38 Works

Data from: Stronger selective constraint on downstream genes in the oxidative phosphorylation pathway of cetaceans

Ran Tian, Shixia Xu, Simin Chai, Daiqing Yin, Harold Zakon & Guang Yang
The oxidative phosphorylation (OXPHOS) pathway is an efficient way to produce energy via adenosine triphosphate (ATP), which is critical for sustaining an energy supply for cetaceans in a hypoxic environment. Several studies have shown that natural selection may shape the evolution of the genes involved in OXPHOS. However, how network architecture drives OXPHOS protein sequence evolution remains poorly explored. Here, we investigated the evolutionary patterns of genes in the OXPHOS pathway across six cetacean genomes...

Data from: Phenotypic plasticity drives a depth gradient in male conspicuousness in threespine stickleback, Gasterosteus aculeatus

Chad D. Brock, Molly E. Cummings & Daniel I. Bolnick
Signal evolution is thought to depend on both a signal's detectability or conspicuousness (signal design) as well as any extractable information it may convey to a potential receiver (signal content). While theoretical and empirical work in sexual selection has largely focused on signal content, there has been a steady accrual of evidence that signal design is also important for trait evolution. Despite this, relatively little attention has been paid to spatial variation in the conspicuousness...

Data from: How bird clades diversify in response to climatic and geographic factors

Genoveva Rodriguez-Castaneda, Anouschka R. Hof & Roland Jansson
While the environmental correlates of global patterns in standing species richness are well understood, it is poorly known which environmental factors promote diversification (speciation minus extinction) in clades. We tested several hypotheses for how geographic and climatic variables should affect diversification using a large dataset of bird sister genera endemic to the New World. We found support for the area, evolutionary speed, environmental predictability and climatic stability hypotheses, but productivity and topographic complexity were rejected...

Data from: Body temperature distributions of active diurnal lizards in three deserts: skewed up or skewed down?

Raymond B. Huey & Eric R. Pianka
1. The performance of ectotherms integrated over time depends in part on the position and shape of the distribution of body temperatures (Tb) experienced during activity. For several complementary reasons, physiological ecologists have long expected that Tb distributions during activity should have a long left tail (left-skewed); but only infrequently have they quantified the magnitude and direction of Tb skewness in nature. 2. To evaluate whether left-skewed Tb distributions are general for diurnal desert lizards,...

Data from: Transcriptome dynamics over a lunar month in a broadcast spawning Acroporid coral

Matthew J. Oldach, Matthew Workentine, Mikhail V. Matz, Tung-Yung Fan & Peter D. Vize
On one night per year, at a specific point in the lunar cycle, one of the most extraordinary reproductive events on the planet unfolds as hundreds of millions of broadcast spawning corals release their trillions of gametes into the waters of the tropical seas. Each species spawns on a specific night within the lunar cycle, typically from full moon to third quarter moon, and in a specific time window after sunset. This accuracy is essential...

Data from: Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium)

Oscar M. Vargas, Edgardo M. Ortiz & Beryl B. Simpson
High-throughput sequencing is helping biologists to overcome the difficulties of inferring the phylogenies of recently diverged taxa. The present study analyzes the phylogenetic signal of genomic regions with different inheritance patterns using genome skimming and ddRAD-seq in a species-rich Andean genus (Diplostephium) and its allies. We analyzed the complete nuclear ribosomal cistron, the complete chloroplast genome, a partial mitochondrial genome, and a nuclear-ddRAD matrix separately with phylogenetic methods. We applied several approaches to understand the...

Data from: Genome reduction and microbe-host interactions drive adaptation of a sulfur-oxidizing bacterium associated with a cold seep sponge

Ren-Mao Tian, Weipeng Zhang, Lin Cai, Yue-Him Wong, Wei Ding & Pei-Yuan Qian
As the most ancient metazoan, sponges have established close relationships with particular microbial symbionts. However, the characteristics and physiology of thioautotrophic symbionts in deep-sea sponges are largely unknown. Using a tailored “differential coverage binning” method on 22-Gb metagenomic sequences, we recovered the nearly complete genome of a sulfur-oxidizing bacterium (SOB) that dominates the microbiota of the cold seep sponge Suberites sp. Phylogenetic analyses suggested that this bacterium (an unclassified gammaproteobacterium termed “Gsub”) may represent a...

Data from: Natural selection on MHC IIβ in parapatric lake and stream stickleback: balancing, divergent, both or neither?

William E. Stutz & Daniel I. Bolnick
Major histocompatibility (MHC) genes encode proteins that play a central role in vertebrates’ adaptive immunity to parasites. MHC loci are among the most polymorphic in vertebrates’ genomes, inspiring many studies to identify evolutionary processes driving MHC polymorphism within populations, and divergence between populations. Leading hypotheses include balancing selection favoring rare alleles within populations, and spatially divergent selection. These hypotheses do not always produce diagnosably distinct predictions, causing many studies of MHC to yield inconsistent or...

Data from: The within-host dynamics of infection in trans-generationally primed flour beetles

Ann T. Tate, Peter Andolfatto, Jeffery P. Demuth & Andrea L. Graham
Many taxa exhibit plastic immune responses initiated after primary microbial exposure that provide increased protection against disease-induced mortality and the fitness costs of infection. In several arthropod species, this protection can even be passed from parents to offspring through a phenomenon called trans-generational immune priming. Here, we first demonstrate that trans-generational priming is a repeatable phenomenon in flour beetles (Tribolium castaneum) primed and infected with Bacillus thuringiensis (Bt). We then quantify the within-host dynamics of...

Data from: Predators regulate prey species sorting and spatial distribution in microbial landscapes

George Livingston, Kayoko Fukumori, Diogo Provete, Masanobu Kawachi, Noriko Takamura, Mathew Leibold & Mathew A. Leibold
1. The role of predation in determining the metacommunity assembly model of prey communities is understudied relative to that of interspecific competition among prey. Previous work on metacommunity dynamics of competing species has shown that sorting by habitat patch type and spatial patterning can be affected by disturbances. 2. Microcosms offer a useful model system to test the effect of multi-trophic interactions and disturbance on metacommunity dynamics. Here, we investigated the potential role of predators...

Data from: Adding landscape genetics and individual traits to the ecosystem function paradigm reveals the importance of species functional breadth

Antonio R. Castilla, Nathaniel S. Pope, Megan O´Connell, María F. Rodriguez, Laurel Treviño, Alonso Santos & Shalene Jha
Animal pollination mediates both reproduction and gene flow for the majority of plant species across the globe. However, past functional studies have focused largely on seed production; although useful, this focus on seed set does not provide information regarding species-specific contributions to pollen-mediated gene flow. Here we quantify pollen dispersal for individual pollinator species across more than 690 ha of tropical forest. Specifically, we examine visitation, seed production, and pollen-dispersal ability for the entire pollinator...

Data from: Many-to-one form-to-function mapping weakens parallel morphological evolution

Cole J. Thompson, Newaz Ahmed, Thor Veen, Catherine Lynn Peichel, Andrew P. Hendry, Daniel I. Bolnick & Yoel E. Stuart
Evolutionary ecologists aim to explain and predict evolutionary change under different selective regimes. Theory suggests that such evolutionary prediction should be more difficult for biomechanical systems in which different trait combinations generate the same functional output: “many-to-one mapping”. Many-to-one mapping of phenotype to function enables multiple morphological solutions to meet the same adaptive challenges. Therefore, many-to-one mapping should undermine parallel morphological evolution, and hence evolutionary predictability, even when selection pressures are shared among populations. Studying...

Data from: Field-based high throughput phenotyping rapidly identifies genomic regions controlling yield components in rice

Paul Tanger, Stephen Klassen, Julius P. Mojica, John T. Lovell, Brook T. Moyers, Marietta Baraoidan, Maria Elizabeth B. Naredo, Kenneth L. McNally, Jesse Poland, Daniel R. Bush, Hei Leung, Jan E. Leach & John K. McKay
To ensure food security in the face of population growth, decreasing water and land for agriculture, and increasing climate variability, crop yields must increase faster than the current rates. Increased yields will require implementing novel approaches in genetic discovery and breeding. Here we demonstrate the potential of field-based high throughput phenotyping (HTP) on a large recombinant population of rice to identify genetic variation underlying important traits. We find that detecting quantitative trait loci (QTL) with...

Data from: Resolution of a global mango and fig pest identity crisis

Andrew J. Johnson, Miloš Knížek, Thomas H. Atkinson, Bjarte H. Jordal, Randy C. Ploetz & Jiri Hulcr
Hypocryphalus Hopkins, 1915 and Cryphalus Erichson, 1836 (Curculionidae: Scolytinae: Cryphalini) are significant pests of fig, mango, and other economically important fruit trees, yet have received little attention from systematists. An integrated approach using molecular and morphological evidence resolved the identities of the species feeding on mango and fig. The following taxonomic changes are proposed: Hypocryphalus mangiferae (Stebbing, 1914), stat. rev.; Hypocryphalus dilutus (Eichhoff, 1878a), stat. rev. (=Cryphalus dilutusEichhoff, 1878b, syn. n.); Hypocryphalus discretus (Eichhoff, 1878a),...

Data from: Idiosyncratic responses to climate-driven forest fragmentation and marine incursions in reed frogs from Central Africa and the Gulf of Guinea Islands

Rayna C. Bell, Juan L. Parra, Gabriel Badjedjea, Michael F. Barej, David C. Blackburn, Marius Burger, Alan Channing, J. Maximilian Dehling, Eli Greenbaum, Václav Gvoždík, Jos Kielgast, Chifundera Kusamba, Stefan Lötters, Patrick J. McLaughlin, Zoltán T. Nagy, Mark-Oliver Rödel, Daniel M. Portik, Bryan L. Stuart, Jeremy VanDerWal, Ange-Ghislain Zassi Boulou & Kelly R. Zamudio
Organismal traits interact with environmental variation to mediate how species respond to shared landscapes. Thus, differences in traits related to dispersal ability or physiological tolerance may result in phylogeographic discordance among co-distributed taxa, even when they are responding to common barriers. We quantified climatic suitability and stability, and phylogeographic divergence within three reed frog species complexes across the Guineo-Congolian forests and Gulf of Guinea archipelago of Central Africa to investigate how they responded to a...

Data from: Complex selection on a regulator of social cognition: evidence of balancing selection, regulatory interactions and population differentiation in the prairie vole Avpr1a locus

Alejandro Berrio, Rafael F. Guerrero, Galina V. Aglyamova, Mariam Okhovat, Mikhail V. Matz & Steven M. Phelps
Adaptive variation in social behavior depends upon standing genetic variation, but we know little about how evolutionary forces shape genetic diversity relevant to brain and behavior. In prairie voles (Microtus ochrogaster), variants at the Avpr1a locus predict expression of the vasopressin 1a receptor in the retrosplenial cortex (RSC), a brain region that mediates spatial and contextual memory; cortical V1aR abundance in turn predicts diversity in space-use and sexual fidelity in the field. To examine the...

Data from: Gene expression stasis and plasticity following migration into a foreign environment

Brian K. Lohman, William E. Stutz & Daniel I. Bolnick
Selection against migrants is key to maintaining genetic differences between populations linked by dispersal. However, migrants may mitigate fitness costs by proactively choosing among available habitats, or by phenotypic plasticity. We previously reported that a reciprocal transplant of lake and stream stickleback (Gasterosteus aculeatus) found little support for divergent selection. Here, we revisit that experiment to test whether phenotypic plasticity in gene expression may have helped migrants adjust to unfamiliar habitats. We measured gene expression...

Data from: Asgard archaea illuminate the origin of eukaryotic cellular complexity

Katarzyna Zaremba-Niedzwiedzka, Eva F. Caceres, Jimmy H. Saw, Disa Bäckström, Lina Juzokaite, Emmelien Vancaester, Kiley W. Seitz, Karthik Anantharaman, Piotr Starnawski, Kasper U. Kjeldsen, Matthew B. Stott, Takuro Nunoura, Jillian F. Banfield, Andreas Schramm, Brett J. Baker, Anja Spang & Thijs J. G. Ettema
The origin and cellular complexity of eukaryotes represent a major enigma in biology. Current data support scenarios in which an archaeal host cell and an alphaproteobacterial (mitochondrial) endosymbiont merged together, resulting in the first eukaryotic cell. The host cell is related to Lokiarchaeota, an archaeal phylum with many eukaryotic features. The emergence of the structural complexity that characterizes eukaryotic cells remains unclear. Here we describe the ‘Asgard’ superphylum, a group of uncultivated archaea that, as...

Data from: Population structure and connectivity of the mountainous star coral, Orbicella faveolata, throughout the wider Caribbean region

John P. Rippe, Mikhail V. Matz, Elizabeth A. Green, Mónica Medina, Nida Z. Khawaja, Thanapat Pongwarin, Jorge H. Pinzón C., Karl D. Castillo & Sarah W. Davies
As coral reefs continue to decline worldwide, it becomes ever more necessary to understand the connectivity between coral populations to develop efficient management strategies facilitating survival and adaptation of coral reefs in the future. Orbicella faveolata is one of the most important reef-building corals in the Caribbean and has recently experienced severe population reductions. Here, we utilize a panel of nine microsatellite loci to evaluate the genetic structure of O. faveolata and to infer connectivity...

Data from: Widespread chemical detoxification of alkaloid venom by formicine ants

Edward G. LeBrun, Peter J. Diebold, Matthew R. Orr & Lawrence E. Gilbert
The ability to detoxify defensive compounds of competitors provides key ecological advantages that can influence community-level processes. Although common in plants and bacteria, this type of detoxification interaction is extremely rare in animals. Here, using laboratory behavioral assays and analyses of videotaped interactions in South America, we report widespread venom detoxification among ants in the subfamily Formicinae. Across both data sets, nine formicine species, representing all major clades, used a stereotyped grooming behavior to self-apply...

Data from: Hierarchical social networks shape gut microbial composition in wild Verreaux's sifaka

Amanda C. Perofsky, Rebecca J. Lewis, Laura A. Abondano, Anthony Di Fiore & Lauren Ancel Meyers
In wild primates, social behaviour influences exposure to environmentally acquired and directly transmitted microorganisms. Prior studies indicate that gut microbiota reflect pairwise social interactions among chimpanzee and baboon hosts. Here, we demonstrate that higher-order social network structure—beyond just pairwise interactions—drives gut bacterial composition in wild lemurs, which live in smaller and more cohesive groups than previously studied anthropoid species. Using 16S rRNA gene sequencing and social network analysis of grooming contacts, we estimate the relative...

Data from: Plastome sequencing of ten nonmodel crop species uncovers a large insertion of mitochondrial DNA in cashew

Samar O. Rabah, Chaehee Lee, Nahid H. Hajrah, Rania M. Makki, Hesham F. Alharby, Alawiah M. Alhebshi, Jamal S. M. Sabir, Robert K. Jansen, Tracey A. Ruhlman & Jamal S.M. Sabir
In plant evolution, intracellular gene transfer (IGT) is a prevalent, ongoing process. While nuclear and mitochondrial genomes are known to integrate foreign DNA via IGT and horizontal gene transfer (HGT), plastid genomes (plastomes) have resisted foreign DNA incorporation and only recently has IGT been uncovered in the plastomes of a few land plants. In this study, we completed plastome sequences for l0 crop species and describe a number of structural features including variation in gene...

Data from: Frequency dependence limits divergent evolution by favouring rare immigrants over residents

Daniel I. Bolnick & William E. Stutz
Two distinct forms of natural selection promote adaptive biological diversity. Divergent selection occurs when different environments favour different phenotypes, leading to increased differences between populations. Negative frequency-dependent selection occurs when rare variants within a population are favoured over common ones, increasing diversity within populations. These two diversifying forces promote genetic variation at different spatial scales, and may act in opposition, but their relative effects remain unclear because they are rarely measured concurrently. Here we show...

Data from: Aggression supersedes individual oxygen demand to drive group air-breathing in a social catfish

Shaun S. Killen, Andrew J. Esbaugh, Nicolas Martins, F. Tadeau Rantin, David J. McKenzie, Nicolas F. Martins & F. Tadeu Rantin
1) Group-living is widespread among animals and comes with numerous costs and benefits. To date, research examining group-living has focused on trade-offs surrounding foraging, while other forms of resource acquisition have been largely overlooked. 2) Air breathing has evolved in many fish lineages, allowing animals to obtain oxygen in hypoxic aquatic environments. Breathing air increases the threat of predation, so some species perform group air breathing, to reduce individual risk. Within species, air breathing can...

Data from: Early antiretroviral therapy and potent second-line drugs could decrease HIV incidence of drug resistance

Mingwang Shen, Yanni Xiao, Libin Rong, Lauren Ancel Meyers, Steve E. Bellan & Steven E. Bellan
Early initiation of antiretroviral therapy (ART) reduces the risk of drug-sensitive HIV transmission but may increase the transmission of drug-resistant HIV. We used a mathematical model to estimate the long-term population-level benefits of ART and determine the scenarios under which earlier ART (treatment at 1 year post-infection, on average) could decrease simultaneously both total and drug-resistant HIV incidence (new infections). We constructed an infection-age-structured mathematical model that tracked the transmission rates over the course of...

Registration Year

  • 2017

Resource Types

  • Dataset


  • The University of Texas at Austin
  • University of California, Berkeley
  • University of Florida
  • University of Wyoming
  • University of Bern
  • King Abdulaziz University
  • Smithsonian Tropical Research Institute
  • James Cook University
  • University of Bath
  • Sun Yat-sen University