Data from: Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L.Nora Mitchell, Paul O. Lewis, Emily Moriarty Lemmon, Alan R. Lemmon & Kent E. Holsinger
PREMISE OF THE STUDY: Estimating phylogenetic relationships in relatively recent evolutionary radiations is challenging, especially if short branches associated with recent divergence result in multiple gene tree histories. We combine anchored enrichment next-generation sequencing with species tree analyses to produce a robust estimate of phylogenetic relationships in the genus Protea (Proteaceae), an iconic radiation in South Africa. METHODS: We sampled multiple individuals within 59 out of 112 species of Protea and 6 outgroup species for...
Why are some traits and trait combinations exceptionally common across the tree of life, whereas others are vanishingly rare? The distribution of trait diversity across a clade at any time depends on the ancestral state of the clade, the rate at which new phenotypes evolve, the differences in speciation and extinction rates across lineages, and whether an equilibrium has been reached. Here we examine the role of transition rates, differential diversification (speciation minus extinction), and...
Data from: The contribution of marine aggregate-associated bacteria to the accumulation of pathogenic bacteria in oysters: an agent-based modelAndrew M. Kramer, J. Evan Ward, Fred C. Dobbs, Melissa L. Pierce & John M. Drake
Bivalves process large volumes of water, leading to their accumulation of bacteria, including potential human pathogens (e.g., vibrios). These bacteria are captured at low efficiencies when freely suspended in the water column, but they also attach to marine aggregates, which are captured with near 100% efficiency. For this reason, and because they are often enriched with heterotrophic bacteria, marine aggregates have been hypothesized to function as important transporters of bacteria into bivalves. The relative contribution...
Data from: Targeted reforestation could reverse declines in connectivity for understory birds in a tropical habitat corridorMatthew E. Fagan, Ruth S. DeFries, Steven E. Sesnie, J. Pablo Arroyo-Mora & Robin L. Chazdon
Re-establishing connectivity between protected areas isolated by habitat clearing is a key conservation goal in the humid tropics. In northeastern Costa Rica, payments for environmental services (PES) and a government ban on deforestation have subsidized forest protection and reforestation in the San Juan–La Selva Biological Corridor (SJLSBC), resulting in a decline in mature forest loss and the expansion of tree plantations. We use field studies and graph models to assess how conservation efforts have altered...
Data from: Evaluating carbon storage, timber harvest, and habitat possibilities for a western Cascades (US) forest landscapeJeffrey Kline, Mark Harmon, Thomas Spies, Anita Morzillo, Robert Pabst, Brenda McComb, Frank Schnekenburger, Keith Olsen, Blair Csuti, Jody Vogeler, Jeffrey D. Kline, Thomas A. Spies, Brenda C. McComb, Anita T. Morzillo, Mark E. Harmon, Robert J. Pabst, Keith A. Olsen & Jody C. Vogeler
Forest policymakers and managers have long sought ways to evaluate the capability of forest landscapes to jointly produce timber, habitat, and other ecosystem services in response to forest management. Currently, carbon is of particular interest as policies for increasing carbon storage on federal lands are being proposed. However, a challenge in joint production analysis of forest management is adequately representing ecological conditions and processes that influence joint production relationships. We used simulation models of vegetation...
Data from: Processes of community assembly in an environmentally heterogeneous, high biodiversity regionMatthew E. Aiello-Lammens, Jasper A. Slingsby, Cory Merow, Hayley Kilroy Mollmann, Douglas Euston-Brown, Cynthia S. Jones, & John A. Silander
Despite decades of study, the relative importance of niche-based versus neutral processes in community assembly remains largely ambiguous. Recent work suggests niche-based processes are more easily detectable at coarser spatial scales, while neutrality dominates at finer scales. Analyses of functional traits with multi-year multi-site biodiversity inventories may provide deeper insights into assembly processes and the effects of spatial scale. We examined associations between community composition, species functional traits, and environmental conditions for plant communities in...
Data from: Intruder colour and light environment jointly determine how nesting male stickleback respond to simulated territorial intrusionsDaniel I. Bolnick, Kimberly Hendrix, Lyndon Alexander Jordan, Thor Veen & Chad D. Brock
Variation in male nuptial colour signals might be maintained by negative frequency-dependent selection. This can occur if males are more aggressive towards rivals with locally common colour phenotypes. To test this hypothesis, we introduced red or melanic three-dimensional printed-model males into the territories of nesting male stickleback from two optically distinct lakes with different coloured residents. Red-throated models were attacked more in the population with red males, while melanic models were attacked more in the...
Data from: How the aridification of Australia structured the biogeography and influenced the diversification of a large lineage of Australian cicadasChristopher L. Owen, David C. Marshall, Kathy B. R. Hill & Chris Simon
Over the last 30 million years, Australia’s landscape has undergone dramatic cooling and drying due to the establishment of the Antarctic Circumpolar Current and change in global CO2 levels. Studies have shown that many Australian organisms went extinct during these major cooling events, while others experienced adaptive radiations and increases in diversification rates as a result of exploiting new niches in the arid zone. Despite the many studies on diversification and biogeography in Australia, few...
Data from: Hiding in plain sight: Koshicola spirodelophila gen. et sp. nov. (Chaetopeltidales, Chlorophyceae), a novel green alga associated with the aquatic angiosperm Spirodela polyrhizaShin Watanabe, Karolina Fucikova, Louise A. Lewis & Paul O. Lewis
Premise of the study: Discovery and morphological characterization of a novel epiphytic aquatic green alga increases our understanding of Chaetopeltidales, a poorly known order in Chlorophyceae. Chloroplast genomic data from this taxon reveals an unusual architecture previously unknown in green algae. Methods: Using light and electron microscopy, we characterized the morphology and ultrastructure of a novel taxon of green algae. Bayesian phylogenetic analyses of nuclear and plastid genes were used to test the hypothesized membership...
Land-use change occurs nowhere more rapidly than in the tropics, where the imbalance between deforestation and forest regrowth has large consequences for the global carbon cycle1. However, considerable uncertainty remains about the rate of biomass recovery in secondary forests, and how these rates are influenced by climate, landscape, and prior land use2, 3, 4. Here we analyse aboveground biomass recovery during secondary succession in 45 forest sites and about 1,500 forest plots covering the major...
Data from: Population and phylogenomic decomposition via genotyping-by-sequencing in Australian PelargoniumAdrienne B. Nicotra, Caroline Chong, Jason G. Bragg, Chong Ren Ong, Nicola C. Aitken, Aaron Chuah, Brendan Lepschi & Justin O. Borevitz
Species delimitation has seen a paradigm shift as increasing accessibility of genomic-scale data enables separation of lineages with convergent morphological traits and the merging of recently diverged ecotypes that have distinguishing characteristics. We inferred the process of lineage formation among Australian species in the widespread and highly variable genus Pelargonium by combining phylogenomic and population genomic analyses along with breeding system studies and character analysis. Phylogenomic analysis and population genetic clustering supported seven of the...
An emerging hypothesis in fire ecology is that pyrodiversity increases species diversity. We test whether pyrodiversity—defined as the standard deviation of fire severity—increases avian biodiversity at two spatial scales, and whether and how this relationship may change in the decade following fire. We use a dynamic Bayesian community model applied to a multi-year dataset of bird surveys at 1106 points sampled across 97 fires in montane California. Our results provide strong support for a positive...
University of Connecticut12
United States Department of Agriculture2
National Autonomous University of Mexico2
University of Maryland, College Park2
University of Kansas1
Federal University of Southern Bahia1
The University of Texas at Austin1
Centre for Australian National Biodiversity Research1
University of Georgia1