model to include the three simplest ecological relationships between two species coexisting as metapopulations: competition, predation, and mutualism. The chapter focuses primarily on predator–prey relationships in spatially explicit metapopulation models. The types of models discussed in this chapter have been studied over the years from a large variety of perspectives and interests. However, in order to present a thematically unified discussion, the chapter describes these models from the point of view of the consequences of changes in the amount of suitable habitat on the abundances of the species and on their persistence.

Controlling for non-independence in comparative analysis of patterns across populations within species

How do we quantify patterns (such as responses to local selection) sampled across multiple populations within a single species? Key to this question is the extent to which populations within species represent statistically independent data points in our analysis. Comparative analyses across species and higher taxa have long recognized the need to control for the non-independence of species data that arises through patterns of shared common ancestry among them (phylogenetic non-independence), as have quantitative genetic studies of individuals linked by a pedigree. Analyses across populations lacking pedigree information fall in the middle, and not only have to deal with shared common ancestry, but also the impact of exchange of migrants between populations (gene flow). As a result, phenotypes measured in one population are influenced by processes acting on others, and may not be a good guide to either the strength or direction of local selection. Although many studies examine patterns across populations within species, few consider such non-independence. Here, we discuss the sources of non-independence in comparative analysis, and show why the phylogeny-based approaches widely used in cross-species analyses are unlikely to be useful in analyses across populations within species. We outline the approaches (intraspecific contrasts, generalized least squares, generalized linear mixed models and autoregression) that have been used in this context, and explain their specific assumptions. We highlight the power of ‘mixed models’ in many contexts where problems of non-independence arise, and show that these allow incorporation of both shared common ancestry and gene flow. We suggest what can be done when ideal solutions are inaccessible, highlight the need for incorporation of a wider range of population models in intraspecific comparative methods and call for simulation studies of the error rates associated with alternative approaches.

Rate of rbcL Gene Sequence Evolution and Species Diversification in Flowering Plants (Angiosperms)

In sister taxa comparisons, there is a significant, positive correlation between the rate of evolution of the rbcL chloroplast gene within families of flowering plants (angiosperms), and the number of species in those families. We briefly discuss alternative evolutionary scenarios which may have generated this relation between species diversification and molecular evolution in flowering plants.