Background: Sex presents evolutionary costs and benefits, leading to the expectation that the amount of genetic exchange should vary in conditions with contrasting cost-benefit equations. Like eukaryotes, viruses also engage in sex, but the rate of genetic exchange is often assumed to be a relatively invariant property of a particular virus. However, the rates of genetic exchange can vary within one type of virus according to geography, as highlighted by phylogeographic studies of cystoviruses. Here...

George Gaylord Simpson famously postulated that much of life's diversity originated as adaptive radiations—more or less simultaneous divergences of numerous lines from a single ancestral adaptive type. However, identifying adaptive radiations has proven difficult due to a lack of broad-scale comparative datasets. Here, we use phylogenetic comparative data on body size and shape in a diversity of animal clades to test a key model of adaptive radiation, in which initially rapid morphological evolution is followed...

Tests of the genetic structure of empirical populations typically focus on the correlative relationships between population connectivity and geographic and/or environmental factors in landscape genetics. However, such tests may overlook or misidentify the impact of such factors on genetic structure, especially when connectivity patterns differ between past and present populations because of shifting environmental conditions over time. Here we account for the underlying demographic component of population connectivity associated with a temporarily dynamic landscape in...

On Bioko Island, Equatorial Guinea, indoor residual spraying (IRS) has been part of the Bioko Island Malaria Control Project since early 2004. Despite success in reducing childhood infections, areas of high transmission remained on the island. We therefore examined fluctuations in the effective population size (N_e) of the malaria vector Anopheles gambiae in an area of persistent high transmission over two spray rounds. We analyzed data for 13 microsatellite loci from 791 An. gambiae specimens...

With increases in both the size and scope of phylogenetic trees, we are afforded a renewed opportunity to address long standing comparative questions, such as whether particular fruit characters account for much of the variation in diversity among flowering plant clades. Studies to date have reported conflicting results, largely as a consequence of taxonomic scale and a reliance on potentially conservative statistical measures. Here we examine a larger and older angiosperm clade, the Campanulidae, and...

The primary Afrotropical malaria mosquito vector Anopheles gambiae sensu stricto has a complex population structure. In western Africa, this species is split into two molecular forms and displays local and regional variation in chromosomal arrangements and behaviours. To investigate patterns of macro-geographic population substructure, 25 An. gambiae samples from 12 African countries were genotyped at 13 microsatellite loci. This analysis detected the presence of additional population structuring, with the M-form being subdivided into distinct west,...

The branching structure of biological evolution confers statistical dependencies on phenotypic trait values in related organisms. For this reason, comparative macroevolutionary studies usually begin with an inferred phylogeny that describes the evolutionary relationships of the organisms of interest. The probability of the observed trait data can be computed by assuming a model for trait evolution, such as Brownian motion, over the branches of this fixed tree. However, the phylogenetic tree itself contributes statistical uncertainty to...

The constant darkness of caves and other subterranean habitats imposes sensory constraints that offer a unique opportunity to examine evolution of sensory modalities. Hearing in cavefishes has not been well explored, and here we show that cavefishes in the family Amblyopsidae are not only blind but have also lost a significant portion of their hearing range. Our results showed that cave and surface amblyopsids shared the same audiogram profile at low frequencies but only surface...

Despite theoretical understanding and empirical detection of local adaptation in natural environments, our knowledge of such divergence in fragmented habitats remains limited, especially in the context of microgeographic spatial scales and contemporary time scales. I used a combination of reciprocal transplant and common garden exposure experiments to evaluate potential microgeographic divergence in a pool-breeding amphibian occupying a landscape fragmented by roads. As indicated by reduced rates of survival and increased rates of malformation, I found...

Understanding the history that underlies patterns of species richness across the Tree of Life requires an investigation of the mechanisms that not only generate young species-rich clades, but also those that maintain species-poor lineages over long stretches of evolutionary time. However, diversification dynamics that underlie ancient species-poor lineages are often hidden due to a lack of fossil evidence. Using information from the fossil record and time calibrated molecular phylogenies, we investigate the history of lineage...

Statistical species delimitation usually relies on singular data, primarily genetic, for detecting putative species and individual assignment to putative species. Given the variety of speciation mechanisms, singular data may not adequately represent the genetic, morphological and ecological diversity relevant to species delimitation. We describe a methodological framework combining multivariate and clustering techniques that uses genetic, morphological and ecological data to detect and assign individuals to putative species. Our approach recovers a similar number of species...

Many studies of offspring size focus on differences in maternal investment that arise from ecological factors such as predation or competition. Classic theory predicts that these ecological factors will select for an optimal offspring size, and therefore that variation in a given environment will be minimized. Yet recent evidence suggests maternal traits such as size or age could also drive meaningful variation in offspring size. The generality of this pattern is unclear, as some studies...

The presumed affinities of the Terminal Neoproterozoic Ediacara biota have been much debated. However, even in the absence of concrete evidence for phylogenetic affinity, numerical paleoecological approaches can be effectively used to make inferences about organismal biology, the nature of biotic interactions, and life history. Here, we examine the population structure of three Ediacaran rangeomorph taxa (Fractofusus, Beothukis, and Pectinofrons), and one non-rangeomorph taxon (Thectardis) across five fossil surfaces around the Avalon Peninsula, Newfoundland, through...

Squirrelfishes and soldierfishes (Holocentridae) are among the most conspicuous species in the nocturnal reef fish community. However, there is no clear consensus regarding their evolutionary relationships, which is reflected in a complicated taxonomic history. We collected DNA sequence data from multiple single copy nuclear genes and one mitochondrial gene sampled from over fifty percent of the recognized holocentrid species and infer the first species-level phylogeny of the Holocentridae. Our results strongly support the monophyly of...

Microgeographic adaptation occurs when populations evolve divergent fitness advantages across the spatial scales at which focal organisms regularly disperse. Although an increasing number of studies find evidence for microgeographic adaptation, the underlying causes often remain unknown. Adaptive divergence requires some combination of limited gene flow and strong divergent natural selection among populations. In this study, we estimated the relative influence of selection, gene flow and the spatial arrangement of populations in shaping patterns of adaptive...

The alteration of paleodrainage river connections has shaped patterns of speciation, genetic diversity, and the geographic distribution of the species-rich freshwater fauna of North America. The integration of ancestral range reconstruction methods and divergence time estimates provides an opportunity to infer paleodrainage connectivity and test alternative paleodrainage hypotheses. Members of the Orangethroat Darter clade, Ceasia, are endemic to southeastern North America and occur north and south of the Pleistocene glacial front, a distributional pattern that...

The growth of phylogenetic trees in scope and in size is promising from the standpoint of understanding a wide variety of evolutionary patterns and processes. With trees comprised of larger, older, and globally distributed clades, it is likely that the lability of a binary character will differ significantly among lineages, which could lead to errors in estimating transition rates and the associated inference of ancestral states. Here we develop and implement a new method for...

Succulent water storage is a prominent feature among plants adapted to arid zones, but we know little about how succulence evolves and how it is integrated into organs already tasked with multiple functions. Increased volume in succulent leaves, for example, may result in longer transport distances between veins and the cells that they supply, which in turn could negatively impact photosynthesis [1, 2, 3 and 4]. We quantified water storage [5] in a group of...

1. Body size is of fundamental importance to the structure and function of natural systems, yet the factors selecting for certain body sizes are still not well understood. Resource supply levels clearly play a role in setting size, but in current theory, optimality functions for body size are not tied to the population dynamics that govern resource supply, minimizing our ability to understand how body size evolves in response to ecological context. 2. We integrated...

Throughout the developing world, urban centres with sprawling slum settlements are rapidly expanding and invading previously forested ecosystems. Slum communities are characterized by untended refuse, open sewers and overgrown vegetation, which promote rodent infestation. Norway rats (Rattus norvegicus) are reservoirs for epidemic transmission of many zoonotic pathogens of public health importance. Understanding the population ecology of R. norvegicus is essential to formulate effective rodent control strategies, as this knowledge aids estimation of the temporal stability...

The Earth’s islands harbor a distinct, yet highly threatened biological and cultural diversity that has been shaped by geographic isolation and unique environments. Island systems are key natural laboratories for testing theory in ecology and evolution. However, despite their potential usefulness for research, a quantitative description of island environments and an environmental classification are still lacking. Here, we prepare a standardized dataset and perform a comprehensive global environmental island characterization for 17,883 of the world’s...

Spiny-rayed fishes, or acanthomorphs, comprise nearly one-third of all living vertebrates. Despite their dominant role in aquatic ecosystems, the evolutionary history and tempo of acanthomorph diversification is poorly understood. We investigate the pattern of lineage diversification in acanthomorphs by using a well-resolved time-calibrated phylogeny inferred from a nuclear gene supermatrix that includes 520 acanthomorph species and 37 fossil age constraints. This phylogeny provides resolution for what has been classically referred to as the “bush at...

Cichlid fishes are a key model system in the study of adaptive radiation, speciation and evolutionary developmental biology. More than 1600 cichlid species inhabit freshwater and marginal marine environments across several southern landmasses. This distributional pattern, combined with parallels between cichlid phylogeny and sequences of Mesozoic continental rifting, has led to the widely accepted hypothesis that cichlids are an ancient group whose major biogeographic patterns arose from Gondwanan vicariance. Although the Early Cretaceous (ca 135...

A major challenge in conservation biology is the need to broadly prioritize conservation efforts when demographic data are limited. One method to address this challenge is to use population genetic data to define groups of populations linked by migration and then use demographic information from monitored populations to draw inferences about the status of unmonitored populations within those groups. We applied this method to anadromous alewife (Alosa pseudoharengus) and blueback herring (Alosa aestivalis), species for...

1. The leaf economics spectrum (LES) has been an organizing framework of plant functional ecology for the past decade. The LES describes a set of trade-offs among traits related to plant carbon balance. Species with a long leaf lifespan (LLS) invest additional material for leaf protection and structural support, and consequently tend to have a lower leaf photosynthetic rate per unit mass than species with a shorter LLS. 2. While the LES is most apparent...