38 Works

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: 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: 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: 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: 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: 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...

Data from: Impact of the Late Triassic mass extinction on functional diversity and composition of marine ecosystems

Alexander M. Dunhill, William J. Foster, James Sciberras & Richard J. Twitchett
Mass extinctions have profoundly influenced the history of life, not only through the death of species but also through changes in ecosystem function and structure. Importantly, these events allow us the opportunity to study ecological dynamics under levels of environmental stress for which there are no recent analogues. Here, we examine the impact and selectivity of the Late Triassic mass extinction event on the functional diversity and functional composition of the global marine ecosystem, and...

Data from: New records of the late Pliensbachian to early Toarcian (Early Jurassic) gladius-bearing coleoid cephalopods from the Ya Ha Tinda Lagerstätte, Canada

Selva M. Marroquín, Rowan C. Martindale & Dirk Fuchs
The Ya Ha Tinda Lagerstätte from Alberta, Canada, is the first Jurassic marine Konservat-Lagerstätte from North America and hosts a substantial collection of exceptionally preserved fossil Vampyropoda specimens. Vampyropods are soft-bodied cephalopods (coleoids) characterized by eight arms and an internalized chitinous shell (gladius). Due to their lack of hard parts, Vampyropoda have a fragmentary fossil record, largely limited to exceptional Lagerstätten deposits. Excavations at Ya Ha Tinda have uncovered sixteen vampyropod fossils from Pliensbachian and...

Data from: DNA sequencing of fish eggs and larvae reveals high species diversity and seasonal changes in spawning activity in the southeastern Gulf of California

Ana L.M. Ahern, Jaime Gómez-Gutiérrez, Octavio J. Aburto-Oropeza, Ricardo J. Saldierna-Martínez, Andrew F. Johnson, Alice E. Harada, Arturo R. Sánchez-Uvera, Brad Erisman, David I. Castro Arvizú & Ronald S. Burton
Ichthyoplankton studies can provide valuable information on the species richness and spawning activity of fishes, complementing estimations done using trawls and diver surveys. Zooplankton samples were collected weekly between January and December 2014 in Cabo Pulmo National Park, Gulf of California, Mexico (n=48). Fish larvae and particularly eggs are difficult to identify morphologically, therefore the DNA barcoding method was employed to identify 4,388 specimens, resulting in 158 Operational Taxonomic Units (OTUs) corresponding to species. Scarus...

Data from: Chromosomal speciation in the genomics era: disentangling phylogenetic evolution of rock-wallabies

Sally Potter, Jason G. Bragg, Mozes P. Blom, Janine E. Deakin, Mark Kirkpatrick, Mark D. Eldridge, Craig Moritz, Mozes P. K. Blom & Mark D. B. Eldridge
The association of chromosome rearrangements with speciation is well established, and there is a long history of theory and evidence relating to “chromosomal speciation”. Genomic sequencing has the potential to provide new insights into how reorganization of genome structure promotes divergence, and in model systems has demonstrated reduced gene flow in rearranged segments. However, there are limits to what we can understand from a small number of model systems, which each only tell us about...

Data from: Plasticity contributes to a fine-scale depth gradient in sticklebacks’ visual system

Thor Veen, Chad Brock, Diana Rennison & Daniel Bolnick
The light environment influences an animal’s ability to forage, evade predators, and find mates, and consequently is known to drive local adaptation of visual systems. However, the light environment may also vary over fine spatial scales at which genetic adaptation is difficult. For instance, in aquatic systems the available wavelengths of light change over a few meters depth. Do animals plastically adjust their visual system to such small-scale environmental light variation? Here, we show that...

Data from: Effects of hypoxia and ocean acidification on the upper thermal niche boundaries of coral reef fishes

Rasmus Ern, Jacob L. Johansen, Jodie L. Rummer & Andrew J. Esbaugh
Rising ocean temperatures are predicted to cause a poleward shift in the distribution of marine fishes occupying the extent of latitudes tolerable within their thermal range boundaries. A prevailing theory suggests that the upper thermal limits of fishes are constrained by hypoxia and ocean acidification. However, some eurythermal fish species do not conform to this theory, and maintain their upper thermal limits in hypoxia. Here we determine if the same is true for stenothermal species....

Data from: Exceptional preservation and the fossil record of tetrapod integument

Chad M. Eliason, Leah Hudson, Taylor Watts, Hector Garza & Julia A. Clarke
The fossil record of exceptionally preserved soft tissues in Konservat-Lagerstätten provides rare yet significant insight into past behaviours and ecologies. Such deposits are known to occur in bursts rather than evenly through time, but reasons for this pattern and implications for the origins of novel structures remain unclear. Previous assessments of these records focused on marine environments preserving chemically heterogeneous tissues from across animals. Here, we investigate the preservation of skin and keratinous integumentary structures...

Data from: Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary

Yan-Jie Feng, David C. Blackburn, Dan Liang, David M. Hillis, David B. Wake, David C. Cannatella & Peng Zhang
Frogs (Anura) are one of the most diverse groups of vertebrates and comprise nearly 90% of living amphibian species. Their worldwide distribution and diverse biology make them well-suited for assessing fundamental questions in evolution, ecology, and conservation. However, despite their scientific importance, the evolutionary history and tempo of frog diversification remain poorly understood. By using a molecular dataset of unprecedented size, including 88-kb characters from 95 nuclear genes of 156 frog species, in conjunction with...

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: Mating status correlates with dorsal brightness in some but not all poison frog populations

Corinna E. Dreher, Ariel Rodríguez, Molly E. Cummings & Heike Pröhl
Sexual signals are important for intraspecific communication and mate selection, but their evolution may be driven by both natural and sexual selection, and stochastic processes. Strawberry poison frogs (Oophaga pumilio) show strong color divergence among populations, but coloration also varies among individuals of the same population. The importance of coloration for female mate choice has been studied intensely, and sexual selection seems to affect color divergence in strawberry poison frogs. However, the effect of coloration...

Data from: The melanocortin system regulates body pigmentation and social behaviour in a colour polymorphic cichlid fish

Peter D. Dijkstra, Sean M. Maguire, Rayna M. Harris, Agosto A. Rodriguez, Ross S. DeAngelis, Stephanie A. Flores & Hans A. Hofmann
The melanocortin system is a neuroendocrine system that regulates a range of physiological and behavioural processes. We examined the extent to which the melanocortin system simultaneously regulates colour and behaviour in the cichlid fish Astatotilapia burtoni. We found that yellow males are more aggressive than blue males, in line with previous studies. We then found that exogenous α-melanocyte-stimulating hormone (α-MSH) increases yellowness of the body and dispersal of xanthophore pigments in both morphs. However, α-MSH...

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: 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: 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: 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: 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: 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: 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...

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