20 Works

Data from: An expanded plastid phylogeny of Marsilea with emphasis on North American species

W. Mark Whitten, Colette C. Jacono & Nathalie S. Nagalingum
Ferns of the genus Marsilea (water clover) are potentially invasive aquatic and wetland plants. They are difficult to identify to species because of subtle diagnostic characters, the sterile condition of many specimens, and unresolved taxonomic problems. We sequenced four plastid regions (rbcL, rps4, rps4-trnS spacer, and trnL-F spacer) from 223 accessions across ca. 38 species. Our goals were to: 1) attempt to identify problematic Marsilea specimens from the southeastern U.S., and 2) assess species delimitation...

Data from: Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK

Kurt M. Neubig, W. Mark Whitten, Barbara S. Carlsward, Mario A. Blanco, Lorena Endara, Norris H. Williams & Michael Moore
Plastid DNA sequences have been widely used by systematists for reconstructing plant phylogenies. The utility of any DNA region for phylogenetic analysis is determined by ease of amplification and sequencing, confidence of assessment in phylogenetic character alignment, and by variability across broad taxon sampling. Often, a compromise must be made between using relatively highly conserved coding regions or highly variable introns and intergenic spacers. Analyses of a combination of these types of DNA regions yield...

Data from: A jungle in there: bacteria in belly buttons are highly diverse, but predictable

Jiri Hulcr, Andrew M. Latimer, Jessica B. Henley, Nina R. Rountree, Noah Fierer, Andrea Lucky, Margaret D. Lowman & Robert R. Dunn
The belly button is one of the habitats closest to us, and yet it remains relatively unexplored. We analyzed bacteria and arachaea from the belly buttons of humans from two different populations sampled within a nation-wide citizen science project. We examined bacterial and archaeal phylotypes present and their diversity using multiplex pyrosequencing of 16S rDNA libraries. We then tested the oligarchy hypothesis borrowed from tropical macroecology, namely that the frequency of phylotypes in one sample...

Data from: Turning the crown upside down: gene tree parsimony roots the eukaryotic tree of life

Laura A. Katz, Jessica R. Grant, Laura Wegener Parfrey & J. Gordon Burleigh
The first analyses of gene sequence data indicated that the eukaryotic tree of life consisted of a long stem of microbial groups ‘topped’ by a crown containing plants, animals, and fungi and their microbial relatives. While more recent multigene concatenated analyses have refined the relationships among the many branches of eukaryotes, the root of the eukaryotic tree of life has remained elusive. Inferring the root of extant eukaryotes is challenging because of the age of...

Data from: Genetic variation in the Yolk protein expression network of Drosophila melanogaster: sex-biased negative correlations with longevity

Aaron M. Tarone, Lauren M. Mcintyre, Lawrence G. Harshman, Sergey V. Nuzhdin, A M Tarone, L G Harshman, L M McIntyre & S V Nuzhdin
One of the persistent problems in biology is understanding how genetic variation contributes to phenotypic variation. Associations at many levels have been reported, and yet causal inference has remained elusive. We propose to rely on the knowledge of causal relationships established by molecular biology approaches. The existing molecular knowledge forms a firm backbone upon which hypotheses connecting genetic variation, transcriptional variation and phenotypic variation can be built. The sex determination pathway is a well-established molecular...

Data from: Montane refugia predict population genetic structure in the Large-blotched Ensatina salamander

Thomas J. Devitt, Susan E. Cameron Devitt, Bradford D. Hollingsworth, Jimmy A. McGuire, Craig Moritz & Susan E. Cameron Devitt
Understanding the biotic consequences of Pleistocene range shifts and fragmentation remains a fundamental goal in historical biogeography and evolutionary biology. Here, we combine species distribution models (SDM) from the present and two late Quaternary time periods with multilocus genetic data (mitochondrial DNA and microsatellites) to evaluate the effect of climate-induced habitat shifts on population genetic structure in the Large-blotched Ensatina (Ensatina eschscholtzii klauberi), a plethodontid salamander endemic to middle and high-elevation conifer forest in the...

Data from: Assessing parameter identifiability in phylogenetic models using Data Cloning

José Miguel Ponciano, J. Gordon Burleigh, Edward L. Braun, Mark Taper & Mark L. Taper
The success of model-based methods in phylogenetics has motivated much research aimed at generating new, biologically informative models. This new computer-intensive approaches to phylogenetics demands validation studies and sound measures of performance. To date such work has consisted only of simulation studies, estimation of known phylogenies and difficult mathematical analyses assessing the estimability of parameters. Little practical guidance has been available to practitioners and theoreticians alike as to when and why the parameters in a...

Data from: Recurrent evolution of dioecy in bryophytes

Stuart F. McDaniel, John Atwood & J. Gordon Burleigh
The origin and maintenance of separate sexes (dioecy) is an enduring evolutionary puzzle. Although both hermaphroditism and dioecy occur in many diverse clades, we know little about the long-term evolutionary consequences of changing sexual system. Here we find evidence for at least 133 transitions between sexual systems in mosses, representing an almost unparalleled lability in the evolution of their sexual systems. Furthermore, in contrast to predictions, the transition rate from hermaphroditism to dioecy was approximately...

Data from: Primer development for the plastid region ycf1 in Annonaceae and other magnoliids

Kurt M. Neubig & J. Richard Abbott
PREMISE OF THE STUDY: Primers were developed for a portion of the ycf1 plastid gene in magnoliid taxa to investigate the utility of ycf1 in phylogenetic analyses. METHODS AND RESULTS: Twenty-six species across six families within the magnoliid group (Canellales, Piperales, Laurales, and Magnoliales) were sampled to examine the ability to amplify ycf1. Additionally, 29 accessions of Asimina and Deeringothamnus (Annonaceae) were sequenced to assess levels of variation in ycf1 compared to matK and trnL-F....

Data from: Ratite non-monophyly: independent evidence from 40 novel loci

Jordan V. Smith, Edward L. Braun & Rebecca T. Kimball
Large-scale multi-locus studies have become common in the field of molecular phylogenetics, but the best way to interpret these studies when their results strongly conflict with prior information about phylogeny remains unclear. An example of such a conflict is provided by the ratites (the large flightless birds of southern land masses, including ostriches, emus, and rheas). Ratite monophyly is strongly supported by both morphological data and many earlier molecular studies and is used as a...

Data from: Resilient networks of ant-plant mutualists in Amazonian forest fragments

Heather A. Passmore, Emilio M. Bruna, Sylvia M. Heredia & Heraldo L. Vasconcelos
BACKGROUND: The organization of networks of interacting species, such as plants and animals engaged in mutualisms, strongly influences the ecology and evolution of partner communities. Habitat fragmentation is a globally pervasive form of spatial heterogeneity that could profoundly impact the structure of mutualist networks. This is particularly true for biodiversity-rich tropical ecosystems, where the majority of plant species depend on mutualisms with animals and it is thought that changes in the structure of mutualist networks...

Data from: A three-stage symbiosis forms the foundation of seagrass ecosystems

Tjisse Van Der Heide, Laura L. Govers, Jimmy De Fouw, Han Olff, Matthijs Van Der Geest, Marieke M. Van Katwijk, Theunis Piersma, Johan Van De Koppel, Brian R. Silliman, Alfons J. P. Smolders & Jan A. Van Gils
Seagrasses evolved from terrestrial plants into marine foundation species around 100 million years ago. Their ecological success, however, remains a mystery because natural organic matter accumulation within the beds should result in toxic sediment sulfide levels. Using a meta-analysis, a field study, and a laboratory experiment, we reveal how an ancient three-stage symbiosis between seagrass, lucinid bivalves, and their sulfide-oxidizing gill bacteria reduces sulfide stress for seagrasses. We found that the bivalve–sulfide-oxidizer symbiosis reduced sulfide...

Data from: Species and phylogenetic nomenclature

Nico Cellinese, David A. Baum, Mishler D. Brent & Brent D. Mishler
The motivation for the development of phylogenetic nomenclature (originally called “phylogenetic taxonomy”) was to allow biological classification (or “systematization”) to represent phylogenetic relationships, and to embody important principles such as “the untenability of paraphyletic groups” (de Queiroz and Gauthier 1990). From this starting point de Queiroz and Gauthier developed a creative new basis for systematization in which the entities are not ranked taxa but clades (de Queiroz and Gauthier 1990, 1992, 1994; de Queiroz 1992,...

Data from: Short-term effects of elevated precipitation and nitrogen on soil fertility and plant growth in a Neotropical savanna

Stella M. Copeland, Emilio M. Bruna, Laura V. Barbosa Silva, Michelle C. Mack & Heraldo L. Vasconcelos
Increasing nitrogen (N) deposition and changing precipitation patterns in Neotropical savannas could alter plant growth, reproduction, and nutrients by altering soil nutrient and water availability. We examined the potential for simulated N deposition and increased dry season precipitation to have interactive effects on reproduction and growth of two abundant native Cerrado (Brazilian savanna) grasses – Loudetiopsis chrysothrix and Tristachya leiostachya – via feedbacks with soil nutrient status. Plant growth and reproduction responses consistently varied by...

Data from: Oxidative damage increases with reproductive energy expenditure and is reduced by food-supplementation

Quinn E. Fletcher, Colin Selman, Stan Boutin, Andrew G. McAdam, Sarah B. Woods, Arnold Y. Seo, Christiaan Leeuwenburgh, John R. Speakman & Murray M. Humphries
A central principle in life-history theory is that reproductive effort negatively affects survival. Costs of reproduction are thought to be physiologically-based, but the underlying mechanisms remain poorly understood. Using female North American red squirrels (Tamiasciurus hudsonicus), we test the hypothesis that energetic investment in reproduction overwhelms investment in antioxidant protection, leading to oxidative damage. In support of this hypothesis we found that the highest levels of plasma protein oxidative damage in squirrels occurred during the...

Data from: High diversity and widespread occurrence of mitotic spore mats in ectomycorrhizal Pezizales

Rosanne A. Healy, Matthew E. Smith, Gregory M. Bonito, Donald H. Pfister, Gonzalo G. Guevara, Caroline Hobart, Leticia Kumar, Thai Lee, Katherine Stafford, Zai-Wei Ge, Rytas Vilgalys, Gwendolyn Williams, James Trappe, David J. McLaughlin, D. H. Pfister, , G. M. Bonito, G. Williams, K. Stafford, R. Vilgalys, J. Trappe, R. A. Healy, L. Kumar, T. Lee, D. J. McLaughlin … & C. Hobart
Fungal mitospores may function as dispersal units and/ or spermatia and thus play a role in distribution and/or mating of species that produce them. Mitospore production in ectomycorrhizal (EcM) Pezizales is rarely reported, but here we document mitospore production by a high diversity of EcM Pezizales on three continents, in both hemispheres. We sequenced the internal transcribed spacer (ITS) and partial large subunit (LSU) nuclear rDNA from 292 spore mats (visible mitospore clumps) collected in...

Data from: A maximum likelihood approach to generate hypotheses on the evolution and historical biogeography in the Lower Volga Valley regions (southwest Russia)

Evgeny V. Mavrodiev, Alexy P. Laktionov & Nico Cellinese
The evolution of the diverse flora in the Lower Volga Valley (LVV) (southwest Russia) is complex due to the composite geomorphology and tectonic history of the Caspian Sea and adjacent areas. In the absence of phylogenetic studies and temporal information, we implemented a maximum likelihood (ML) approach and stochastic character mapping reconstruction aiming at recovering historical signals from species occurrence data. A taxon-area matrix of 13 floristic areas and 1018 extant species was constructed and...

Data from: Greenhouse biogeography: the relationship of geographic range to invasion and extinction in the Cretaceous Western Interior Seaway

Corinne E. Myers, , Bruce S. Lieberman & Richard A. MacKenzie
Significant warming of Earth's climate in the near term seems increasingly likely. If significant enough, this climatic regime could, in the long term, come to resemble previous greenhouse intervals in earth history. Consequently, analysis of the fossil record during periods of extreme warmth may provide important lessons for species biology, including biogeography, in a much warmer world. To explore this issue, we analyzed the biogeographic response of 63 molluscan species to the long-term global warmth...

Data from: Molecular phylogenetics and the evolution of fruit and leaf morphology of Dichaea (Orchidaceae: Zygopetalinae)

Kurt M. Neubig, Norris H. Williams, W. Mark Whitten & Franco Pupulin
BACKGROUND AND AIMS: The orchid genus Dichaea, with over 100 species found throughout the neotropics, is easily recognized by distichous leaves on long stems without pseudobulbs and flowers with infrastigmatic ligules. The genus has previously been divided into four sections based primarily on presence of ovary bristles and a foliar abscission layer. The aim of this work is to use DNA sequence data to estimate phylogenetic relationships within Dichaea and map the distribution of major...

Data from: Patterns of reproductive isolation in Nolana (Chilean Bellflower)

Cathleen Jewell, Amy Douglas Papineau, Rosanna Freyre & Leonie Clare Moyle
We examined reproductive isolating barriers at four postmating stages among 11 species from the morphologically diverse genus Nolana (Solanaceae). At least one stage was positively correlated with both genetic and geographic distance between species. Postzygotic isolation was generally stronger and faster evolving than postmating prezygotic isolation. In addition, there was no evidence for mechanical isolation or for reproductive character displacement in floral traits that can influence pollinator isolation. In general, among the potential isolating stages...

Registration Year

  • 2012

Resource Types

  • Dataset


  • University of Florida
  • Florida Museum of Natural History
  • University of Colorado Boulder
  • Eastern Illinois University
  • Federal University of Uberlândia
  • University of Kansas
  • University of Massachusetts Amherst
  • Duke University
  • Oregon State University
  • University of Groningen