42 Works

Data from: X-rays and virtual taphonomy resolve the first Cissus (Vitaceae) macrofossils from Africa as early diverging members of the genus

Neil F. Adams, Margaret E. Collinson, Selena Y. Smith, Marion K. Bamford, Félix Forest, Panagiota Malakasi, Federica Marone & Dan Sykes
PREMISE OF THE STUDY: Fossilized seeds similar to Cissus (Vitaceae) have been recognized from the Miocene of Kenya, though some were previously assigned to the Menispermaceae. We undertook a comparative survey of extant African Cissus seeds to identify the fossils and consider their implications for the evolution and biogeography of Cissus and for African early Miocene paleoenvironments. METHODS: Micro-computed tomography (µCT) and synchrotron-based X-ray tomographic microscopy (SRXTM) were used to study seed morphology and anatomy....

Data from: Phylogenetic stability, tree shape, and character compatibility: a case study using early tetrapods

Massimo Bernardi, Kenneth D. Angielczyk, Jonathan S. Mitchell & Marcello Ruta
Phylogenetic tree shape varies as the evolutionary processes affecting a clade change over time. In this study, we examined an empirical phylogeny of fossil tetrapods during several time intervals, and studied how temporal constraints manifested in patterns of tree imbalance and character change. The results indicate that the impact of temporal constraints on tree shape is minimal and highlights the stability through time of the reference tetrapod phylogeny. Unexpected values of imbalance for Mississippian and...

Data from: Can longitudinal generalized estimating equation models distinguish network influence and homophily? an agent-based modeling approach to measurement characteristics

Kori Sauser Zachrison, Theodore J. Iwashyna, Achamyeleh Gebremariam, Meghan Hutchins & Joyce M. Lee
Background: Connected individuals (or nodes) in a network are more likely to be similar than two randomly selected nodes due to homophily and/or network influence. Distinguishing between these two influences is an important goal in network analysis, and generalized estimating equation (GEE) analyses of longitudinal dyadic network data are an attractive approach. It is not known to what extent such regressions can accurately extract underlying data generating processes. Therefore our primary objective is to determine...

Data from: Fitness costs of animal medication: antiparasitic plant chemicals reduce fitness of monarch butterfly hosts

Leiling Tao, Kevin M. Hoang, Mark D. Hunter & Jacobus C. De Roode
The emerging field of ecological immunology demonstrates that allocation by hosts to immune defence against parasites is constrained by the costs of those defences. However, the costs of non-immunological defences, which are important alternatives to canonical immune systems, are less well characterized. Estimating such costs is essential for our understanding of the ecology and evolution of alternative host defence strategies. Many animals have evolved medication behaviours, whereby they use antiparasitic compounds from their environment to...

Data from: Haplotype-phased synthetic long reads from short-read sequencing

James A. Stapleton, Jeongwoon Kim, John P. Hamilton, Ming Wu, Luiz C. Irber, Rohan Maddamsetti, Bryan Briney, Linsey Newton, Dennis R. Burton, C. Titus Brown, Christina Chan, C. Robin Buell & Timothy A. Whitehead
Next-generation DNA sequencing has revolutionized the study of biology. However, the short read lengths of the dominant instruments complicate assembly of complex genomes and haplotype phasing of mixtures of similar sequences. Here we demonstrate a method to reconstruct the sequences of individual nucleic acid molecules up to 11.6 kilobases in length from short (150-bp) reads. We show that our method can construct 99.97%-accurate synthetic reads from bacterial, plant, and animal genomic samples, full-length mRNA sequences...

Data from: Powerful methods for detecting introgressed regions from population genomic data

Benjamin K. Rosenzweig, James B. Pease, Nora J. Besansky & Matthew H. Hahn
Understanding the types and functions of genes that are able to cross species boundaries—and those that are not—is an important step in understanding the forces maintaining species as largely independent lineages across the remainder of the genome. With large next-generation sequencing data sets we are now able to ask whether introgression has occurred across the genome, and multiple methods have been proposed to detect the signature of such events. Here, we introduce a new summary...

Data from: Inordinate spinescence: taxonomic revision and microtomography of the Pheidole cervicornis species group (Hymenoptera, Formicidae)

Eli M. Sarnat, Georg Fischer & Evan P. Economo
The ant genus Pheidole—for all of its hyperdiversity and global ubiquity—is remarkably conservative with regard to morphological disparity. A striking exception to this constrained morphology is the spinescent morphotype, which has evolved multiple times across distantly related lineages of Indoaustralian Pheidole. The Pheidole cervicornis group contains perhaps the most extraordinary spinescent forms of all Pheidole. Here we present a taxonomic revision of the P. cervicornis group, and use microtomographic scanning technology to investigate the internal...

Data from: Multi-scale heterogeneity in vegetation and soil carbon in exurban residential land of southeastern Michigan, USA

William S. Currie, Sarah Kiger, Joan I. Nassauer, Meghan Hutchins, Lauren L. Marshall, Daniel G. Brown, Rick L. Riolo, Derek T. Robinson & Stephanie K. Hart
Exurban residential land (one housing unit per 0.2–16.2 ha) is growing in importance as a human-dominated land use. Carbon storage in the soils and vegetation of exurban land is poorly known, as are the effects on C storage of choices made by developers and residents. We studied C storage in exurban yards in southeastern Michigan, USA, across a range of parcel sizes and different types of neighborhoods. We divided each residential parcel into ecological zones...

Data from: Bayesian model selection with BAMM: effects of the model prior on the inferred number of diversification shifts

Jonathan S. Mitchell & Daniel L. Rabosky
1. Understanding variation in rates of speciation and extinction -- both among lineages and through time -- is critical to the testing of many hypotheses about macroevolutionary processes. BAMM is a flexible Bayesian framework for inferring the number and location of shifts in macroevolutionary rate across phylogenetic trees and has been widely used in empirical studies. BAMM requires that researchers specify a prior probability distribution on the number of diversification rate shifts before conducting an...

Data from: Fine with heat, problems with water: microclimate alters water loss in a thermally adapted insular lizard

Anat Belasen, Kinsey Brock, Binbin Li, Dimitra Chremou, Efstratios Valakos, Panayiotis Pafilis, Barry Sinervo & Johannes Foufopoulos
Global change, including habitat isolation and climate change, has both short- and long-term impacts on wildlife populations. For example, genetic drift and inbreeding result in genetic impoverishment in small, isolated populations, while species undergo range shifts or adaptive phenotypic change in response to shifts in environmental temperatures. In this study, we utilize a model system in which Holocene landscape changes have occurred to examine long-term effects of population isolation. To examine how isolation may constrain...

Data from: Mechanical conflict system: a novel operant method for the assessment of nociceptive behavior

Steven Harte, Jessica B. Meyers, Renee R. Donahue, Bradley K. Taylor, Thomas J. Morrow & Steven E. Harte
A new operant test for preclinical pain research, termed the Mechanical Conflict System (MCS), is presented. Rats were given a choice either to remain in a brightly lit compartment or to escape to a dark compartment by crossing an array of height-adjustable nociceptive probes. Latency to escape the light compartment was evaluated with varying probe heights (0, .5, 1, 2, 3, and 4 mm above compartment floor) in rats with neuropathic pain induced by constriction...

Data from: Parasite transmission in a natural multihost-multiparasite community

Stuart K. Auld, Catherine L. Searle & Meghan A. Duffy
Understanding the transmission and dynamics of infectious diseases in natural communities requires understanding the extent to which the ecology, evolution and epidemiology of those diseases are shaped by alternative hosts. We performed laboratory experiments to test how parasite spillover affected traits associated with transmission in two co-occurring parasites: the bacterium Pasteuria ramosa and the fungus Metschnikowia bicuspidata. Both parasites were capable of transmission from the reservoir host (Daphnia dentifera) to the spillover host (Ceriodaphnia dubia),...

Data from: Foliar damage beyond species distributions is partly explained by distance dependent interactions with natural enemies

Daniel S. W. Katz & Inés Ibáñez
Plant distributions are expected to shift in response to climate change, and range expansion dynamics will be shaped by the performance of individuals at the colonizing front. These plants will encounter new biotic communities beyond their range edges, and the net outcome of these encounters could profoundly affect colonization success. However, little is known about how biotic interactions vary across range edges and this has hindered efforts to predict changes in species distributions in response...

Data from: Genetic basis of octanoic acid resistance in Drosophila sechellia: functional analysis of a fine-mapped region

Jose M. Andrade López, Stephen M. Lanno, Jeremy M. Auerbach, Eva C. Moskowitz, Laura A. Sligar, Patricia J. Wittkopp & Joseph D. Coolon
Drosophila sechellia is a species of fruit fly endemic to the Seychelles islands. Unlike its generalist sister species, D. sechellia has evolved to be a specialist on the host plant Morinda citrifolia. This specialization is interesting because the plant's fruit contains secondary defense compounds, primarily octanoic acid (OA), that are lethal to most other Drosophilids. Although ecological and behavioral adaptations to this toxic fruit are known, the genetic basis for evolutionary changes in OA resistance...

Data from: Assessing the effects of a sequestered germline on interdomain lateral gene transfer in Metazoa

Lindy M Jensen, Jessica R Grant, , Laura A. Katz & Lindy Jensen
A sequestered germline in Metazoa has been argued to be an obstacle to lateral gene transfer (LGT), though few studies have specifically assessed this claim. Here we test the hypothesis that the origin of a sequestered germline reduced LGT events in Bilateria (i.e. triploblast lineages) as compared to early-diverging Metazoa (i.e. Ctenophora, Cnidaria, Porifera, and Placozoa). We analyze single-gene phylogenies generated with over 900 species, sampled from among Bacteria, Archaea and Eukaryota to identify well-supported...

Data from: Convergent evolution in social swallows (Aves: Hirundinidae)

Allison E. Johnson, Jonathan S. Mitchell & Mary Bomberger Brown
Behavioral shifts can initiate morphological evolution by pushing lineages into new adaptive zones. This has primarily been examined in ecological behaviors, such as foraging, but social behaviors may also alter morphology. Swallows and martins (Hirundinidae) are aerial insectivores that exhibit a range of social behaviors, from solitary to colonial breeding and foraging. Using a well-resolved phylogenetic tree, a database of social behaviors, and morphological measurements, we ask how shifts from solitary to social breeding and...

Data from: A resurrection experiment finds evidence of both reduced genetic diversity and potential adaptive evolution in the agricultural weed Ipomoea purpurea

Adam Kuester, Ariana Wilson, Shu-Mei Chang & Regina S. Baucom
Despite the negative economic and ecological impact of weeds, relatively little is known about the evolutionary mechanisms that influence their persistence in agricultural fields. Here, we use a resurrection approach to examine the potential for genotypic and phenotypic evolution in Ipomoea purpurea, an agricultural weed that is resistant to glyphosate, the most widely used herbicide in current-day agriculture. We found striking reductions in allelic diversity between cohorts sampled nine years apart (2003 vs. 2012), suggesting...

Registration Year

  • 2016

Resource Types

  • Dataset


  • University of Michigan-Ann Arbor
  • University of Georgia
  • Okinawa Institute of Science and Technology
  • Purdue University
  • Indiana University Bloomington
  • University of Hong Kong
  • Georgia Southern University
  • University of the Basque Country
  • University of Massachusetts Amherst
  • Field Museum of Natural History