16 Works

Data from: Detecting spatial genetic signatures of local adaptation in heterogeneous landscapes

Brenna R. Forester, Matthew R. Jones, Stéphane Joost, Erin L. Landguth & Jesse R. Lasky
The spatial structure of the environment (e.g., the configuration of habitat patches) may play an important role in determining the strength of local adaptation. However, previous studies of habitat heterogeneity and local adaptation have largely been limited to simple landscapes, which poorly represent the multi-scale habitat structure common in nature. Here, we use simulations to pursue two goals: (1) we explore how landscape heterogeneity, dispersal ability, and selection affect the strength of local adaptation, and...

Data from: Quantifying the human impacts on Papua New Guinea reef fish communities across space and time

Joshua A. Drew, Ruth A. Hufbauer & Kathryn L. Amatangelo
Describing the drivers of species loss and of community change are important goals in both conservation and ecology. However, it is difficult to determine whether exploited species decline due to direct effects of harvesting or due to other environmental perturbations brought about by proximity to human populations. Here we quantify differences in species richness of coral reef fish communities along a human population gradient in Papua New Guinea to understand the relative impacts of fishing...

Data from: Genetics, morphology, advertisement calls, and historical records distinguish six new polyploid species of African clawed frog (Xenopus, Pipidae) from West and Central Africa

Ben J. Evans, Timothy F. Carter, Eli Greenbaum, Václav Gvoždík, Darcy B. Kelley, Patrick J. McLaughlin, Olivier S. G. Pauwels, Daniel M. Portik, Edward L. Stanley, Richard C. Tinsley, Martha L. Tobias & David C. Blackburn
African clawed frogs, genus Xenopus, are extraordinary among vertebrates in the diversity of their polyploid species and the high number of independent polyploidization events that occurred during their diversification. Here we update current understanding of the evolutionary history of this group and describe six new species from west and central sub-Saharan Africa, including four tetraploids and two dodecaploids. We provide information on molecular variation, morphology, karyotypes, vocalizations, and estimated geographic ranges, which support the distinctiveness...

Data from: The fitness consequences of kin-biased dispersal in a cooperatively breeding bird

Lea Pollack & Dustin R. Rubenstein
Cooperative alliances among kin may not only lead to indirect fitness benefits for group-living species, but can also provide direct benefits through access to mates or higher social rank. However, the immigrant sex in most species loses any potential benefits of living with kin unless immigrants disperse together or recruit relatives into the group in subsequent years. To look for evidence of small subgroups of related immigrants within social groups (kin substructure), we used microsatellites...

Data from: Can the source-sink hypothesis explain macrofaunal abundance patterns in the abyss? A modeling test

Sarah M. Hardy, Craig R. Smith & Andreas M. Thurnherr
Low food availability is a major structuring force in deep-sea benthic communities, sustaining only very low densities of organisms in parts of the abyss. These low population densities may result in an Allee effect, whereby local reproductive success is inhibited, and populations are maintained by larval dispersal from bathyal slopes. This slope–abyss source–sink (SASS) hypothesis suggests that the abyssal seafloor constitutes a vast sink habitat with macrofaunal populations sustained only by an influx of larval...

Data from: Soil nutrients influence growth response of temperate tree species to drought

Mathieu Lévesque, Lorenz Walthert & Pascale Weber
Soil properties can buffer forest response to global climate change. However, it is unclear how soil characteristics, water availability and their interactions can affect drought response of trees. The aim of this study was to assess the influence of soil nutrients and physical soil properties on the growth sensitivity of Fagus sylvatica, Quercus spp., Fraxinus excelsior, Abies alba, Picea abies and Pinus sylvestris to drought in Central Europe. Yearly growth data from increment cores were...

Data from: Agricultural intensification and the functional capacity of soil microbes on smallholder African farms

Stephen A. Wood, Mark A. Bradford, Jack A. Gilbert, Krista L. McGuire, Cheryl A. Palm, Katherine L. Tully, Jizhong Zhou & Shahid Naeem
1. Fertilization may impact ecosystem processes that sustain agriculture, such as nutrient cycling, by altering the composition of soil microbial communities that regulate such processes. These processes are crucial to low-input, smallholder tropical agriculture, which supports 900 million of the world's poorest people. Yet little is known about how efforts to increase crop yield on such farms will affect the capacity of soil microbial communities to carry out ecosystem processes. 2. We studied the diversity...

Data from: Gene-wise association of variants in four lysosomal storage disorder genes in neuropathologically confirmed Lewy Body disease

Lorraine N. Clark, Robin Chan, Rong Cheng, Xinmin Liu, Naeun Park, Nancy Parmalee, Sergey Kisselev, Etty Cortes, Paola A. Torres, Gregory M. Pastores, Jean P. Vonsattel, Roy Alcalay, Karen Marder, Lawrence L. Honig, Stanley Fahn, Richard Mayeux, Michael Shelanski, Gilbert Di Paolo & Joseph H. Lee
Objective: Variants in GBA are associated with Lewy Body (LB) pathology. We investigated whether variants in other lysosomal storage disorder (LSD) genes also contribute to disease pathogenesis. Methods: We performed a genetic analysis of four LSD genes including GBA, HEXA, SMPD1, and MCOLN1 in 231 brain autopsies. Brain autopsies included neuropathologically defined LBD without Alzheimer Disease (AD) changes (n = 59), AD without significant LB pathology (n = 71), Alzheimer disease and lewy body variant...

Data from: Environmental gradients and the evolution of successional habitat specialization: a test case with 14 Neotropical forest sites

Susan G. Letcher, Jesse R. Lasky, Robin L. Chazdon, Natalia Norden, S. Joseph Wright, Jorge A. Meave, Eduardo A. Pérez-García, Rodrigo Muñoz, Eunice Romero-Pérez, Ana Andrade, José Luis Andrade, Patricia Balvanera, Justin M. Becknell, Tony V. Bentos, Radika Bhaskar, Frans Bongers, Vanessa Boukili, Pedro H. S. Brancalion, Ricardo G. César, Deborah A. Clark, David B. Clark, Dylan Craven, Alexander DeFrancesco, Juan M. Dupuy, Bryan Finegan … & G. Bruce Williamson
1. Successional gradients are ubiquitous in nature, yet few studies have systematically examined the evolutionary origins of taxa that specialize at different successional stages. Here we quantify successional habitat specialization in Neotropical forest trees and evaluate its evolutionary lability along a precipitation gradient. Theoretically, successional habitat specialization should be more evolutionarily conserved in wet forests than in dry forests due to more extreme microenvironmental differentiation between early and late successional stages in wet forest. 2....

Data from: Sex-specific fitness effects of unpredictable early life conditions are associated with DNA methylation in the avian glucocorticoid receptor

Dustin R. Rubenstein, Hannah Skolnik, Alejandro Berrio, Frances A. Champagne, Steven Phelps & Joseph Solomon
Organisms can adapt to variable environments by using environmental cues to modulate developmental gene expression. In principle, maternal influences can adaptively adjust offspring phenotype when early life and adult environments match, but they may be maladaptive when future environments are not predictable. One of the best-studied ‘maternal effects’ is through modification of the offspring's hypothalamic–pituitary–adrenal (HPA) axis, the neuroendocrine system that controls responses to stress. In addition to the direct transfer of glucocorticoids from mother...

Data from: Understanding the dominant controls on litter decomposition

Mark A. Bradford, Bjorn Berg, Daniel S. Maynard, William R. Wieder & Stephen A. Wood
Litter decomposition is a biogeochemical process fundamental to element cycling within ecosystems, influencing plant productivity, species composition and carbon storage. Climate has long been considered the primary broad-scale control on litter decomposition rates, yet recent work suggests that plant litter traits may predominate. Both decomposition paradigms, however, rely on inferences from cross-biome litter decomposition studies that analyse site-level means. We re-analyse data from a classical cross-biome study to demonstrate that previous research may falsely inflate...

Data from: Reproductive skew drives patterns of sexual dimorphism in sponge-dwelling snapping shrimps

Solomon Tin Chi Chak, J. Emmett Duffy & Dustin R. Rubenstein
Sexual dimorphism is typically a result of strong sexual selection on male traits used in male–male competition and subsequent female choice. However, in social species where reproduction is monopolized by one or a few individuals in a group, selection on secondary sexual characteristics may be strong in both sexes. Indeed, sexual dimorphism is reduced in many cooperatively breeding vertebrates and eusocial insects with totipotent workers, presumably because of increased selection on female traits. Here, we...

Data from: Stable recombination hotspots in birds

Sonal Singhal, Ellen M. Leffler, Keerthi Sannareddy, Isaac Turner, Oliver Venn, Daniel M. Hooper, Alva I. Strand, Qiye Li, Brian Raney, Christopher N. Balakrishnan, Simon C. Griffith, Gil McVean & Molly Przeworski
The DNA-binding protein PRDM9 has a critical role in specifying meiotic recombination hotspots in mice and apes, but it appears to be absent from other vertebrate species, including birds. To study the evolution and determinants of recombination in species lacking the gene that encodes PRDM9, we inferred fine-scale genetic maps from population resequencing data for two bird species: the zebra finch, Taeniopygia guttata, and the long-tailed finch, Poephila acuticauda. We found that both species have...

Data from: Genome-environment associations in sorghum landraces predict adaptive traits

Jesse R. Lasky, Hari D. Upadhyaya, Punna Ramu, Santosh Deshpande, C. Tom Hash, Jason Bonnette, Thomas E. Juenger, Katie Hyma, Charlotte Acharya, Sharon E. Mitchell, Edward S. Buckler, Zachary Brenton, Stephen Kresovich & Geoffrey P. Morris
Improving environmental adaptation in crops is essential for food security under global change, but phenotyping adaptive traits remains a major bottleneck. If associations between single-nucleotide polymorphism (SNP) alleles and environment of origin in crop landraces reflect adaptation, then these could be used to predict phenotypic variation for adaptive traits. We tested this proposition in the global food crop Sorghum bicolor, characterizing 1943 georeferenced landraces at 404,627 SNPs and quantifying allelic associations with bioclimatic and soil...

Data from: Keeping cool: enhanced optical reflection and heat dissipation in silver ants

Norman Nan Shi, Cheng-Chia Tsai, Fernando Camino, Gary D. Bernard, Nanfang Yu & Rüdiger Wehner
Saharan silver ants, Cataglyphis bombycina, forage under extreme temperature conditions in the African desert. We show that the ants’ conspicuous silvery appearance is created by a dense array of triangular hairs with two thermoregulatory effects. They enhance not only the reflectivity of the ant’s body surface in the visible and near-infrared range of the spectrum, where solar radiation culminates, but also the emissivity of the ant in the mid-infrared. The latter effect enables the animals...

Data from: Characterization of a novel fusion gene EML4-NTRK3 in a case of recurrent congenital fibrosarcoma

Sarah Tannenbaum-Dvir, Julia L. Glade Bender, Alanna J. Church, Katherine A. Janeway, Marian H. Harris, Mahesh M. Mansukhani, Peter L. Nagy, Stuart J. Andrews, Vundavalli V. Murty, Angela Kadenhe-Chiweshe, Eileen P. Connolly, Andrew L. Kung & Filemon S. Dela Cruz
We describe the clinical course of a recurrent case of congenital fibrosarcoma diagnosed in a 9-mo-old boy with a history of hemimelia. Following complete surgical resection of the primary tumor, the patient subsequently presented with bulky bilateral pulmonary metastases 6 mo following surgery. Molecular characterization of the tumor revealed the absence of the prototypical ETV6-NTRK3 translocation. However, tumor characterization incorporating cytogenetic, array comparative genomic hybridization, and RNA sequencing analyses, revealed a somatic t(2;15)(2p21;15q25) translocation resulting...

Registration Year

  • 2015
    16

Resource Types

  • Dataset
    16

Affiliations

  • Columbia University
    16
  • The University of Texas at Austin
    2
  • Yale University
    2
  • Museo de Historia Natural Noel Kempff Mercado
    1
  • University of Montana
    1
  • University of Washington
    1
  • Federal University of São Carlos
    1
  • Department of Plant Biology
    1
  • Del Rosario University
    1
  • University of Minnesota
    1