1. Agriculture now constitutes 40–50% of terrestrial land use globally. By enhancing habitat suitability and connectivity, restoration within agricultural landscapes could have a major influence on biodiversity conservation. However, habitat management within intensive agricultural landscapes may primarily boost abundances of common, highly mobile generalists, rather than vulnerable or endangered species. We studied pollinator community response to small-scale habitat restoration in the intensively farmed Central Valley of California to determine whether restoration could also promote more...

We explore the estimation of uncertainty in evolutionary parameters using a recently devised approach for resampling entire additive genetic variance–covariance matrices (G). Large-sample theory shows that maximum-likelihood estimates (including restricted maximum likelihood, REML) asymptotically have a multivariate normal distribution, with covariance matrix derived from the inverse of the information matrix, and mean equal to the estimated G. This suggests that sampling estimates of G from this distribution can be used to assess the variability of...

In many species with internal fertilization, molecules transferred in the male ejaculate trigger and interact with physiological changes in females. It is controversial to what extent these interactions between the sexes act synergistically to mediate the female switch to a reproductive state or instead reflect sexual antagonism evolved as a byproduct of sexual selection on males. To address this question, we eliminated sexual selection by enforcing monogamy in populations of Drosophila melanogaster for 65 generations...

Global climate change and increases in sea levels will affect coastal marine communities. The conservation of these ecologically important areas will be a challenge because of their wide geographic distribution, ecological diversity and species richness. To address this problem, we need to better understand how the genetic variation of the species in these communities is distributed within local populations, among populations and between distant regions. In this study we apply genotyping by sequencing (GBS) and...

Background: Using molecular data generated by high throughput next generation sequencing (NGS) platforms to infer phylogeny is becoming common as costs go down and the ability to capture loci from across the genome goes up. While there is a general consensus that greater numbers of independent loci should result in more robust phylogenetic estimates, few studies have compared phylogenies resulting from smaller datasets for commonly used genetic markers with the large datasets captured using NGS....

Speed regulations of watercraft in protected areas are designed to reduce lethal collisions with wildlife but can have economic consequences. We present a quantitative framework for investigating the risk of deadly collisions between boats and wildlife. We apply encounter rate theory to demonstrate how marine mammal-boat encounter rate can be used to predict the expected number of deaths associated with management scenarios. We illustrate our approach with management scenarios for two endangered species: the Florida...

Studies of the adaptive significance of variation among conspecific populations often focus on a single ecological factor. However, habitats rarely differ in only a single ecological factor, creating a challenge for identifying the relative importance of the various ecological factors that might be maintaining local adaptation. Here we investigate the ecological factors associated with male body shape variation among nine populations of the poeciliid fish, Heterandria formosa, from three distinct habitats and combine those results...

Selection can vary geographically across environments and temporally over the lifetime of an individual. Unlike geographic contexts, where different selective regimes can act on different alleles, age-specific selection is constrained to act on the same genome by altering age-specific expression. Snake venoms are exceptional traits for studying ontogeny because toxin expression variation directly changes the phenotype; relative amounts of venom components determine, in part, venom efficacy. Phenotypic integration is the dependent relationship between different traits...

The swamp type of the Asian water buffalo is assumed to have been domesticated by about 4000 years BP, following the introduction of rice cultivation. Previous localizations of the domestication site were based on mitochondrial DNA (mtDNA) variation within China, accounting only for the maternal lineage. We carried out a comprehensive sampling of China, Taiwan, Vietnam, Laos, Thailand, Nepal and Bangladesh and sequenced the mtDNA Cytochrome b gene and control region and the Y-chromosomal ZFY,...

The purpose of this study was to delineate the topological dynamics of pain and discomfort during constant exercise performed until volitional exhaustion. Eleven physical education students were tested while cycling and running at a “hard” intensity level (e.g., corresponding to Borg’s RPE (6–20) = 15). During the tests, participants reported their discomfort and pain on a body map every 15s. “Time on task” for each participant was divided into five equal non-overlapping temporal windows within...

Precise exponential scaling with size is a fundamental aspect of phenotypic variation. These allometric power laws are often invariant across taxa and have long been hypothesized to reflect developmental constraints. Here we test this hypothesis by investigating the evolutionary potential of an allometric scaling relationship in drosophilid wing shape that is nearly invariant across 111 species separated by at least 50 million years of evolution. In only 26 generations of artificial selection in a population...

East Africa is a drought prone, food and water insecure region with a highly variable climate. This complexity makes rainfall estimation challenging, and this challenge is compounded by low rain gauge densities and inhomogeneous monitoring networks. The dearth of observations is particularly problematic over the past decade, since the number of records in globally accessible archives has fallen precipitously. This lack of data coincides with an increasing scientific and humanitarian need to place recent seasonal...

Delimiting species is important to every subfield in biology. Templeton's cohesion species concept uses genetic and ecological exchangeability to identify sets of populations that ought to be considered as the same species, and the lack of exchangeability helps determine which populations can be grouped as evolutionarily significant units (ESU) in conservation science. However, previous work assessing genetic and ecological interchangeability among populations has been limited in scope. Here, we provide a method for assessing exchangeability...

Fragmented species complexes provide an interesting system for investigating biogeographic history and the present distribution of genetic variation. Recent advances in sequencing technology and statistical phylogeography enable the collection and rigorous analysis of large multilocus data sets, but designing studies that produce meaningful phylogeographic inferences remains challenging. We implemented a Bayesian model comparison approach to investigate previous biogeographic hypotheses while simultaneously inferring the presence of genetic structure in a chorus frog species complex. The Illinois...

Despite considerable progress in unravelling the phylogenetic relationships of microhylid frogs, relationships among subfamilies remain largely unstable and many genera are not demonstrably monophyletic. Here, we used five alternative combinations of DNA sequence data (ranging from seven loci for 48 taxa to up to 73 loci for as many as 142 taxa) generated using the anchored phylogenomics sequencing method (66 loci, derived from conserved genome regions, for 48 taxa) and Sanger sequencing (seven loci for...

We calculated the linkage disequilibrium between all pairs of variants in the Drosophila Genome Reference Panel with minor allele count ≥5. We used r2 ≥ 0.5 as the cutoff for a highly correlated SNP. We make available the list of all highly correlated SNPs for use in association studies. Seventy-six percent of variant SNPs are highly correlated with at least one other SNP, and the mean number of highly correlated SNPs per variant over the...

Background: The past decade has witnessed remarkable progress towards resolution of the Tree of Life. However, despite the increased use of genomic scale datasets, some phylogenetic relationships remain difficult to resolve. Here we employ anchored phylogenomics to capture 107 nuclear loci in 29 species of acanthomorph teleost fishes, with 25 of these species sampled from the recently delimited clade Ovalentaria. Previous studies employing multilocus nuclear exon datasets have not been able to resolve the nodes...

The importance of intraspecific variation has emerged as a key question in community ecology, helping to bridge the gap between ecology and evolution. Although much of this work has focused on plant species, recent syntheses have highlighted the prevalence and potential importance of morphological, behavioral, and life history variation within animals for ecological and evolutionary processes. Many small-bodied consumers live on the plant that they consume, often resulting in host plant-associated trait variation within and...