48 Works

Data from: Spatially explicit analysis sheds new light on the Pleistocene megafaunal extinction in North America

Meaghan M. Emery-Wetherell, Brianna K. McHorse & Edward Byrd Davis
The late Pleistocene megafaunal extinctions may have been the first extinctions directly related to human activity, but in North America the close temporal proximity of human arrival and the Younger Dryas climate event has hindered efforts to identify the ultimate extinction cause. Previous work evaluating the roles of climate change and human activity in the North American megafaunal extinction has been stymied by a reliance on geographic binning, yielding contradictory results among researchers. We used...

Data from: Ranking and characterization of established BMI and lipid associated loci as candidates for gene-environment interactions

Dmitry Shungin, Wei Q. Deng, Tibor V. Varga, Jian'an Luan, Evelin Mihailov, Andres Metspalu, Andrew P. Morris, Nita G. Forouhi, Cecilia Lindgren, Patrik K. E. Magnusson, Nancy L. Pedersen, Göran Hallmans, Audrey Y. Chu, Anne E. Justice, Mariaelisa Graff, Thomas W. Winkler, Lynda M. Rose, Claudia Langenberg, L. Adrienne Cupples, Paul M. Ridker, Nicholas J. Wareham, Ken K. Ong, Ruth J. F. Loos, Daniel I. Chasman, Erik Ingelsson … & Paul W. Franks
Phenotypic variance heterogeneity across genotypes at a single nucleotide polymorphism (SNP) may reflect underlying gene-environment (G·E) or gene-gene interactions. We modeled variance heterogeneity for blood lipids and BMI in up to 44,211 participants and investigated relationships between variance effects (Pv), G·E interaction effects (with smoking and physical activity), and marginal genetic effects (Pm). Correlations between Pv and Pm were stronger for SNPs with established marginal effects (Spearman's ρ=0.401 for triglycerides, and ρ=0.236 for BMI) compared...

Data from: Temporal specificity of the initial adaptive response in motor adaptation

Wilsaan M. Joiner, Gary C. Sing & Maurice A. Smith
Repeated exposure to a novel physical environment eventually leads to a mature adaptive response whereby feedforward changes in motor output mirror both the amplitude and temporal structure of the environmental perturbations. However, adaptive responses at the earliest stages of learning have been found to be not only smaller, but systematically less specific in their temporal structure compared to later stages of learning. This observation has spawned a lively debate as to whether the temporal structure...

Data from: Habitat patterns in tropical rain forests: a comparison of 105 plots in northwest Borneo

Matthew D. Potts, Peter S. Ashton, Les S. Kaufman & Joshua B. Plotkin
Understanding the maintenance of high tropical tree species diversity requires disentangling the effects of habitat vs. geographic distance. Using floristic, topographic, and soil nutrient data from 105 0.6-ha plots in mixed dipterocarp forest throughout Sarawak, Malaysian Borneo, we explore the degree to which floristic patterns are habitat-driven from local to landscape scales. We assess how the floristic influence of geographic distance vs. abiotic factors varies from local to regional scales. We employ several multivariate analytical...

Data from: Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates

Zachary Baker, Molly Schumer, Yuki Haba, Lisa Bashkirova, Chris Holland, Gil G Rosenthal & Molly Przeworski
Studies of highly diverged species have revealed two mechanisms by which meiotic recombination is directed to the genome—through PRDM9 binding or by targeting promoter-like features—that lead to dramatically different evolutionary dynamics of hotspots. Here, we identify PRDM9 orthologs from genome and transcriptome data in 225 species. We find the complete PRDM9 ortholog across distantly related vertebrates but, despite this broad conservation, infer a minimum of six partial and three complete losses. Strikingly, taxa carrying the...

Data from: Edge effects on components of diversity and above-ground biomass in a tropical rainforest

Onja H. Razafindratsima, Kerry A. Brown, Fabio Carvalho, Steig E. Johnson, Patricia C. Wright & Amy E. Dunham
1. Edge effects are among the most significant consequences of forest fragmentation. Therefore, understanding the impacts of edge creation on biodiversity is crucial for forest management and biological conservation. 2. In this study, we used trait-based and phylogenetic approaches to examine the effects of fragmentation on components of diversity and above-ground biomass of rainforest tree communities in Madagascar in forest edge vs. interior habitats. 3. Tree communities in forest edges showed lower phylogenetic diversity relative...

Data from: Walking like an ant: a quantitative and experimental approach to understanding locomotor mimicry in the jumping spider Myrmarachne formicaria

Paul S. Shamble, Ron R. Hoy, Itai Cohen & Tsevi Beatus
Protective mimicry, in which a palatable species avoids predation by being mistaken for an unpalatable model, is a remarkable example of adaptive evolution. These complex interactions between mimics, models and predators can explain similarities between organisms beyond the often-mechanistic constraints typically invoked in studies of convergent evolution. However, quantitative studies of protective mimicry typically focus on static traits (e.g. colour and shape) rather than on dynamic traits like locomotion. Here, we use high-speed cameras and...

Data from: Conserved non-exonic elements: a novel class of marker for phylogenomics

Scott V. Edwards, Alison Cloutier & Allan J. Baker
Noncoding markers have a particular appeal as tools for phylogenomic analysis because, at least in vertebrates, they appear less subject to strong variation in GC content among lineages. Thus far, ultraconserved elements (UCEs) and introns have been the most widely used noncoding markers. Here we analyze and study the evolutionary properties of a new type of noncoding marker, conserved non-exonic elements (CNEEs), which consists of noncoding elements that are estimated to evolve slower than the...

Data from: X-ray microtomography for ant taxonomy: an exploration and case study with two new Terataner (Hymenoptera, Formicidae, Myrmicinae) species from Madagascar

Francisco Hita Garcia, Georg Fischer, Cong Liu, Tracy L. Audisio, Gary D. Alpert, Brian L. Fisher & Evan P. Economo
We explore the potential of x-ray micro computed tomography (μCT) for the field of ant taxonomy by using it to enhance the descriptions of two remarkable new species of the ant genus Terataner: T. balrog sp. n. and T. nymeria sp. n.. We provide an illustrated worker-based species identification key for all species found on Madagascar, as well as detailed taxonomic descriptions, which include diagnoses, discussions, measurements, natural history data, high-quality montage images and distribution...

Data from: Demographic stochasticity and resource autocorrelation control biological invasions in heterogeneous landscapes

Andrea Giometto, Florian Altermatt & Andrea Rinaldo
Mounting theoretical evidence suggests that demographic stochasticity, environmental heterogeneity and biased movement of organisms individually affect the dynamics of biological invasions and range expansions. Studies of species spread in heterogeneous landscapes have traditionally characterized invasion velocities as functions of the mean resource density throughout the landscape, thus neglecting higher-order moments of the spatial resource distribution. Here, we show theoretically that different spatial arrangements of resources lead to different spread velocities even if the mean resource...

Data from: Archipelagic genetics in a widespread Caribbean anole

Robert Graham Reynolds, Tanner R. Strickland, Jason J. Kolbe, Bryan G. Falk, Gad Perry, Liam J. Revell & Jonathan B. Losos
Aim We examine the influence of fluctuating sea levels in a land-bridge archipelago on the apportioning of intraspecific genetic diversity and divergence in the widespread Puerto Rican crested anole (Anolis cristatellus). We compare three alternative scenarios for genetic diversification in an archipelagic species that contrast the relative influences of periodic isolation versus island connectedness driven by fluctuating sea levels. Our approach combines information from geography and population genetics to assess the influence of island size,...

Data from: Repeated evolution of vertebrate pollination syndromes in a recently diverged Andean plant clade

Laura P. Lagomarsino, Elisabeth J. Forrestel, Nathan Muchhala & Charles C. Davis
While specialized interactions, including those involving plants and their pollinators, are often invoked to explain high species diversity, they are rarely explored at macroevolutionary scales. We investigate the dynamic evolution of hummingbird and bat pollination syndromes in the centropogonid clade (Lobelioideae: Campanulaceae), an Andean-centered group of ∼550 angiosperm species. We demonstrate that flowers hypothesized to be adapted to different pollinators based on flower color fall into distinct regions of morphospace, and this is validated by...

Data from: Anchored hybrid enrichment provides new insights into the phylogeny and evolution of longhorned beetles (Cerambycidae)

Stephanie Haddad, Seunggwan Shin, Alan R. Lemmon, Emily Moriarty Lemmon, Petr Svacha, Brian Farrell, Adam Ślipiński, Donald Windsor & Duane D. McKenna
Cerambycidae is a species-rich family of mostly wood-feeding (xylophagous) beetles containing nearly 35 000 known species. The higher-level phylogeny of Cerambycidae has never been robustly reconstructed using molecular phylogenetic data or a comprehensive sample of higher taxa, and its internal relationships and evolutionary history remain the subjects of ongoing debate. We reconstructed the higher-level phylogeny of Cerambycidae using phylogenomic data from 522 single copy nuclear genes, generated via anchored hybrid enrichment. Our taxon sample (31...

Data from: The AAA protein Msp1 mediates clearance of excess tail-anchored proteins from the peroxisomal membrane

Nicholas R. Weir, Roarke A. Kamber, James S. Martenson & Vladimir Denic
Msp1 is a conserved AAA ATPase in budding yeast localized to mitochondria where it prevents accumulation of mistargeted tail-anchored (TA) proteins, including the peroxisomal TA protein Pex15. Msp1 also resides on peroxisomes but it remains unknown how native TA proteins on mitochondria and peroxisomes evade Msp1 surveillance. We used live-cell quantitative cell microscopy tools and drug-inducible gene expression to dissect Msp1 function. We found that a small fraction of peroxisomal Pex15, exaggerated by overexpression, is...

Data from: Dispersing hydrophobic natural colorant β-carotene in shellac particles for enhanced stability and tunable color

Dong Chen, Chun-Xia Zhao, Camille Lagoin, Mingtan Hai, Laura R. Arriaga, Stephan Koehler, Alireza Abbaspourrad & David A. Weitz
Color is one of the most important visual attributes of food and is directly related to the perception of food quality. The interest in natural colorants, especially β-carotene that not only imparts color but also has well-documented health benefits, has triggered the research and development of different protocols designed to entrap these hydrophobic natural molecules to improve their stability against oxidation. Here, we report a versatile microfluidic approach that utilizes single emulsion droplets as templates...

Data from: The role of sexual and natural selection in shaping patterns of sexual dichromatism in the largest family of songbirds (Aves: Thraupidae)

Allison J. Shultz & Kevin J. Burns
Males and females can be under different evolutionary pressures if sexual and natural selection is differentially operating in each sex. As a result, many species have evolved sexual dichromatism, or differences in coloration between sexes. Although sexual dichromatism is often used as an index of the magnitude of sexual selection, sexual dichromatism is a composite trait. Here, we examine the evolution of sexual dichromatism in one of the largest and most ecologically diverse families of...

Data from: Sexual selection constrains the body mass of male but not female mice

James S. Ruff, Douglas H. Cornwall, Linda C. Morrison, Joseph W. Cauceglia, Adam C. Nelson, Shannon M. Gaukler, Shawn Meagher, Lara S. Carroll & Wayne K. Potts
Sexual size dimorphism results when female and male body size is influenced differently by natural and sexual selection. Typically, in polygynous species larger male body size is thought to be favored in competition for mates and constraints on maximal body size are due to countervailing natural selection on either sex; however, it has been postulated that sexual selection itself may result in stabilizing selection at an optimal mass. Here we test this hypothesis by retrospectively...

Data from: Migration in geographic and ecological space by a large herbivore

Wibke Peters, Mark Hebblewhite, Atle Mysterud, Derek Spitz, Stefano Focardi, Ferdinando Urbano, Nicolas Morellet, Marco Heurich, Petter Kjellander, John D.C. Linnell, Francesca Cagnacci & John D. C. Linnell
Partial migration, when only part of the population migrates seasonally while the other part remains resident on the shared range, is the most common form of migration in ungulates. Migration is often defined by spatial separation of seasonal ranges and consequently, classification of individuals as migrants or residents is usually only based on geographic criteria. However, the underlying mechanism for migration is hypothesized to be movement in response to spatiotemporal resource variability and thus, migrants...

Data from: Ant-plant mutualism: a dietary by-product of a tropical ant's macronutrient requirements

Lina M. Arcila Hernández, Jon G. Sanders, Gabriel A. Miller, Alison Ravenscraft & Megan E. Frederickson
Many arboreal ants depend on myrmecophytic plants for both food and shelter; in return, these ants defend their host plants against herbivores, which are often insects. Ant-plant and other mutualisms do not necessarily involve the exchange of costly rewards or services; they may instead result from by-product benefits, or positive outcomes that do not entail a cost for one or both partners. Here, we examined whether the plant-ant Allomerus octoarticulatus pays a short-term cost to...

Data from: Outlier analyses to test for local adaptation to breeding grounds in a migratory arctic seabird

Anna Tigano, Allison J. Shultz, Scott V. Edwards, Gregory J. Robertson & Vicki L. Friesen
Investigating the extent (or the existence) of local adaptation is crucial to understanding how populations adapt. When experiments or fitness measurements are difficult or impossible to perform in natural populations, genomic techniques allow us to investigate local adaptation through the comparison of allele frequencies and outlier loci along environmental clines. The thick-billed murre (Uria lomvia) is a highly philopatric colonial arctic seabird that occupies a significant environmental gradient, shows marked phenotypic differences among colonies, and...

Data from: Origins of lymphatic and distant metastases in human colorectal cancer

Kamila Naxerova, Johannes G. Reiter, Elena Brachtel, Jochen K. Lennerz, Marc Van De Wetering, Andrew Rowan, Tianxi Cai, Hans Clevers, Charles Swanton, Martin A. Nowak, Stephen J. Elledge & Rakesh K. Jain
The spread of cancer cells from primary tumors to regional lymph nodes is often associated with reduced survival. One prevailing model to explain this association posits that fatal, distant metastases are seeded by lymph node metastases. This view provides a mechanistic basis for the TNM staging system and is the rationale for surgical resection of tumor-draining lymph nodes. Here we examine the evolutionary relationship between primary tumor, lymph node, and distant metastases in human colorectal...

Data from: Excavation and aggregation as organizing factors in de novo construction by mound-building termites

Ben Green, Paul Bardunias, J. Scott Turner, Radhika Nagpal & Justin Werfel
Termites construct complex mounds that are orders of magnitude larger than any individual and fulfil a variety of functional roles. Yet the processes through which these mounds are built, and by which the insects organize their efforts, remain poorly understood. The traditional understanding focuses on stigmergy, a form of indirect communication in which actions that change the environment provide cues that influence future work. Termite construction has long been thought to be organized via a...

Data from: Early photosynthetic eukaryotes inhabited low-salinity habitats

Patricia Sánchez-Baracaldo, John A. Raven, Davide Pisani & Andrew H. Knoll
The early evolutionary history of the chloroplast lineage remains an open question. It is widely accepted that the endosymbiosis that established the chloroplast lineage in eukaryotes can be traced back to a single event, in which a cyanobacterium was incorporated into a protistan host. It is still unclear, however, which Cyanobacteria are most closely related to the chloroplast, when the plastid lineage first evolved, and in what habitats this endosymbiotic event occurred. We present phylogenomic...

Data from: Genomic footprints of adaptation in a cooperatively breeding tropical bird across a vegetation gradient

Flavia Termignoni-Garcia, Juan P. Jaramillo-Correa, Juan Chablé-Santos, Mark Liu, Allison J. Shultz, Scott V. Edwards, Patricia Escalante Pliego & Patricia Escalante-Pliego
Identifying the genetic basis of phenotypic variation and its relationship with the environment is key to understanding how local adaptations evolve. Such patterns are especially interesting among populations distributed across habitat gradients, where genetic structure can be driven by isolation by distance (IBD) and/or isolation by environment (IBE). Here, we used variation in ~1,600 high-quality SNPs derived from paired-end sequencing of double-digest restriction site-associated DNA (ddRAD-Seq) to test hypotheses related to IBD and IBE in...

Data from: Ecophysiological variation across a forest-ecotone gradient produces divergent climate change vulnerability within species

Félix Landry Yuan, Adam H. Freedman, Laurent Chirio, Matthew LeBreton & Timothy C. Bonebrake
Climate change related risks and impacts on ectotherms will be mediated by habitats and their influence on local thermal environments. While many studies have documented morphological and genetic aspects of niche divergence across habitats, few have examined thermal performance across such gradients and directly linked this variation to contemporary climate change impacts. In this study, we quantified variation in thermal performance across a gradient from forest to gallery forest-savanna mosaic in Cameroon for a skink...

Registration Year

  • 2017
    48

Resource Types

  • Dataset
    48

Affiliations

  • Harvard University
    48
  • University of Montana
    3
  • Massachusetts Institute of Technology
    3
  • National Museum
    2
  • Rice University
    2
  • Princeton University
    2
  • University of Michigan-Ann Arbor
    2
  • University of Queensland
    2
  • University of North Carolina
    2
  • University of California, Berkeley
    2