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

Dengue is a systemic viral infection transmitted between humans by Aedes mosquitoes. For some patients, dengue is a life-threatening illness. There are currently no licensed vaccines or specific therapeutics, and substantial vector control efforts have not stopped its rapid emergence and global spread. The contemporary worldwide distribution of the risk of dengue virus infection and its public health burden are poorly known. Here we undertake an exhaustive assembly of known records of dengue occurrence worldwide, and use a formal modelling framework to map the global distribution of dengue risk. We then pair the resulting risk map with detailed longitudinal information from dengue cohort studies and population surfaces to infer the public health burden of dengue in 2010. We predict dengue to be ubiquitous throughout the tropics, with local spatial variations in risk influenced strongly by rainfall, temperature and the degree of urbanization. Using cartographic approaches, we estimate there to be 390 million (95% credible interval 284-528) dengue infections per year, of which 96 million (67-136) manifest apparently (any level of disease severity). This infection total is more than three times the dengue burden estimate of the World Health Organization. Stratification of our estimates by country allows comparison with national dengue reporting, after taking into account the probability of an apparent infection being formally reported. The most notable differences are discussed. These new risk maps and infection estimates provide novel insights into the global, regional and national public health burden imposed by dengue. We anticipate that they will provide a starting point for a wider discussion about the global impact of this disease and will help to guide improvements in disease control strategies using vaccine, drug and vector control methods, and in their economic evaluation.

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The global distribution and burden of dengue

Model selection is a topic of special relevance in molecular phylogenetics that affects many, if not all, stages of phylogenetic inference. Here we discuss some fundamental concepts and techniques of model selection in the context of phylogenetics. We start by reviewing different aspects of the selection of substitution models in phylogenetics from a theoretical, philosophical and practical point of view, and summarize this comparison in table format. We argue that the most commonly implemented model selection approach, the hierarchical likelihood ratio test, is not the optimal strategy for model selection in phylogenetics, and that approaches like the Akaike Information Criterion (AIC) and Bayesian methods offer important advantages. In particular, the latter two methods are able to simultaneously compare multiple nested or nonnested models, assess model selection uncertainty, and allow for the estimation of phylogenies and model parameters using all available models (model-averaged inference or multimodel inference). We also describe how the relative importance of the different parameters included in substitution models can be depicted. To illustrate some of these points, we have applied AIC-based model averaging to 37 mitochondrial DNA sequences from the subgenus Ohomopterus (genus Carabus) ground beetles described by Sota and Vogler (2001). (AIC; Bayes factors; BIC; likelihood ratio tests; model averaging; model uncertainty; model selection; multimodel inference.) It is clear that models of nucleotide substitution (henceforth models of evolution) play a significant role in molecular phylogenetics, particularly in the context of distance, maximum likelihood (ML), and Bayesian es- timation. We know that the use of one or other model affects many, if not all, stages of phylogenetic inference. For example, estimates of phylogeny, substitution rates, bootstrap values, posterior probabilities, or tests of the molecular clock are clearly influenced by the model of evolution used in the analysis (Buckley, 2002; Buckley

Model Selection and Model Averaging in Phylogenetics: Advantages of Akaike Information Criterion and Bayesian Approaches Over Likelihood Ratio Tests

Genetics and analysis of quantitative traits

We studied the molecular phylogeny of the carabid subgenus Ohomopterus (genus Carabus), using two mitochondrial (mt) DNA regions (16SrRNA and NADH dehydrogenase subunit 5) and three nuclear DNA regions (wingless, phosphoenolpyruvate carboxykinase, and an anonymous locus). We revisited the previously reported incongruence between the distribution of mtDNA markers and morphologically defined species (Su et al., 1996; J. Mol. Evol. 43:662-671), which those authors attributed to "type switching", a concerted change in many morphological characters that results in the repeated evolution of a particular morphological type. Our mtDNA gene tree obtained from 44 individuals representing all 15 currently recognized species of Ohomopterus revealed that haplotypes isolated from individuals of a single "species" were frequently separated into distant clades, confirming the previous report. The three nuclear markers generally conformed better-with the morphologically defined species than did the mitochondrial markers. The phylogenetic signal in mtDNA and nuclear DNA data differed strongly, and these two partitions were significantly incongruent with each other according to the incongruence length difference test of Farris et al. (1994; Cladistics 10:315-320), although the three nuclear partitions were not homogeneous either. Our results did not support the type-switching hypothesis that had been proposed to fit the morphological data to the mitochondrial gene tree: The incongruence of the mtDNA tree with other nuclear markers indicates that the mtDNA-based tree does not reflect species history any better than the morphological data do. Incongruence of gene trees in Ohomopterus may have been promoted by the complex processes of geographic isolation and hybridization in the Japanese Archipelago that have led to occasional gene flow and recombination between separated entities. The occurrence of reticulate patterns in this group is intriguing, because species of Ohomopterus exhibit extremely divergent genitalic structures that represent a highly efficient reproductive isolation mechanism.

Incongruence of Mitochondrial and Nuclear Gene Trees in the Carabid Beetles Ohomopterus

We demonstrate experimentally that differences in genital characters impose a direct cost of interspecific copulation on two closely related carabid species, Carabus (Ohomopterus) maiyasanus and C. (O.) iwawakianus, that share a narrow hybrid zone. Males of both species attempted copulation indiscriminately between conspecific and heterospecific females. Females experiencing heterospecific mating often suffered mortality due to rupture of their vaginal membranes. Those without fatal injury laid eggs which developed into F1 adults, but the fertilization rate was much lower than for intraspecific pairs. Males of C. maiyasanus, but not C. iwawakianus, often had broken genital parts (copulatory pieces) following interspecific copulations, which may prevent normal copulation in subsequent matings. Because of female mortality and low fertilization rate, the estimated fitness cost of interspecific mating was very large in terms of the reduction in the number of offspring (hatching larvae) for both sexes and both species. Thus, genital lock-and-key appears to exert significant selection against hybridization in the hybrid zone of these carabid beetles.

Genital lock-and-key as a selective agent against hybridization.

Survival times of eggs under three humidity conditions (42%, 68%, 88% RH) were investigated among Aedes (Stegomyia) mosquitoes from temperate and tropical zones (5 species and 20 geographical strains). This subgenus tends to occupy small aquatic sites as larvae, where desiccation resistance of eggs is necessary during habitat drought. Interspecific comparison showed that the egg survival time was correlated with egg volume and dryness of source locality, and probably with habitat. Aedes aegypti is associated most with arid climate and human-disturbed habitats — its large eggs survived the longest periods at all humidities. Aedes albopictus ranges from tropics to temperate zones and inhabits both disturbed and forest habitats — its eggs were less desiccation-resistant than A. aegypti eggs. The survival times for forest species eggs (A. riversi, A. galloisi, A. flavopictus) were variable at high humidities but at the lowest humidity were consistently shorter than for eggs of A. aegypti and A. albopictus.

Interspecific variation in desiccation survival time of Aedes (Stegomyia) mosquito eggs is correlated with habitat and egg size

The escalation of defensive/offensive arms is ubiquitous in prey‐predator evolutionary interactions. However, there may be a geographically varying imbalance in the armaments of participating species that affects the outcome of local interactions. In a system involving the Japanese camellia (Camellia japonica) and its obligate seed predator, the camellia weevil (Curculio camelliae), we investigated the geographic variation in physical defensive/offensive traits and that in natural selection on the plant’s defense among 17 populations over a 700‐km‐wide area in Japan. The sizes of the plant defensive apparatus (pericarp thickness) and the weevil offensive apparatus (rostrum length) clearly correlated with each other across populations. Nevertheless, the balance in armaments between the two species was geographically structured. In the populations for which the balance was relatively advantageous for the plant’s defense, natural selection on the trait was stronger because in the other populations,...

https://www.jstor.org/stable/10.1086/498277

Imbalance of predator and prey armament: geographic clines in phenotypic interface and natural selection.

The evolution of flight is a key innovation that may enable the extreme diversification of insects. Nonetheless, many species-rich, winged insect groups contain flightless lineages. The loss of flight may promote allopatric differentiation due to limited dispersal power and may result in a high speciation rate in the flightless lineage. Here we show that loss of flight accelerates allopatric speciation using carrion beetles (Coleoptera: Silphidae). We demonstrate that flightless species retain higher genetic differentiation among populations and comprise a higher number of genetically distinct lineages than flight-capable species, and that the speciation rate with the flightless state is twice that with the flight-capable state. Moreover, a meta-analysis of 51 beetle species from 15 families reveals higher genetic differentiation among populations in flightless compared with flight-capable species. In beetles, which represent almost one-fourth of all described species, repeated evolution of flightlessness may have contributed to their steady diversification since the Mesozoic era.

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Teiji Sota

Papers

Incongruence of Mitochondrial and Nuclear Gene Trees in the Carabid Beetles Ohomopterus

Genital lock-and-key as a selective agent against hybridization.

Interspecific variation in desiccation survival time of Aedes (Stegomyia) mosquito eggs is correlated with habitat and egg size

Imbalance of predator and prey armament: geographic clines in phenotypic interface and natural selection.

Loss of flight promotes beetle diversification