15 Works

Data from: Shifting baselines on a tropical forest frontier: extirpations drive declines in local ecological knowledge

Zhong Kai, Teoh Shu Woan, Li Jie, Eben Goodale, Kaoru Kitajima, Robert Bagchi, Rhett D. Harrison & Zhang Kai
The value of local ecological knowledge (LEK) to conservation is increasingly recognised, but LEK is being rapidly lost as indigenous livelihoods change. Biodiversity loss is also a driver of the loss of LEK, but quantitative study is lacking. In our study landscape in SW China, a large proportion of species have been extirpated. Hence, we were interested to understand whether species extirpation might have led to an erosion of LEK and the implications this might...

Data from: Do habitat shifts drive the diversity in teleost fishes? An example from the pufferfishes (Tetraodontidae)

Francesco Santini, Mai T. T. Nguyen, Laurie Sorenson, Thomas B. Waltzek, Jessica W. Lynch Alfaro, Jonathan M. Eastman & Michael E. Alfaro
Habitat shifts are implicated as the cause of many vertebrate radiations, yet relatively few empirical studies quantify patterns of diversification following colonization of new habitats in fishes. The pufferfishes (family Tetraodontidae) occur in several habitats, including coral reefs and freshwater, which are thought to provide ecological opportunity for adaptive radiation, and thus provide a unique system for testing the hypothesis that shifts to new habitats alter diversification rates. To test this hypothesis we sequenced eight...

Data from: From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

Brad R. Ruhfel, Matthew A. Gitzendanner, Pamela S. Soltis, Douglas E. Soltis & J. Gordon Burleigh
Background: Next-generation sequencing has provided a wealth of plastid genome sequence data from an increasingly diverse set of green plants (Viridiplantae). Although these data have been useful for reconstructing the phylogeny of numerous clades of photosynthetic organisms (e.g., green algae, angiosperms, and gymnosperms), their utility for inferring relationships across all green plants is uncertain. Viridiplantae originated 700-1500 million years ago and may comprise as many as 500,000 species. This clade represents a major source of...

Data from: Three keys to the radiation of angiosperms into freezing environments

Amy E. Zanne, David C. Tank, William K. Cornwell, Jonathan M. Eastman, Stephen A. Smith, Richard G. FitzJohn, Daniel J. McGlinn, Brian C. O'Meara, Angela T. Moles, Peter B. Reich, Dana L. Royer, Douglas E. Soltis, Peter F. Stevens, Mark Westoby, Ian J. Wright, Lonnie Aarssen, Robert I. Bertin, Andre Calaminus, Rafaël Govaerts, Frank Hemmings, Michelle R. Leishman, Jacek Oleksyn, Pamela S. Soltis, Nathan G. Swenson, Laura Warman … & Alejandro Ordonez
Early flowering plants are thought to have been woody species restricted to warm habitats1, 2, 3. This lineage has since radiated into almost every climate, with manifold growth forms4. As angiosperms spread and climate changed, they evolved mechanisms to cope with episodic freezing. To explore the evolution of traits underpinning the ability to persist in freezing conditions, we assembled a large species-level database of growth habit (woody or herbaceous; 49,064 species), as well as leaf...

Data from: Phylogenetic relationships and character evolution analysis of Saxifragales using a supermatrix approach

Douglas E. Soltis, Mark E. Mort, Maribeth Latvis, Evgeny V. Mavrodiev, Brian C. O'Meara, Pamela S. Soltis, J. Gordon Burleigh & Rafael Rubio De Casas
Premise of the study: We sought novel evolutionary insights for the highly diverse Saxifragales by constructing a large phylogenetic tree encompassing 36.8% of the species-level biodiversity. Methods: We built a phylogenetic tree for 909 species of Saxifragales and used this hypothesis to examine character evolution for: annual or perennial habit, woody or herbaceous habit, ovary position, petal number, carpel number, and stamen: petal ratio. We employed likelihood approaches to investigate the effect of habit and...

Data from: Evolution of Manduca sexta hornworms and relatives: biogeographical analysis reveals an ancestral diversification in Central America

Akito Y. Kawahara, Jesse W. Breinholt, Francesca V. Ponce, Jean Haxaire, Lei Xiao, Greg P. A. Lamarre, Daniel Rubinoff & Ian J. Kitching
The hawkmoth genus Manduca is a diverse group of very large, conspicuous moths that has served as an important model across many biological disciplines. Two species in particular, the tobacco hornworm (Manduca sexta) and the tomato hornworm (Manduca quinquemaculatus) have been researched extensively. Studies across biological fields have referred to these two species as being closely related or even sister species, but the extent to which these two model organisms are related remains largely unknown....

Data from: Low plant density enhances gene dispersal in the Amazonian understory herb Heliconia acuminata

Marina Corrêa Côrtes, María Uriarte, Maristerra R. Lemes, Rogério Gribel, W. John Kress, Peter E. Smouse & Emilio M. Bruna
In theory, conservation genetics predicts that forest fragmentation will reduce gene dispersal, but in practice, genetic and ecological processes are also dependent on other population characteristics. We used Bayesian genetic analyses to characterize parentage and propagule dispersal in Heliconia acuminata L. C. Richard (Heliconiaceae), a common Amazonian understory plant that is pollinated and dispersed by birds. We studied these processes in two continuous forest sites and three 1-ha fragments in Brazil's Biological Dynamics of Forest...

Data from: Phylogeny and evolutionary history of glycogen synthase kinase 3/SHAGGY-like kinase genes in land plants

Xinshuai Qi, André S. Chanderbali, Gane Ka-Shu Wong, Douglas E. Soltis & Pamela S. Soltis
Background: GSK3 (glycogen synthase kinase 3) genes encode signal transduction proteins with roles in a variety of biological processes in eukaryotes. In contrast to the low copy numbers observed in animals, GSK3 genes have expanded into a multi-gene family in land plants (embryophytes), and have also evolved functions in diverse plant specific processes, including floral development in angiosperms. However, despite previous efforts, the phylogeny of land plant GSK3 genes is currently unclear. Here, we analyze...

Data from: One phase of the dormancy developmental pathway is critical for the evolution of insect seasonality

Crista B. Wadsworth, , Daniel A. Hahn, Erik B. Dopman & W. A. Woods
Evolutionary change in the timing of dormancy enables animals and plants to adapt to changing seasonal environments and can result in ecological speciation. Despite its clear biological importance, the mechanisms underlying the evolution of dormancy timing in animals remain poorly understood because of a lack of anatomical landmarks to discern which phase of dormancy an individual is experiencing. Taking advantage of the nearly universal characteristic of metabolic suppression during insect dormancy (diapause), we use patterns...

Data from: Evolutionary hotspots in the Mojave Desert

Amy G. Vandergast, Richard D. Inman, Kelly R. Barr, Kenneth E. Nussear, Todd C. Esque, Stacie A. Hathaway, Dustin A. Wood, Philip A. Medica, Jesse W. Breinholt, Catherine L. Stephen, Andrew D. Gottscho, Sharyn B. Marks, W. Bryan Jennings, Robert N. Fisher, Jesse Breinholt, Andrew Gottscho, Sharyn Marks, W. Jennings, Amy Vandergast, Richard Inman, Kelly Barr, Kenneth Nussear, Todd Esque, Stacie Hathaway, Dustin Wood … & Catherine Stephen
Genetic diversity within species provides the raw material for adaptation and evolution. Just as regions of high species diversity are conservation targets, identifying regions containing high genetic diversity and divergence within and among populations may be important to protect future evolutionary potential. When multiple co-distributed species show spatial overlap in high genetic diversity and divergence, these regions can be considered evolutionary hotspots. We mapped spatial population genetic structure for 17 animal species across the Mojave...

Data from: Molecular phylogenetics of Maxillaria and related genera (Orchidaceae: Cymbidieae) based on combined molecular data sets

W. Mark Whitten, Mario A. Blanco, Norris H. Williams, Samantha Koehler, Germán Carnevali, Rodrigo B. Singer, Lorena Endara & Kurt M. Neubig
The orchid genus Maxillaria is one of the largest and most common of neotropical orchid genera, but its current generic boundaries and relationships have long been regarded as artificial. Phylogenetic relationships within subtribe Maxillariinae sensu Dressler (1993) with emphasis on Maxillaria s.l. were inferred using parsimony analyses of individual and combined DNA sequence data. We analyzed a combined matrix of nrITS DNA, the plastid matK gene and flanking trnK intron, and the plastid atpB-rbcL intergenic...

Data from: Paleoenvironmental and paleobiogeographical implications of a Middle Pleistocene mollusc assemblage from the marine terraces of Baía das Pipas, southwest Angola

Jocelyn A. Sessa, Pedro M. Callapez, Pedro A. Dinis & Austin J. W. Hendy
Quaternary raised marine terraces containing the remains of diverse, shallow water marine invertebrate faunas are widespread across coastal Angola. These deposits and faunas have not been studied in the same detail as contemporaneous features in northwest and southernmost Africa. We analyzed the fossil assemblages and sedimentology of two closely spaced Middle Pleistocene marine terrace deposits in Baía das Pipas, southwest Angola. This revealed 46 gastropod and 29 bivalve species, along with scleractinian corals, encrusting bryozoans,...

Data from: Rates of genomic divergence in humans, chimpanzees and their lice

Kevin P. Johnson, Julie M. Allen, Brett P. Olds, Lawrence Mugisha, David L. Reed, Ken N. Paige & Barry R. Pittendrigh
The rate of DNA mutation and divergence is highly variable across the tree of life. However, the reasons underlying this variation are not well understood. Comparing the rates of genetic changes between hosts and parasite lineages that diverged at the same time is one way to begin to understand differences in genetic mutation and substitution rates. Such studies have indicated that the rate of genetic divergence in parasites is often faster than that of their...

Data from: The hindgut-lumen prokaryotic microbiota of the lignocellulose-degrading termite Reticulitermes flavipes and its responses to dietary lignocellulose composition

Drion G. Boucias, Yunpeng Cai, Yijun Sun, Verena-Ulrike Lietze, Ruchira Sen, Rhitoban Raychoudhury & Michael E. Scharf
Reticulitermes flavipes (Isoptera: Rhinotermitidae) is a highly eusocial insect that thrives on recalcitrant lignocellulosic diets through nutritional symbioses with gut-dwelling prokaryotes and eukaryotes. In the R. flavipes hindgut, there are up to 12 eukaryotic protozoan symbionts; the number of prokaryotic symbionts has been estimated in the hundreds. Despite its biological relevance, this diverse community, to date, has been investigated only by culture- and cloning-dependent methods. Moreover, it is unclear how termite gut microbiomes respond to...

Data from: DNA barcoding reveals a largely unknown fauna of Gracillariidae leaf-mining moths in the Neotropics

D. C. Lees, A. Y. Kawahara, R. Rougerie, I. Ohshima, A. Kawakita, O. Bouteleux, J. De Prins & C. Lopez-Vaamonde
Higher taxa often show increasing species richness towards tropical low latitudes, a pattern known as the latitudinal biodiversity gradient (LBG). A rare reverse LBG (with greater richness towards temperate high latitudes) is exhibited by Gracillariidae leaf-mining moths, in which most described species occur in northern temperate areas. We carried out the first assessment of gracillariid species diversity in two Neotropical regions to test whether the relatively low tropical species diversity of this family is genuine...

Registration Year

  • 2013

Resource Types

  • Dataset


  • University of Florida
  • Florida Museum of Natural History
  • Smithsonian Institution
  • University of Tennessee at Knoxville
  • University of Idaho
  • Royal Museum for Central Africa
  • University of Kansas
  • National Evolutionary Synthesis Center
  • Zhejiang University
  • University of Washington