### Data from: The phenology-substrate-match hypothesis explains decomposition rates of evergreen and deciduous oak leaves.

Ian S. Pearse, Richard C. Cobb & Richard Karban
1. There is substantial evidence that the rate of litter decomposition is affected by the match between the litter substrate and the soil matrix (decomposer community). We introduce and test the phenology-substrate-match hypothesis, which predicts that both litter composition and soil matrix will change over the course of the year, and that a lagged match between litter type and soil matrix will result in an optimal decomposition environment. 2. We conducted a decomposition experiment in...

### 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...

### Data from: Understanding the contribution of habitats and regional variation to long-term population trends in tricolored blackbirds

Emilie E. Graves, Marcel Holyoak, T. Rodd Kelsey & Robert J. Meese
Population trends represent a minimum amount of information required to assess the conservation status of a species. However, understanding and detecting trends can be complicated by variation among habitats and regions, and by dispersal connecting habitats through source-sink dynamics. We analyzed trends in breeding populations between habitats and regions to better understand the overall dynamics of a species' decline. Specifically, we analyzed historical trends in breeding populations of tricolored blackbirds (Agelaius tricolor) using breeding records...

### Data from: Genomics of Compositae crops: reference transcriptome assemblies, and evidence of hybridization with wild relatives

Kathryn A. Hodgins, Zhao Lai, Luiz O. Oliveira, David W. Still, Moira Scascitelli, Michael S. Barker, Nolan C. Kane, Hannes Dempewolf, Alex Kozik, Richard V. Kesseli, John M. Burke, Richard W. Michelmore & Loren H. Rieseberg
Although the Compositae harbours only two major food crops, sunflower and lettuce, many other species in this family are utilized by humans and have experienced various levels of domestication. Here we have used next generation sequencing technology to develop 15 reference transcriptome assemblies for Compositae crops or their wild relatives. These data allow us to gain insight into the evolutionary and genomic consequences of plant domestication. Specifically, we performed Illumina sequencing of Cichorium endivia, Cichorium...

### Data from: Local adaptation when competition depends on phenotypic similarity

Scott C. Burgess, Robin S. Waples & Marissa L. Baskett
Recent work incorporating demographic–genetic interactions indicates the importance of population size, gene flow, and selection in influencing local adaptation. This work typically assumes that density-dependent survival affects individuals equally, but individuals in natural population rarely compete equally. Among-individual differences in resource use generate stronger competition between more similar phenotypes (frequency-dependent competition) but it remains unclear how this additional form of selection changes the interactions between population size, gene flow, and local stabilizing selection. Here, we...

### Data from: Evolution and spread of glyphosate resistance in Conyza canadensis in California

Miki Okada, Bradley D. Hanson, Kurt J. Hembree, Yanhui Peng, Anil Shrestha, , Steven D. Wright, Marie Jasieniuk & Charles Neal Stewart
Recent increases in glyphosate use in perennial crops of California, USA, are hypothesized to have led to an increase in selection and evolution of resistance to the herbicide in Conyza canadensis populations. To gain insight into the evolutionary origins and spread of resistance and to inform glyphosate resistance management strategies, we investigated the geographical distribution of glyphosate resistance in C. canadensis across and surrounding the Central Valley, its spatial relationship to groundwater protection areas (GWPA),...

### Data from: Hybridization and adaptation to introduced balloon vines in an Australian soapberry bug

Jose A. Andrés, Prasobh R. Thampy, Michael T. Mathieson, Jenella Loye, Myron P. Zalucki, Hugh Dingle & Scott P. Carroll
Contemporary adaptation of plant feeding insects to introduced hosts provides clear cases of ecologically based population divergence. In most cases the mechanisms permitting rapid differentiation are not well known. Here we study morphological and genetic variation associated with recent shifts by the Australian soapberry bug Leptocoris tagalicus onto two naturalized Neotropical balloon vines, Cardiospermum halicacabum and C. grandiflorum that differ in time since introduction. Our results show that these vines have much larger fruits than...

### Data from: Multilocus analyses reveal little evidence for lineage wide adaptive evolution within major clades of soft pines (Pinus subgenus Strobus)

Andrew J. Eckert, Andrew D. Bower, Kathleen D. Jermstad, Jill L. Wegrzyn, Brian J. Knaus, John V. Syring & David B. Neale
Estimates from molecular data for the fraction of new nonsynonymous mutations that are adaptive vary strongly across plant species. Much of this variation is due to differences in life-history strategies as they influence the effective population size (Ne). Ample variation for these estimates, however, remains even when comparisons are made across species with similar values of Ne. An open question thus remains as to why the large disparity for estimates of adaptive evolution exists among...

### 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: A quantitative genetic basis for leaf morphology in a set of precisely defined tomato introgression lines

Daniel H. Chitwood, Ravi Kumar, Lauren R. Headland, Aashish Ranjan, Michael F. Covington, Yasunori Ichihashi, Daniel Fulop, José M. Jiménez-Gómez, Jie Peng, Julin N. Maloof & Neelima R. Sinha
Introgression lines (ILs), in which genetic material from wild tomato species is introgressed into a domesticated background, have been used extensively in tomato (Solanum lycopersicum) improvement. Here, we genotype an IL population derived from the wild desert tomato Solanum pennellii at ultrahigh density, providing the exact gene content harbored by each line. To take advantage of this information, we determine IL phenotypes for a suite of vegetative traits, ranging from leaf complexity, shape, and size...

### Data from: Complex patterns of local adaptation in Teosinte

Tanja Pyhäjärvi, Matthew B. Hufford, Sofiane Mezmouk & Jeffrey Ross-Ibarra
Populations of widely distributed species encounter and must adapt to local environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome wide genotype data, multiple sampled populations, and an understanding of population structure and potential selection pressures. Here, we used SNP genotyping and data on numerous environmental variables to describe the genetic basis of local adaptation in 21 populations of teosinte, the wild ancestor of maize. We found complex hierarchical...

### 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: The influence of gene flow on species tree estimation: a simulation study

Adam D. Leaché, Rebecca B. Harris, Bruce Rannala & Ziheng Yang
Gene flow among populations or species and incomplete lineage sorting (ILS) are two evolutionary processes responsible for generating gene tree discordance and therefore hindering species tree estimation. Numerous studies have evaluated the impacts of ILS on species tree inference, yet the ramifications of gene flow on species trees remain less studied. Here, we simulate and analyze multilocus sequence data generated with ILS and gene flow to quantify their impacts on species tree inference. We characterize...

### Data from: Functional and population genomic divergence within and between two species of killifish adapted to different osmotic niches

Genevieve M. Kozak, Reid S. Brennan, Emma L. Berdan, Rebecca C. Fuller & Andrew Whitehead
Adaptation to salinity affects species distributions, promotes speciation, and guides many evolutionary patterns in fishes. To uncover the basis of a complex trait like osmoregulation, genome-level analyses are sensible. We combine population genomic scans with genome expression profiling to discover candidate genes and pathways associated with divergence between osmotic environments. We compared transcriptome sequence divergence between multiple freshwater and saltwater populations of the rainwater killifish, Lucania parva. We also compared sequence divergence between L. parva...

### Data from: When genes move farther than offspring: gene flow by male gamete dispersal in the highly philopatric bat species Thyroptera tricolor

Michael R. Buchalski, Gloriana Chaverri & Maarten J. Vonhof
For species characterized by philopatry of both sexes, mate selection represents an important behavior for inbreeding avoidance, yet the implications for gene flow are rarely quantified. Here we present evidence of male gamete mediated gene flow resulting from extra-group mating in Spix’s disk-winged bat, Thyroptera tricolor, a species which demonstrates all-offspring philopatry. We used microsatellite and capture-recapture data to characterize social group structure and the distribution of mated pairs at two sites in southwestern Costa...

### Data from: Genomics assisted ancestry deconvolution in grape

Jason K. Sawler, Bruce Reisch, Mallikarjuna K. Aradhya, Bernard Prins, Gan-Yuan Zhong, Heidi Schwaninger, Charles Simon, Edward Buckler, Sean Myles & Jason Sawler
The genus Vitis (the grapevine) is a group of highly diverse, diploid woody perennial vines consisting of approximately 60 species from across the northern hemisphere. It is the world’s most valuable horticultural crop with ~8 million hectares planted, most of which is processed into wine. To gain insights into the use of wild Vitis species during the past century of interspecific grape breeding and to provide a foundation for marker-assisted breeding programmes, we present a...

### Data from: Mechanisms of biotic resistance across complex life cycles

Marc Rius, Elaine E. Potter, John J. Stachowicz & J. David Aguirre
1. Biotic resistance is the ability of communities to inhibit the establishment, spread or impact of novel species. However, the interactions that underlie biotic resistance depend heavily on the contexts in which species interact. Consequently, studies of biotic resistance that consider single processes, patches, species or life-history stages may provide an incomplete picture of the capacity for communities to resist invasion. 2. Many organisms have multiphasic life cycles, where individuals can occupy distinct niches at...

### Data from: Morphological analysis of phylogenetic relationships among extant rhynchonellide brachiopods

Holly A. Schreiber, Maria Aleksandra Bitner & Sandra J. Carlson
Rhynchonellida is the stratigraphically oldest and phylogenetically most basal of the extant rhynchonelliform brachiopod orders, yet phylogenetic relationships among rhynchonellides are poorly known. The fourteen named rhynchonellide superfamilies (four of which have extant representatives) were defined primarily on the basis of features of the dorsal cardinalia, particularly crural morphology, but their homology and polarity have not been investigated rigorously. Superfamily monophyly is unclear, as is the evolution of several distinctive rhynchonellide morphological features, such as...

### Data from: The link between host density and egg production in a parasitoid insect: comparison between agricultural and natural habitats

Michal Segoli & Jay A. Rosenheim
1. Theory predicts that organisms should invest in overcoming a factor that may limit their reproductive success in direct proportion to their probability of being limited by it. The occurrence of egg limitation (where female insects deplete their eggs while oviposition opportunities are still available) is predicted to impose selection for increased fecundity at the expense of other fitness components. 2. We tested the hypothesis that the fecundity of a proovigenic parasitoid (where females emerge...

### Data from: Increased accuracy of species lists developed for alpine lakes using morphology and cytochrome oxidase I for identification of specimens

Kristy Deiner, Roland A. Knapp, Daniel M. Boiano & Bernie May
The first step in many community ecology studies is to produce a species list from a sample of individuals. Community ecologists now have two viable ways of producing a species list: morphological and barcode identification. In this study, we compared the taxonomic resolution gained by a combined use of both methods and tested whether a change in taxonomic resolution significantly impacted richness estimates for benthic macroinvertebrates sampled from ten lakes in Sequoia National Park, USA....

### Data from: Molecular phylogeny and SNP variation of polar bears (Ursus maritimus), brown bears (U. arctos) and black bears (U. americanus) derived from genome sequences

Matthew A. Cronin, Gonzalo Rincon, Robert W. Meredith, Michael D. MacNeil, Alma Islas-Trejo, Angela Canovas & Juan F. Medrano
We assessed the relationships of polar bears (Ursus maritimus), brown bears (U. arctos), and black bears (U. americanus) with high throughput genomic sequencing data with an average coverage of 25X for each species. A total of 1.4 billion 100-bp paired-end reads was assembled using the polar bear and annotated giant panda (Ailuropoda melanoleuca) genome sequences as references. We identified 13.8 million single nucleotide polymorphisms (SNP) in the three species aligned to the polar bear genome....

### Data from: Association between integration structure and functional evolution in the opercular four-bar apparatus of the threespine stickleback, Gasterosteus aculeatus (Pisces: Gasterosteidae)

Heather A. Jamniczky, Emily E. Harper, Rebecca Garner, William A. Cresko, Peter C. Wainwright, Benedikt Hallgrimsson & Charles B. Kimmel
Phenotypes may evolve to become integrated in response to functional demands. Once evolved, integrated phenotypes, often modular, can also influence the trajectory of subsequent responses to selection. Clearly, connecting modularity and functionally adaptive evolution has been challenging. The teleost skull and jaw structures are useful for understanding this connection because of the key roles that these structures play in feeding in novel environments with different prey resources. In the present study, we examined such a...

### Data from: Strong assortative mating by diet, color, size, and morphology but limited progress toward sympatric speciation in a classic example: Cameroon crater lake cichlids

Christopher H. Martin
Models predict that sympatric speciation depends on restrictive parameter ranges, such as sufficiently strong disruptive selection and assortative mating, but compelling examples in nature have rarely been used to test these predictions. I measured the strength of assortative mating within a species complex of Tilapia in Lake Ejagham, Cameroon, a celebrated example of incipient sympatric adaptive radiation. This species complex is in the earliest stages of speciation: morphological and ecological divergence are incomplete, species differ...

### Data from: The effect of Wolbachia on the lifetime reproductive success of its insect host in the field

Michal Segoli, Richard Stouthamer, Corinne M. Stouthamer, Paul Rugman-Jones & Jay A. Rosenheim
Wolbachia is a widespread endosymbiont that induces dramatic manipulations of its host's reproduction. Although there has been substantial progress in the developing theory for Wolbachia–host interactions and in measuring the effects of Wolbachia on host fitness in the laboratory, there is a widely recognized need to quantify the effects of Wolbachia on the host fitness in the field. The wasp Anagrus sophiae, an egg parasitoid of planthoppers, carries a Wolbachia strain that induces parthenogenesis, but...

### Data from: Evolutionary change during experimental ocean acidification

Melissa H. Pespeni, Eric Sanford, Tessa M. Hill, Jessica D. Hosfelt, Hannah K. Jaris, Michele LaVigne, Brian Gaylord, Elizabeth A. Lenz, Ann D. Russell, Megan K. Young & Stephen R. Palumbi
Rising atmospheric carbon dioxide (CO2) conditions are driving unprecedented changes in seawater chemistry, resulting in reduced pH and carbonate ion concentrations in the Earth’s oceans. This ocean acidification has negative but variable impacts on individual performance in many marine species. However, little is known about the adaptive capacity of species to respond to an acidified ocean, and as a result, predictions regarding future ecosystem responses remain incomplete. Here we demonstrate that ocean acidification generates striking...

• 2013
33

• Dataset
33

#### Affiliations

• University of California, Davis
33
• University of California, Berkeley
3
• University of Queensland
2
• Dalhousie University
2
• United States Department of Agriculture
2
• University of Tennessee at Knoxville
2
• Indiana University Bloomington
2