458 Works

Data from: Heterochronic shifts and conserved embryonic shape underlie crocodylian craniofacial disparity and convergence

Zachary S. Morris, Kent A. Vliet, Arkhat Abzhanov & Stephanie E. Pierce
The distinctive anatomy of the crocodylian skull is intimately linked with dietary ecology, resulting in repeated convergence on blunt- and slender-snouted ecomorphs. These evolutionary shifts depend upon modifications of the developmental processes which direct growth and morphogenesis. Here we examine the evolution of cranial ontogenetic trajectories to shed light on the mechanisms underlying convergent snout evolution. We use geometric morphometrics to quantify skeletogenesis in an evolutionary context and reconstruct ancestral patterns of ontogenetic allometry to...

Data from: A Palaeozoic stem-group to mite harvestmen revealed through integration of phylogenetics and development

Russell J. Garwood, Prashant P. Sharma, Jason A. Dunlop & Gonzalo Giribet
Successfully placing fossils in phylogenies is integral to understanding the tree of life. Crown-group Paleozoic members of the arachnid order Opiliones are indicative of ancient origins and one of the earliest arthropod terrestrialization events. Opiliones epitomize morphological stasis, and all known fossils have been placed within the four extant suborders. Here we report a Carboniferous harvestman species, Hastocularis argusgen. nov., sp. nov., reconstructed with microtomography (microCT). Phylogenetic analysis recovers this species, and the Devonian Eophalangium...

Data from: Resolving the evolutionary relationships of molluscs with phylogenomic tools

Stephen A. Smith, Casey W. Dunn, Nerida G. Wilson, Freya E. Goetz, Caitlin Feehery, Sónia C. S. Andrade, Greg W. Rouse & Gonzalo Giribet
Molluscs (snails, octopuses, clams, and relatives) have great body plan disparity, and among animals only arthropods surpass them in species number. This diversity has made Mollusca one of the best-studied groups of animals, yet their evolutionary relationships remain poorly resolved. Open questions have important implications for the origin of Mollusca and morphological evolution within the group. These include whether the shell-less vermiform aplacophoran molluscs diverged prior to the origin of the shelled molluscs (Conchifera), or...

Data from: A NGS approach to the encrusting Mediterranean sponge Crella elegans (Porifera, Demospongiae, Poecilosclerida): transcriptome sequencing, characterization and overview of the gene expression along three life cycle stages

Alicia R. Pérez-Porro, Daniel Navarro-Gómez, Maria J. Uriz & Gonzalo Giribet
Sponges can be dominant organisms in many marine and freshwater habitats where they play essential ecological roles. They also represent a key group to address important questions in early metazoan evolution. Recent approaches for improving knowledge on sponge biological and ecological functions as well as on animal evolution have focused on the genetic toolkits involved in ecological responses to environmental changes (biotic and abiotic), development and reproduction. These approaches are possible thanks to newly available,...

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: 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: Ant and mite diversity drives toxin variation in the Little Devil poison frog

Jenna R. McGugan, Gary D. Bryd, Alexandre B. Roland, Stephanie N. Caty, Nisha Kabir, Elicio E. Tapia, Sunia A. Trauger, Luis A. Coloma, Lauren A. O'Connell & Gary D. Byrd
Poison frogs sequester chemical defenses from arthropod prey, although the details of how arthropod diversity contributes to variation in poison frog toxins remains unclear. We characterized skin alkaloid profiles in the Little Devil poison frog, Oophaga sylvatica (Dendrobatidae), across three populations in northwestern Ecuador. Using gas chromatography/mass spectrometry, we identified histrionicotoxins, 3,5- and 5,8-disubstituted indolizidines, decahydroquinolines, and lehmizidines as the primary alkaloid toxins in these O. sylvatica populations. Frog skin alkaloid composition varied along a...

Data from: Examining the full effects of landscape heterogeneity on spatial genetic variation: a multiple matrix regression approach for quantifying geographic and ecological isolation

Ian J. Wang
Understanding the effects of landscape heterogeneity on spatial genetic variation is a primary goal of landscape genetics. Ecological and geographic variables can contribute to genetic structure through geographic isolation, in which geographic barriers and distances restrict gene flow, and ecological isolation, in which gene flow among populations inhabiting different environments is limited by selection against dispersers moving between them. Although methods have been developed to study geographic isolation in detail, ecological isolation has received much...

Data from: Why close relatives make bad neighbors: phylogenetic conservatism in niche preferences and dispersal disproves Darwin’s Naturalization Hypothesis in the thistle tribe

Daniel S. Park & Daniel Potter
The number of exotic plant species that have been introduced into the United States far exceeds that of other groups of organisms, and many of these have become invasive. As in many regions of the globe, invasive members of the thistle tribe, Cardueae, are highly problematic in the California Floristic Province, an established biodiversity hotspot. While Darwin's naturalization hypothesis posits that plant invaders closely related to native species would be at a disadvantage, evidence has...

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: Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas

Bastien Llamas, Lars Fehren-Schmitz, Guido Valverde, Julien Soubrier, Swapan Mallick, Nadin Rohland, Susanne Nordenfelt, Cristina Valdiosera, Stephen M. Richards, Adam Rohrlach, Maria Inés Barreto Romero, Isabel Flores Espinoza, Elsa Tomasto Cagigao, Lucía Watson Jiménez, Krzysztof Makowski, Ilán Santiago Leboreiro Reyna, Josefina Mansilla Lory, Julio Alejandro Ballivián Torrez, Mario A. Rivera, Richard L. Burger, Maria Constanza Ceruti, Johan Reinhard, R. Spencer Wells, Gustavo Politis, Calogero M. Santoro … & Wolfgang Haak
The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native...

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: 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: 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: The role of isoforms in the evolution of cryptic coloration in Peromyscus mice

Ricardo Mallarino, Tess A. Linden, Catherine R. Linnen & Hopi E. Hoekstra
A central goal of evolutionary biology is to understand the molecular mechanisms underlying phenotypic adaptation. While the contribution of protein-coding and cis-regulatory mutations to adaptive traits has been well documented, additional sources of variation – such as the production of alternative RNA transcripts from a single gene, or isoforms – have been understudied. Here, we focus on the pigmentation gene Agouti, known to express multiple alternative transcripts, to investigate the role of isoform usage in...

Data from: Pathogen burden, co-infection and major histocompatibility complex variability in the European badger (Meles meles)

Yung Wa Sin, Geetha Annavi, Hannah L. Dugdale, Chris Newman, Terry Burke & David W. Macdonald
Pathogen-mediated selection is thought to maintain the extreme diversity in the major histocompatibility complex (MHC) genes, operating through the heterozygote advantage, rare-allele advantage and fluctuating selection mechanisms. Heterozygote advantage (i.e., recognizing and binding a wider range of antigens than homozygotes) is expected to be more detectable when multiple pathogens are considered simultaneously. Here, we test if MHC diversity in a wild population of European badgers (Meles meles) is driven by pathogen-mediated selection. We examined individual...

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: 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: 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: Early bursts of body size and shape evolution are rare in comparative data

Luke J. Harmon, Jonathan B. Losos, T. Jonathan Davies, Rosemary G. Gillespie, John L. Gittleman, W. Bryan Jennings, Kenneth H. Kozak, Mark A. McPeek, Franck Moreno-Roark, Thomas J. Near, Andy Purvis, Robert E. Ricklefs, Dolph Schluter, , Ole Seehausen, Brian L. Sidlauskas, Omar Torres-Carvajal, Jason T. Weir & Arne Ø. Mooers
George Gaylord Simpson famously postulated that much of life's diversity originated as adaptive radiations—more or less simultaneous divergences of numerous lines from a single ancestral adaptive type. However, identifying adaptive radiations has proven difficult due to a lack of broad-scale comparative datasets. Here, we use phylogenetic comparative data on body size and shape in a diversity of animal clades to test a key model of adaptive radiation, in which initially rapid morphological evolution is followed...

Data from: Step matrices and the interpretation of homoplasy

Richard H. Ree & Michael J. Donoghue
Assumptions about the costs of character change, coded in the form of a step matrix, determine most-parsimonious inferences of character evolution on phylogenies. We present a graphical approach to exploring the relationship between cost assumptions and evolutionary inferences from character data. The number of gains and losses of a binary trait on a phylogeny can be plotted over a range of cost assumptions, to reveal the inflection point at which there is a switch from...

Data from: Does ecological specialization transcend scale? Habitat partitioning among individuals and species of Anolis lizards

Ambika Kamath & Jonathan B. Losos
Ecological specialization is common across all levels of biological organization, raising the question of whether the evolution of specialization at one scale in a taxon is linked to specialization at other scales. Anolis lizards have diversified repeatedly along axes of habitat use, but it remains unknown if this diversification into habitat use specialists is underlain by individual specialization. From repeated observations of individuals in a population of Anolis sagrei in Florida, we show that the...

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: Protein pheromone expression levels predict and respond to the formation of social dominance networks

Adam C. Nelson, Christopher B. Cunningham, James S. Ruff & Wayne K. Potts
Communication signals are key regulators of social networks and are thought to be under selective pressure to honestly reflect social status, including dominance status. The odours of dominants and nondominants differentially influence behaviour, and identification of the specific pheromones associated with, and predictive of, dominance status is essential for understanding the mechanisms of network formation and maintenance. In mice, major urinary proteins (MUPs) are excreted in extraordinary large quantities and expression level has been hypothesized...

Data from: Testing for phylogenetic conflict among molecular data sets in the Tribe Triticeae (Gramineae)

Roberta J. Mason-Gamer & Elizabeth A. Kellogg
Four molecular data sets are available for the diploid intersterile genera of the cereal grain tribe Triticeae, and there are numerous differences among the four published trees. All six pairwise combinations of data sets were examined using tree comparisons, the incongruence length difference test, the Wilcoxon signed ranks test, and a permutation test. We describe some advantages, disadvantages, and properties of the different comparison methods. Test results provide no evidence for significant differences in the...

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