184 Works

Data from: Antagonistic pleiotropy and mutation accumulation contribute to age-related decline in stress response

Elizabeth Rose Everman & Theodore J. Morgan
As organisms age, the effectiveness of natural selection weakens, leading to age-related decline in fitness-related traits. The evolution of age-related changes associated with senescence is likely influenced by mutation accumulation (MA) and antagonistic pleiotropy (AP). MA predicts that age-related decline in fitness components is driven by age-specific sets of alleles, non-negative genetic correlations within trait across age, and an increase in the coefficient of genetic variance. AP predicts that age-related decline in a trait is...

Data from: Synthesis of phylogeny and taxonomy into a comprehensive tree of life

Cody E. Hinchliff, Stephen A. Smith, James F. Allman, J. Gordon Burleigh, Ruchi Chaudhary, Lyndon M. Coghill, Keith A. Crandall, Jiabin Deng, Bryan T. Drew, Romina Gazis, Karl Gude, David S. Hibbett, Laura A. Katz, , Emily Jane McTavish, Peter E. Midford, Christopher L. Owen, Richard H. Ree, Jonathan A. Rees, Douglas E. Soltis, Tiffani Williams & Karen Ann Cranston
Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly...

Data from: Conservation genetics of Australasian sailfin lizards: flagship species threatened by coastal development and insufficient protected area coverage

Cameron D. Siler, Andrés Lira-Noriega & Rafe M. Brown
Despite rampant coastal development throughout Southeast Asia and the Pacific, studies of conservation genetics and ecology of vulnerable, coastal species are rare. Large bodied vertebrates with highly specialized habitat requirements may be at particular risk of extinction due to habitat degradation and fragmentation, especially if these habitats are naturally patchily distributed, marginal, or otherwise geographically limited, or associated in space with high human population densities or heavy anthropogenic disturbance. Particularly telling examples of these conservation...

Data from: From success to persistence: Identifying an evolutionary regime shift in the diverse Paleozoic aquatic arthropod group Eurypterida, driven by the Devonian biotic crisis

James C. Lamsdell & Paul A. Selden
Mass extinctions have altered the trajectory of evolution a number of times over the Phanerozoic. During these periods of biotic upheaval a different selective regime appears to operate, although it is still unclear whether consistent survivorship rules apply across different extinction events. We compare variations in diversity and disparity across the evolutionary history of a major Paleozoic arthropod group, the Eurypterida. Using these data, we explore the group's transition from a successful, dynamic clade to...

Data from: Synchrony is more than its top-down and climatic parts: interacting Moran effects on phytoplankton in British seas

Lawrence William Sheppard, Emma J. Defriez, Philip Christopher Reid & Daniel C. Reuman
Large-scale spatial synchrony is ubiquitous in ecology. We examined 56 years of data representing chlorophyll density in 26 areas in British seas monitored by the Continuous Plankton Recorder survey. We used wavelet methods to disaggregate synchronous fluctuations by timescale and determine that drivers of synchrony include both biotic and abiotic variables. We tested these drivers for statistical significance by comparison with spatially synchronous surrogate data. We generated timescale-specific models, accounting for 61% of long-timescale (>...

Data from: Sun skink landscape genomics: assessing how microevolutionary processes shape genetic and phenotypic diversity across a heterogeneous and fragmented landscape

Anthony J. Barley, Patrick J. Monnahan, Robert C. Thomson, L. Lee Grismer & Rafe M. Brown
Incorporating genomic data sets into landscape genetic analyses allows for powerful insights into population genetics, explicitly geographical correlates of selection, and morphological diversification of organisms across the geographical template. Here, we utilize an integrative approach to examine gene flow and detect selection, and we relate these processes to genetic and phenotypic population differentiation across South-East Asia in the common sun skink, Eutropis multifasciata. We quantify the relative effects of geographic and ecological isolation in this...

Data from: Tectonic collision and uplift of Wallacea triggered the global songbird radiation

Robert G. Moyle, Carl H. Oliveros, Michael J. Andersen, Peter A. Hosner, Brett W. Benz, Joseph D. Manthey, Scott L. Travers, Rafe M. Brown & Brant C. Faircloth
Songbirds (oscine passerines) are the most species rich and cosmopolitan bird group, comprising almost half of global avian species diversity. Because of their diversity and ubiquity, songbirds are used extensively in studies of evolutionary ecology, diversification, and ethology. Songbirds originated in Australia, but the evolutionary trajectory from a single species in an isolated continent to worldwide proliferation is poorly understood. Prior research suggested songbird diversification scenarios that are largely uncoupled from Earth history, including extensive...

Data from: Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity

Brian C. O'Meara, Stacey D. Smith, W. Scott Armbruster, Lawrence D. Harder, Christopher R. Hardy, Lena C. Hileman, Larry Hufford, Amy Litt, Susana Magallon, Stephen A. Smith, Peter F. Stevens, Charles B. Fenster & Pamela K. Diggle
Why are some traits and trait combinations exceptionally common across the tree of life, whereas others are vanishingly rare? The distribution of trait diversity across a clade at any time depends on the ancestral state of the clade, the rate at which new phenotypes evolve, the differences in speciation and extinction rates across lineages, and whether an equilibrium has been reached. Here we examine the role of transition rates, differential diversification (speciation minus extinction), and...

Data from: Evolution of codfishes (Teleostei: Gadinae) in geographical and ecological space: evidence that physiological limits drove diversification of subarctic fishes

Hannah L. Owens
Aim: To develop a holistic biogeographical history of codfishes in the subfamily Gadinae based on historical relationships, ecological niche, and evolution of physiological tolerances. Two alternative diversification scenarios were tested in two co-distributed, Northern Hemisphere clades: (1) clade ancestors were temperate, and environmental niche has been conserved over evolutionary time, implying that speciation was driven by vicariance associated with ice sheet formation; and (2) clade ancestors were Arctic, and species convergently adapted to temperate environmental...

Data from: Placing cryptic, recently extinct, or hypothesized taxa into an ultrametric phylogeny using continuous character data: A case study with the lizard Anolis roosevelti

Liam J. Revell, D. Luke Mahler, Robert Graham Reynolds & Graham James Slater
In recent years, enormous effort and investment has been put into assembling the tree of life: a phylogenetic history for all species on Earth. Overwhelmingly, this progress toward building an ever increasingly complete phylogeny of living things has been accomplished through sophisticated analysis of molecular data. In the modern genomic age, molecular genetic data have become very easy and inexpensive to obtain for many species. However, some lineages are poorly represented in or absent from...

Data from: Life history traits and phenotypic selection among sunflower crop-wild hybrids and their wild counterpart: implications for crop allele introgression

Matthew A. Kost, Helen M. Alexander, D. Jason Emry & Kristin L. Mercer
Hybridization produces strong evolutionary forces. In hybrid zones, selection can differentially occur on traits and selection intensities may differ among hybrid generations. Understanding these dynamics in crop-wild hybrid zones can clarify crop-like traits likely to introgress into wild populations and the particular hybrid generations through which introgression proceeds. In a field experiment with four crop-wild hybrid Helianthus annuus (sunflower) cross types, we measured growth and life history traits and performed phenotypic selection analysis on early...

Data from: Crop-associated virus infection in a native perennial grass: reduction in plant fitness and dynamic patterns of virus detection

Helen M. Alexander, Emily Bruns, Hayley Schebor & Carolyn M. Malmstrom
To understand the eco-evolutionary significance of plant viruses in nature, we must (i) quantify the effects of infection on plant fitness and (ii) recognize that native plants are increasingly exposed to crop-associated viruses. Studies of perennials are particularly needed: most of our knowledge of plant-virus interactions is from annuals, yet long-lived species dominate landscapes. Here we used aster models for life-history analysis and longitudinal measures of plant virus status to evaluate multi-year consequences of crop...

Data from: Automated identification of insect vectors of Chagas disease in Brazil and Mexico: the Virtual Vector Lab

Rodrigo Gurgel-Gonçalves, Ed Komp, Lindsay P. Campbell, Ali Khalighifar, Jarrett Mellenbruch, Vagner José Mendonça, Hannah L. Owens, Keynes De La Cruz Felix, A. Townsend Peterson & Janine M. Ramsey
Identification of arthropods important in disease transmission is a crucial, yet difficult, task that can demand considerable training and experience. An important case in point is that of the 150+ species of Triatominae, vectors of Trypanosoma cruzi, causative agent of Chagas disease across the Americas. We present a fully automated system that is able to identify triatomine bugs from Mexico and Brazil with an accuracy consistently above 80%, and with considerable potential for further improvement....

Data from: Non-clonal coloniality: genetically chimeric colonies through fusion of sexually produced polyps in the hydrozoan Ectopleura larynx

E. Sally Chang, Maria E. Orive & Paulyn Cartwright
Hydrozoans typically develop colonies through asexual budding of polyps. Although colonies of Ectopleura are similar to other hydrozoans in that they consist of multiple polyps physically connected through continuous epithelia and shared gastrovascular cavity, Ectopleura larynx does not asexually bud polyps indeterminately. Instead, after an initial phase of limited budding in a young colony, E. larynx achieves its large colony size through the aggregation and fusion of sexually (non-clonally) produced polyps. The apparent chimerism within...

Data from: An ancient origin for the enigmatic Flat-Headed Frogs (Bombinatoridae: Barbourula) from the islands of Southeast Asia

David C. Blackburn, David P. Bickford, Arvin C. Diesmos, Djoko T. Iskandar & Rafe M. Brown
Background: The complex history of Southeast Asian islands has long been of interest to biogeographers. Dispersal and vicariance events in the Pleistocene have received the most attention, though recent studies suggest a potentially more ancient history to components of the terrestrial fauna. Among this fauna is the enigmatic archaeobatrachian frog genus Barbourula, which only occurs on the islands of Borneo and Palawan. We utilize this lineage to gain unique insight into the temporal history of...

Data from: Multilocus phylogeny and Bayesian estimates of species boundaries reveal hidden evolutionary relationships and cryptic diversity in Southeast Asian monitor lizards

Luke J. Welton, Cameron D. Siler, Jamie R. Oaks, Arvin C. Diesmos & Rafe M. Brown
Recent conceptual, technological, and methodological advances in phylogenetics have enabled increasingly robust statistical species delimitation in studies of biodiversity. As the variety of evidence purporting species diversity has increased, so too have the kinds of tools and inferential power of methods for delimiting species. Here we showcase an organismal system for a data-rich, comparative molecular approach to evaluating strategies of species delimitation among monitor lizards of the genus Varanus. The water monitors (Varanus salvator Complex),...

Data from: Fitness consequences of outcrossing in a social spider with an inbreeding mating system

Reut Berger-Tal, Cristina Tuni, Yael Lubin, Debroah Smith, Trine Bilde & Deborah Smith
Inbreeding mating systems are uncommon because of inbreeding depression. Mating among close relatives can evolve, however, when outcrossing is constrained. Social spiders show obligatory mating among siblings. In combination with a female-biased sex ratio, sib-mating results in small effective populations. In such a system high genetic homozygosity is expected, and drift may cause population divergence. We tested the effect of outcrossing in the social spider Stegodyphus dumicola. Females were mated to sib-males, to a non-nestmate...

Data from: A Bayesian method for the joint estimation of outcrossing rate and inbreeding depression

John K. Kelly, Vanessa A. Koelling & Patrick J. Monnahan
The population outcrossing rate (t) and adult inbreeding coefficient (F) are key parameters in mating system evolution. The magnitude of inbreeding depression as expressed in the field can be estimated given t and F via the method of Ritland (1990). For a given total sample size, the optimal design for the joint estimation of t and F requires sampling large numbers of families (100-400) with fewer offspring (1-4) per family. Unfortunately, the standard inference procedure...

Data from: Greenhouse biogeography: the relationship of geographic range to invasion and extinction in the Cretaceous Western Interior Seaway

Corinne E. Myers, , Bruce S. Lieberman & Richard A. MacKenzie
Significant warming of Earth's climate in the near term seems increasingly likely. If significant enough, this climatic regime could, in the long term, come to resemble previous greenhouse intervals in earth history. Consequently, analysis of the fossil record during periods of extreme warmth may provide important lessons for species biology, including biogeography, in a much warmer world. To explore this issue, we analyzed the biogeographic response of 63 molluscan species to the long-term global warmth...

Data from: Quantifying morphological change during an evolutionary radiation of Devonian trilobites

Francine R. Abe & Bruce S. Lieberman
The fossil record provides an important source of data on adaptive radiations, and indeed some of the earliest theoretical insights on the nature of these radiations were made by paleontologists. Here we focus on the diverse Devonian Metacryphaeus group calmoniid trilobites, known from the Malvinokaffric Realm; these have been considered a classic example of an adaptive radiation preserved in the fossil record. A geometric morphometric analysis is used in conjunction with phylogenetic and biogeographic patterns...

Data from: Evidence for repeated acquisition and loss of complex body form characters in an insular clade of Southeast Asian semi-fossorial skinks

Cameron David Siler & Rafe M. Brown
Evolutionary simplification, or loss of complex characters, is a major theme in studies of body form evolution. The apparently infrequent evolutionary reacquisition of complex characters has led to the assertion (Dollo’s Law) that once lost, complex characters may be impossible to re-evolve, at least via the exact same evolutionary process. Here we provide one of the most comprehensive, fine-scale analyses of squamate body-form evolution to date, introducing a new model system of closely related, morphologically...

Data from: Archipelago-wide survey of Philippine forest dragons (Agamidae: Gonocephalus): multilocus phylogeny uncovers unprecedented levels of genetic diversity in a biodiversity hotspot

Luke J. Welton, Cameron D. Siler, L. L. Grismer, Arvin C. Diesmos, Jack W. Sites & Rafe M. Brown
We utilize robust geographical genetic sampling, a multilocus dataset, and coalescent-based species delimitation statistics to provide the first phylogenetic inferences of relationships of Philippine Gonocephalus, combined with estimates of putative species diversity in this virtually unknown island radiation. Our results reveal startling levels of undocumented diversity, genetically partitioned at a number of geographic levels across the archipelago. In this paper we present the first survey of genetic lineage diversity, coupled with an archipelago-wide elucidation of...

Data from: A genomic approach for distinguishing between recent and ancient admixture as applied to cattle

Emily Jane McTavish & David M. Hillis
Genomic data facilitate opportunities to track complex population histories of divergence and gene flow. We developed a metric, scaled block size (SBS), that uses the unrecombined block size of introgressed regions of chromosomes to differentiate between recent and ancient admixture, and applied it to reconstructing admixture in cattle. Cattle are descendants of two independently domesticated lineages, taurine and indicine, that diverged 200,000 or more years ago. Several breeds have hybrid ancestry between these divergent lineages....

Data from: Greater host breadth still not associated with increased diversification rate in the Nymphalidae – a response to Janz et al

Christopher Alan Hamm & James Andrew Fordyce
In their technical comment, Janz et al. take issue with our recent study examining the association between host breadth and diversification rates in the brush footed butterflies (Lepidoptera: Nymphalidae) (Hamm and Fordyce 2015). Specifically, they are concerned that we misrepresent their “oscillation hypothesis” (OH) (Janz et al. 2016; Janz and Nylin 2008) and that one of our models was inadequate to test hypotheses regarding host breadth and diversification rate. Given our mutual interests in the...

Data from: MycoDB, a global database of plant response to mycorrhizal fungi

V. Bala Chaudhary, Megan A. Rúa, Anita Antoninka, James D. Bever, Jeffery Cannon, Ashley Craig, Jessica Duchicela, Alicia Frame, Monique Gardes, Catherine Gehring, Michelle Ha, Miranda Hart, Jacob Hopkins, Baoming Ji, Nancy Collins Johnson, Wittaya Kaonongbua, Justine Karst, Roger T. Koide, Louis J. Lamit, James Meadow, Brook G. Milligan, John C. Moore, , Bridget Piculell, Blake Ramsby … & Jason D. Hoeksema
Plants form belowground associations with mycorrhizal fungi in one of the most common symbioses on Earth. However, few large-scale generalizations exist for the structure and function of mycorrhizal symbioses, as the nature of this relationship varies from mutualistic to parasitic and is largely context-dependent. We announce the public release of MycoDB, a database of 4,010 studies (from 438 unique publications) to aid in multi-factor meta-analyses elucidating the ecological and evolutionary context in which mycorrhizal fungi...

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