21 Works

Data from: Hybrid origin of European Vipers (Vipera magnifica and Vipera orlovi) from the Caucasus determined using genomic scale DNA markers.

Oleksandr Zinenko, Michael Sovic, Ulrich Joger & H. Lisle Gibbs
Background: Studying patterns of introgression can illuminate the role of hybridization in speciation, and help guide decisions relevant to the conservation of rare taxa. Vipera magnifica and Vipera orlovi are small vipers that have high conservation status due to their rarity and restricted distributions in an area of the Caucasus region where two other related species are present – V. kaznakovi and V. renardi. Despite numerous observations of hybridization between different species of small vipers,...

Data from: Relative performance of non-local cultivars and local, wild populations of switchgrass (Panicum virgatum) in competition experiments

Destiny J. Palik, Allison A. Snow, Amy L. Stottlemyer, Maria N. Miriti & Emily A. Heaton
The possibility of increased invasiveness in cultivated varieties of native perennial species is a question of interest in biofuel risk assessment. Competitive success is a key factor in the fitness and invasive potential of perennial plants, and thus the large-scale release of high-yielding biomass cultivars warrants empirical comparisons with local conspecifics in the presence of competitors. We evaluated the performance of non-local cultivars and local wild biotypes of the tallgrass species Panicum virgatum L. (switchgrass)...

Data from: Identifying cryptic diversity with predictive phylogeography

Anahí Espíndola, Megan Ruffley, Megan L. Smith, Bryan C. Carstens, David C. Tank & Jack Sullivan
Identifying units of biological diversity is a major goal of organismal biology. An increasing literature has focused on the importance of cryptic diversity, defined as the presence of deeply diverged lineages within a single species. While most discoveries of cryptic lineages proceed on a taxon-by-taxon basis, rapid assessments of biodiversity are needed to inform conservation policy and decision-making. Here, we introduce a predictive framework for phylogeography that allows rapidly identifying cryptic diversity. Our approach proceeds...

Data from: The impact of reconstruction methods, phylogenetic uncertainty and branch lengths on inference of chromosome number evolution in American daisies (Melampodium, Asteraceae)

Jamie McCann, Gerald M. Schneeweiss, Tod F. Stuessy, Jose L. Villaseñor & Hanna Weiss-Schneeweiss
Chromosome number change (polyploidy and dysploidy) plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse plant genus Melampodium (Asteraceae) as model group, we assess the impact of reconstruction method (maximum parsimony, maximum likelihood, Bayesian methods), branch length model (phylograms versus chronograms) and phylogenetic...

Data from: Relative importance of abiotic, biotic, and disturbance drivers of plant community structure in the sagebrush steppe

Rachel M. Mitchell, Jonathan D. Bakker, John B. Vincent & G. Matt Davies
Abiotic conditions, biotic factors, and disturbances can act as filters that control community structure and composition. Understanding the relative importance of these drivers would allow us to understand and predict the causes and consequences of changes in community structure. We used long-term data (1989-2002) from the sagebrush steppe in Washington state, USA, to ask three questions: 1) What are the key drivers of community-level metrics of community structure? 2) Do community-level metrics and functional groups...

Data from: Demographic consequences of greater clonal than sexual reproduction in Dicentra canadensis

Chia-Hua Lin, Maria N. Miriti & Karen Goodell
Clonality is a widespread life history trait in flowering plants that may be essential for population persistence, especially in environments where sexual reproduction is unpredictable. Frequent clonal reproduction, however, could hinder sexual reproduction by spatially aggregating ramets that compete with seedlings and reduce inter-genet pollination. Nevertheless, the role of clonality in relation to variable sexual reproduction in population dynamics is often overlooked. We combined population matrix models and pollination experiments to compare the demographic contributions...

Data from: Phylogeographic concordance factors quantify phylogeographic congruence among co-distributed species in the Sarracenia alata pitcher plant system

Jordan D. Satler & Bryan Charles Carstens
Comparative phylogeographic investigations have identified congruent phylogeographic breaks in co-distributed species in nearly every region of the world. The qualitative assessments of phylogeographic patterns traditionally used to identify such breaks, however, are limited because they rely on identifying monophyletic groups across species and do not account for coalescent stochasticity. Only long-standing phylogeographic breaks are likely to be obvious; many species could have had a concerted response to more recent landscape events, yet possess subtle signs...

Data from: Cryptic sex? Estimates of genome exchange in unisexual mole salamanders (Ambystoma sp.)

H. Lisle Gibbs & Robert D. Denton
Cryptic sex has been argued to explain the exceptional longevity of certain parthenogenetic vertebrate lineages, yet direct measurements of genetic exchange between sexual and apparently parthenogenetic forms are rare. Female unisexual mole salamanders (Ambystoma sp.) are the oldest known unisexual vertebrate lineage (~5 million years), and one hypothesis for their persistence is that allopolyploid female unisexuals periodically exchange haploid genomes ‘genome exchange’ during gynogenetic reproduction with males from sympatric sexual species. We test this hypothesis...

Data from: Bayesian estimation of fossil phylogenies and the evolution of early to middle Paleozoic crinoids (Echinodermata)

David F. Wright
Knowledge of phylogenetic relationships among species is fundamental to understanding basic patterns in evolution and underpins nearly all research programs in biology and paleontology. However, most methods of phylogenetic inference typically used by paleontologists do not accommodate the idiosyncrasies of fossil data and therefore do not take full advantage of the information provided by the fossil record. The advent of Bayesian ‘tip-dating’ approaches to phylogeny estimation is especially promising for paleosystematists because time-stamped comparative data...

Data from: Genetic diversity in migratory bats: results from RADseq data for three tree bat species at an Ohio windfarm

Michael G. Sovic, Bryan C. Carstens & H. Lisle Gibbs
Genetic analyses can identify the scale at which wildlife species are impacted by human activities, and provide demographic information useful for management. Here, we use thousands of nuclear DNA genetic loci to assess whether genetic structure occurs within Lasiurus cinereus (Hoary Bat), L. borealis (Red Bat), and Lasionycteris noctivagans (Silver-Haired Bat) bats found at a wind turbine site in Ohio, and to also estimate demographic parameters in each of these three groups. Our specific goals...

Data from: Community trees: identifying codiversification in the páramo dipteran community

Bryan Charles Carstens, Michael Gruenstaeudl & Noah M. Reid
Groups of codistributed species that responded in a concerted manner to environmental events are expected to share patterns of evolutionary diversification. However, the identification of such groups has largely been based on qualitative, post hoc analyses. We develop here two methods (PPS, K-F ANOVA) for the analysis of codistributed species that, given a group of species with a shared pattern of diversification, allow empiricists to identify those taxa that do not codiversify (i.e., "outlier" species)....

Data from: Model-based analysis supports interglacial refugia over long-dispersal events in the diversification of two South American cactus species

Manolo Perez, Isabel A. S. Bonatelli, Evandro Moraes & Bryan C. Carstens
Pilosocereus machrisii and P. aurisetus are cactus species within the P. aurisetus complex, a group of eight cacti that are restricted to rocky habitats within the Neotropical savannas of eastern South America. Previous studies have suggested that diversification within this complex was driven by distributional fragmentation, isolation leading to allopatric differentiation, and secondary contact among divergent lineages. These events have been associated with Quaternary climatic cycles, leading to the hypothesis that the xerophytic vegetation patches...

Data from: Phylogeny and morphologic evolution of the Ordovician Camerata (Class Crinoidea, Phylum Echinodermata)

Selina R. Cole
The subclass Camerata (Crinoidea, Echinodermata) is a major group of Paleozoic crinoids that represents an early divergence in the evolutionary history and morphologic diversification of class Crinoidea, yet phylogenetic relationships among early camerates remain unresolved. This study conducted a series of quantitative phylogenetic analyses using parsimony methods to infer relationships of all well-preserved Ordovician camerate genera (52 taxa), establish the branching sequence of early camerates, and test the monophyly of traditionally recognized higher taxa, including...

Data from: Origin of a cryptic lineage in a threatened reptile through isolation and historical hybridization

Michael G. Sovic, Anthony C. Fries & H. Lisle Gibbs
Identifying phylogenetically distinct lineages and understanding the evolutionary processes by which they have arisen are important goals of phylogeography. This information can also help define conservation units in endangered species. Such analyses are being transformed by the availability of genomic-scale data sets and novel analytical approaches for statistically comparing different historical scenarios as causes of phylogeographic patterns. Here, we use genomic-scale restriction-site-associated DNA sequencing (RADseq) data to test for distinct lineages in the endangered Eastern...

Data from: Locomotor endurance predicts differences in realized dispersal between sympatric sexual and unisexual salamanders

Robert D. Denton, Katherine R. Greenwald & H. Lisle Gibbs
Dispersal is the central mechanism that determines connectivity between populations yet few studies connect the mechanisms of movement with realized dispersal in natural populations. To make such a link, we assessed how physiological variation among individuals predicted dispersal in natural populations of unisexual (all-female) and sexual Ambystoma salamanders on the same fragmented landscape in Ohio. Specifically, we assessed variation in a trait that influences long-distance animal movement (locomotor endurance) and determined whether variation in endurance...

Data from: Sub-lethal effects on fish provide insight into a biologically-relevant threshold of hypoxia

Allison R. Hrycik, L. Zoe Almeida & Tomas O. Hӧӧk
Hypoxia (low dissolved oxygen) is a mounting concern for aquatic ecosystems as its prevalence increases with rising anthropogenic nutrient inputs. Hypoxia is most commonly defined as 2.0 mg l–1 of dissolved oxygen, although this level varies widely across studies and agency regulations. Such definitions may be too conservative, as ecologically-relevant non-lethal effects (e.g. consumption and growth) of hypoxia on important aquatic species, such as fish, often occur at oxygen levels much higher than 2.0 mg...

Data from: The cutaneous lipid composition of bat wing and tail membranes: a case of convergent evolution with birds

Miriam Ben-Hamo, Agusti Muñoz-Garcia, Paloma Larrain, Berry Pinshow, Carmi Korine & Joseph Williams
The water vapour permeability barrier of mammals and birds resides in the stratum corneum (SC), the outermost layer of the epidermis. The molar ratio and molecular arrangement of lipid classes in the SC determine the integrity of this barrier. Increased chain length and polarity of ceramides, the most abundant lipid class in mammalian SC, contribute to tighter packing and thus to reduced cutaneous evaporative water loss (CEWL). However, tighter lipid packing also causes low SC...

Data from: Coevolution of venom function and venom resistance in a rattlesnake predator and its squirrel prey

Matthew L. Holding, James E. Biardi & H. Lisle Gibbs
Measuring local adaptation can provide insights into how coevolution occurs between predators and prey. Specifically, theory predicts that local adaptation in functionally-matched traits of predators and prey will not be detected when coevolution is governed by escalating arms races, whereas it will be present when coevolution occurs through an alternate mechanism of phenotype matching. Here, we analyze local adaptation in venom activity and prey resistance across 12 populations of Northern Pacific rattlesnakes and California ground...

Data from: Phylogeographic model selection leads to insight into the evolutionary history of four-eyed frogs

Maria Tereza C. Thome & Bryan C. Carstens
Phylogeographic research investigates biodiversity at the interface between populations and species, in a temporal and geographic context. Phylogeography has benefited from analytical approaches that allow empiricists to estimate parameters of interest from the genetic data (e.g., θ = 4Neμ, population divergence, gene flow), and the widespread availability of genomic data allow such parameters to be estimated with greater precision. However, the actual inferences made by phylogeographers remain dependent on qualitative interpretations derived from these parameters’...

Data from: Restriction site associated DNA (RAD) for de novo sequencing and marker discovery in sugarcane borer, Diatraea saccharalis Fab. (Lepidoptera: Crambidae)

Vitor A.C. Pavinato, Gabriel R.A. Margarido, Asela J. Wijeratne, Saranga Wijeratne, Tea Meulia, Anete P. Souza, Andrew P. Michel, Maria I. Zucchi & V. A. C. Pavinato
We present the development of a genomic library using RADseq (restriction site associated DNA sequencing) protocol for marker discovery that can be applied on evolutionary studies of the sugarcane borer Diatraea saccharalis, an important South American insect pest. A RADtag protocol combined with Illumina paired-end sequencing allowed de novo discovery of 12 811 SNPs and a high-quality assembly of 122.8M paired-end reads from six individuals, representing 40 Gb of sequencing data. Approximately 1.7 Mb of...

Data from: Phylogenomic analyses support traditional relationships within Cnidaria

Felipe Zapata, Freya E. Goetz, Stephen A. Smith, Mark Howison, Stefan Siebert, Samuel H. Church, Steven M. Sanders, Cheryl Lewis Ames, Catherine S. McFadden, Scott C. France, Marymegan Daly, Allen G. Collins, Steven H. D. Haddock, Casey W. Dunn & Paulyn Cartwright
Cnidaria, the sister group to Bilateria, is the most diverse group of animals in terms of morphology, lifecycles, ecology, and development. How this diversity originated and evolved is not well understood because phylogenetic relationships among major cnidarian lineages are unclear, and recent studies present contrasting phylogenetic hypotheses. Here, we use transcriptome data from 15 newly-sequenced species in combination with 26 publicly available genomes and transcriptomes to assess phylogenetic relationships among major cnidarian lineages. Phylogenetic analyses...

Registration Year

  • 2016

Resource Types

  • Dataset


  • The Ohio State University
  • University of Kansas
  • Sao Paulo State University
  • University of Washington
  • Duke University
  • Federal University of São Carlos
  • University of Vermont
  • National Autonomous University of Mexico
  • University of Louisiana at Lafayette
  • Purdue University