The demand that anatomical structures work together to perform biological functions is thought to impose strong limits on morphological evolution. Breakthroughs in diversification can occur, however, when functional integration among structures is relaxed. Although such transitions are expected to generate variation in morphological diversification across the tree of life, empirical tests of this hypothesis are rare. Here we show that transitions between suction-based and biting modes of prey capture, which require different degrees of coordination...

The repeated occurrence of abnormal amphibians in nature points to ecological imbalance, yet identifying causes of these abnormalities has proved complex. Multiple studies have linked amphibian abnormalities to chemically contaminated areas, but inference about causal mechanisms is lacking. Here we use a high incidence of abnormalities in Alaskan wood frogs to strengthen inference about the mechanism for these abnormalities. We suggest that limb abnormalities are caused by a combination of multiple stressors. Specifically, toxicants lead...

Temporal priority can affect individual performance and reproduction, as well as community assembly, but whether these effects persist over time remains unclear, and their demographic mechanisms have been little explored. The continued dominance of exotic annual grasses in California has been commonly attributed to their demonstrated early germination and rapid early growth relative to native perennial grasses. This advantage may play a crucial role in the structure of California exotic annual grasslands, as well as...

Organisms across the tree of life use a variety of mechanisms to respond to stress-inducing fluctuations in osmotic conditions. Cellular response mechanisms and phenotypes associated with osmoadaptation also play important roles in bacterial virulence, human health, agricultural production and many other biological systems. To improve understanding of osmoadaptive strategies, we have generated 59 high-quality draft genomes for the haloarchaea (a euryarchaeal clade whose members thrive in hypersaline environments and routinely experience drastic changes in environmental...

1. Human impacts are often thought of as homogenizing natural communities, but it is unclear how these impacts interact to alter the beta diversity (spatial variability) of plant communities. 2. In a grassland with high beta diversity along a soil fertility gradient, we asked which combinations of nutrient enrichment, precipitation enhancement, and disturbance would homogenize communities along the gradient by allowing dominant species from one part of the gradient to increase their abundances in other...

The Bayesian method of species delimitation (Yang and Rannala, 2010) uses a so-called guide tree to reduce the number of models to be evaluated in the reversible-jump Markov chain Monte Carlo (rjMCMC) algorithm (Green, 1995). It has been pointed out that the method tends to over-split if a random population tree is used as the guide tree (Fujita and Leaché, 2011). Here we conduct a simulation study to examine the performance of the method under...

Although Madagascar is an ancient fragment of Gondwana, the majority of taxa studied thus far appear to have reached the island through dispersal from Cenozoic times. Ancient lineages may have experienced a different history compared to more recent Cenozoic arrivals, as such lineages would have encountered geoclimatic shifts over an extended time period. The motivation for this study was to unravel the signature of diversification in an ancient lineage by comparing an area known for...

Gelatinous polymers including extracellular polymeric substances (EPSs) are fundamental to biophysical processes in aquatic habitats, including mediating aggregation processes and functioning as the matrix of biofilms. Yet insight into the impact of these sticky molecules on the environmental transmission of pathogens in the ocean is limited. We used the zoonotic parasite Toxoplasma gondii as a model to evaluate polymer-mediated mechanisms that promote transmission of terrestrially derived pathogens to marine fauna and humans. We show that...

In theory, predator-prey pairs with extinction-prone local populations can persist through metapopulation dynamics, wherein local populations fluctuate asynchronously, occasionally providing dispersers that prevent permanent extinction in all patches. A few studies have shown that spatial structure can extend predator-prey persistence. However, no studies have unequivocally demonstrated the asynchrony among patches, low dispersal rates, and rescue effects that prove metapopulation dynamics extend persistence. We used a protist predator-prey pair to show that spatial subdivision lengthens persistence...

Characterizations of coy females and ardent males are rooted in models of sexual selection that are increasingly outdated. Evolutionary feedbacks can strongly influence the sex roles and subsequent patterns of sex differentiated investment in mating effort, with a key component being the adult sex ratio (ASR). Using data from eight Makushi communities of southern Guyana, characterized by varying ASRs contingent on migration, we show that even within a single ethnic group, male mating effort varies...

1. Ecological filter models derived from community assembly theory can inform restoration planning by highlighting management actions most likely to affect community composition. Despite growing interest in these models, many restoration studies solely manipulate a single filter—the biotic filter by altering interspecific competition in studies—while ignoring abiotic and dispersal filters that may also influence restoration success. 2. To examine how manipulating all three filters (biotic, abiotic, dispersal) affected restoration in an annual-type grassland, we seeded...

Background Army ants are dominant invertebrate predators in tropical and subtropical terrestrial ecosystems. Their close relatives within the dorylomorph group of ants are also highly specialized predators, although much less is known about their biology. We analyzed molecular data generated from 11 nuclear genes to infer a phylogeny for the major dorylomorph lineages, and incorporated fossil evidence to infer divergence times under a relaxed molecular clock. Results Because our results indicate that one subfamily and...

Parasitic flowering plants are one of the most destructive agricultural pests and have major impact on crop yields throughout the world. Being dependent on finding a host plant for growth, parasitic plants penetrate their host using specialized organs called haustoria. Haustoria establish vascular connections with the host, which enable the parasite to steal nutrients and water. The underlying molecular and developmental basis of parasitism by plants is largely unknown. In order to investigate the process...

Adaptive radiation is recognized by a rapid burst of phenotypic, ecological, and species diversification. However, it is unknown whether different species within an adaptive radiation evolve reproductive isolation at different rates. We compared patterns of genetic differentiation among nascent species within an adaptive radiation of Cyprinodon pupfishes using genotyping by sequencing. Similar to classic adaptive radiations, this clade exhibits rapid morphological diversification rates and two species are novel trophic specialists, a scale-eater and hard-shelled prey...

Both landscape structure and population size fluctuations influence population genetics. While independent effects of these factors on genetic patterns and processes are well studied, a key challenge is to understand their interaction, as populations are simultaneously exposed to habitat fragmentation and climatic changes that increase variability in population size. In a population network of an alpine butterfly, abundance declined 60–100% in 2003 because of low over-winter survival. Across the network, mean microsatellite genetic diversity did...

There is considerable interest in the genetics of wolves (Canis lupus) because of their close relationship to domestic dogs (C. familiaris) and the need for informed conservation and management. This includes wolf populations in Southeast Alaska for which we determined genotypes of 305 wolves at 173662 single nucleotide polymorphism (SNP) loci. After removal of invariant and linked SNP, 123801 SNP were used to quantify genetic differentiation of wolves in Southeast Alaska and wolves, coyotes (C....

Advances in sequencing technology have forced a quantitative revolution in Evolutionary Biology. One important feature of this renaissance is that comprehensive genomic resources can be obtained quickly for almost any taxon, thus speeding the development of new model organisms. Here, we analyze 20 RNA-seq libraries from morphologically, sexually, and genetically distinct polyp types from the gonochoristic colonial hydrozoan, Hydractinia symbiolongicarpus (Cnidaria). Analyses of these data using weighted gene co-expression networks highlight deeply conserved genetic elements...

Drosophila suzukii recently invaded North America and Europe. Populations in Hawaii, California, New York and Nova Scotia are polymorphic for Wolbachia, typically with <20% infection frequency. The Wolbachia in D. suzukii, denoted wSuz, is closely related to wRi, the variant prevalent in continental populations of D. simulans. wSuz is also nearly identical to Wolbachia found in D. subpulchrella, plausibly D. suzukii's sister species. This suggests vertical Wolbachia transmission through cladogenesis (“cladogenic transmission”). The widespread occurrence...

Many species of large wildlife have declined drastically worldwide. These reductions often lead to profound shifts in the ecology of entire communities and ecosystems. However, the effects of these large wildlife declines on other taxa likely hinge upon both underlying abiotic properties of these systems and on the types of secondary anthropogenic changes associated with wildlife loss, making impacts difficult to predict. To better understand how these important contextual factors determine the consequences of large-wildlife...

Widely distributed taxa provide an opportunity to compare biogeographic responses to climatic fluctuations on multiple continents and to investigate speciation. We conducted the most geographically and genomically comprehensive study to date of the red fox (Vulpes vulpes), the world's most widely distributed wild terrestrial carnivore. Analyses of 697 bp of mitochondrial sequence in ~1000 individuals suggested an ancient Middle Eastern origin for all extant red foxes and a 400 kya (SD = 139 kya) origin...

1. Plant communities are structured by complex interactions between multiple factors, which veil our understanding of the effects of environmental changes on communities and ecosystems. Besides the relative role of biotic and abiotic factors as community-structuring processes, addressing how they jointly affect the ecological resilience and resistance of plant communities is crucial to understand better the long-term response of communities facing global changes. 2. Here, we used the results from a long-term (23 years) perturbation...

Background: Safflower (Carthamus tinctorius L.) is an oilseed crop in the Compositae (a.k.a. Asteraceae) that is valued for its oils rich in unsaturated fatty acids. Here, we present an analysis of the genetic architecture of safflower domestication and compare our findings to those from sunflower (Helianthus annuus L.), an independently domesticated oilseed crop within the same family. We mapped quantitative trait loci (QTL) underlying 24 domestication-related traits in progeny from a cross between safflower and...

Environmental variation drives ecological and phenotypic change. How predictable is differentiation in response to environmental change? Answering this question requires the development and testing of multifarious a priori predictions in natural systems. We employ this approach using Gobiomorus dormitor populations that have colonized inland blue holes differing in the availability of fish prey. We evaluated predictions of differences in demographics, habitat use, diet, locomotor and trophic morphology, and feeding kinematics and performance between G. dormitor...

Next generation sequencing and the application of population genomic and association approaches have made it possible to detect selection and unravel the genetic basis to variable phenotypic traits. Using the two approaches in parallel is an especially attractive approach in non-models organisms that lack a sequenced and annotated genome, but only works well when population structure is not confounded with the phenotype of interest. Herein, we use population genomics in a non-model fish species, rainbow...

Mimulus guttatus and M. nasutus are an evolutionary and ecological model sister species pair differentiated by ecology, mating system, and partial reproductive isolation. Despite extensive research on this system, the history of divergence and differentiation in this sister pair is unclear. We present and analyze a population genomic data set which shows that M. nasutus budded from a central Californian M. guttatus population within the last 200 to 500 thousand years. In this time, the...