32 Works

Data from: Mating preference for novel phenotypes can be explained by general neophilia in female guppies

Mitchel J. Daniel, Laura Koffinas & Kimberly Hughes
Understanding how genetic variation is maintained in ecologically-important traits is a fundamental question in evolutionary biology. Male Trinidadian guppies (Poecilia reticulata) exhibit extreme genetic diversity in color patterns within populations, which is believed to be promoted by a female mating preference for rare or novel patterns. However, the origins of this preference remain unclear. Here, we test the hypothesis that mating preference for novel phenotypes is a by-product of general neophilia that evolved in response...

Data for: The scales of coevolution: comparative phylogeography and genetic demography of a locally adapted venomous predator and its prey

Matthew Holding
Coevolutionary theory predicts that differences in the genetic demography of interacting species can influence patterns of local adaptation by affecting the potential of local populations to respond to selection. We conducted a comparative phylogeographic study of venomous rattlesnakes and their venom-resistant ground squirrel prey across California, and assessed how effective population size (Ne) estimates correspond with a previously documented pattern of rattlesnake local adaptation. Using RAD-seq markers, we detected lineage relationships among both the rattlesnakes...

Data from: Out of sight, out of mind: Widespread nuclear and plastid-nuclear discordance in the flowering plant genus Polemonium (Polemoniaceae) suggests widespread historical gene flow despite limited nuclear signal

Jeffrey Rose, Cassio Toledo, Emily Lemmon, Alan Lemmon & Kenneth Sytsma
Phylogenomic data from a rapidly increasing number of studies provide new evidence for resolving relationships in recently radiated clades, but they also pose new challenges for inferring evolutionary histories. Most existing methods for reconstructing phylogenetic hypotheses rely solely on algorithms that only consider incomplete lineage sorting as a cause of intra- or inter-genomic discordance. Here, we utilize a variety of methods, including those to infer phylogenetic networks, to account for both incomplete lineage sorting and...

Integrating top-down and bottom-up effects of local density across scales and a complex life cycle

Jessie Mutz, Nora Underwood & Brian Inouye
Effects of group size (local conspecific density) on individual performance can be substantial, yet it is unclear how these translate to larger-scale and longer-term outcomes. Effects of group size can be mediated by both top-down and bottom-up interactions, can change in type or direction across the life cycle, and can depend on the spatial scale at which group size is assessed. Only by determining how these different processes combine can we make predictions about how...

The role of cloud–infrared radiation feedback in tropical cyclone development

J.H. Ruppert, A.A. Wing, X. Tang & E.L. Duran
This archive contains the data and code used by Ruppert et al. (2020) in their journal publication (DOI placeholder; "The role of cloud–infrared radiation feedback in tropical cyclone development"). It contains 1) the WRF model code and namelist files required to run the pre-processing and simulations of Typhoon Haiyan and Hurricane Maria, and 2) the forcing and circulation output from Sawyer–Eliassen equation computations. Gridded output files are in NetCDF format. Additional datasets required to conduct...

Data from: Gene flow and species delimitation in fishes of Western North America: Flannelmouth (Catostomus latipinnis) and Bluehead sucker (C. Pantosteus discobolus)

Max Bangs, Marlis Douglas, Tyler Chafin & Michael Douglas
The delimitation of species-boundaries, particularly those obscured by reticulation, is a critical step in contemporary biodiversity assessment. It is especially relevant for conservation and management of indigenous fishes in western North America, represented herein by two species with dissimilar life-histories co-distributed in the highly modified Colorado River (i.e., Flannelmouth Sucker, Catostomus latipinnis; Bluehead Sucker, C. (Pantosteus) discobolus). To quantify phylogenomic patterns and examine proposed taxonomic revisions, we first employed double-digest restriction-site associated DNA sequencing (ddRAD),...

Data from: Inbreeding shapes the evolution of marine invertebrates

Kevin Olsen, Will Ryan, Alice Winn, Ellen Kosman, Jose Moscoso, Stacy Krueger-Hadfield, Scott Burgess, David Carlon, Richard Grosberg, Susan Kalisz & Don Levitan
Inbreeding is a potent evolutionary force shaping the distribution of genetic variation within and among populations of plants and animals. Yet, our understanding of the forces shaping the expression and evolution of non-random mating in general, and inbreeding in particular, remains remarkably incomplete. Most research on plant mating systems focuses on self-fertilization and its consequences for automatic selection, inbreeding depression, purging, and reproductive assurance, whereas studies of animal mating systems have often assumed that inbreeding...

Data from: Kin recognition in guppies uses self-referencing on olfactory cues

Mitchel Daniel & F. Helen Rodd
Kin recognition plays an important role in social behavior and evolution, but the proximate mechanisms by which individuals recognize kin remain poorly understood. In many species, individuals form a “kin template” that they compare against conspecifics’ phenotypes to assess phenotypic similarity–and by association, relatedness. Individuals may form a kin template through self-inspection (i.e. self-referencing) and/or by observing their rearing associates (i.e. family-referencing). However, despite much interest, few empirical studies have successfully disentangled self- and family-referencing....

Data from: Large-scale connectivity, cryptic population structure, and relatedness in Eastern Pacific olive ridley sea turtles (Lepidochelys olivacea)

Ian Silver-Gorges, Julianne Koval, Clara Rodriguez-Zarate, Frank Paladino & Mark Jordan
Endangered species are grouped into genetically discrete populations to direct conservation efforts. Mitochondrial Control Region (mtCR) haplotypes are used to elucidate deep divergences between populations, as compared to nuclear microsatellites that can detect recent structuring. When prior populations are unknown, it is useful to subject microsatellite data to clustering and/or ordination population inference. Olive ridley sea turtles (Lepidochelys olivacea) are the most abundant sea turtle, yet few studies have characterized olive ridley population structure. Recently,...

Data from: Predicting multivariate responses of sexual dimorphism to direct and indirect selection

David Houle & Changde Cheng
Sexual dimorphism is often assumed to result from balancing the strength of antagonistic selection in favor of dimorphism against the degree of constraint imposed by the shared genome of the sexes, reflected in the B matrix of genetic inter-sexual covariances. To investigate the totality of forces shaping dimorphism, we reparameterized the Lande equation to predict changes in trait averages and trait differences between the sexes. As genetic constraints on the evolution of dimorphism in response...

Supplementary information for: Using networks to identify structure in phylogenetic tree sets

Jeremy Brown, Melissa Marchand, Wen Huang, Guifang Zhou, Genevieve Mount, Jeremy Ash, Kyle Gallivan & James Wilgenbusch
Modern phylogenomic studies produce large sets of trees that can represent variation in inferred phylogenies across genes, uncertainty in estimated phylogenies for a given gene, or both. Standard practice is to condense this variation down to a small set of point estimates or consensus trees in order to facilitate display and interpretation. However, doing so results in the loss of enormous amounts of information about the structure of the underlying tree set. Here, we propose...

Data from: Phylogenomic data reveal reticulation and incongruence among mitochondrial candidate species in Dusky Salamanders (Desmognathus)

Robert Alexander Pyron, Kyle A. O'Connell, Emily Moriarty Lemmon, Alan R. Lemmon & David A. Beamer
Gene flow between evolutionarily distinct lineages is increasingly recognized as a common occurrence. Such processes distort our ability to diagnose and delimit species, as well as confound attempts to estimate phylogenetic relationships. A conspicuous example is Dusky Salamanders (Desmognathus), a common model-system for ecology, evolution, and behavior. Only 22 species are described; 7 in the last 40 years. However, mitochondrial datasets indicate the presence of up to 45 “candidate species” presenting a complex history of...

Data from: Are you more than the sum of your parents’ genes? phenotypic plasticity in a clonal vertebrate and F1 hybrids of its parental species

Amber M. Makowicz & Joseph Travis
All known vertebrate clones have originated from hybridization events and some have produced distinct evolutionary lineages via hybrid speciation. Amazon mollies (Poecilia formosa) present an excellent study system to investigate how clonal species have adapted to heterogeneous environments because they are the product of a single hybridization event between male sailfin mollies (P. latipinna) and female Atlantic mollies (P. mexicana). Here we ask whether the hybrid species differs from the combination of its parental species’...

Data from: Congruence and conflict in the higher-level phylogenetics of squamate reptiles: an expanded phylogenomic perspective

Sonal Singhal, Timothy Colston, Maggie Grundler, Stephen Smith, Gabriel Costa, Guarino Colli, Craig Moritz, Alexander Pyron & Daniel Rabosky
Genome-scale data have the potential to clarify phylogenetic relationships across the tree of life, but have also revealed extensive gene tree conflict. This seeming paradox, whereby larger datasets both increase statistical confidence and uncover significant discordance, suggests that understanding sources of conflict is important for accurate reconstruction of evolutionary history. We explore this paradox in squamate reptiles, the vertebrate clade comprising lizards, snakes, and amphisbaenians. We collected an average of 5103 loci for 91 species...

Data from: Environmental change, if unaccounted, prevents detection of cryptic evolution in a wild population

Tomos Potter, Ronald D. Bassar, Paul Bentzen, Emily W. Ruell, Julián Torres-Dowdall, Corey A. Handelsman, Cameron K. Ghalambor, Joseph Travis, David N. Reznick & Tim Coulson
Detecting contemporary evolution requires demonstrating that genetic change has occurred. Mixed-effects models allow estimation of quantitative genetic parameters and are widely used to study evolution in wild populations. However, predictions of evolution based on these parameters frequently fail to match observations. Furthermore, such studies often lack an independent measure of evolutionary change against which to verify predictions. Here, we applied three commonly used quantitative genetic approaches to predict the evolution of size at maturity in...

Data from: Bee phenology is predicted by climatic variation and functional traits

Michael Stemkovski, Will Pearse, Sean Griffin, Gabriella Pardee, Jason Gibbs, Terry Griswold, John Neff, Ryan Oram, Molly RightMyer, Cory Sheffield, Karen Wright, Brian Inouye, David Inouye & Rebecca Irwin
Climate change is shifting the environmental cues that determine the phenology of interacting species. Plant-pollinator systems may be susceptible to temporal mismatch if bees and flowering plants differ in their phenological responses to warming temperatures. While the cues that trigger flowering are well-understood, little is known about what determines bee phenology. Using Generalized Additive Models, we analyzed time-series data representing 67 bee species collected over nine years in the Colorado Rocky Mountains to perform the...

Phylogenomics, biogeography and taxonomic revision of New Guinean pythons (Pythonidae, Leiopython) harvested for international trade

Damien Esquerre, Daniel J. D. Natusch, Jessica A. Lyons, Amir Hamidy, Alan R. Lemmon, Emily M. Lemmon, Awal Riyanto, J. Scott Keogh & Stephen Donnellan
The large and enigmatic New Guinean pythons in the genus Leiopython are harvested from the wild to supply the international trade in pets. Six species are currently recognized (albertisii, biakensis, fredparkeri, huonensis, meridionalis, montanus) but the taxonomy of this group has been controversial. We combined analysis of 421 nuclear loci and complete mitochondrial genomes with morphological data to construct a detailed phylogeny of this group, understand their biogeographic patterns and establish the systematic diversity of...

Data from: Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment

David Gray, David Weissman, Jeffrey Cole, Emily Lemmon & Alan Lemmon
We present the first comprehensive molecular phylogeny of Gryllus field cricket species found in the United States and Canada, select additional named Gryllus species found in Mexico and the Bahamas, plus the European field cricket G. campestris Linnaeus and the Afro-Eurasian cricket G. bimaculatus De Geer. Acheta, Teleogryllus, and Nigrogryllus were used as outgroups. Anchored hybrid enrichment was used to generate 492,531 base pairs of DNA sequence from 563 loci. RAxML analysis of concatenated sequence...

Cohesin depleted cells rebuild functional nuclear compartments after endomitosis

Marion Cremer, Katharina Brandstetter, Andreas Maiser, Suhas S P Rao, Volker Schmid, Miguel Guirao-Ortiz, Namita Mitra, Stefania Mamberti, Kyle N Klein, David Gilbert, Heinrich Leonhardt, Maria Cristina Cardoso, Erez Lieberman Aiden, Hartmann Harz & Thomas Cremer
Cohesin plays an essential role in chromatin loop extrusion, but its impact on a compartmentalized nuclear architecture is debatable. Using live-cell and super-resolved 3D microscopy, we demonstrate that cohesin-depleted cells pass through an endomitosis and rebuild a single multilobulated nucleus (MLN) with chromosome territories (CTs) pervaded by interchromatin channels. CTs contain chromatin domain clusters with a zonal organization of repressed chromatin domains in the interior and transcriptionally competent domains located at the periphery. Splicing speckles...

The perfect storm: Gene tree estimation error, incomplete lineage sorting, and ancient gene flow explain the most recalcitrant ancient angiosperm clade, Malpighiales

Liming Cai, Zhenxiang Xi, Emily Lemmon, Alan Lemmon, Austin Mast, Christopher Buddenhagen, Liang Liu & Charles Davis
The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent (MSC) model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data...

Data from: Evolutionary and plastic phenotypic change can be just as fast as changes in population densities

Michael Cortez & Guenchik Grosklos
Evolution and plasticity can drive population-level phenotypic change (e.g., changes in the mean phenotype) on time scales comparable to changes in population densities. However, it is unclear if phenotypic change has the potential to be just as fast as changes in densities, or if comparable rates of change only occur when densities are changing slow enough for phenotypes to keep pace. Moreover, it is unclear if this depends on the mode of adaptation. Using scaling...

Data from: Comparing the indirect effects between exploiters in predator-prey and host-pathogen systems

Michael H. Cortez & Meghan Duffy
DataS1 These files are Maple and Matlab scripts for analyzing the predator-prey and host-pathogen models in "Comparing the indirect effects between exploiters in predator-prey and host-pathogen systems" and generating the figures in that study.

Data from: When does growth rate influence fitness in a colonial marine invertebrate?

Scott Burgess & Marília Bueno
Growth rate affects body size, and larger body sizes are often associated with the capacity to produce more surviving offspring. However, the assumption that growth rate should positively relate to fitness is rarely tested, especially in colonial marine invertebrates where size and age can be decoupled. We measured growth, survival, and reproduction through repeated census of 97 colonies from two populations of a marine bryozoan in the field from settlement to the end of their...

Clinical trial generalizability assessment in the big data era: a review

Zhe He, Xiang Tang, Kelsa Bartley, Xi Yang, Yi Guo, Thomas J. George, Neil Charness, William R Hogan & Jiang Bian
Clinical studies, especially randomized controlled trials, are essential for generating evidence for clinical practice. However, generalizability is a long-standing concern when applying trial results to real-world patients. Generalizability assessment is thus important, nevertheless, not consistently practiced. We performed a systematic scoping review to understand the practice of generalizability assessment. We identified 187 relevant papers and systematically organized these studies in a taxonomy with three dimensions: (1) data availability (i.e., before or after trial [a priori...

Sibship reconstruction with SNPs illuminates the scope of a cryptic invasion of Asian Swamp Eels (Monotperus albus) in Georgia, USA

Andrew Taylor, Max Bangs & James Long
Cryptic invasive species are particularly problematic to study, manage, and control because of the difficulty detecting these species within their invaded habitats. Such is the case of the Asian Swamp Eel (Monopterus albus; ASE) where it is established in vegetated marshes along the Chattahoochee River, Georgia. Adult eels have been nearly impossible to detect or quantify with traditional sampling, although leaf-litter trapping of juvenile ASEs has been somewhat successful.In this study, we leveraged a collection...

Registration Year

  • 2020
    32

Resource Types

  • Dataset
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Affiliations

  • Florida State University
    32
  • Utah State University
    2
  • Australian National University
    2
  • Dalhousie University
    2
  • University of California, Riverside
    2
  • University of California, Davis
    2
  • California State University, Northridge
    1
  • University of Alabama at Birmingham
    1
  • University of Phayao
    1
  • The University of Texas at Austin
    1