16 Works

Data from: A total evidence approach to understanding phylogenetic relationships and ecological diversity in Selaginella subg. Tetragonostachys

Nils Arrigo, James Therrien, Cajsa Lisa Anderson, Michael D. Windham, Christopher H. Haufler & Michael S. Barker
Premise of the Study: Several members of Selaginella are renowned for their ability to survive extreme drought and “resurrect” when conditions improve. Many of these belong to subgenus Tetragonostachys, a group of ∼45 species primarily found in North and Central America, with substantial diversity in the Sonoran and Chihuahuan Deserts. We evaluated the monophyly and the age of subgenus Tetragonostachys and assess how drought tolerance contributed to the evolution of this clade. Methods: Our study...

Data from: The tree of life and a new classification of bony fishes

Ricardo Betancur-R., Adela Roa-Varon, Nancy I. Holcroft, W. Calvin Borden, Terry Grande, Kent Carpenter, Millicent Sanciangco, Chenhong Li, Dahiana Arcila, Jesus A Ballesteros, Guillermo Ortí, J. Andrés López, Matthew A. Campbell, Edward O. Wiley, Gloria Arratia, Guoqing Lu, Stuart Willis, Richard E. Broughton, , Feifei Zhang & Daniel J. Hough
The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The situation is most critical for a large clade of spiny-finned fishes, traditionally referred to as percomorphs, whose uncertain relationships have plagued ichthyologists for over a century. Most of what we know about the higher-level relationships among fish lineages has been based on morphology, but rapid influx of molecular studies is...

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: Cryptic diversity and population genetic structure in the rare, endemic, forest-obligate, slender geckos of the Philippines

Cameron D. Siler, T. Alex Dececchi, Chris L. Merkord, Drew R. Davis, Tony J. Christiani & Rafe M. Brown
Recent studies of forest lizards in Southeast Asia have highlighted spectacular morphological and cryptic genetic diversity in several poorly known clades. Unfortunately, many of the included species have microhabitat preferences for forested environments, and therefore they are threatened by extensive forest destruction throughout the region. This is particularly true in the Philippines, an archipelago with a strikingly high proportion (84%) of endemic geckos. Abundances inferred from historical museum collections suggests that we are in a...

Data from: Conservation genetics of Australasian sailfin lizards: flagship species threatened by coastal development and insufficient protected area coverage

Cameron D. Siler, Andrés Lira-Noriega & Rafe M. Brown
Despite rampant coastal development throughout Southeast Asia and the Pacific, studies of conservation genetics and ecology of vulnerable, coastal species are rare. Large bodied vertebrates with highly specialized habitat requirements may be at particular risk of extinction due to habitat degradation and fragmentation, especially if these habitats are naturally patchily distributed, marginal, or otherwise geographically limited, or associated in space with high human population densities or heavy anthropogenic disturbance. Particularly telling examples of these conservation...

Data from: Multilocus phylogeny and Bayesian estimates of species boundaries reveal hidden evolutionary relationships and cryptic diversity in Southeast Asian monitor lizards

Luke J. Welton, Cameron D. Siler, Jamie R. Oaks, Arvin C. Diesmos & Rafe M. Brown
Recent conceptual, technological, and methodological advances in phylogenetics have enabled increasingly robust statistical species delimitation in studies of biodiversity. As the variety of evidence purporting species diversity has increased, so too have the kinds of tools and inferential power of methods for delimiting species. Here we showcase an organismal system for a data-rich, comparative molecular approach to evaluating strategies of species delimitation among monitor lizards of the genus Varanus. The water monitors (Varanus salvator Complex),...

Data from: Fitness consequences of outcrossing in a social spider with an inbreeding mating system

Reut Berger-Tal, Cristina Tuni, Yael Lubin, Debroah Smith, Trine Bilde & Deborah Smith
Inbreeding mating systems are uncommon because of inbreeding depression. Mating among close relatives can evolve, however, when outcrossing is constrained. Social spiders show obligatory mating among siblings. In combination with a female-biased sex ratio, sib-mating results in small effective populations. In such a system high genetic homozygosity is expected, and drift may cause population divergence. We tested the effect of outcrossing in the social spider Stegodyphus dumicola. Females were mated to sib-males, to a non-nestmate...

Data from: Stochastic faunal exchanges drive diversification in widespread Wallacean and Pacific island lizards (Squamata: Scincidae: Lamprolepis smaragdina)

Charles W. Linkem, Rafe M. Brown, Cameron D. Siler, Ben J. Evans, Christopher C. Austin, Djoko T. Iskandar, Arvin C. Diesmos, Jatna Supriatna, Noviar Andayani, Jimmy A. McGuire & Malte Ebach
Aim: Widespread species found in disturbed habitats are often expected to be human commensals. In island systems, this association predicts that dispersal will be mediated by humans. We investigated the biogeographical relationships among populations of a widespread tree skink that inhabits coastal forest and human-cultivated plantations in Southeast Asia. We sought to determine whether populations of the emerald tree skink, Lamprolepis smaragdina, dis- persed via mechanisms that were not human-mediated (‘natural’ dispersal) or whether dispersal...

Data from: Anolis sex chromosomes are derived from a single ancestral pair

Tony Gamble, Anthony J. Geneva, Richard E. Glor & David Zarkower
To explain the frequency and distribution of heteromorphic sex chromosomes in the lizard genus Anolis we compared the relative roles of sex chromosome conservation vs. turnover of sex determining mechanisms. We used model based comparative methods to reconstruct karyotype evolution and the presence of heteromorphic sex chromosomes onto a newly generated Anolis phylogeny. We found that heteromorphic sex chromosomes evolved multiple times in the genus. Fluorescent in situ hybridization (FISH) of repetitive DNA showed variable...

Data from: Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution

Richard E. Broughton, Ricardo Betancur-R., Chenhong Li, Gloria Arratia & Guillermo Orti
Over half of all vertebrates are “fishes”, which exhibit enormous diversity in morphology, physiology, behavior, reproductive biology, and ecology. Investigation of fundamental areas of vertebrate biology depend critically on a robust phylogeny of fishes, yet evolutionary relationships among the major actinopterygian and sarcopterygian lineages have not been conclusively resolved. Although a consensus phylogeny of teleosts has been emerging recently, it has been based on analyses of various subsets of actinopterygian taxa, but not on a...

Data from: An adaptive radiation of frogs in a Southeast Asian island archipelago

David C. Blackburn, Cameron D. Siler, Arvin C. Diesmos, Jimmy A. McGuire, David C. Cannatella & Rafe M. Brown
Living amphibians exhibit a diversity of ecologies, life histories, and species-rich lineages that offers opportunities for studies of adaptive radiation. We characterize a diverse clade of frogs (Kaloula, Microhylidae) in the Philippine island archipelago as an example of an adaptive radiation into three primary habitat specialists or ecotypes. We use a novel phylogenetic estimate for this clade to evaluate the tempo of lineage accumulation and morphological diversification. Because species-level phylogenetic estimates for Philippine Kaloula are...

Data from: Spotted stream frog diversification at the Australasian faunal zone interface, mainland versus island comparisons, and a test of the Philippine ‘dual-umbilicus’ hypothesis

Rafe M. Brown & Cameron D. Siler
Aim: We utilize comprehensive geographical sampling and a new, multilocus dataset to re-examine the biogeography of spotted stream frogs throughout Southeast Asia. We compare patterns of diversification among stream frog populations on land-bridge islands and oceanic islands and we reevaluate a previous ‘dual-invasion’ hypothesis for the origins of several endemic Philippine taxa. Location: Southeast Asia, Sundaland, and the Philippines. Methods: Stream frogs were collected and sequenced for two mitochondrial and two nuclear gene regions. We...

Data from: The challenge of species delimitation at the extremes: diversification without morphological change in Philippine sun skinks

Anthony J. Barley, Jordan White, Arvin C. Diesmos & Rafe M. Brown
Species represent one of the fundamental units of the evolutionary process, and an accurate understanding of species diversity is essential to studies across a wide range of biological subdisciplines. However, delimiting species remains challenging in evolutionary radiations where morphological diversification is rapid and accompanied by little genetic differentiation or when genetic lineage divergence is not accompanied by morphological change. We investigate the utility of a variety of recently developed approaches to examine genetic and morphological...

Data from: Critically endangered island endemic or peripheral population of a widespread species? Conservation genetics of Kikuchi’s gecko and the global challenge of protecting peripheral oceanic island endemic vertebrates

Cameron D. Siler, Jamie R. Oaks, Kerry Cobb, Hidetoshi Ota & Rafe M. Brown
Aim: To highlight the significant conservation challenge of evaluating peripheral endemic vertebrates in island archipelago systems and to assess empirically the complexities of approaches to conservation genetic studies across political and biogeographic boundaries. To demonstrate the poignant need for international collaboration and coordination when species delimitation problems with high conservation concern involve island endemics with biogeographically peripheral ranges. Location: Southeast Asia, Lanyu Island, Taiwan, and the Philippines. Methods: Genetic samples were collected and sequenced for...

Data from: Brazilian marsupial frogs are diphyletic (Anura: Hemiphractidae: Gastrotheca)

David C. Blackburn & William E. Duellman
Molecular phylogenetic analyses based on expanded taxonomic and geographic sampling support the monophyly of the marsupial frog genera (family Hemiphractidae), resolve six geographically circumscribed lineages within Gastrotheca, and, for the first time, reveal that two divergent lineages of Gastrotheca inhabit the Atlantic Coastal Forests of Brazil. Within Gastrotheca, the earliest diverging clade is confined to northeastern Brazil, whereas the three subsequent diverging lineages are restricted to northern Venezuela (G. walkeri), southeastern Brazil, and northwestern South...

Data from: The genetic architecture of methotrexate toxicity is similar in Drosophila melanogaster and humans

Galina Kislukhin, Elizabeth G. King, Kelli N. Walters, Stuart J. Macdonald & Anthony D. Long
The severity of the toxic side effects of chemotherapy varies among patients, and much of this variation is likely genetically based. Here, we use the model system Drosophila melanogaster to genetically dissect the toxicity of methotrexate (MTX), a drug used primarily to treat childhood acute lymphoblastic leukemia and rheumatoid arthritis. We use the Drosophila Synthetic Population Resource, a panel of recombinant inbred lines derived from a multiparent advanced intercross, and quantify MTX toxicity as a...

Registration Year

  • 2013

Resource Types

  • Dataset


  • University of Kansas
  • University of Oklahoma
  • National Museum
  • University of South Dakota
  • George Washington University
  • University of California, Berkeley
  • Shanghai Ocean University
  • National Evolutionary Synthesis Center
  • Institut Teknologi Bandung
  • University of Washington