51 Works

Data from: The interplay of past diversification and evolutionary isolation with present imperilment across the amphibian tree of life

Walter Jetz & R. Alexander Pyron
Human activities continue to erode the tree of life, requiring us to prioritize research and conservation. Amphibians represent key victims and bellwethers of global change, and the need for action to conserve them is drastically outpacing knowledge. We provide a phylogeny incorporating nearly all extant amphibians (7,238 species). Current amphibian diversity is composed of both older, depauperate lineages and extensive, more recent tropical radiations found in select clades. Frog and salamander diversification increased strongly after...

Data from: The Palaeozoic colonization of the water column and the rise of global nekton

Christopher D. Whalen, Derek E.G. Briggs & Derek E. G. Briggs
The colonization of the water column is among the most important transformations in the evolution of animal life and global ecosystems. The Devonian Nekton Revolution (DNR) has been identified as a major macroevolutionary event signifying the sudden occupation of the water column by independent radiations of swimming animals. Using new data, an expanded taxonomic coverage, sample standardization, and increased ecological resolution, we reanalysed the timing, duration, and magnitude of this event. We find that nekton...

Data from: Genetic diversity and population structure of the tsetse fly Glossina fuscipes fuscipes (Diptera: Glossinidae) in Northern Uganda: implications for vector control

Robert Opiro, Norah P. Saarman, Richard Echodu, Elizabeth A. Opiyo, Kirstin Dion, Alexis Halyard, Augustine W. Dunn, Serap Aksoy, Adalgisa Caccone & Philippe Solano
Uganda is the only country where the chronic and acute forms of human African Trypanosomiasis (HAT) or sleeping sickness both occur and are separated by < 100 km in areas north of Lake Kyoga. In Uganda, Glossina fuscipes fuscipes is the main vector of the Trypanosoma parasites responsible for these diseases as well for the animal African Trypanosomiasis (AAT), or Nagana. We used highly polymorphic microsatellite loci and a mitochondrial DNA (mtDNA) marker to provide...

Data from: Organic matter and nutrient inputs from large wildlife influence ecosystem function in the Mara River, Africa

Amanda L. Subalusky, Christopher L. Dutton, Laban Njoroge, Emma J. Rosi & David M. Post
Animals can be important vectors for the movement of resources across ecosystem boundaries. Animals add resources to ecosystems primarily through egestion, excretion and carcasses, and the stoichiometry and bioavailability of these inputs likely interacts with characteristics of the recipient ecosystem to determine their effects on ecosystem function. We studied the influence of hippopotamus excretion/egestion and wildebeest carcasses, and their interactions with discharge, in the Mara River, Kenya. We measured nutrient dissolution and decomposition rates of...

Data from: Phylogeography of a widespread eastern North American shrub, Viburnum lantanoides

Brian Park & Michael J. Donoghue
Premise of the Study: There have been relatively few phylogeographic studies of eastern North American plants, especially of animal‐dispersed shrubby species, and this leaves a significant gap in our understanding of how such species were affected by glacial events. Here, we analyzed the phylogeography of the widespread understory shrub Viburnum lantanoides. Methods: We generated RADseq data and paleoclimatic species distribution models (SDMs) to identify the locations of refugia where V. lantanoides may have survived the...

Data from: The influence of a semi-arid sub-catchment on suspended sediments in the Mara River, Kenya

Christopher L. Dutton, Amanda L. Subalusky, Shimon C. Anisfeld, Laban Njoroge, Emma J. Rosi & David M. Post
The Mara River Basin in East Africa is a trans-boundary basin of international significance experiencing excessive levels of sediment loads. Sediment levels in this river are extremely high (turbidities as high as 6,000 NTU) and appear to be increasing over time. Large wildlife populations, unregulated livestock grazing, and agricultural land conversion are all potential factors increasing sediment loads in the semi-arid portion of the basin. The basin is well-known for its annual wildebeest (Connochaetes taurinus)...

Data from: An inverse latitudinal gradient in speciation rate for marine fishes

Daniel L. Rabosky, Jonathan Chang, Pascal O. Title, Peter F. Cowman, Lauren Sallan, Matt Friedman, Kristin Kaschner, Cristina Garilao, Thomas J. Near, Marta Coll & Michael E. Alfaro
Far more species of organisms are found in the tropics than in temperate and polar regions, but the evolutionary and ecological causes of this pattern remain controversial1,2. Tropical marine fish communities are much more diverse than cold-water fish communities found at higher latitudes3,4, and several explanations for this latitudinal diversity gradient propose that warm reef environments serve as evolutionary ‘hotspots’ for species formation5,6,7,8. Here we test the relationship between latitude, species richness and speciation rate...

Data from: Global geographic patterns in the colours and sizes of animal‐dispersed fruits

Miranda A. Sinnott-Armstrong, Alexander E. Downie, Sarah Federman, Alfredo Valido, Pedro Jordano & Michael J. Donoghue
Aim. Fruit colours attract animal seed dispersers, yet the causes of fruit colour diversity remain controversial. The lack of knowledge of large-scale spatial patterns in fruit colours has limited our ability to formulate and test alternative hypotheses to explain fruit colour, fruit size, and fruit colour diversity. We describe spatial (especially latitudinal) variation in fruit colour, colour diversity, and length, and test for correlations between fruit colour, length, and plant habit. Location. Global. Time period....

Data from: Population genomics through time provides insights into the consequences of decline and rapid demographic recovery through head-starting in a Galapagos giant tortoise

Evelyn L. Jensen, Danielle L. Edwards, Ryan C. Garrick, Joshua M. Miller, James P. Gibbs, Linda J. Cayot, Washington Tapia, Aldalgisa Caccone, Michael A. Russello & Adalgisa Caccone
Population genetic theory related to the consequences of rapid population decline is well-developed, but there are very few empirical studies where sampling was conducted before and after a known bottleneck event. Such knowledge is of particular importance for species restoration, given links between genetic diversity and the probability of long-term persistence. To directly evaluate the relationship between current genetic diversity and past demographic events, we collected genome-wide single nucleotide polymorphism data from pre-bottleneck historical (c.1906)...

Data from: Genetic effects of anthropogenic habitat fragmentation on remnant animal and plant populations: a meta-analysis

Daniel R. Schlaepfer, Brigitte Braschler, Hans-Peter Rusterholz & Bruno Baur
Habitat loss and fragmentation are among the biggest threats to biodiversity. Anthropogenic habitat fragmentation leads to small and isolated remnant plant and animal populations. The combination of increased random genetic drift, inbreeding, and reduced gene flow may substantially reduce genetic variation of remnant populations. However, the magnitude of these responses may depend on several poorly understood factors including organism group, habitat type of both the fragment and the surrounding matrix, life‐history traits, and time since...

Data from: Retracing the Hawaiian silversword radiation despite phylogenetic, biogeographic, and paleogeographic uncertainty

Michael J. Landis, William A. Freyman & Bruce G. Baldwin
The Hawaiian silversword alliance (Asteraceae) is an iconic adaptive radiation. However, like many island plant lineages, no fossils have been assigned to the clade. As a result, the clade's age and diversification rate are not known precisely, making it difficult to test biogeographic hypotheses about the radiation. Without fossils, paleogeographically structured biogeographic processes may inform species divergence times; for example, an island must first exist for a clade to radiate upon it. We date the...

Data from: Tracing the diversification history of a Neogene rodent invasion into South America

Renan Maestri, Nathan S. Upham & Bruce D. Patterson
We investigated spatial patterns of evolutionary relatedness and diversification rates to test hypotheses about the historical biogeographic processes underlying the radiation of Neotropical rats and mice (Sigmodontinae, ~400 species). A negative correlation between mean phylogenetic distance and diversification rates of rodent assemblages reveals a pattern of species co-occurrence in which assemblages of closely related species are also the fastest diversifying ones. Subregions of the Neotropics occupied by distantly related species that are on average more...

Data from: The diversity of population responses to environmental change

Fernando Colchero, Owen R. Jones, Dalia A. Conde, Dave Hodgson, Felix Zajitschek, Benedikt R. Schmidt, Aurelio F. Malo, Susan C. Alberts, Peter H. Becker, Sandra Bouwhuis, Anne M. Bronikowski, Kristel M. De Vleeschouwer, Richard J. Delahay, Stefan Dummermuth, Eduardo Fernández-Duque, John Frisenvænge, Martin Hesselsøe, Sam Larson, Jean-Francois Lemaitre, Jennifer McDonald, David A.W. Miller, Colin O'Donnell, Craig Packer, Becky E. Raboy, Christopher J. Reading … & Chris J. Reading
The current extinction and climate change crises pressure us to predict population dynamics with ever-greater accuracy. Although predictions rest on the well-advanced theory of age-structured populations, two key issues remain poorly-explored. Specifically, how the age-dependency in demographic rates and the year-to-year interactions between survival and fecundity affect stochastic population growth rates. We use inference, simulations, and mathematical derivations to explore how environmental perturbations determine population growth rates for populations with different age-specific demographic rates and...

Data from: The function of the ophiuroid nerve ring: how a decentralized nervous system controls coordinated locomotion

Elizabeth G. Clark, Daichi Kanauchi, Takeshi Kano, Hitoshi Aonuma, Derek E. G. Briggs & Akio Ishiguro
Echinoderms lack a centralized nervous control system yet each extant echinoderm class has evolved unique and effective strategies for locomotion. Brittle stars (Ophiuroidea) stride swiftly over the seafloor by coordinating motions of their five muscular arms. Their arms consist of many repeating segments, requiring them to use a complex control system to coordinate motions among segments and between arms. We conducted in vivo experiments with brittle stars to analyze the functional role of the nerve...

Data from: A phylogenomic resolution of the sea urchin tree of life

Nicolás Mongiardino Koch, Simon E. Coppard, Harilaos A. Lessios, Derek E.G. Briggs, Rich Mooi & Greg W. Rouse
Background: Echinoidea is a clade of marine animals including sea urchins, heart urchins, sand dollars and sea biscuits. Found in benthic habitats across all latitudes, echinoids are key components of marine communities such as coral reefs and kelp forests. A little over 1,000 species inhabit the oceans today, a diversity that traces its roots back at least to the Permian. Although much effort has been devoted to elucidating the echinoid tree of life using a...

Data from: Urban rat races: spatial population genomics of brown rats (Rattus norvegicus) compared across multiple cities

Matthew Combs, Kaylee A. Byers, Bruno M. Ghersi, Michael J. Blum, Adalgisa Caccone, Federico Costa, Chelsea G. Himsworth, Jonathan L. Richardson & Jason Munshi-South
Urbanization often substantially influences animal movement and gene flow. However, few studies to date have examined gene flow of the same species across multiple cities. In this study, we examine brown rats (Rattus norvegicus) to test hypotheses about the repeatability of neutral evolution across four cities: Salvador, Brazil; New Orleans, USA; Vancouver, Canada; New York City, USA. At least 150 rats were sampled from each city and genotyped for a minimum of 15,000 genome-wide SNPs....

Data from: Molecular evolution of key metabolic genes during transitions to C4 and CAM photosynthesis

Eric W. Goolsby, Abigail J. Moore, Lillian P. Hancock, Jurriaan M. De Vos & Erika J. Edwards
PREMISE OF THE STUDY: Next-generation sequencing facilitates rapid production of well-sampled phylogenies built from very large genetic datasets, which can then be subsequently exploited to examine the molecular evolution of the genes themselves. We present an evolutionary analysis of 83 gene families (19 containing carbon-concentrating mechanism (CCM) genes, 64 containing non-CCM genes) in the portullugo clade (Caryophyllales), a diverse lineage of mostly arid-adapted plants that contains multiple evolutionary origins of all known photosynthesis types in...

Data from: Genome-wide assessment of diversity and divergence among extant Galápagos giant tortoise species

Joshua M. Miller, Maud C. Quinzin, Danielle L. Edwards, Deren A.R. Eaton, Evelyn L. Jensen, Michael A. Russello, James P. Gibbs, Washington Tapia, Danny Rueda, Adalgisa Caccone, James P Gibbs, Joshua M Miller, Maud C Quinzin, Deren A R Eaton, Danielle L Edwards, Evelyn L Jensen & Michael A Russello
Genome-wide assessments allow for fuller characterization of genetic diversity, finer-scale population delineation, and better detection of demographically significant units to guide conservation compared to those based on “traditional” markers. Galapagos giant tortoises (Chelonoidis spp.) have long provided a case study for how evolutionary genetics may be applied to advance species conservation. Ongoing efforts to bolster tortoise populations, which have declined by 90%, have been informed by analyses of mitochondrial DNA sequence and microsatellite genotypic data,...

Data from: Destabilizing mutations encode nongenetic variation that drives evolutionary innovation

Katherine L. Petrie, Nathan D. Palmer, Daniel T. Johnson, Sarah J. Medina, Stephanie J. Yan, Victor Li, Alita R. Burmeister & Justin R. Meyer
Evolutionary innovations are often achieved by repurposing existing genes to perform new functions; however, the mechanisms enabling the transition from old to new remain controversial. We identified mutations in bacteriophage λ’s host-recognition gene J that confer enhanced adsorption to λ’s native receptor, LamB, and the ability to access a new receptor, OmpF. The mutations destabilize particles and cause conformational bistability of J, which yields progeny of multiple phenotypic forms, each proficient at different receptors. This...

Data from: Genomic analysis of morphometric traits in bighorn sheep using the Ovine Infinium® HD SNP BeadChip

Joshua M. Miller, Marco Festa-Bianchet & David W. Coltman
Elucidating the genetic basis of fitness-related traits is a major goal of molecular ecology. Traits subject to sexual selection are particularly interesting, as non-random mate choice should deplete genetic variation and thereby their evolutionary benefits. We examined the genetic basis of three sexually selected morphometric traits in bighorn sheep (Ovis canadensis): horn length, horn base circumference, and body mass. These traits are of specific concern in bighorn sheep as artificial selection through trophy hunting opposes...

Data from: Despite high levels of expression in thymic epithelial cells, miR-181a1 and miR-181b1 are not required for thymic development

Heather E. Stefanski, Yan Xing, Patricia A. Taylor, Stefano Maio, Jorge Henao-Meija, Adam Williams, Richard A. Flavell, Georg A. Hollander & Bruce R. Blazar
MicroRNAs (miRNAs) have been shown to be key modulators of post-transcriptional gene silencing in many cellular processes. In previous studies designed to understand the role of miRNAs in thymic development, we globally deleted miRNA exclusively in thymic epithelial cells (TECs), which are critical in thymic selection. This resulted in the loss of stromal cells that instruct T cell lineage commitment and affect thymocyte positive selection, required for mature T cell development. Since murine miR-181 is...

Data from: Increased temperature disrupts the biodiversity-ecosystem functioning relationship

Elodie C. Parain, Rudolf P. Rohr, Sarah M. Gray & Louis-Félix Bersier
Gaining knowledge of how ecosystems provide essential services to humans is of primary importance, especially with the current threat of climate change. Yet, little is known about how increased temperature will impact the biodiversity-ecosystem functioning (BEF) relationship. We tackled this subject theoretically and experimentally. We developed a BEF theory based on mechanistic population dynamic models, which allows the inclusion of the effect of temperature. Using experimentally established relationships between attack rate and temperature, the model...

Data from: Phylogenomic signatures of ancient introgression in a rogue lineage of darters (Teleostei: Percidae)

Daniel J. MacGuigan & Thomas J. Near
Evolutionary history is typically portrayed as a branching phylogenetic tree, yet not all evolution proceeds in a purely bifurcating manner. Introgressive hybridization is one process that results in reticulate evolution. Most known examples of genome-wide introgression occur among closely related species with relatively recent common ancestry; however, we present evidence for ancient hybridization and genome-wide introgression between major stem lineages of darters, a species-rich clade of North American freshwater fishes. Previous attempts to resolve the...

Data from: Cross-biome patterns in soil microbial respiration predictable from evolutionary theory on thermal adaptation

Mark A. Bradford, Rebecca L. McCulley, Thomas W. Crowther, Emily E. Oldfield, Stephen A. Wood & Noah Fierer
Climate warming may stimulate microbial metabolism of soil carbon, causing a carbon cycle-climate feedback whereby carbon is redistributed from soil to atmospheric CO2. The magnitude of this feedback is uncertain, in part because warming-induced shifts in microbial physiology and/or community composition could retard or accelerate soil carbon losses. Here, we measure microbial respiration rates for soils collected from 22 sites in each of three years, at locations spanning boreal to tropical climates. Respiration was measured...

Data from: Developmental shifts in social cognition: socio-emotional biases across the lifespan in rhesus monkeys

Alexandra G. Rosati, Alyssa M. Arre, Michael L. Platt & Laurie R. Santos
Humans exhibit a suite of developmental changes in social cognition across the lifespan. To what extent are these developmental patterns unique? We first review several social domains in which humans undergo critical ontogenetic changes in socio-cognitive processing, including social attention and theory of mind. We then examine whether one human developmental transition—a shift in socioemotional preferences—also occurs in nonhuman primates. Specifically, we experimentally measured socioemotional processing in a large population of rhesus macaques (Macaca mulatta)...

Registration Year

  • 2018
    51

Resource Types

  • Dataset
    51

Affiliations

  • Yale University
    51
  • University of Michigan-Ann Arbor
    6
  • University of Pennsylvania
    4
  • University of California, San Diego
    3
  • University of Minnesota
    3
  • Cary Institute of Ecosystem Studies
    3
  • University of Basel
    3
  • Gulu University
    3
  • University of California Los Angeles
    3
  • National Museums of Kenya
    3