### Data from: Improving transcriptome assembly through error correction of high-throughput sequence reads

Matthew D. MacManes & Michael B. Eisen
The study of functional genomics, particularly in non-model organisms, has been dramatically improved over the last few years by the use of transcriptomes and RNAseq. While these studies are potentially extremely powerful, a computationally intensive procedure, the de novo construction of a reference transcriptome must be completed as a prerequisite to further analyses. The accurate reference is critically important as all downstream steps, including estimating transcript abundance are critically dependent on the construction of an...

### 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: Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote

Gerald Schönknecht, Wei-Hua Chen, Chad M. Ternes, Guillaume G. Barbier, Roshan P. Shrestha, Mario Stanke, Andrea Bräutigam, Brett J. Baker, Jillian F. Banfield, R. Michael Garavito, Kevin Carr, Curtis Wilkerson, Stefan A. Rensing, David Gagneul, Nicholas E. Dickenson, Christine Oesterhelt, Martin J. Lercher & Andreas P. M. Weber
Some microbial eukaryotes, such as the extremophilic red alga Galdieria sulphuraria, can live in hot, toxic metal-rich, acidic environments. To elucidate the underlying molecular mechanisms of adaptation, we sequenced the 13.7 Mb genome of G. sulphuraria. This alga shows an enormous metabolic flexibility, growing either photoautotrophically or heterotrophically on more than 50 carbon sources. Environmental adaptation seems to have been facilitated by horizontal gene transfer from various bacteria and archaea, often followed by gene family...

### Data from: Efficient exploration of the space of reconciled gene trees

Gergely J. Szöllősi, Wojciech Rosikiewicz, Bastien Boussau, Eric Tannier & Vincent Daubin
Gene trees record the combination of gene-level events, such as duplication, transfer and loss, and species-level events, such as speciation and extinction. Gene tree-species tree reconciliation methods model these processes by drawing gene trees into the species tree using a series of gene and species level events. The reconstruction of gene trees based on sequence alone almost always involves choosing between statistically equivalent or weakly distinguishable relationships that could be much better resolved based on...

### Data from: Stage and size structure of three species of oaks in central coastal California

Ian S. Pearse, Sophie Griswold, Desirree Pizarro & Walter D. Koenig
Oaks are foundational species in much of California, and many oak populations in the state may be in jeopardy due to a lack of recruitment of young trees. Despite considerable interest in this problem, there have been few comprehensive surveys of all stages of oak development. We surveyed all stages of three oaks: Quercus lobata, Q. douglasii, and Q. agrifolia in a forest plot with mixed land-use in central coastal California. We found abundant seedlings...

### Data from: Robustness to divergence time underestimation when inferring species trees from estimated gene trees

Michael DeGiorgio & James H. Degnan
To infer species trees from gene trees estimated from phylogenomic data sets, tractable methods are needed that can handle dozens to hundreds of loci. We examine several computationally efficient approaches—MP-EST, STAR, STEAC, STELLS, and STEM—for inferring species trees from gene trees estimated using maximum likelihood (ML) and Bayesian approaches. Among the methods examined, we found that topology-based methods often performed better using ML gene trees and methods employing coalescent times typically performed better using Bayesian...

### Data from: Population genetic analyses provide insights on the introduction pathway and spread patterns of the North American forest pathogen Heterobasidion irregulare in Italy

Matteo Garbelotto, Fabio Guglielmo, Silvia Mascheretti, Peter J. P. Croucher & Paolo Gonthier
A population genetics approach is used to identify the most likely introduction site and introduction pathway for the North American forest pathogen Heterobasidion irregulare using 101 isolates from six sites in Italy and 34 isolates from five sites in North America. Diversity indices based on sequences from ten loci indicate the highest diversity in Italy is found in Castelfusano/Castelporziano and that diversity progressively decreases with increasing distance from that site. AMOVA, Bayesian clustering and principal...

### Data from: Bayesian analysis of biogeography when the number of areas is large

Michael J. Landis, Nicholas J. Matzke, Brian R. Moore & John P. Huelsenbeck
Historical biogeography is increasingly studied from an explicitly statistical perspective, using stochastic models to describe the evolution of species range as a continuous-time Markov process of dispersal between and extinction within a set of discrete geographic areas. The main constraint of these methods is the computational limit on the number of areas that can be specified. We propose a Bayesian approach for inferring biogeographic history that extends the application of biogeographic models to the analysis...

### Data from: Early warning signals and the prosecutor's fallacy

Carl Boettiger & Alan Hastings
Early warning signals have been proposed to forecast the possibility of a critical transition, such as the eutrophication of a lake, the collapse of a coral reef or the end of a glacial period. Because such transitions often unfold on temporal and spatial scales that can be difficult to approach by experimental manipulation, research has often relied on historical observations as a source of natural experiments. Here, we examine a critical difference between selecting systems...

### Data from: Population dynamics of an Arctiid caterpillar-tachinid parasitoid system using state-space models

Richard Karban & Perry De Valpine
1. Population dynamics of insect host–parasitoid systems are important in many natural and managed ecosystems and have inspired much ecological theory. However, ecologists have a limited knowledge about the relative strengths of species interactions, abiotic effects and density dependence in natural host–parasitoid dynamics. Statistical time-series analyses would be more informative by incorporating multiple factors, measurement error and noisy dynamics. 2. We use a novel maximum likelihood and model-selection analysis of a state-space model for host–parasitoid...

### Data from: Early bursts of body size and shape evolution are rare in comparative data

Luke J. Harmon, Jonathan B. Losos, T. Jonathan Davies, Rosemary G. Gillespie, John L. Gittleman, W. Bryan Jennings, Kenneth H. Kozak, Mark A. McPeek, Franck Moreno-Roark, Thomas J. Near, Andy Purvis, Robert E. Ricklefs, Dolph Schluter, , Ole Seehausen, Brian L. Sidlauskas, Omar Torres-Carvajal, Jason T. Weir & Arne Ø. Mooers
George Gaylord Simpson famously postulated that much of life's diversity originated as adaptive radiations—more or less simultaneous divergences of numerous lines from a single ancestral adaptive type. However, identifying adaptive radiations has proven difficult due to a lack of broad-scale comparative datasets. Here, we use phylogenetic comparative data on body size and shape in a diversity of animal clades to test a key model of adaptive radiation, in which initially rapid morphological evolution is followed...

### Data from: Urban land use limits regional bumble bee gene flow

Shalene Jha & Claire Kremen
Potential declines in native pollinator communities and increased reliance on pollinator-dependent crops have raised concerns about native pollinator conservation and dispersal across human-altered landscapes. Bumble bees are one of the the most effective native pollinators, and are often the first to be extirpated in human-altered habitats, yet little is known about how bumble bees move across fine spatial scales and what landscapes promote or limit their gene flow. In this study, we examine regional genetic...

### Data from: Unlocking the vault: next generation museum population genomics

Ke Bi, Tyler Linderoth, Dan Vanderpool, Jeffrey M. Good, Rasmus Nielsen & Craig Moritz
Natural history museum collections provide unique resources for understanding how species respond to environmental change, including the abrupt, anthropogenic climate change of the past century. Ideally, researchers would conduct genome-scale screening of museum specimens to explore the evolutionary consequences of environmental changes, but to date such analyses have been severely limited by the numerous challenges of working with the highly degraded DNA typical of historic samples. Here we circumvent these challenges by using custom, multiplexed,...

### 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: Mice infected with low-virulence strains of Toxoplasma gondii lose their innate aversion to cat urine, even after extensive parasite clearance

Wendy Marie Ingram, Leeanne M. Goodrich, Ellen A. Robey & Michael B. Eisen
Toxoplasma gondii chronic infection in rodent secondary hosts has been reported to lead to a loss of innate, hard-wired fear toward cats, its primary host. However the generality of this response across T. gondii strains and the underlying mechanism for this pathogen-mediated behavioral change remain unknown. To begin exploring these questions, we evaluated the effects of infection with two previously uninvestigated isolates from the three major North American clonal lineages of T. gondii, Type III...

### Data from: Pollinator interactions with yellow starthistle (Centaurea solstitialis) across urban, agricultural, and natural landscapes

Misha Leong, Claire Kremen & George K. Roderick
Pollinator-plant relationships are found to be particularly vulnerable to land use change. Yet despite extensive research in agricultural and natural systems, less attention has focused on these interactions in neighboring urban areas and its impact on pollination services. We investigated pollinator-plant interactions in a peri-urban landscape on the outskirts of the San Francisco Bay Area, California, where urban, agricultural, and natural land use types interface. We made standardized observations of floral visitation and measured seed...

### Data from: Extending ecological niche models to the past 120 000 years corroborates the lack of strong phylogeographic structure in the Crested Drongo (Dicrurus forficatus forficatus) on Madagascar

Jérôme Fuchs, Juan L. Parra, Steven M. Goodman, Marie Jeanne Raherilalao, Jeremy Vanderwal & Rauri C. K. Bowie
We conduct a phylogeographic study of the Crested Drongo (Dicrurus forficatus forficatus), a broadly distributed bird species on Madagascar. We first determined the demographic and spatial pattern inferred from mitochondrial and nuclear data, and then compared these results with predictions from a present to 0.120-Myr-old reconstruction of the spatial dynamics of the range of D. f. forficatus on Madagascar, enabling putative areas of stability (lineage persistence) to be detected. Weak genetic structure along an east–west...

### Data from: No early warning signals for stochastic transitions: insights from large deviation theory

Carl Boettiger & Alan Hastings
Code to replicate the analysis and generate Figure 1A dynamic document for running the analysis and generating the data and graphs shown in Figure 1. After installing the packages indicated, this code can be run by copy-pasting the code blocks into any R terminal, or compiled at once by running knit("Figure1.Rmd") in the R terminal using the knitr package.Figure1.RmdData from: No early warning signals for stochastic transitions: insights from large deviation theoryA csv file containing...

• 2013
18

• Dataset
18

#### Affiliations

• University of California, Berkeley
18
• University of California System
3
• University of California, Davis
3
• University of Kansas
2
• National Museum
2
• National Evolutionary Synthesis Center
1
• Howard Hughes Medical Institute
1
• University of Montana
1
• Institut Teknologi Bandung
1
• The University of Texas at Austin
1