56 Works

Data from: Prolific fruit output by the invader Bellucia pentamera (Melastomataceae) is enhanced by selective logging disturbance

Christopher Dillis, Andrew J. Marshall, Campbell O. Webb & Mark N. Grote
Selective logging in tropical rain forests may promote population growth of invasive plants. The ability of invaders to respond, specifically in reproductive traits, to increases in resource abundance may allow them to increase their presence in the seed rain of recipient communities. The invasive pioneer tree Bellucia pentamera (Melastomataceae) is currently spreading within Gunung Palung National Park in West Kalimantan, Indonesia. The park has also experienced periods of illegal, small-scale, selective logging that seem to...

Data from: The spectre of too many species

Adam D. Leache, Tianqi Zhu, Bruce Rannala & Ziheng Yang
Recent simulation studies examining the performance of Bayesian species delimitation as implemented in the BPP program have suggested that BPP may detect population splits but not species divergences and that it tends to over-split when data of many loci are analyzed. Here we confirm these results and provide the mathematical justifications. We point out that the distinction between population and species splits made in the protracted speciation model has no influence on the generation of...

Data from: GlobTherm, a global database on thermal tolerances for aquatic and terrestrial organisms

Joanne M. Bennett, Piero Calosi, Susana Clusella-Trullas, Brezo Martínez, Jennifer Sunday, Adam C. Algar, Miguel B. Araújo, Bradford A. Hawkins, Sally Keith, Ingolf Kühn, Carsten Rahbek, Laura Rodríguez, Alexander Singer, Fabricio Villalobos, Miguel Ángel Olalla-Tárraga & Ignacio Morales-Castilla
How climate affects species distributions is a longstanding question receiving renewed interest owing to the need to predict the impacts of global warming on biodiversity. Is climate change forcing species to live near their critical thermal limits? Are these limits likely to change through natural selection? These and other important questions can be addressed with models relating geographical distributions of species with climate data, but inferences made with these models are highly contingent on non-climatic...

Data from: Herbarium specimens reveal increasing herbivory over the past century

Emily K. Meineke, Aimee T. Classen, Nathan J. Sanders & T. Jonathan Davies
Predicting how ecological interactions will respond to global change is a major challenge. Plants and their associated insect herbivores compose much of macroscopic diversity, yet how their interactions have been altered by recent environmental change remains underexplored. To address this gap, we quantified herbivory on herbarium specimens of four plant species with records extending back 112 years. Our study focused on the northeastern US, where temperatures have increased rapidly over the last few decades. This...

Data from: Tetraconatan phylogeny with special focus on Malacostraca and Branchiopoda—Highlighting the strength of taxon-specific matrices in phylogenomics

Martin Schwentner, Stefan Richter, D. Christopher Rogers & Gonzalo Giribet
Understanding the evolution of Tetraconata or Pancrustacea —the clade that includes crustaceans and insects—requires a well-resolved hypothesis regarding the relationships within and among its constituent taxa. Herein, we assembled a taxon-rich phylogenomic data set focusing on crustacean lineages based solely on genomes and new-generation Illumina-generated transcriptomes, including 89 representatives of Tetraconata. This constitutes the first phylogenomic study specifically addressing internal relationships of Malacostraca (with 26 species included) and Branchiopoda (36 species). Seven matrices comprising 81...

Data from: Global macroevolution and macroecology of passerine song

William David Pearse, Ignacio Morales-Castilla, Logan S. James, Maxwell Farrell, Frédéric Boivin & T. Jonathan Davies
Studying the macroevolution of the songs of Passeriformes (perching birds) has proved challenging. The complexity of the task stems not just from the macroevolutionary and macroecological challenge of modelling so many species, but also from the difficulty in collecting and quantifying birdsong itself. Using machine learning techniques, we extracted songs from a large citizen science dataset, and then analysed the evolution, and biotic and abiotic predictors of variation in birdsong across 578 passerine species. Contrary...

Data from: Identification of a transporter complex responsible for the cytosolic entry of nitrogen-containing-bisphosphonates

Zhou Yu, Lauren E. Surface, Chong Yon Park, Max A Horlbeck, Gregory A Wyant, Monther Abu-Remaileh, Timothy R. Peterson, David M. Sabatini, Jonathan S. Weissman & Erin K. O'Shea
Nitrogen-containing-bisphosphonates (N-BPs) are widely prescribed to treat osteoporosis and other bone-related diseases. Although previous studies established that N-BPs function by inhibiting the mevalonate pathway in osteoclasts, the mechanism by which N-BPs enter the cytosol from the extracellular space to reach their molecular target is not understood. Here we implemented a CRISPRi-mediated genome-wide screen and identified SLC37A3 (solute carrier family 37 member A3) as a gene required for the action of N-BPs in mammalian cells. We...

Data from: Locality or habitat? Exploring predictors of biodiversity in Amazonia

Camila D. Ritter, Alexander Zizka, Christopher Barnes, R. Henrik Nilsson, Fabian Roger & Alexandre Antonelli
Amazonia is an environmentally heterogeneous and biologically megadiverse region, and its biodiversity varies considerably over space. However, existing knowledge on Amazonian biodiversity and its environmental determinants stems almost exclusively from studies of macroscopic above‐ground organisms, notably vertebrates and trees. In contrast, diversity patterns of most other organisms remain elusive, although some of them, for instance microorganisms, constitute the overwhelming majority of taxa in any given location, both in terms of diversity and abundance. Here, we...

Data from: The relationship between post-mating reproductive isolation and reinforcement in Phlox

Sevan S. Suni & Robin Hopkins
The process of speciation involves the accumulation of reproductive isolation (RI) between diverging lineages. Selection can favor increased RI via the process of reinforcement, whereby costs to hybridization impose selection for increased prezygotic RI. Reinforcement results in phenotypic divergence within at least one taxon, as a result of costly hybridization between sympatric taxa. The strength of selection driving reinforcement is determined by the cost of hybridization and the frequency of hybridization. We investigated the cost...

Data from: Social behavior in bees influences the abundance of Sodalis (Enterobacteriaceae) symbionts

Benjamin E. R. Rubin, Jon G. Sanders, Kyle M. Turner, Naomi E. Pierce & Sarah D. Kocher
Social interactions can facilitate transmission of microbes between individuals, reducing variation in gut communities within social groups. Thus, the evolution of social behaviors and symbiont community composition have the potential to be tightly linked. We explored this connection by characterizing the diversity of bacteria associated with both eusocial and solitary bee species within the behaviorally variable family Halictidae using 16S amplicon sequencing. Contrary to expectations, we found few differences in bacterial abundance or variation between...

Data from: The effects of skeletal asymmetry on interpreting biological variation and taphonomy in the fossil record

Brandon P. Hedrick, Emma R. Schachner, Gabriel Rivera, Peter Dodson & Stephanie E. Pierce
Biological asymmetry is present in all bilaterally symmetric organisms as a result of normal developmental instability. However, fossilized organisms, which have undergone distortion due to burial, may have additional asymmetry as a result of taphonomic processes. To investigate this issue, we evaluated the magnitude of shape variation resulting from taphonomy on vertebrate bone using a novel application of fluctuating asymmetry. We quantified the amount of total variance attributed to asymmetry in a taphonomically distorted fossil...

Data from: The International Tree-Ring Data Bank (ITRDB) revisited: data availability and global ecological representativity

Shoudong Zhao, Neil Pederson, Loïc D'Orangeville, Janneke HilleRisLambers, Emery Boose, Caterina Penone, Bruce Bauer, Yuan Jiang & Rubén D. Manzanedo
Aim: The International Tree-Ring Data Bank (ITRDB) is the most comprehensive database of tree growth. To evaluate its usefulness and improve its accessibility to the broad scientific community, we aimed to: i) quantify its biases, ii) assess how well it represents global forests, iii) develop tools to identify priority areas to improve its representativity, and iv) make available the corrected database. Location: Worldwide. Time period: Contributed datasets between 1974 and 2017. Major taxa studied: Trees....

Data from: Structural complexity of hunting habitat and territoriality increase the reversed sexual size dimorphism in diurnal raptors

Lorenzo Pérez-Camacho, Sara Martínez-Hesterkamp, Salvador Rebollo, Gonzalo García-Salgado & Ignacio Morales-Castilla
Despite numerous efforts and many hypotheses to explain the selective pressures that may have favoured reversed sexual dimorphism (RSD) in raptors ‐ i.e. that the female is larger than the male ‐ some drivers of RSD are still unknown. Here we analyse how much variation in RSD is explained by hunting habitat structure, territoriality or territory size. We do so using data on diurnal raptors from the New World and the Western Palearctic – i.e....

Data from: MADA: Malagasy Animal trait Data Archive

Onja H. Razafindratsima, Yasmin Yacoby & Daniel S. Park
Species are characterized by their behavioral, physiological and ecological attributes, which determine their role in ecosystems. In turn, ecosystems and their functions are defined by the species that inhabit them. Thus, evaluating the functional diversity and distributions of species is of utmost importance to studies of biogeography, community ecology, macroevolution, and conservation. The functional diversity of species are determined by traits such as diet, foraging strata, trophic level, activity cycle, litter size, generation length, habitat...

Data from: The unrealized potential of herbaria in global change biology

Emily K. Meineke, Charles C. Davis & T. Jonathan Davies
Plant and fungal specimens in herbaria are becoming primary resources for investigating how plant phenology and geographic distributions shift with climate change, greatly expanding inferences across spatial, temporal, and phylogenetic dimensions. However, these specimens contain a wealth of additional data—including nutrients, defensive compounds, herbivore damage, disease lesions, and signatures of physiological processes—that capture ecological and evolutionary responses to the Anthropocene but which are less frequently utilized. Here, we outline the diversity of herbarium data, global...

Data from: Comprehensive experimental fitness landscape and evolutionary network for small RNA

José I. Jimenez, Ramon Xulvi-Brunet, Gregory W. Campbell, Rebecca Turk-MacLeod & Irene A. Chen
The origin of life is believed to have progressed through an RNA world, in which RNA acted as both genetic material and functional molecules. The structure of the evolutionary fitness landscape of RNA would determine natural selection for the first functional sequences. Fitness landscapes are the subject of much speculation, but their structure is essentially unknown. Here we describe a comprehensive map of a fitness landscape, exploring nearly all of sequence space, for short RNAs...

Data from: Early arrival and climatically-linked geographic expansion of New World monkeys from tiny African ancestors

Daniele Silvestro, Marcelo F. Tejedor, Martha L. Serrano-Serrano, Oriane Loiseau, Victor Rossier, Jonathan Rolland, Alexander Zizka, Sebastian Höhna, Alexandre Antonelli & Nicolas Salamin
New World monkeys (platyrrhines) are one of the most diverse groups of primates, occupying today a wide range of ecosystems in the American tropics and exhibiting large variations in ecology, morphology, and behavior. Although the relationships among the almost 200 living species are relatively well understood, we lack robust estimates of the timing of origin, ancestral morphology, and geographic range evolution of the clade. Here we integrate paleontological and molecular evidence to assess the evolutionary...

Data from: PHYLACINE 1.2: The Phylogenetic Atlas of Mammal Macroecology

Søren Faurby, Matt Davis, Rasmus Østergaard Pedersen, Simon D. Schowanek, Alexandre Antonelli & Jens-Christian Svenning
Data needed for macroecological analyses are difficult to compile and often hidden away in supplementary material under non-standardized formats. Phylogenies, range data, and trait data often use conflicting taxonomies and require ad hoc decisions to synonymize species or fill in large amounts of missing data. Furthermore, most available data sets ignore the large impact that humans have had on species ranges and diversity. Ignoring these impacts can lead to drastic differences in diversity patterns and...

Data from: The evolutionary history of dogs in the Americas

Máire Ní Leathlobhair, Angela R. Perri, Evan K. Irving-Pease, Kelsey E. Witt, Anna Linderholm, James Haile, Ophelie Lebrasseur, Carly Ameen, Jeffrey Blick, Adam R. Boyko, Selina Brace, Yahaira Nunes Cortes, Susan J. Crockford, Alison Devault, Evangelos A. Dimopoulos, Morley Eldridge, Jacob Enk, Shyam Gopalakrishnan, Kevin Gori, Vaughan Grimes, Eric Guiry, Anders J. Hansen, Ardern Hulme-Beaman, John Johnson, Andrew Kitchen … & Laurent A. F. Frantz
Dogs were present in the Americas prior to the arrival of European colonists, but the origin and fate of these pre-contact dogs are largely unknown. We sequenced 71 mitochondrial and seven nuclear genomes from ancient North American and Siberian dogs spanning ~9,000 years. Our analysis indicates that American dogs were not domesticated from North American wolves. Instead, American dogs form a monophyletic lineage that likely originated in Siberia and dispersed into the Americas alongside people....

Data from: Phylogenomic data yield new and robust insights into the phylogeny and evolution of weevils

Seunggwan Shin, Dave J. Clarke, Alan R. Lemmon, Emily Moriarty Lemmon, Alexander L. Aitken, Stephanie Haddad, Brian D. Farrell, Adriana E. Marvaldi, Rolf G. Oberprieler & Duane D. McKenna
The phylogeny and evolution of weevils (the beetle superfamily Curculionoidea) has been extensively studied, but many relationships, especially in the large family Curculionidae (true weevils; > 50000 species), remain uncertain. We used phylogenomic methods to obtain DNA sequences from 522 protein coding genes for representatives of all families of weevils and all subfamilies of Curculionidae. Most of our phylogenomic results had strong statistical support, and the inferred relationships were generally congruent with those reported in...

Data from: Adaptation and constraint in the evolution of the mammalian backbone

Katrina E. Jones, Lorena Benitez, Kenneth D. Angielczyk & Stephanie E. Pierce
Background: The axial skeleton consists of repeating units (vertebrae) that are integrated through their development and evolution. Unlike most tetrapods, vertebrae in the mammalian trunk are subdivided into distinct thoracic and lumbar modules, resulting in a system that is constrained in terms of count but highly variable in morphology. This study asks how thoracolumbar regionalization has impacted adaptation and evolvability across mammals. Using geometric morphometrics, we examine evolutionary patterns in five vertebral positions from diverse...

Data from: The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history

Danièle L. Filiault, Evangeline S. Ballerini, Terezie Mandakova, Gökçe Aköz, Nathan J. Derieg, Jeremy Schmutz, Jerry Jenkins, Jane Grimwood, Shengqiang Shu, Richard D. Hayes, Uffe Hellsten, Kerrie Barry, Juying Yan, Sirma Mihaltcheva, Miroslava Karafiatova, Viktoria Nizhynska, Elena M. Kramer, Martin A. Lysak, Scott A. Hodges & Magnus Nordborg
The columbine genus Aquilegia is a classic example of an adaptive radiation, involving a wide variety of pollinators and habitats. Here we present the genome assembly of A. coerulea 'Goldsmith', complemented by high-coverage sequencing data from 10 wild species covering the world-wide distribution. Our analyses reveal extensive allele sharing among species, and demonstrate that introgression and selection played a role in the Aquilegia radiation. We also present the remarkable discovery that the evolutionary history of...

Data from: Regional population structure of the endangered Bridle Shiner (Notropis bifrenatus)

Anthony J. Geneva, Andrea M. Kreit, Shane Neiffer, Susan Tsang & Richard J. Horwitz
In the last 100 years, the Bridle Shiner has declined over significant parts of its range. We used mitochondrial and nuclear microsatellite markers to investigate population structure of this species. Tissue samples were collected from populations in six drainages in PA, NJ, NY and CT. One predominant haplotype was observed in the Delaware, Housatonic, Passaic, and Raritan specimens. Specimens from the Hudson and St. Lawrence drainages had a separate unique haplotype. Microsatellite loci revealed low...

Data from: Linking a mutation to survival in wild mice

Rowan D. H. Barrett, Stefan Laurent, Ricardo Mallarino, Susanne P. Pfeifer, Charles C. Y. Xu, Matthieu Foll, Kazumasa Wakamatsu, Jonathan S. Duke-Cohan, Jeffrey D. Jensen & Hopi E. Hoekstra
Adaptive evolution in new or changing environments can be difficult to predict because the functional connections between genotype, phenotype, and fitness are complex. Here, we make these explicit connections by combining field and laboratory experiments in wild mice. We first directly estimate natural selection on pigmentation traits and an underlying pigment locus, Agouti, by using experimental enclosures of mice on different soil colors. Next, we show how a mutation in Agouti associated with survival causes...

Data from: Male harassment, female movements, and genetic diversity in a fragmented metapopulation

Paul M. Severns & Greg A. Breed
Interactions with males often alter the short‐term behaviors of reproductive females. Yet, the influence of different internal and external factors, such as sexual conflict, on animal movement and patch dynamics is not well understood. We studied associations between courtship, movements of reproductive females, and genetic diversity in a small, fragmented network of Euphydras editha taylori (Taylor's checkerspot butterfly). In the absence of courtship, female movements (step lengths) were restricted (< 2 m) and tortuous, and...

Registration Year

  • 2018
    56

Resource Types

  • Dataset
    56

Affiliations

  • Harvard University
    56
  • University of British Columbia
    5
  • McGill University
    4
  • University of Gothenburg
    4
  • University of Cambridge
    3
  • Indiana University Bloomington
    3
  • Yale University
    3
  • University of Washington
    2
  • University of Michigan-Ann Arbor
    2
  • Field Museum of Natural History
    2