187 Works

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...

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...

Data from: Effect of mutualist partner identity on plant demography

Emilio M. Bruna, Thiago Junqueira Izzo, Brian D. Inouye & Heraldo L. Vasconcelos
Mutualisms play a central role in the origin and maintenance of biodiversity. Because many mutualisms have strong demographic effects, interspecific variation in partner quality could have important consequences for population dynamics. Nevertheless, few studies have quantified how a mutualist partner influences population growth rates, and still fewer have compared the demographic impacts of multiple partner species. We used integral projection models parameterized with three years of census data to compare the demographic effects of two...

Data from: Contemporary population structure and post-glacial genetic demography in a migratory marine species, the blacknose shark, Carcharhinus acronotus

David Portnoy, Christopher Hollenbeck, Carolyn Belcher, , Bryan Frazier, Jim Gelsleichter, R. D. Grubbs, John Gold, D. S. Portnoy, C. M. Hollenbeck, J. R. Gold, C. N. Belcher, B. S. Frazier & W. B. Driggers
Patterns of population structure and historical genetic demography of blacknose sharks in the western North Atlantic Ocean were assessed using variation in nuclear-encoded microsatellites and sequences of mitochondrial (mt)DNA. Significant heterogeneity and/or inferred barriers to gene flow, based on microsatellites and/or mtDNA, revealed the occurrence of five genetic populations localized to five geographic regions: the southeastern U.S Atlantic coast, the eastern Gulf of Mexico, the western Gulf of Mexico, Campeche Bay in the southern Gulf...

Data from: Correlated evolution of mating system and floral display traits in flowering plants and its implications for the distribution of mating system variation

Carol Goodwillie, Risa D. Sargent, Susan Kalisz, Richard H. Ree, David A. Moeller, Mario Vallejo-Marin, Christopher G. Eckert, Alice A. Winn, Elizabeth Elle, Monica A. Geber & Mark O. Johnston
Reduced allocation to structures for pollinator attraction is predicted in selfing species. We explored the association between outcrossing and floral display in a broad sample of angiosperms. We used the demonstrated relationship to test for bias against selfing species in the outcrossing rate distribution, the shape of which has relevance for the stability of mixed mating. Relationships between outcrossing rate, flower size, flower number and floral display, measured as the product of flower size and...

Data from: Origins of the Greenland shark (Somniosus microcephalus): impacts of ice-olation and introgression

Ryan P. Walter, Denis Roy, Nigel E. Hussey, Björn Stelbrink, Kit M. Kovacs, Christian Lydersen, Bailey C. McMeans, Jörundur Svavarsson, Steven T. Kessel, Sebastian Biton Porsmoguer, Sharon Wildes, Cindy A. Tribuzio, Steven E. Campana, Stephen D. Petersen, R. Dean Grubbs, Daniel D. Heath, Kevin J. Hedges & Aaron T. Fisk
Herein, we use genetic data from 277 sleeper sharks to perform coalescent-based modeling to test the hypothesis of early Quaternary emergence of the Greenland shark (Somniosus microcephalus) from ancestral sleeper sharks in the Canadian Arctic-Subarctic region. Our results show that morphologically cryptic somniosids S. microcephalus and Somniosus pacificus can be genetically distinguished using combined mitochondrial and nuclear DNA markers. Our data confirm the presence of genetically admixed individuals in the Canadian Arctic and sub-Arctic, and...

Data from: Local adaptation in dispersal in multi-resource landscapes

Meredith Lane Cenzer & Leithen K. M'Gonigle
The distribution of resources in space has important consequences for the evolution of dispersal-related traits. Dispersal moderates patterns of gene flow and, consequently, the potential for local adaptation to spatially differentiated resource types. We lack both models and experiments that evaluate how dispersal evolves in landscapes with multiple resources. Here, we investigate the evolution of dispersal in landscapes that contain two resource types that differ in their spatial autocorrelations. Individuals may possess ecological traits that...

Data from: Effectiveness of phylogenomic data and coalescent species-tree methods for resolving difficult nodes in the phylogeny of advanced snakes (Serpentes: Caenophidia)

R. Alexander Pyron, Catriona R. Hendry, Vincent M. Chou, Emily M. Lemmon, Alan R. Lemmon & Frank T. Burbrink
Next-generation genomic sequencing promises to quickly and cheaply resolve remaining contentious nodes in the Tree of Life, and facilitates species-tree estimation while taking into account stochastic genealogical discordance among loci. Recent methods for estimating species trees bypass full likelihood-based estimates of the multi-species coalescent, and approximate the true species-tree using simpler summary metrics. These methods converge on the true species-tree with sufficient genomic sampling, even in the anomaly zone. However, no studies have yet evaluated...

Data from: The evolution of gametic compatibility and compatibility groups in the sea urchin Mesocentrotus franciscanus: an avenue for speciation in the sea

Don R. Levitan, Rebecca Buchwalter & Yueling Hao
The generation of reproductive incompatibility between groups requires a rare genotype with low compatibility to increase in frequency. We tested the hypothesis that sexual conflict driven by the risk of polyspermy can generate compatibility groups in gamete recognition proteins (GRPs) in the sea urchin Mesocentrotus franciscanus. We examined variation in the sperm (bindin) and egg (EBR1) GRPs, how this variation influences fertilization success and how allele frequencies shift in these GRPs over time. The EBR1...

Data from: Natatanuran frogs used the Indian Plate to step-stone disperse and radiate across the Indian Ocean

Zhi-Yong Yuan, Bao-Lin Zhang, Christopher J. Raxworthy, David W. Weisrock, Paul M. Hime, Jie-Qiong Jin, Emily M. Lemmon, Alan R. Lemmon, Sean D. Holland, Michelle L. Kortyna, Wei-Wei Zhou, Min-Sheng Peng, Jing Che & Elizabeth Prendini
Natatanura raw assembled sequencesNatatanura_seqs.zip

Data from: Skeletal microstructure of Stenopterygius quadriscissus (Reptilia, Ichthyosauria) from the Posidonienschiefer (Posidonia Shale, Lower Jurassic) of Germany

Katherine L. Anderson, Patrick S. Druckenmiller, Gregory M. Erickson & Erin E. Maxwell
Ichthyosaurians (Ichthyosauria) are a major clade of secondarily aquatic marine tetrapods that occupied several major predatory niches during the Mesozoic Era. Multiple lines of evidence including isotopic, body shape and swimming modality analyses suggest they exhibited elevated growth and metabolic rates, and body temperatures. However, applications of osteohistological methods to test hypotheses regarding their physiology are few. Previous studies focused on the humeri, vertebrae and ribs from a small number of taxa. Here, we use...

Data from: A hybrid phylogenetic–phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification

Adam D. Leaché, Philipp Wagner, Charles W. Linkem, Wolfgang Böhme, Theodore J. Papenfuss, Rebecca A. Chong, Brian R. Lavin, Aaron M. Bauer, Stuart V. Nielsen, Eli Greenbaum, Mark-Oliver Rödel, Andreas Schmitz, Matthew LeBreton, Ivan Ineich, Laurent Chirio, Caleb Ofori-Boateng, Edem A. Eniang, Sherif Baha El Din, Alan R. Lemmon & Frank T. Burbrink
Africa is renowned for its biodiversity and endemicity, yet little is known about the factors shaping them across the continent. African Agama lizards (45 species) have a pan-continental distribution, making them an ideal model for investigating biogeography. Many species have evolved conspicuous sexually dimorphic traits, including extravagant breeding coloration in adult males, large adult male body sizes, and variability in social systems among colorful versus drab species. We present a comprehensive time-calibrated species tree for...

Data from: The Centennial Trends Greater Horn of Africa precipitation dataset

Chris C. Funk, Sharon E. Nicholson, Martin Landsfeld, Douglas Klotter, Pete Peterson & Laura Harrison
East Africa is a drought prone, food and water insecure region with a highly variable climate. This complexity makes rainfall estimation challenging, and this challenge is compounded by low rain gauge densities and inhomogeneous monitoring networks. The dearth of observations is particularly problematic over the past decade, since the number of records in globally accessible archives has fallen precipitously. This lack of data coincides with an increasing scientific and humanitarian need to place recent seasonal...

Data from: Anchored hybrid enrichment for massively high-throughput phylogenomics

Alan R. Lemmon, Sandra Emme, Emily Moriarty Lemmon & Sandra A. Emme
The field of phylogenetics is on the cusp of a major revolution, enabled by new methods of data collection that leverage both genomic resources and recent advances in DNA sequencing. Previous phylogenetic work has required labor-intensive marker development coupled with single-locus PCR and DNA sequencing on a clade-by-clade and marker-by-marker basis. Here, we present a new, cost-efficient, and rapid approach to obtaining data from hundreds of genes for potentially hundreds of individuals for deep and...

Data from: Phylogeographic inference using Bayesian model comparison across a fragmented chorus frog species complex

Lisa N. Barrow, Alyssa T. Bigelow, Christopher A. Phillips & Emily Moriarty Lemmon
Fragmented species complexes provide an interesting system for investigating biogeographic history and the present distribution of genetic variation. Recent advances in sequencing technology and statistical phylogeography enable the collection and rigorous analysis of large multilocus data sets, but designing studies that produce meaningful phylogeographic inferences remains challenging. We implemented a Bayesian model comparison approach to investigate previous biogeographic hypotheses while simultaneously inferring the presence of genetic structure in a chorus frog species complex. The Illinois...

Data from: Genomic basis of life history evolution in Drosophila melanogaster

Silvia C. Remolina, Peter L. Chang, Jeff Leips, Sergey V. Nuzhdin & Kimberly A. Hughes
Natural diversity in aging and other life history patterns is a hallmark of organismal variation. Related species, populations, and individuals within populations show genetically based variation in life span and other aspects of age-related performance. Population differences are especially informative because these differences can be large relative to within-population variation and because they occur in organisms with otherwise similar genomes. We used experimental evolution to produce populations divergent for life span and late-age fertility and...

Data from: Phylogenomic data yield new and robust insights into the phylogeny and evolution of weevils

Seunggwan Shin, Dave J. Clarke, Alan R. Lemmon, Emily Moriarty Lemmon, Alexander L. Aitken, Stephanie Haddad, Brian D. Farrell, Adriana E. Marvaldi, Rolf G. Oberprieler & Duane D. McKenna
The phylogeny and evolution of weevils (the beetle superfamily Curculionoidea) has been extensively studied, but many relationships, especially in the large family Curculionidae (true weevils; > 50000 species), remain uncertain. We used phylogenomic methods to obtain DNA sequences from 522 protein coding genes for representatives of all families of weevils and all subfamilies of Curculionidae. Most of our phylogenomic results had strong statistical support, and the inferred relationships were generally congruent with those reported in...

Data from: Geographic variation in the Pine Barrens Treefrog (Hyla andersonii): concordance of genetic, morphometric, and acoustic signal data

Alexa R. Warwick, Joseph Travis & Emily Moriarty Lemmon
Delimiting species is important to every subfield in biology. Templeton's cohesion species concept uses genetic and ecological exchangeability to identify sets of populations that ought to be considered as the same species, and the lack of exchangeability helps determine which populations can be grouped as evolutionarily significant units (ESU) in conservation science. However, previous work assessing genetic and ecological interchangeability among populations has been limited in scope. Here, we provide a method for assessing exchangeability...

Data from: Life history evolution in guppies VIII: the demographics of density regulation in guppies (Poecilia reticulata)

David N. Reznick, Ronald D. Bassar, Joseph Travis & F. Helen Rodd
In prior research, we found the way guppy life histories evolve in response to living in environments with a high or low risk of predation is consistent with life history theory that assumes no density-dependence. We later found that guppies from high predation environments experience higher mortality rates than those from low predation environments, but the increased risk was evenly distributed across all age/size classes. Life history theory that assumes density-independent population growth predicts that...

Data from: The evolution of coexistence: reciprocal adaptation promotes the assembly of a simple community

Ronald D. Bassar, Troy Simon, William Roberts, Joseph Travis & David N. Reznick
Species coexistence may result by chance when co-occurring species do not strongly interact or it may be an evolutionary outcome of strongly interacting species adapting to each other. While patterns like character displacement indicate that coexistence has often been an evolutionary outcome, it is unclear how often the evolution of coexistence represents adaptation in only one species or reciprocal adaptation among all interacting species. Here we demonstrate a strong role for evolution in the coexistence...

Data from: The phylogeny and biogeography of Hakea (Proteaceae) reveals the role of biome shifts in a continental plant radiation

Marcel Cardillo, Peter H. Weston, Zoe K.M. Reynolds, Peter M. Olde, Austin R. Mast, Emily Lemmon, Alan Richard Lemmon, Lindell Bromham, Emily M. Lemmon & Zoe K. M. Reynolds
The frequency of evolutionary biome shifts during diversification has important implications for our ability to explain geographic patterns of plant diversity. Recent studies present several examples of biome shifts, but whether frequencies of biome shifts closely reflect geographic proximity or environmental similarity of biomes remains poorly known. We explore this question by using phylogenomic methods to estimate the phylogeny of Hakea, a diverse Australian genus occupying a wide range of biomes. Model-based estimation of ancestral...

Data from: Short-term, low-level nitrogen deposition dampens a trophic cascade between bears and plants

Joshua B. Grinath
Human activities have substantially increased atmospheric nitrogen (N) deposition in ecosystems worldwide, often leading to higher plant quality for herbivores and greater herbivory. Predators frequently suppress herbivores and indirectly benefit plants via ‘trophic cascades’, and the strength of these interactions can also depend on N availability. However, the evidence for N deposition effects on cascades primarily comes from studies of high-level N deposition. Most terrestrial ecosystems currently receive elevated, but low-level N deposition, and it...

Data from: In love and war: the morphometric and phylogenetic basis of ornamentation, and the evolution of male display behavior, in the livebearer genus Poecilia

Daniel Lorenz Goldberg, Joseph Alex Landy, Joseph Travis, Mark S. Springer & David N. Reznick
Exaggerated male traits under sexual selection are often used for both competition and courtship, raising the question of whether ornaments evolved simultaneously for both functions, or if use in one context preceded use in another. Here we apply a phylogenetic approach to study the evolution of ornamental dorsal fins in male poeciliid fish of the subgenera Mollienesia and Limia, which exhibit convergent development of an enlarged dorsal fin, and often direct erect-fin displays to male...

Data from: Sudden collapse of a mesopredator reveals its complementary role in mediating rocky reef regime shifts

Jenn M. Burt, Tim M. Tinker, Daniel K. Okamoto, Kyle W. Demes, Keith Holmes & Anne K. Salomon
While changes in the abundance of keystone predators can have cascading effects resulting in regime shifts, the role of mesopredators in these processes remains underexplored. We conducted annual surveys of rocky reef communities that varied in the recovery of a keystone predator (sea otters Enhydra lutris) and the mass mortality of a mesopredator (sunflower sea star Pycnopodia helianthoides) due to an infectious wasting disease. By fitting a population model to empirical data, we show that...

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...

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