19 Works

Data from: Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa

Tod W. Reeder, Ted M. Townsend, Daniel G. Mulcahy, Brice P. Noonan, Perry L. Wood, , John J. Wiens & Jack W. Sites
Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological...

Data from: Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

Simon Roux, Steven J. Hallam, Tanja Woyke & Matthew B. Sullivan
The ecological importance of viruses is now widely recognized, yet our limited knowledge of viral sequence space and virus-host interactions precludes accurate prediction of their roles and impacts. Here we mined publicly available bacterial and archaeal genomic datasets to identify 12,498 high‑confidence viral genomes linked to their microbial hosts. These data augment public datasets 10-fold, provide first viral sequences for 13 new bacterial phyla including ecologically abundant phyla, and help taxonomically identify 7-38% of 'unknown'...

Data from: The transcriptomic and evolutionary signature of social interactions regulating honey bee caste development

Svjetlana Vojvodic, Brian R. Johnson, Brock A. Harpur, Clement F. Kent, Amro Zayed, Kirk E. Anderson & Timothy A. Linksvayer
The caste fate of developing female honey bee larvae is strictly socially regulated by adult nurse workers. As a result of this social regulation, nurse-expressed genes as well as larval-expressed genes may affect caste expression and evolution. We used a novel transcriptomic approach to identify genes with putative direct and indirect effects on honey bee caste development, and we subsequently studied the relative rates of molecular evolution at these caste-associated genes. We experimentally induced the...

Data from: When do species-tree and concatenated estimates disagree? An empirical analysis with higher-level scincid lizard phylogeny

Shea M. Lambert, Tod W. Reeder & John J. Wiens
Simulation studies suggest that coalescent-based species-tree methods are generally more accurate than concatenated analyses. However, these species-tree methods remain impractical for many large datasets. Thus, a critical but unresolved issue is when and why concatenated and coalescent species-tree estimates will differ. We predict such differences for branches in concatenated trees that are short, weakly supported, and have conflicting gene trees. We test these predictions in Scincidae, the largest lizard family, with data from 10 nuclear...

Data from: Frost sensitivity of leaves and flowers of subalpine plants is related to tissue type and phenology

Paul J. CaraDonna & Justin A. Bain
Harsh abiotic conditions–such as low temperatures that lead to spring and summer frost events in high-elevation and high-latitude ecosystems–can have strong negative consequences for plant growth, survival, and reproduction. Despite the predicted increase in episodic frost events under continued climate change in some ecosystems, our general understanding of the factors associated with frost sensitivity of reproductive and vegetative plant structures in natural plant communities is limited. The timing of growth and reproduction may be an...

Data from: How and when do insects rely on endogenous protein and lipid resources during lethal bouts of starvation? a new application for 13C-breath testing

Marshall D. McCue, R. Marena Guzzman, Celeste A. Passement & Goggy Davidowitz
Most of our understanding about the physiology of fasting and starvation comes from studies of vertebrates; however, for ethical reasons, studies that monitor vertebrates through the lethal endpoint are scant. Insects are convenient models to characterize the comparative strategies used to cope with starvation because they have diverse life histories and have evolved under the omnipresent challenge of food limitation. Moreover, we can study the physiology of starvation through its natural endpoint. In this study...

Crust-Mantle Interactions during Continental Growth and High-Pressure Rock Exhumation at an Oblique Arc-Continent Collision Zone: SE Caribbean Margin

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Passive array deployment to investigate tectonics of the SE Caribbean region. Array will be a 2D array with USArray scale station spacing covering most of the country of Venezuela.

Data from: Re-growing a tropical dry forest: functional plant trait composition and community assembly during succession

Vanessa Buzzard, Catherine M. Hulshof, Trevor Birt, Cyrille Violle & Brian J. Enquist
A longstanding goal of ecology and conservation biology is to understand the environmental and biological controls of forest succession. However, the patterns and mechanisms that guide successional trajectories, especially within tropical forests, remain unclear. We collected leaf functional trait and abiotic data across a 110-year chronosequence within a tropical dry forest in Costa Rica. Focusing on six key leaf functional traits related to resource acquisition and competition, along with measures of forest stand structure, we...

Data from: Shaping species with ephemeral boundaries: the distribution and genetic structure of the desert tortoise (Gopherus morafkai) in the Sonoran Desert region

Taylor Edwards, Mercy Vaughn, Philip C. Rosen, Cristina Meléndez Torres, Alice E. Karl, Melanie Culver & Robert W. Murphy
Aim: We examine the role biogeographical features played in the evolution of Morafka's desert tortoise (Gopherus morafkai) and test the hypothesis that G. morafkai maintains genetically distinct lineages associated with different Sonoran Desert biomes. Increased knowledge of the past and present distribution of the Sonoran Desert region's biota provides insight into the forces that drive and maintain its biodiversity. Location: Sonoran Desert biogeographical region; Sonora and Sinaloa, Mexico and Arizona, USA. Methods: We examined wild...

Data from: Range and niche shifts in response to past climate change in the desert horned lizard (Phrynosoma platyrhinos)

Tereza Jezkova, Jef Jaeger, Viktoria Oláh-Hemmings, K. Bruce Jones, Rafael A. Lara-Resendiz, Daniel G. Mulcahy, Brett R. Riddle & Jef R. Jaeger
During climate change, species are often assumed to shift their geographic distributions (geographic ranges) in order to track environmental conditions – niches – to which they are adapted. Recent work, however, suggests that the niches do not always remain conserved during climate change but shift instead, allowing populations to persist in place or expand into new areas. We assessed the extent of range and niche shifts in response to the warming climate after the Last...

Data from: Pseudomonas syringae enhances herbivory by suppressing the reactive oxygen burst in Arabidopsis

Simon C. Groen, Parris T. Humphrey, Daniela Chevasco, Frederick M. Ausubel, Naomi E. Pierce & Noah K. Whiteman
Plant-herbivore interactions have evolved in the presence of plant-colonizing microbes. These microbes can have important third-party effects on herbivore ecology, as exemplified by drosophilid flies that evolved from ancestors feeding on plant-associated microbes. Leaf-mining flies in the genus Scaptomyza, which is nested within the paraphyletic genus Drosophila, show strong associations with bacteria in the genus Pseudomonas, including Pseudomonas syringae. Adult females are capable of vectoring these bacteria between plants and larvae show a preference for...

Data from: Connecting proximate mechanisms and evolutionary patterns: pituitary gland size and mammalian life history

Jason M. Kamilar & Stacey R. Tecot
At the proximate level, hormones are known to play a critical role in influencing the life history of mammals, including humans. The pituitary gland is directly responsible for producing several hormones, including those related to growth and reproduction. Although we have a basic understanding of how hormones affect life history characteristics, we still have little knowledge of this relationship in an evolutionary context. We used data from 129 mammal species representing 14 orders to investigate...

Data from: The devil is in the details: genetic variation in introduced populations and its contributions to invasion

Katrina M. Dlugosch, Samantha R. Anderson, Joseph Braasch, F. Alice Cang & Heather D. Gillette
The influence of genetic variation on invasion success has captivated researchers since the start of the field of invasion genetics 50 years ago. We review the history of work on this question and conclude that genetic variation—as surveyed with molecular markers—appears to shape invasion rarely. Instead, there is a significant disconnect between marker assays and ecologically relevant genetic variation in introductions. We argue that the potential for adaptation to facilitate invasion will be shaped by...

Data from: Insecticides promote viral outbreaks by altering herbivore competition

Huipeng Pan, Evan L. Preisser, Dong Chu, Shaoli Wang, Qingjun Wu, Yves Carrière, Xuguo Zhou & Youjun Zhang
While the management of biological invasions is often characterized by a series of single-species decisions, invasive species exist within larger food webs. These biotic interactions can alter the impact of control/eradication programs and may cause suppression efforts to inadvertently facilitate invasion spread and impact. We document the rapid replacement of the invasive Bemisia MEAM1 cryptic species by the cryptic MED species throughout China, and demonstrate that MED is more tolerant of insecticides and a better...

Data from: Assessing models of speciation under different biogeographic scenarios; an empirical study using multi-locus and RNA-seq analyses

Taylor Edwards, Marc Tollis, PingHsun Hsieh, Ryan N. Gutenkunst, Zhen Liu, Kenro Kusumi, Melanie Culver & Robert W. Murphy
Evolutionary biology often seeks to decipher the drivers of speciation, and much debate persists over the relative importance of isolation and gene flow in the formation of new species. Genetic studies of closely related species can assess if gene flow was present during speciation, because signatures of past introgression often persist in the genome. We test hypotheses on which mechanisms of speciation drove diversity among three distinct lineages of desert tortoise in the genus Gopherus....

Data from: Geographies of an online social network

Balázs Lengyel, Attila Varga, Bence Ságvári, Ákos Jakobi & János Kertész
How is online social media activity structured in the geographical space? Recent studies have shown that in spite of earlier visions about the “death of distance”, physical proximity is still a major factor in social tie formation and maintenance in virtual social networks. Yet, it is unclear, what are the characteristics of the distance dependence in online social networks. In order to explore this issue the complete network of the former major Hungarian online social...

Data from: Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species

Yuchi Zheng & John J. Wiens
Two common approaches for estimating phylogenies in species-rich groups are to: (i) sample many loci for few species (e.g. phylogenomic approach), or (ii) sample many species for fewer loci (e.g. supermatrix approach). In theory, these approaches can be combined to simultaneously resolve both higher-level relationships (with many genes) and species-level relationships (with many taxa). However, fundamental questions remain unanswered about this combined approach. First, will higher-level relationships more closely resemble those estimated from many genes...

Data from: Colour learning when foraging for nectar and pollen: bees learn two colours at once

Felicity Muth, Daniel R. Papaj & Anne S. Leonard
Bees are model organisms for the study of learning and memory, yet nearly all such research to date has used a single reward, nectar. Many bees collect both nectar (carbohydrates) and pollen (protein) on a single foraging bout, sometimes from different plant species. We tested whether individual bumblebees could learn colour associations with nectar and pollen rewards simultaneously in a foraging scenario where one floral type offered only nectar and the other only pollen. We...

Data from: How should genes and taxa be sampled for phylogenomic analyses with missing data? An empirical study in iguanian lizards

Jeffrey W. Streicher, James A. Schulte & John J. Wiens
Targeted sequence capture is becoming a widespread tool for generating large phylogenomic data sets to address difficult phylogenetic problems. However, this methodology often generates data sets in which increasing the number of taxa and loci increases amounts of missing data. Thus, a fundamental (but still unresolved) question is whether sampling should be designed to maximize sampling of taxa or genes, or to minimize the inclusion of missing data cells. Here, we explore this question for...

Registration Year

  • 2015

Resource Types

  • Dataset


  • University of Arizona
  • Royal Ontario Museum
  • University of Nevada Reno
  • Smithsonian Institution
  • San Diego State University
  • University of Massachusetts Amherst
  • Rice University
  • University of Pennsylvania
  • University of Rhode Island
  • University of California, San Diego