### 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: 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: 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: Disentangling the effects of geographic and ecological isolation on genetic differentiation

Gideon S. Bradburd, Peter L. Ralph & Graham M. Coop
Populations can be genetically isolated by both geographic distance and by differences in their ecology or environment that decrease the rate of successful migration. Empirical studies often seek to investigate the relationship between genetic differentiation and some ecological variable(s) while accounting for geographic distance, but common approaches to this problem (such as the partial Mantel test) have a number of drawbacks. In this article, we present a Bayesian method that enables users to quantify the...

### Data from: A new multiplex SNP genotyping assay for detecting hybridization and introgression between the M and S molecular forms of Anopheles gambiae

Yoosook Lee, Clare D. Marsden, Catelyn Nieman & Gregory C. Lanzaro
The M and S forms of A. gambiae have been the subject of intense study, but are morphologically indistinguishable and can only be identified using molecular techniques. PCR-based assays to distinguish the two forms have been designed and applied widely. However, the application of these assays towards identifying hybrids between the two forms, and backcrossed hybrids in particular, has been problematic as the currently available diagnostic assays are based on single loci, and/or are located...

### Data from: Kin recognition affects plant communication and defence

Richard Karban, Kaori Shiojiri, Satomi Ishizaki, William C. Wetzel & Richard Y. Evans
The ability of many animals to recognize kin has allowed them to evolve diverse cooperative behaviours; such ability is less well studied for plants. Many plants, including Artemisia tridentata, have been found to respond to volatile cues emitted by experimentally wounded neighbours to increase levels of resistance to herbivory. We report that this communication was more effective among A. tridentata plants that were more closely related based on microsatellite markers. Plants in the field that...

### Data from: Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting

Matt Friedman, Benjamin P. Keck, Alex Dornburg, Ron I. Eytan, Christopher H. Martin, C. Darrin Hulsey, Peter C. Wainwright & Thomas J. Near
Cichlid fishes are a key model system in the study of adaptive radiation, speciation and evolutionary developmental biology. More than 1600 cichlid species inhabit freshwater and marginal marine environments across several southern landmasses. This distributional pattern, combined with parallels between cichlid phylogeny and sequences of Mesozoic continental rifting, has led to the widely accepted hypothesis that cichlids are an ancient group whose major biogeographic patterns arose from Gondwanan vicariance. Although the Early Cretaceous (ca 135...

### Data from: Localized hotspots drive continental geography of abnormal amphibians on U.S. wildlife refuges

Mari K. Reeves, Kimberly A. Medley, Alfred E. Pinkney, Marcel Holyoak, Pieter T. J. Johnson & Michael J. Lannoo
Amphibians with missing, misshapen, and extra limbs have garnered public and scientific attention for two decades, yet the extent of the phenomenon remains poorly understood. Despite progress in identifying the causes of abnormalities in some regions, a lack of knowledge about their broader spatial distribution and temporal dynamics has hindered efforts to understand their implications for amphibian population declines and environmental quality. To address this data gap, we conducted a nationwide, 10-year assessment of 62,947...

### 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...

### Data from: Vitis phylogenomics: hybridization intensities from a SNP array outperform genotype calls

Allison J. Miller, Naim Matasci, Heidi Schwaninger, Mallikarjuna K. Aradhya, Bernard Prins, Gan-Yuan Zhong, Charles Simon, Edward S. Buckler & Sean Myles
Understanding relationships among species is a fundamental goal of evolutionary biology. Single nucleotide polymorphisms (SNPs) identified through next generation sequencing and related technologies enable phylogeny reconstruction by providing unprecedented numbers of characters for analysis. One approach to SNP-based phylogeny reconstruction is to identify SNPs in a subset of individuals, and then to compile SNPs on an array that can be used to genotype additional samples at hundreds or thousands of sites simultaneously. Although powerful and...

### Data from: Exceptional convergence on the macroevolutionary landscape in island lizard radiations

D. Luke Mahler, Travis Ingram, Liam J. Revell & Jonathan B. Losos
G. G. Simpson, one of the chief architects of evolutionary biology’s modern synthesis, proposed that diversification occurs on a macroevolutionary adaptive landscape, but landscape models are seldom used to study adaptive divergence in large radiations. We show that for Caribbean Anolis lizards, diversification on similar Simpsonian landscapes leads to striking convergence of entire faunas on four islands. Parallel radiations unfolding at large temporal scales shed light on the process of adaptive diversification, indicating that the...

### Data from: Leaf drop affects herbivory in oaks

Ian S. Pearse & Richard Karban
Leaf phenology is important to herbivores, but the timing and extent of leaf drop has not played an important role in our understanding of herbivore interactions with deciduous plants. Using phylogenetic general least squares regression, we compared the phenology of leaves of 55 oak species in a common garden with the abundance of leaf miners on those trees. Mine abundance was highest on trees with an intermediate leaf retention index, i.e. trees that lost most,...

### 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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...

• 2013
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• Dataset
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#### 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
• University of Colorado Boulder
2
• University of Arizona
2
• University of Massachusetts Boston
2