28 Works

A rodent anchored hybrid enrichment probe set for a range of phylogenetic utility – from order to species

Max Bangs & Scott Steppan
Rodents are the largest order of mammals and contain several model organisms important to scientific research in a variety of fields, yet no large set of genomic markers have been designed for this group to date, hindering evolutionary studies into relationships of the group as a whole. Here we present a genomic probe set designed and optimized for rodents with a protocol easy to replicate with little laboratory investment. This design utilizes an anchored hybrid...

Coprophagy in Caribbean parrotfishes

Joshua Manning & Sophie McCoy
Parrotfishes are widely considered to be important grazers on coral reefs that remove autotrophic biomass from the reef substrate and create bare space that is conducive to larval coral settlement and recruitment. Because of the top-down effects associated with their benthic foraging, this has been a major focus of parrotfish research. Another aspect of parrotfish foraging and trophic ecology that has received very little attention is coprophagy, the consumption of fecal matter. The feces of...

Anchored phylogenomics and a revised classification of the Planidial Larva Clade of Jewel Wasps (Hymenoptera: Chalcidoidea)

JUNXIA ZHANG, John Heraty, Christopher Darling, Robert Kresslein, Austin Baker, Javier Torréns, Jean-Yves Rasplus, Alan Lemmon & Emily Lemmon
Planidia are free-living, mobile first-instar larvae that are notable in their ability to transition on a single host between different larval stadia, and for completing their development on the host prepupa as ectoparasitoids, effectively acting as larval-pupal external koinobionts. Within Chalcidoidea, a mega-diverse superfamily of parasitoid wasps, taxa with a planidium form a monophyletic group, the Planidial-Larva-Clade (PLC), which has been comprised of three recognized groups: Eutrichosomatinae (Pteromalidae), Perilampidae (Chrysolampinae, Perilampinae, Philomidinae and the unplaced...

Living and fossil Ginkgo leaves

Luke Mander, Haibin Hang, Martin Bauer & Washington Mio
The data presented here are a collection of images of living and fossil Ginkgo leaves. Mature and fully expanded leaves were harvested from a reproductively immature Ginkgo biloba tree growing in partial shade as a specimen on the campus of The Open University, UK. The specimen was ascended using a ladder and seven branches growing towards the West at approximately halfway up the specimen were removed from the trunk using a saw. Every leaf growing...

Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis

Eva Koch, Hernán Morales, Jenny Larsson, Anja Westram, Rui Faria, Alan Lemmon, Emily Lemmon, Kerstin Johannesson & Roger Butlin
Chromosomal inversion polymorphisms, segments of chromosomes that are flipped in orientation and occur in reversed order in some individuals, have long been recognized to play an important role in local adaptation. They can reduce recombination in heterozygous individuals and thus help to maintain sets of locally adapted alleles. In a wide range of organisms, populations adapted to different habitats differ in frequency of inversion arrangements. However, getting a full understanding of the importance of inversions...

Data from: Ancestral ecological regime shapes reaction to food limitation in the Least Killifish, Heterandria formosa

Anja Felmy, Jeff Leips & Joseph Travis
Populations with different densities often show genetically-based differences in life histories. The divergent life histories could be driven by several agents of selection, one of which is variation in per-capita food levels. Its relationship with population density is complex, as it depends on overall food availability, individual metabolic demand, and food-independent factors potentially affecting density, such as predation intensity. Here we present a case study of two populations of a small live-bearing freshwater fish, one...

Dose relationships can exacerbate, mute, or reverse the impact of heterospecific host density on infection prevalence

Patrick Clay, Michael Cortez & Meghan Duffy
The likelihood an individual becomes infected depends on the community in which it is embedded. For environmentally transmitted parasites, host community composition can alter host density, the density of parasites that hosts encounter in the environment, and the dose to which hosts are subsequently exposed. While some multi-host theory incorporates some of these factors (e.g., competition among hosts), it does not currently consider the nonlinear relationships between parasite exposure dose and per-propagule infectivity (dose-infectivity relationships),...

The evolution of size-dependent competitive interactions promotes species coexistence

Jaime Mauricio Anaya-Rojas, Ronald D Bassar, Tomos Potter, Allison Blanchette, Shay Callahan, Nick Framstead, David Reznick & Joseph Travis
1. Theory indicates that competing species coexist in a community when intraspecific competition is stronger than interspecific competition. When body size determines the outcome of competitive interactions between individuals, coexistence depends also on how resource use and the ability to compete for these resources change with body size. Testing coexistence theory in size-structured communities, therefore, requires disentangling the effects of size-dependent competitive abilities and niche shifts. 2. Here, we tested the hypothesis that the evolution...

Using Delaunay triangulation to sample whole-specimen color from digital images

Jennifer Valvo, J. Aponte, Mitch Daniel, Kenna Dwinell, Helen Rodd, David Houle & Kimberly Hughes
1. Color variation is one of the most obvious examples of variation in nature, but biologically meaningful quantification and interpretation of variation in color and complex patterns is challenging. Many current methods for assessing variation in color patterns classify color patterns using categorical measures, provide aggregate measures that ignore spatial pattern, or both, losing potentially important aspects of color pattern. 2. Here, we present Colormesh, a novel method for analyzing complex color patterns that offers...

A new sectional classification of Lachenalia (Asparagaceae) based on a multilocus DNA phylogeny

Graham D. Duncan, Carl D. Schlichting, Felix Forest, Allan G. Ellis, Alan R. Lemmon, Emily Moriarty Lemmon & G. Anthony Verboom
Lachenalia J.Jacq. ex Murray (Asparagaceae; Scilloideae; Hyacintheae) is a large and morphologically diverse genus of more than 140 bulbous species endemic to southern Africa. Previous attempts to infer a well resolved and robustly supported phylogeny of Lachenalia using Sanger sequencing of candidate loci and/or morphological characters have been largely unsuccessful. Consequently, the current infrageneric classification is artificial and there is a need to explore alternative avenues to produce a phylogenetic classification. In this paper we...

Phylogenetically diverse diets favor more complex venoms in North American pitvipers

Matthew Holding & Christopher Parkinson
The role of natural selection in the evolution of trait complexity can be characterized by testing hypothesized links between complex forms and their functions across species. Predatory venoms are traits composed of multiple proteins that collectively function to incapacitate prey. Venom complexity fluctuates considerably over evolutionary timescales, with apparent increases and decreases in complexity, yet the evolutionary causes of this variation is unclear. Here, we tested alternative hypotheses for the link between venom complexity and...

Individual variation in marine larval-fish swimming speed and the emergence of dispersal kernels

Scott Burgess, Michael Bode, Jeffrey Leis & Luciano Mason
Dispersal emerges as a consequence of how an individual’s phenotype interacts with the environment. Not all dispersing individuals have the same phenotype, and variation among individuals can generate complex variation in the distribution of dispersal distances and directions. While active locomotion performance is an obvious candidate for a dispersal phenotype, its effects on dispersal are difficult to measure or predict, especially in small organisms dispersing in wind or currents. Therefore, we analyzed the effects of...

Diversification of a polyploid complex: the biogeography and acoustic communication evolution of North American gray treefrogs throughout the Quaternary

William Booker, Emily Lemmon, Alan Lemmon, Margaret Ptacek, Alyssa Hassinger, Johannes Schul & H. Carl Gerhardt
Polyploid speciation and whole genome duplications are major drivers of biological diversity. After polyploid species are formed, the interactions between diploid and polyploid lineages may generate additional diversity in novel cytotypes and phenotypes. In anurans, mate choice by acoustic communication is the primary method by which individuals identify their own species and assess suitable mates. As such, the evolution of acoustic signals is an important mechanism for contributing to reproductive isolation and diversification in this...

Sex differences in the plasticity of life history in response to social environment

Elizabeth Lange, Margaret Ptacek, Joseph Travis & Kimberly Hughes
Predicting how social environment affects life history variation is critical to understanding if, and when, selection favors alternative life history development, especially in systems in which social interactions change over time or space. While sexual selection theory predicts that males and females should respond differently to variation in the social environment, few studies have examined the responses of both male and female phenotypes to the same gradient of social environment. In this study, we used...

Response diversity in corals: hidden differences in bleaching mortality among cryptic Pocillopora species

Scott Burgess, Erika Johnston, Alex Wyatt, James Leichter & Peter Edmunds
Variation among functionally similar species in their response to environmental stress buffers ecosystems from changing states. Functionally similar species may often be cryptic species representing evolutionarily distinct genetic lineages that are morphologically indistinguishable. However, the extent to which cryptic species differ in their response to stress, and could therefore provide a source of response diversity, remains unclear because they are often not identified or are assumed to be ecologically equivalent. Here, we uncover differences in...

Niche differences in co-occurring cryptic coral species (Pocillopora spp.)

Erika Johnston, Alex Wyatt, James Leichter & Scott Burgess
Cryptic species that are morphologically similar co-occur because either the rate of competitive exclusion is very slow, or because they are not, in fact, ecologically similar. The processes that maintain cryptic local diversity may, therefore, be particularly subtle and difficult to identify. Here, we uncover differences among several cryptic species in their relative abundance across a depth gradient within a dominant and ecologically important genus of hard coral, Pocillopora. From extensive sampling unbiased towards morphological...

Metabolic depression in sea urchin barrens associated with food deprivation

Nathan Spindel, Lynn Lee & Daniel Okamoto
The proliferation of sea urchins can decimate macroalgal forests in coastal ecosystems, leading to persistent barren seascapes. While kelp forests are among the most productive ecosystems on the planet, productivity in these urchin barrens is dramatically reduced. Moreover, urchins inhabiting these food-depauperate barrens face starvation and many survive in these barrens for years or decades. Urchins in barrens can persist by eating food subsidies from drift algae, pelagic salps, tubeworms, as well as encrusting and...

Direct observation of hyperpolarization breaking through the spin diffusion barrier

Quentin Stern, Samuel F. Cousin, Frederic Mentink-Vigier, Arthur C. Pinon, Stuart J. Elliott, Olivier Cala & Sami Jannin
Dynamic nuclear polarization (DNP) is a widely used tool for overcoming the low intrinsic sensitivity of nuclear magnetic resonance spectroscopy and imaging. Its practical applicability is typically bounded, however, by the so-called ‘spin diffusion barrier’, which relates to the poor efficiency of polarization transfer from highly polarized nuclei close to paramagnetic centers to bulk nuclei. A quantitative assessment of this barrier has been hindered so far by the lack of general methods for studying nuclear-polarization...

A comparative study between outcomes of an in-person vs. online introductory field course

Alexandra Race, Maria De Jesus, Roxanne Beltran & Erika Zavaleta
The COVID-19 pandemic has disrupted many standard approaches to STEM education. Particularly impacted were field courses, which rely on specific natural spaces often accessed through shared vehicles. As in-person field courses have been found to be particularly impactful for undergraduate student success in the sciences, we aimed to compare and understand what factors may have been lost or gained during the conversion of an introductory field course to an online format. Using a mixed methods...

Data from: Signatures of north-eastern expansion and multiple refugia: Genomic phylogeography of the Pine Barrens Treefrog, Hyla andersonii (Anura: Hylidae)

Alexa Warwick, Lisa Barrow, Megan Smith, D. Bruce Means, Alan Lemmon & Emily Lemmon
Range fragmentation poses challenges for species persistence over time and may be caused by both historical and contemporary processes. We combined genomic data, phylogeographic model testing, and paleoclimate niche modeling to infer the evolutionary history of the Pine Barrens Treefrog (Hyla andersonii), a seepage bog specialist, in eastern North America to better understand the historical context of its fragmented distribution. We sampled H. andersonii populations across the three disjunct regions of the species’ range: Alabama/Florida...

Tempo and mode of evolution of Oryzomyine rodents (Rodentia, Cricetidae, Sigmodontinae): a phylogenomic approach

Alexandre Percequillo, Joyce Prado, Edson Abreu, Jeronymo Dalapicolla, Ana Carolina Pavan, Elisandra Chiquito, Pamella Brennand, Scott Steppan, Alan Lemmon & Emily Lemmon
The tribe Oryzomyini is an impressive group of rodents, comprising 30 extant genera and an estimated 147 species. Recent remarkable advances in the understanding of the diversity, taxonomy and systematics of the tribe have mostly derived from analyses of single or few genetic markers. However, the evolutionary history and biogeography of Oryzomyini, its origin and diversification across the Neotropics, remain unrevealed. Here we use a multi-locus dataset (over 400 loci) obtained through anchored phylogenomics to...

Alignments for probes, raw WGS reads, and WGS assemblies

Marie Nydam, Alan Lemmon, Jesse Cherry, Michelle Kortyna, Darragh Clancy, Cecilia Hernandez & C. Sarah Cohen
Ascidians (Phylum Chordata, Class Ascidiacea) are a large group of invertebrates which occupy a central role in the ecology of marine benthic communities. Many ascidian species have become successfully introduced around the world via anthropogenic vectors. The botryllid ascidians (Order Stolidobranchia, Family Styelidae) are a group of 53 colonial species, several of which are widespread throughout temperate or tropical and subtropical waters. However, the systematics and biology of this group of ascidians is not well-understood....

Data from: The context dependent effects of host competence, competition, and the pathogen transmission mode on disease prevalence

Michael Cortez & Meghan Duffy
Biodiversity in communities is changing globally, including the gain and loss of host species in host-pathogen communities. Increased host diversity can cause infection prevalence in a focal host to increase (amplification) or decrease (dilution). However, it is unclear what general rules govern the context dependent effects, in part because theories for pathogens with different transmission modes have developed largely independently. Using a two-host model, we explore how the pathogen transmission mode and characteristics of a...

Analysis of airline boarding changes in response to COVID-19

Ashok Srinivasan, Tasvirul Islam, Mehran Sadeghi Lahijani & Sirish Namilae
Airlines have introduced a back-to-front boarding process in response to the COVID-19 pandemic. We performed pedestrian dynamics simulation using the Constrained Linear Movement (CALM) model to simulate people boarding a 144-seat Airbus 320 airplane using different boarding procedures, including back to front. This data set contains input files, code, and output files from the simulations containing the trajectories of passengers for a parameter sweep consisting of thousands of simulations. It also contains code to perform...

Allometry constrains the evolution of sexual dimorphism in Drosophila across 33 million years of divergence

Jacqueline Sztepanacz & David Houle
Sexual dimorphism is widely viewed as adaptive, reflecting the evolution of males and females towards divergent fitness optima. Its evolution, however, may often be constrained by the shared genetic architecture of the sexes, and by allometry. Here, we investigated the evolution of sexual size dimorphism, shape dimorphism, and their allometric relationship in the wings of 82 taxa in the family Drosophilidae that have been diverging for at least 33 million years. Shape dimorphism among species...

Registration Year

  • 2021

Resource Types

  • Dataset


  • Florida State University
  • Clemson University
  • University of Michigan-Ann Arbor
  • The Hong Kong University of Science and Technology
  • University of Gothenburg
  • University of Toronto
  • University of California, Riverside
  • University of Oxford
  • University of West Florida
  • South African National Biodiversity Institute