Recent advances in high-throughput sequencing library preparation and subgenomic enrichment methods have opened new avenues for population genetics and phylogenetics of non-model organisms. To multiplex large numbers of indexed samples while sequencing predominantly orthologous, targeted regions of the genome, we propose modifications to an existing, in-solution capture that utilizes PCR products as target probes to enrich library pools for the genomic subset of interest. The sequence capture using PCR-generated probes (SCPP) protocol requires no specialized...

Studies on the relationship between the optimal phenotype and its environment have had limited focus on genotype-to-phenotype pathways and their evolutionary consequences. Here, we study how multi-layered trait architecture and its associated constraints prescribe diversity. Using an idealized model of the emotion system in fish, we find that trait architecture yields genetic and phenotypic diversity even in absence of frequency-dependent selection or environmental variation. That is, for a given environment, phenotype frequency distributions are predictable...

1.Pervasive and accelerating changes to ecosystems due to human activities remain major sources of uncertainty in predicting the structure and dynamics of ecological communities. Understanding which biotic interactions within natural multitrophic communities are threatened or augmented by invasions of non-native species in the context of other environmental pressures is needed for effective management. 2.We used multivariate autoregressive models with detailed time-series data from largely freshwater and brackish regions of the upper San Francisco Estuary to...

Animals have evolved intricate search strategies to find new sources of food. Here, we analyze a complex food seeking behavior in the nematode Caenorhabditis elegans (C. elegans) to derive a general theory describing different searches. We show that C. elegans, like many other animals, uses a multi-stage search for food, where they initially explore a small area intensively (‘local search’) before switching to explore a much larger area (‘global search’). We demonstrate that these search...

1. Despite extensive development of successional theory, few empirical studies have evaluated whether existing models are applicable to human-modified landscapes. Seasonally dry tropical forests are experiencing widespread transformation, and represent a critical system to assess in a successional framework to infer the mechanisms that shape assembly of secondary forests post-management. 2. We used a functional trait-based approach to assess changes in community assembly mechanisms along succession in secondary dry forests of varying stages following abandonment...

Should animals operating at great speeds and accelerations use fast or slow muscles? The answer hinges on a fundamental tradeoff: muscles can be maximally fast or forceful, but not both. Direct lever systems offer a straightforward manifestation of this tradeoff, yet the fastest organisms use power amplification, not direct lever action. Power-amplified systems typically use slow, forceful muscles to pre-load springs which then rapidly release elastic potential energy to generate high speeds and accelerations. However,...

The North America deserts were impacted by both Neogene plate tectonics and Quaternary climatic fluctuations, yet it remains unclear how these events influenced speciation in this region. We tested published hypotheses regarding the timing and mode of speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a sand dune specialist endemic to the Mojave Desert of California and Arizona. We sampled 109 individual lizards representing 22 insular dune localities, obtained DNA...

Africa is renowned for its biodiversity and endemicity, yet little is known about the factors shaping them across the continent. African Agama lizards (45 species) have a pan-continental distribution, making them an ideal model for investigating biogeography. Many species have evolved conspicuous sexually dimorphic traits, including extravagant breeding coloration in adult males, large adult male body sizes, and variability in social systems among colorful versus drab species. We present a comprehensive time-calibrated species tree for...

Gaining a genomic perspective on phylogeny requires the collection of data from many putatively independent loci across the genome. Among insects, an increasingly common approach to collecting this class of data involves transcriptome sequencing, because few insects have high-quality genome sequences available; assembling new genomes remains a limiting factor; the transcribed portion of the genome is a reasonable, reduced subset of the genome to target; and the data collected from transcribed portions of the genome...

Particularly intriguing examples of adaptive radiation are those in which lineages show parallel or convergent evolution, suggesting utilization of similar genetic or developmental pathways. The current study focuses on an adaptive radiation of Hawaiian “spiny-leg” spiders in which diversification is associated with repeated convergent evolution leading to similar sets of ecomorphs on each island. However, two species on the oldest islands in the archipelago exhibit variability, occurring as two different ecomorphs. More derived species on...

A new dataset of the highest quality specimens of fully articulated, juvenile and mature exoskeletons of the Czech middle Silurian trilobite Aulacopleura koninckii offers improved resolution of original morphology by all measures considered. The degree of variation in both size and shape among later meraspid instars was constant, and suggesting targeted growth in both attributes. Size-related changes in the shape of the dorsal exoskeleton and of the segment-invariant cephalon were detected in the meraspid stage,...

Neotropical migratory birds are declining across the Western Hemisphere, but conservation efforts have been hampered by the inability to assess where migrants are most limited – the breeding grounds, migratory stopover sites, or wintering areas. A major challenge has been the lack of an efficient, reliable, and broadly applicable method for measuring the strength of migratory connections between populations across the annual cycle. Here we show how high-resolution genetic markers can be used to identify...

Andean uplift and the collision of North and South America are thought to have major implications for the diversification of the Neotropical biota. However, few studies have investigated how these geological events may have influenced diversification. We present a multilocus phylogeny of 102 Protieae taxa (73% of published species), sampled pantropically, to test hypotheses about the relative importance of dispersal, vicariance, habitat specialization, and biotic factors in the diversification of this ecologically dominant tribe of...

Changes in sexual signals have the potential to promote rapid divergence and reproductive isolation among populations of animals. Thus, identifying processes contributing to variation in signals is key to understanding the drivers of speciation. However, it is difficult to identify the processes initiating changes in signals in empirical systems because (1) the demographic history of populations under study is usually unclear, and (2) there is no unified hypothesis-testing framework for evaluating the simultaneous contribution of...

The formation of stable genetic boundaries between emerging species is often diagnosed by reduced hybrid fitness relative to parental taxa. This reduced fitness can arise from endogenous and/or exogenous barriers to gene flow. Although detecting exogenous barriers in nature is difficult, we can estimate the role of ecological divergence in driving species boundaries by integrating molecular and ecological niche modelling tools. Here, we focus on a three-way secondary contact zone between three viper species (Vipera...

The oxidation handicap hypothesis (OHH) proposed that honesty in sexual signals is maintained when testosterone simultaneously promotes the development of elaborate signals and imposes an oxidative cost. Although there is evidence that testosterone enhances display traits in some cases, relatively few studies have tested the prediction that testosterone generates oxidative costs. We tested this prediction experimentally by administering testosterone (n = 14) and control (n = 14) implants to free-living common yellowthroat warblers (Geothlypis trichas)...

1.The trade-off between current reproductive effort and survival is a key concept of life history theory. A variety of studies support the existence of this trade-off but the underlying physiological mechanisms are not well-understood. Oxidative stress has been proposed as a potential mechanism underlying the observed inverse relationship between reproductive investment and lifespan. Prolonged fasting is associated with oxidative stress including increases in the production of reactive oxygen species, oxidative damage and inflammation. 2.Northern elephant...

Next-generation sequencing has made it possible to begin asking questions about the process of divergence at the level of the genome. For example, recently there has been a debate around the role of “genomic islands of divergence” (i.e. blocks of outlier loci) in facilitating the process of speciation-with-gene-flow. The Swainson’s thrush, Catharus ustulatus, is a migratory songbird with two genetically-distinct subspecies that differ in a number of traits known to be involved in reproductive isolation...

Introduction: There is little evidence regarding the influence of conflicts of interest on preclinical research. This study examines whether industry sponsorship is associated with increased risks of bias and/or effect sizes of outcomes in published preclinical thiazolidinedione (TZD) studies. Methods: We identified preclinical TZD studies published between January 1, 1965, and November 14, 2012. Coders independently extracted information on study design criteria aimed at reducing bias, results for all relevant outcomes, sponsorship source and investigator...

Reproductive isolation due to pollinator behavior is considered a key mode of speciation in flowering plants. Although floral scent is thought to mediate pollinator behavior, little is known about its effects on pollinator attraction and floral visitation in the wild. We used field experiments with wild hawkmoths and laboratory experiments with naïve hawkmoths to investigate attraction to and probing of flowers in response to indole, a volatile emitted by Ipomopsis tenuituba but not its close...

Molecular analyses of turtle relationships have overturned prevailing morphological hypotheses and prompted the development of a new taxonomy. Here we provide the first genome-scale analysis of turtle phylogeny. We sequenced 2,381 ultraconserved element (UCE) loci representing a total of 1,718,154 bp of aligned sequence. Our sampling includes 32 turtle taxa representing all 14 recognized turtle families and an additional six outgroups. Maximum likelihood, Bayesian, and species tree methods produce a single resolved phylogeny. This robust...

Visual signaling in animals can serve many uses, including predator deterrence and mate attraction. In many cases, signals used to advertise unprofitability to predators are also used for intraspecific communication. Although aposematism and mate choice are significant forces driving the evolution of many animal phenotypes, the interplay between relevant visual signals remains little explored. Here, we address this question in the aposematic passion-vine butterfly Heliconius erato by using color- and pattern-manipulated models to test the...

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...

Migratory birds often form flocks on their wintering grounds, but important details of social structure such as the patterns of association between individuals are virtually unknown. We analysed networks of co-membership in short-term flocks for wintering golden-crowned sparrows (Zonotrichia atricapilla) across three years and discovered social complexity unsuspected for migratory songbirds. The population was consistently clustered into distinct social communities within a relatively small area (~ 7 ha). Birds returned to the same community across...

1. Life history varies across latitudes, with the ‘pace of life’ being ‘slower’ in tropical regions. Because life history is coupled to energy metabolism via allocation tradeoffs and links between performance capacity and energy use, low metabolic intensity is expected in tropical animals. Low metabolism has been reported for lowland tropical birds, but it is unclear if this is due to ‘slow’ life history or to a warm, stable environment. 2. We measured Basal Metabolic...