44 Works

Data from: Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing

Ya Yang, Michael J. Moore, Samuel F. Brockington, Douglas E. Soltis, Gane Ka-Shu Wong, Eric J. Carpenter, Yong Zhang, Li Chen, Zhixiang Yan, Yinlong Xie, Rowan F. Sage, Sarah Covshoff, Julian M. Hibberd, Matthew N. Nelson & Stephen A. Smith
Many phylogenomic studies based on transcriptomes have been limited to “single-copy” genes due to methodological challenges in homology and orthology inferences. Only a relatively small number of studies have explored analyses beyond reconstructing species relationships. We sampled 69 transcriptomes in the hyperdiverse plant clade Caryophyllales and 27 outgroups from annotated genomes across eudicots. Using a combined similarity- and phylogenetic tree-based approach, we recovered 10,960 homolog groups, where each was represented by at least eight ingroup...

Data from: Feed or fight: testing the impact of food availability and intraspecific aggression on the functional ecology of an island lizard

Colin M. Donihue, Kinsey M. Brock, Johannes Foufopoulos & Anthony Herrel
Body size often varies among insular populations relative to continental conspecifics – the ‘island rule’ – and functional, context-dependent morphological differences tend to track this body size variation on islands. Two hypotheses are often proposed as potential drivers of insular population differences in morphology: one relating to diet and the other involving intraspecific competition and aggression. We directly tested whether differences in morphology and maximum bite capacity were explained by interisland changes in hardness of...

Data from: Pertussis immunity and epidemiology: mode and duration of vaccine-induced immunity

Felicia M. G. Magpantay, Matthieu Domenech De Cellès, Pejman Rohani & Aaron A. King
The resurgence of pertussis in some countries that maintain high vaccination coverage has drawn attention to gaps in our understanding of the epidemiological effects of pertussis vaccines. In particular, major questions surround the nature, degree and durability of vaccine protection. To address these questions, we used mechanistic transmission models to examine regional time series incidence data from Italy in the period immediately following the introduction of acellular pertussis (aP) vaccine. Our results concur with recent...

Data from: Can observation skills of citizen scientists be estimated using species accumulation curves?

Steve Kelling, Alison Johnston, Wesley M. Hochachka, Marshall Iliff, Daniel Fink, Jeff Gerbracht, Carl Lagoze, Frank A. La Sorte, Travis Moore, Andrea Wiggins, Weng-Keen Wong, Chris Wood & Jun Yu
Volunteers are increasingly being recruited into citizen science projects to collect observations for scientific studies. An additional goal of these projects is to engage and educate these volunteers. Thus, there are few barriers to participation resulting in volunteer observers with varying ability to complete the project’s tasks. To improve the quality of a citizen science project’s outcomes it would be useful to account for inter-observer variation, and to assess the rarely tested presumption that participating...

Data from: Paternity analyses in wild-caught and lab-reared Caribbean cricket females reveal the influence of mating environment on post-copulatory sexual selection

Elen Oneal & L. Lacey Knowles
Polyandry is ubiquitous in insects and provides the conditions necessary for male- and female-driven forms of post-copulatory sexual selection to arise. Populations of Amphiacusta sanctaecrucis exhibit significant divergence in portions of the male genitalia that are inserted directly into the female reproductive tract, suggesting that males may exercise some post-copulatory control over fertilization success. We examine the potential for male-male and male-female post-copulatory interactions to influence paternity in wild-caught females of A. sanctaecrucis and contrast...

Data from: Resources, key traits, and the size of fungal epidemics in Daphnia populations

David J. Civitello, Rachel M. Penczykowski, Aimee N. Smith, Marta S. Shocket, Meghan A. Duffy & Spencer R. Hall
1. Parasites can profoundly affect host populations and ecological communities. Thus, it remains critical to identify mechanisms that drive variation in epidemics. Resource availability can drive epidemics via traits of hosts and parasites that govern disease spread. 2. Here, we map resource–trait–epidemic connections to explain variation in fungal outbreaks (Metschnikowia bicuspidata) in a zooplankton host (Daphnia dentifera) among lakes. We predicted epidemics would grow larger in lakes with more phytoplankton via three energetic mechanisms. First,...

Data from: Detecting adaptive evolution in phylogenetic comparative analysis using the Ornstein-Uhlenbeck model

Clayton E. Cressler, Marguerite A. Butler & Aaron A. King
Phylogenetic comparative analysis is an approach to inferring evolutionary process from a combination of phylogenetic and phenotypic data. The last few years have seen increasingly sophisticated models employed in the evaluation of more and more detailed evolutionary hypotheses, including adaptive hypotheses with multiple selective optima and hypotheses with rate variation within and across lineages. The statistical performance of these sophisticated models has received relatively little systematic attention, however. We conducted an extensive simulation study to...

Data from: A molecular genetic time scale demonstrates Cretaceous origins and multiple diversification rate shifts within the order Galliformes (Aves)

R. Will Stein, Joseph W. Brown & Arne Ø. Mooers
The phylogeny of Galliformes (landfowl) has been studied extensively; however, the associated chronologies have been criticized recently due to misplaced or misidentified fossil calibrations. As a consequence, it is unclear whether any crown-group lineages arose in the Cretaceous and survived the Cretaceous–Paleogene (K–Pg; 65.5 Ma) mass extinction. Using Bayesian phylogenetic inference on an alignment spanning 14,539 bp of mitochondrial and nuclear DNA sequence data, four fossil calibrations, and a combination of uncorrelated lognormally distributed relaxed-clock...

Data from: The species versus subspecies conundrum: quantitative delimitation from integrating multiple data types within a single Bayesian approach in Hercules beetles

Jen-Pan Huang & L. Lacey Knowles
With the recent attention and focus on quantitative methods for species delimitation, an overlooked but equally important issue regards what has actually been delimited. This study investigates the apparent arbitrariness of some taxonomic distinctions, and in particular how species and subspecies are assigned. Specifically, we use a recently developed Bayesian model-based approach to show that in the Hercules beetles (genus Dynastes) there is no statistical difference in the probability that putative taxa represent different species,...

Data from: Relationships of diversity, disparity and their evolutionary rates in squirrels (Sciuridae)

Miriam L. Zelditch, Jingchun Li, Lucy A. P. Tran & Donald L. Swiderski
Several theories predict that rapidly diversifying clades will also rapidly diverge phenotypically; yet, there are also reasons for suspecting that diversification and divergence might not be correlated. In the widely distributed squirrel clade (Sciuridae), we test for correlations between per-lineage speciation rates, species richness, disparity and a time-invariant measure of disparity that allows for comparing rates when evolutionary modes differ, as they do in squirrels. We find that species richness and speciation rates are not...

Data from: Challenges in the estimation of extinction from molecular phylogenies: a response to Beaulieu and O'Meara

Daniel L. Rabosky
Time-calibrated phylogenies that contain only living species have been widely used to study the dynamics of speciation and extinction. Concerns about the reliability of phylogenetic extinction estimates were raised by Rabosky (2010), where I suggested that unaccommodated heterogeneity in speciation rate could lead to positively biased extinction estimates. In a recent article, Beaulieu and O'Meara (2015) correctly point out several technical errors in the execution of my 2010 study and concluded that phylogenetic extinction estimates...

Data from: An examination of fitness costs of glyphosate resistance in the common morning glory, Ipomoea purpurea

Catherine L. Debban, Sara Okum, Kathleen E. Pieper, Ariana Wilson & Regina S. Baucom
Fitness costs are frequently invoked to explain the presence of genetic variation underlying plant defense across many types of damaging agents. Despite the expectation that costs of resistance are prevalent, however, they have been difficult to detect in nature. To examine the potential that resistance confers a fitness cost, we examined the survival and fitness of genetic lines of the common morning glory, Ipomoea purpurea, that diverged in the level of resistance to the herbicide...

Data from: Opportunities and challenges of Integral Projection Models for modeling host-parasite dynamics

C. Jessica E. Metcalf, Andrea L. Graham, Micaela Martinez-Bakker & Dylan Z. Childs
Epidemiological dynamics are shaped by and may in turn shape host demography. These feedbacks can result in hard to predict patterns of disease incidence. Mathematical models that integrate infection and demography are consequently a key tool for informing expectations for disease burden and identifying effective measures for control. A major challenge is capturing the details of infection within individuals and quantifying their downstream impacts to understand population-scale outcomes. For example, parasite loads and antibody titres...

Data from: Socially selected ornaments and fitness: signals of fighting ability in paper wasps are positively associated with survival, reproductive success, and rank

Elizabeth Alison Tibbetts, Taylor Forrest, Cassondra Vernier, Judy Jinn & Andrew Madagame
Many animals have ornaments that mediate choice and competition in social and sexual contexts. Individuals with elaborate sexual ornaments typically have higher fitness than those with less elaborate ornaments, but less is known about whether socially selected ornaments are associated with fitness. Here, we test the relationship between fitness and facial patterns that are a socially-selected signal of fighting ability in Polistes dominula wasps. We found wasps that signal higher fighting ability have larger nests,...

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: Minimal effects of latitude on present-day speciation rates in New World birds

Daniel L. Rabosky, Pascal O. Title & Huateng Huang
The tropics contain far greater numbers of species than temperate regions, suggesting that rates of species formation might differ systematically between tropical and non-tropical areas. We tested this hypothesis by reconstructing the history of speciation in New World (NW) land birds using BAMM, a Bayesian framework for modelling complex evolutionary dynamics on phylogenetic trees. We estimated marginal distributions of present-day speciation rates for each of 2571 species of birds. The present-day rate of speciation varies...

Data from: Speciation dynamics during the global radiation of extant bats

Jeff J. Shi & Daniel L. Rabosky
Species richness varies widely across extant clades, but the causes of this variation remain poorly understood. We investigate the role of diversification rate heterogeneity in shaping patterns of diversity across families of extant bats. To provide a robust framework for macroevolutionary inference, we assemble a time-calibrated, species-level phylogeny using a supermatrix of mitochondrial and nuclear sequence data. We analyze the phylogeny using a Bayesian method for modeling complex evolutionary dynamics. Surprisingly, we find that variation...

Data from: Extant-only comparative methods fail to recover the disparity preserved in the bird fossil record

Jonathan S. Mitchell
Most extant species are in clades with poor fossil records, and recent studies of comparative methods show have low power to infer even highly simplified models of trait evolution without fossil data. Birds are a well-studied radiation, yet their early evolutionary patterns are still contentious. The fossil record suggests that birds underwent a rapid ecological radiation after the end-Cretaceous mass extinction, and several smaller, subsequent radiations. This hypothesized series of repeated radiations from fossil data...

Data from: Initial colonization, community assembly, and ecosystem function: fungal colonist traits and litter biochemistry mediate decay rate

Lauren C. Cline & Donald R. Zak
Priority effects are an important ecological force shaping biotic communities and ecosystem processes, in which the establishment of early colonists alters the colonization success of later-arriving organisms via competitive exclusion and habitat modification. However, we do not understand which biotic and abiotic conditions lead to strong priority effects and lasting historical contingencies. Using saprotrophic fungi in a model leaf decomposition system, we investigated whether compositional and functional consequences of initial colonization were dependent on initial...

Data from: No substitute for real data: a cautionary note on the use of phylogenies from birth-death polytomy resolvers for downstream comparative analyses

Daniel L. Rabosky
The statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth-death polytomy resolver is a method of accounting for phylogenetic uncertainty that places missing (unsampled) taxa onto phylogenetic trees, using taxonomic information alone. Recent studies of birds and mammals have used this approach to generate pseudo-posterior distributions of phylogenetic trees that are complete at the species level, even in the absence...

Data from: Expanding the described metabolome of the marine cyanobacterium Moorea producens JHB through orthogonal natural products workflows

Paul D. Boudreau, Emily A. Monroe, Suneet Mehrotra, Shane Desfor, Anton Korobeynikov, David H. Sherman, Thomas F. Murray, Lena Gerwick, Pieter C. Dorrestein & William H. Gerwick
Moorea producens JHB, a Jamaican strain of tropical filamentous marine cyanobacteria, has been extensively studied by traditional natural products techniques. These previous bioassay and structure guided isolations led to the discovery of two exciting classes of natural products, hectochlorin (1) and jamaicamides A (2) and B (3). In the current study, mass spectrometry-based ‘molecular networking’ was used to visualize the metabolome of Moorea producens JHB, and both guided and enhanced the isolation workflow, revealing additional...

Data from: Sex-linked genomic variation and its relationship to avian plumage dichromatism and sexual selection

Huateng Huang & Daniel L. Rabosky
Background: Sexual dichromatism is the tendency for sexes to differ in color pattern and represents a striking form of within-species morphological variation. Conspicuous intersexual differences in avian plumage are generally thought to result from Darwinian sexual selection, to the extent that dichromatism is often treated as a surrogate for the intensity of sexual selection in phylogenetic comparative studies. Intense sexual selection is predicted to leave a footprint on genetic evolution by reducing the relative genetic...

Data from: Avoidable errors in the modeling of outbreaks of emerging pathogens, with special reference to Ebola

Aaron A. King, Matthieu Domenech De Cellès, Felicia M. G. Magpantay, Pejman Rohani & M. Domenech De Celles
As an emergent infectious disease outbreak unfolds, public health response is reliant on information on key epidemiological quantities, such as transmission potential and serial interval. Increasingly, transmission models fit to incidence data are used to estimate these parameters and guide policy. Some widely used modelling practices lead to potentially large errors in parameter estimates and, consequently, errors in model-based forecasts. Even more worryingly, in such situations, confidence in parameter estimates and forecasts can itself be...

Data from: Atmospheric N deposition alters co-occurrence, but not functional potential among saprotrophic bacterial communities

Zachary B. Freedman & Donald R. Zak
The use of co-occurrence patterns to investigate interactions between micro-organisms has provided novel insight into organismal interactions within microbial communities. However, anthropogenic impacts on microbial co-occurrence patterns and ecosystem function remain an important gap in our ecological knowledge. In a northern hardwood forest ecosystem located in Michigan, USA, 20 years of experimentally increased atmospheric N deposition has reduced forest floor decay and increased soil C storage. This ecosystem-level response occurred concomitantly with compositional changes in...

Data from: The geographic mosaic of herbicide resistance evolution in the common morning glory, Ipomoea purpurea: evidence for resistance hotspots and low genetic differentiation across the landscape

Adam Kuester, Shu-Mei Chang & Regina S. Baucom
Strong human-mediated selection via herbicide application in agroecosystems has repeatedly led to the evolution of resistance in weedy plants. Although resistance can occur among separate populations of a species across the landscape, the spatial scale of resistance in many weeds is often left unexamined. We assessed the potential that resistance to the herbicide glyphosate in the agricultural weed Ipomoea purpurea has evolved independently multiple times across its North American range. We examined both adaptive and...

Registration Year

  • 2015

Resource Types

  • Dataset


  • University of Michigan-Ann Arbor
  • University of Georgia
  • University of California System
  • Duke University
  • Oregon State University
  • University of Minnesota
  • University of Florida
  • Oberlin College
  • University of Kansas
  • Menzies School of Health Research