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Made available in DSpace on 2022-04-28T19:52:06Z (GMT). No. of bitstreams: 0 Previous issue date: 2022-03-18 Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural clines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale. Department of Biology University of Toronto Mississauga ON Centre for Urban Environments University of Toronto Mississauga ON Department of Biology University of North Carolina, Chapel Hill Department of Biology University of Louisiana LA Department of Biology Queen's University ON Department of Biology Concordia University QC Department of Biological Sciences DePaul University Department of Biology DePauw University IN Department of Urban Design and Planning, University of Washington, Seattle, WA, USA Colegio de Ciencias Biológicas y Ambientales Universidad San Francisco de Quito USFQ Department of Genetics University of Georgia Department of Ecology and Genetics Evolutionary Biology Centre Uppsala University Field Science Center for Northern Biosphere Hokkaido University Natural History Museum Zoology University of New England NSW Programa de Pós-Graduação em Geografia da UFMT campus de Rondonópolis Department of Botany and Biodiversity Research Centre University of British Columbia Graduate Program in Genome Sciences and Technology Genome Sciences Centre University of British Columbia Department of Microbiology and Immunology University of British Columbia Red de Biología Evolutiva Instituto de Ecología A. C. School of the Environment Yale University CT Departamento de Ciencias Ecológicas Universidad de Chile, Facultad de Ciencias Instituto de Ecología y Biodiversidad Universidad de Chile Department of Biology Mount Allison University Red de Ecoetología Instituto de Ecología A. C. Department of Biology University of Ottawa ON Department of Zoology University of Cambridge Department of Biology, Washington University in St. Louis, St. Louis, MO, USA Department of Biology University of Miami FL Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS) Universidad Bernardo O'Higgins Department of Biology, University of La Verne, La Verne, CA, USA Département des sciences du bois et de la forêt Université Laval QC Evolution & Ecology Research Centre School of Biological Earth and Environmental Sciences UNSW Sydney NSW Department of Biology Ghent University Department of Biology Monmouth University West Long Branch Centre for Ecology Evolution and Environmental Changes Faculdade de Ciências Universidade de Lisboa Lisboa Department of Biology KU Leuven School of Agriculture and Environment Wildlife and Ecology group Massey University, Palmerston North Department of Biological Sciences University of Cape Town Institute of Landscape Ecology University of Münster Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA Department of Biological Sciences University of Alberta AB Louis Calder Center and Department of Biological Sciences, Fordham University, Armonk, NY, USA Departamento de Ecología Tropical, Universidad Autónoma de Yucatán, Mérida, Yucatán, México School of Life Sciences University of Sussex Department of Ecology Environment and Plant Sciences Stockholm University iBIOTROP Instituto de Biodiversidad Tropical Universidad San Francisco de Quito Department of Biology, San Francisco State University, San Francisco, CA, USA Unidad de Recursos Naturales, Centro de Investigación Científica de Yucatán AC, Mérida, Yucatán, México School of Ecological and Environmental Sciences East China Normal University Shanghai Engineering Research Center of Sustainable Plant Innovation Centre for Ecosystem Science School of Biological Earth and Environmental Sciences UNSW Sydney NSW Department of Ecology and Evolutionary Biology University of Michigan MI Department of Biosciences Rice University TX IFEVA Universidad de Buenos Aires Facultad de Agronomía, CONICET Biology Department Saint Mary's University NS Department of Biological Sciences, Universidad de los Andes Department of Biology and Biochemistry University of Houston TX Université de Rennes Department of Zoology and Biodiversity Research Centre University of British Columbia Department of Environmental Studies Dordt University Sioux Center IA Department of Biology Minneapolis Community and Technical College MN Department of Natural Sciences Ecology and Environment Research Centre Manchester Metropolitan University Instituto de Investigaciones en Ecosistemas y Sustentabilidad UNAM Department of Botany School of Biology Aristotle University of Thessaloniki Faculty of Biological and Environmental Science Organismal & Evolutionary Biology Research Programme University of Helsinki Institute of Biodiversity Animal Health and Comparative Medicine University of Glasgow Department of Biology Hendrix College Department of Ecological Science Vrije Universiteit Amsterdam Departamento de Ciencias Biológicas y Agropecuarias Universidad Técnica Particular de Loja Departamento de Biologia Universidade Federal de Santa Maria (UFSM) Department of Plant Sciences School of Biology College of Science University of Tehran NTNU University Museum Norwegian University of Science and Technology Red de Estudios Moleculares Avanzados Instituto de Ecología A. C. School of Biological Sciences, University of Reading, Whiteknights Park, Reading, Berkshire, UK Department of Biology Northern Arizona University AZ Department of Biological Sciences MacEwan University AB Max Planck Institute for Plant Breeding Research Departamento de Ecología Evolutiva Instituto de Ecología Universidad Nacional Autónoma de México Max Planck Institute of Molecular Plant Physiology Potsdam-Golm BIO5 Institute University of Arizona AZ Alaska Center for Conservation Science University of Alaska Anchorage Tropical Diversity, Royal Botanical Garden of Edinburgh Département de biologie Université de Moncton Department of Biological Sciences University of Manitoba MB Departments of Microbiology & Statistics University of Manitoba MB Department of Biology University of New Brunswick Department of Biology Kalamazoo College MI BioProtection Research Centre Lincoln University Departamento de Ciencias Facultad de Artes Liberales Universidad Adolfo Ibáñez Department of Ecology Evolution Behaviour University of Minnesota MN Department of Biological Sciences Brock University Department of Environmental Toxicology, University of California, Davis, CA, USA ICB - University of Talca School of Molecular and Life Science Curtin University College of Science Health Engineering and Education Murdoch University, Murdoch School of Life and Environmental Sciences University of Sydney NSW School of Biological Sciences, Monash University, Melbourne, VIC, Australia Department of Biological Sciences Wayne State University MI Department of Biology Western Oregon University, OR School of Natural Resources and the Environment University of Arizona AZ Departamento de Ecología Humana, Cinvestav Mérida Departamento de Ciencias Biológicas y Departamento de Ecología y Biodiversidad Facultad de Ciencias de la Vida, Universidad Andrés Bello Institute of Ecology and Biodiversity (IEB) Department of Biology Lund University Department of Biology Norwegian University of Science and Technology Escuela Superiro de Desarrollo Sustentable Universidad Autónoma de Guerrero -CONACYT Clarkson Secondary School Peel District School Board ON Homelands Sr. Public School Peel District School Board ON Department of Biological Sciences University of Illinois at Chicago Dufferin-Peel Catholic District School Board, St. James Catholic Global Learning Centre Department of Biosciences University of Calgary AB Ecological Processes Branch U.S. Army ERDC-CERL Department of Biology, Oberlin College, Oberlin, OH, USA Escuela Nacional de Estudios Superiores Unidad Morelia UNAM Institute of Evolution and Ecology University of Tübingen Tübingen Department of Evolutionary Biology and Environmental Studies University of Zurich, Winterthurerstrasse Urban Wildlife Institute Department of Conservation and Science, Lincoln Park Zoo Departamento de Ecología Universidad Católica de la Santísima Concepción Department of Biological Sciences University of Denver CO Department of Biological Sciences Mississippi State University MS Department of Biology Center for Computational & Integrative Biology Rutgers University-Camden Kunming Institute of Botany Chinese Academy of Sciences Department of Chemistry & Biochemistry Laurentian University ON Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University School of BioSciences, University of Melbourne, Melbourne, VIC, Australia Posgrado en Ciencias Biológicas Universidad Nacional Autónoma de México Department of Biological Sciences, Auburn University, Auburn, AL, USA Department of Entomology and Nematology, University of California, Davis, CA, USA Department of Biology University of New Mexico NM Department of Biology University of Wisconsin - Eau Claire Agriculture Institute Iranian Research Organization for Science and Technology (IROST) Department of Biology Colby College ME Instituto de Biología Universidad de Antioquia Department of Biology University of Massachusetts Boston MA Agricultural Biology Colorado State University CO Departamento de Biología Vegetal y Ecología Facultad de Biología Universidad de Sevilla, Av. Reina Mercedes s/n Facultad de Estudios Interdisciplinarios Centro GEMA- Genómica Universidad Mayor Evolutionary Ecology Group Naturalis Biodiversity Center Department of Biology and Chemistry Nipissing University ON, North Bay Center for Ecological Research Kyoto University Bonanza Creek Long Term Ecological Research Program University of Alaska Fairbanks Department of Botany and Molecular Evolution Senckenberg Research Institute and Natural History Museum Frankfurt Departamento de Biodiversidade Instituto de Biociências Univ Estadual Paulista - UNESP Nelson Institute for Environmental Studies University of Wisconsin-Madison WI Department of Biology, California State University, Northridge, Los Angeles, CA, USA Department of Ecology Swedish University of Agricultural Sciences Facultad de Ciencias y Biotecnologia Universidad CES Department of Biology Hofstra University Faculty of Biosciences and Aquaculture Nord University, Bodø Division of Biological Sciences, University of California San Diego, San Diego, CA, USA Department of Biology University of Richmond VA Estación de Biodiversidad Tiputini Colegio de Ciencias Biológicas y Ambientales Universidad San Francisco de Quito USFQ Department of Biological Sciences Institute of Environment Florida International University FL Agronomy Department University of Almería Department of Biological Sciences and Center for Urban Ecology and Sustainability Butler University IN Department of Biological Sciences Louisiana State University LA Faculty of Biological Sciences, Goethe University Frankfurt Institute of Biology Leiden Leiden University Department of Biological and Environmental Science University of Jyväskylä Jyväskylä Department of Biology University of Louisville KY Organization for Programs on Environmental Science University of Tokyo CNRS AgroParisTech Ecologie Systématique et Evolution, Université Paris-Saclay Department of Biology, Providence College, Providence, RI, USA General Zoology Institute for Biology Martin Luther University Halle-Wittenberg International Arctic Research Center University of Alaska Fairbanks Science, Technology and Society Department, Rochester Institute of Technology, Rochester, NY, USA SLU Swedish Species Information Centre Swedish University of Agricultural Sciences Department of Biology Westfield State University MA Centre of New Technologies University of Warsaw Department of Biology, Stanford University, Stanford, CA, USA Plant Biology Department Michigan State University MI Biology Department Davidson College College of Horticulture and Forestry Sciences/ Hubei Engineering Technology Research Center for Forestry Information Huazhong Agricultural University School of Life Sciences Technical University of Munich School of Life Sciences Lanzhou University Institute of Ecology and Evolution University of Bern Department of Evolution Ecology and Behaviour University of Liverpool Departamento de Biodiversidade Instituto de Biociências Univ Estadual Paulista - UNESP

There is intense interest in using genome editing technologies to domesticate wild plants, or accelerate the improvement of weakly domesticated crops, in de novo domestication. Here, we discuss promising genetic strategies, with a focus on plant development. Importantly, genome editing releases us from dependence on random mutagenesis or intraspecific diversity, allowing us to draw solutions more broadly from diversity. However, sparse understanding of the complex genetics of diversity limits innovation. Beyond genetics, we urge the ethical use of indigenous knowledge, indigenous plants, and ethnobotany. De novo domestication still requires conventional breeding by phenotypic selection, especially in the development of crops for diverse environments and cultures. Indeed, uniting genome editing with selective breeding could facilitate faster and better outcomes than either technology alone. Domestication is complex and incompletely understood, involving changes to many aspects of plant biology and human culture. Success in de novo domestication requires careful attention to history and collaboration across traditional boundaries. Expected final online publication date for the

Crop adaptation is required to sustainably increase the rate of yield gains to meet projected future needs under the challenging conditions of climate change and competition for resources. Future adaptation will likely need to harness both highly polygenic traits and genotype-by-environment interactions (GxE), the study of which is aided by complex recombinant populations. We used the diverse Oryza sativa Global Multiparent Advanced Generation InterCross (MAGIC) population to study the genetic architecture and contributions of seedling emergence, establishment, and development to yield components under dry-direct seeding and seedling stage drought across three growing seasons. Dry-direct seeding is an establishment practice that has the potential to reduce methane emissions, water use, and labor demands for rice farmers, but increases the possibility of early-season drought conditions. We found substantial evidence for large roles of environmental variation and GxE in controlling trait variation. Maintenance of shoot growth during seedling stage drought was positively correlated with crown root number and both directly and indirectly influenced agronomic traits. Other than the major green revolution locus sd1, most allelic effects were conditionally neutral (affecting trait values in some environments but not others) and most alleles had their strongest effect in an environmental extreme. This discovery is both a challenge and a potential opportunity: with variable genetic architecture, selection in any one environment may not result in stable trait gains across environments. However, conditionally neutral GxE is a potential route to sustainable yield stability through allele pyramiding.

Decreasing sequencing costs have driven a rapid expansion of novel genotyping methods. One of these methods is the exploitation of restriction enzyme cut sites to generate genome-wide but reduced representation sequencing libraries (RRLs), alternatively termed genotyping by sequencing or restriction-site associated DNA sequencing. Without a reference genome, the resulting short sequence reads must be assembled de novo. There are many possible assembly programs, most not explicitly developed for RRL data, and we know little of their effectiveness. In this issue of Molecular Ecology Resources, LaCava et al. (2020) systematically evaluate six commonly used programs and two commonly varied parameters for complete and accurate assembly of RRLs, using simulated double digests of Homo sapiens and Arabidopsis thaliana genomes with varied mutation rates and types. The authors find substantial variation in performance across assembly programs. The most consistently high-performing assembler is infrequently used in their literature survey (CD-HIT; Li and Godzik, 2006), while several others fail to produce complete, accurate assemblies under many conditions. LaCava et al. additionally recommend best practices in parameter choice and evaluation of future assembly programs-advice that molecular ecologists working to assemble sequences of all kinds should take to heart.

Background and aims The patterning of floral ultraviolet (UV) pigmentation varies both intra- and interspecifically in sunflowers and many other plant species, impacts pollinator attraction, and can be critical to reproductive success and crop yields. However, the genetic basis for variation in UV patterning is largely unknown. This study examines the genetic architecture for proportional and absolute size of the UV bullseye in Helianthus argophyllus , a close relative of the domesticated sunflower. Methods A camera modified to capture UV light (320-380 nm) was used to phenotype floral UV patterning in an F 2 mapping population, then quantitative trait loci (QTL) were identified using genotyping-by-sequencing and linkage mapping. The ability of these QTL to predict the UV patterning of natural population individuals was also assessed. Key results Proportional UV pigmentation is additively controlled by six moderate effect QTL that are predictive of this phenotype in natural populations. In contrast, UV bullseye size is controlled by a single large effect QTL that also controls flowerhead size and co-localizes with a major flowering time QTL in Helianthus . Conclusions The co-localization of the UV bullseye size QTL, flowerhead size QTL and a previously known flowering time QTL may indicate a single highly pleiotropic locus or several closely linked loci, which could inhibit UV bullseye size from responding to selection without change in correlated characters. The genetic architecture of proportional UV pigmentation is relatively simple and different from that of UV bullseye size, and so should be able to respond to natural or artificial selection independently.

International audience; Domesticated plants and animals often display dramatic responses to selection, but the origins of the genetic diversity underlying these responses remain poorly understood. Despite domestication and improvement bottlenecks, the cultivated sunflower remains highly variable genetically, possibly due to hybridization with wild relatives. To characterize genetic diversity in the sunflower and to quantify contributions from wild relatives, we sequenced 287 cultivated lines, 17 Native American landraces and 189 wild accessions representing 11 compatible wild species. Cultivar sequences failing to map to the sunflower reference were assembled de novo for each genotype to determine the gene repertoire, or 'pan-genome', of the cultivated sunflower. Assembled genes were then compared to the wild species to estimate origins. Results indicate that the cultivated sunflower pan-genome comprises 61,205 genes, of which 27% vary across genotypes. Approximately 10% of the cultivated sunflower pan-genome is derived through introgression from wild sunflower species, and 1.5% of genes originated solely through introgression. Gene ontology functional analyses further indicate that genes associated with biotic resistance are over-represented among introgressed regions, an observation consistent with breeding records. Analyses of allelic variation associated with downy mildew resistance provide an example in which such introgressions have contributed to resistance to a globally challenging disease.

Genome-wide association studies (GWAS) have identified loci linked to hundreds of traits in many different species. Yet, because linkage equilibrium implicates a broad region surrounding each identified locus, the causal genes often remain unknown. This problem is especially pronounced in nonhuman, nonmodel species, where functional annotations are sparse and there is frequently little information available for prioritizing candidate genes. We developed a computational approach, Camoco, that integrates loci identified by GWAS with functional information derived from gene coexpression networks. Using Camoco, we prioritized candidate genes from a large-scale GWAS examining the accumulation of 17 different elements in maize (

Significance Local adaptation can occur due to individual genetic variants that increase the fitness of individuals in their home environments but decrease fitness in other environments [genetic trade-offs (GTs)] or genetic variants that increase fitness in one environment but have no effect in other environments [conditional neutrality (CN)]. Here, we show that GT quantitative trait loci (QTLs) for fitness between Italian and Swedish Arabidopsis thaliana exhibit strong population genomic signatures of local adaptation, including elevated levels of allele frequency differentiation, correlations to climatic variables, and recent sweeps. Highly divergent genes between Italy and Sweden populations show evidence of more recent selection in Sweden than Italy, and the biological annotations of these genes suggest interesting mechanisms underlying local adaptation., Evidence for adaptation to different climates in the model species Arabidopsis thaliana is seen in reciprocal transplant experiments, but the genetic basis of this adaptation remains poorly understood. Field-based quantitative trait locus (QTL) studies provide direct but low-resolution evidence for the genetic basis of local adaptation. Using high-resolution population genomic approaches, we examine local adaptation along previously identified genetic trade-off (GT) and conditionally neutral (CN) QTLs for fitness between locally adapted Italian and Swedish A. thaliana populations [Ågren J, et al. (2013) Proc Natl Acad Sci USA 110:21077–21082]. We find that genomic regions enriched in high FST SNPs colocalize with GT QTL peaks. Many of these high FST regions also colocalize with regions enriched for SNPs significantly correlated to climate in Eurasia and evidence of recent selective sweeps in Sweden. Examining unfolded site frequency spectra across genes containing high FST SNPs suggests GTs may be due to more recent adaptation in Sweden than Italy. Finally, we collapse a list of thousands of genes spanning GT QTLs to 42 genes that likely underlie the observed GTs and explore potential biological processes driving these trade-offs, from protein phosphorylation, to seed dormancy and longevity. Our analyses link population genomic analyses and field-based QTL studies of local adaptation, and emphasize that GTs play an important role in the process of local adaptation.

How often does evolution repeat itself? When the same evolutionary strategy arises multiple times, how often are these strategies built on the same genetic foundations? Addressing this question allows us to understand the relative roles of constraint and contingency in the history of life, but (

Four accessions of cultivated sunflower (Helianthus annuus) and silverleaf sunflower (Helianthus argophyllus), were each grown in three locations (Georgia, British Columbia, and Iowa) at different planting densities and phenotyped for biomass-related traits and wood biochemistry. In most environments, H. argophyllus produced significantly more biomass than H. annuus. Cell wall chemistry for a subset of plants grown in Georgia and Iowa was assessed using analytical wet chemistry methods to measure lignin and sugar content/composition. The analysis of lignin and the S/G-lignin ratios for a larger number of samples (n > 250) was also assessed by high-throughput pyrolysis Molecular Beam Mass Spectrometry. Average pyMBMS estimated lignin content (i.e., dry weight fraction) for 60 °C dried basal stem samples of H. annuus and H. argophyllus was 29.6% (range, 24.0%–34.6%) and 28.6% (range, 24.6%–33.3%), respectively when averaged across all environments. The average S/G lignin mass ratio was 1.5 (range, 1.0–2.0) for H. annuus and 1.7 (range, 1.0–2.4) in H. argophyllus. Stem samples from these two species only differed statistically for a few cell wall chemistry traits; however, accession level differences within each species were apparent. Cell wall chemistry in both species was significantly affected by both location and planting density, thus demonstrating the need to select for these traits in the environment for which the crop will be produced. Overall, these results show that cultivated sunflower and silverleaf sunflower both possess the necessary phenotypic diversity to facilitate the development of a hybrid sunflower with improved lignocellulosic biofuels traits, namely increased biomass, decreased lignin, and increased glucan.

Premise of research. The transition from herbaceous annual to woody perennial has occurred numerous times during angiosperm evolution, but the suite of genetic changes that accompanies this life history shift remains poorly understood. Here we analyze genetic sequence and gene expression divergence between the annual Helianthus annuus and a recently diverged woody perennial ecotype from California.Methodology. We grew plants from populations of typical H. annuus and the woody perennial ecotype in a common garden and measured days to flower, mature height, and basal stem density. We looked for evidence of genome size evolution in the woody ecotype using flow cytometry and conducted anatomical observations of stem development in seedlings. We sequenced the aboveground seedling transcriptomes of six individuals of each ecotype and identified genes with high fixation index (FST) and significant divergence in gene expression. Finally, we examined the gene ontology annotation of differentiated genes and assesse...

To ensure food security in the face of population growth, decreasing water and land for agriculture, and increasing climate variability, crop yields must increase faster than the current rates. Increased yields will require implementing novel approaches in genetic discovery and breeding. Here we demonstrate the potential of field-based high throughput phenotyping (HTP) on a large recombinant population of rice to identify genetic variation underlying important traits. We find that detecting quantitative trait loci (QTL) with HTP phenotyping is as accurate and effective as traditional labor-intensive measures of flowering time, height, biomass, grain yield, and harvest index. Genetic mapping in this population, derived from a cross of an modern cultivar (IR64) with a landrace (Aswina), identified four alleles with negative effect on grain yield that are fixed in IR64, demonstrating the potential for HTP of large populations as a strategy for the second green revolution.

Selection on quantitative trait loci (QTL) may vary among natural environments due to differences in the genetic architecture of traits, environment-specific allelic effects or changes in the direction and magnitude of selection on specific traits. To dissect the environmental differences in selection on life history QTL across climatic regions, we grew a panel of interconnected recombinant inbred lines (RILs) of Arabidopsis thaliana in four field sites across its native European range. For each environment, we mapped QTL for growth, reproductive timing and development. Several QTL were pleiotropic across environments, three colocalizing with known functional polymorphisms in flowering time genes (CRY2, FRI and MAF2-5), but major QTL differed across field sites, showing conditional neutrality. We used structural equation models to trace selection paths from QTL to lifetime fitness in each environment. Only three QTL directly affected fruit number, measuring fitness. Most QTL had an indirect effect on fitness through their effect on bolting time or leaf length. Influence of life history traits on fitness differed dramatically across sites, resulting in different patterns of selection on reproductive timing and underlying QTL. In two oceanic field sites with high prereproductive mortality, QTL alleles contributing to early reproduction resulted in greater fruit production, conferring selective advantage, whereas alleles contributing to later reproduction resulted in larger size and higher fitness in a continental site. This demonstrates how environmental variation leads to change in both QTL effect sizes and direction of selection on traits, justifying the persistence of allelic polymorphism at life history QTL across the species range.

The data underlying scientific papers should be accessible to researchers both now and in the future, but how best can we ensure that these data are available? Here we examine the effectiveness of four approaches to data archiving: no stated archiving policy, recommending (but not requiring) archiving, and two versions of mandating data deposition at acceptance. We control for differences between data types by trying to obtain data from papers that use a single, widespread population genetic analysis, STRUCTURE. At one extreme, we found that mandated data archiving policies that require the inclusion of a data availability statement in the manuscript improve the odds of finding the data online almost a thousand-fold compared to having no policy. However, archiving rates at journals with less stringent policies were only very slightly higher than those with no policy at all. At one extreme, we found that mandated data archiving policies that require the inclusion of a data availability statement in the manuscript improve the odds of finding the data online almost a thousand fold compared to having no policy. However, archiving rates at journals with less stringent policies were only very slightly higher than those with no policy at all. We also assessed the effectiveness of asking for data directly from authors and obtained over half of the requested datasets, albeit with about 8 days delay and some disagreement with authors. Given the long term benefits of data accessibility to the academic community, we believe that journal based mandatory data archiving policies and mandatory data availability statements should be more widely adopted.

Hybridization may drive rare taxa to extinction through genetic swamping, where the rare form is replaced by hybrids, or by demographic swamping, where population growth rates are reduced due to the wasteful production of maladaptive hybrids. Conversely, hybridization may rescue the viability of small, inbred populations. Understanding the factors that contribute to destructive versus constructive outcomes of hybridization is key to managing conservation concerns. Here, we survey the literature for studies of hybridization and extinction to identify the ecological, evolutionary, and genetic factors that critically affect extinction risk through hybridization. We find that while extinction risk is highly situation dependent, genetic swamping is much more frequent than demographic swamping. In addition, human involvement is associated with increased risk and high reproductive isolation with reduced risk. Although climate change is predicted to increase the risk of hybridization‐induced extinction, we find little empirical support for this prediction. Similarly, theoretical and experimental studies imply that genetic rescue through hybridization may be equally or more probable than demographic swamping, but our literature survey failed to support this claim. We conclude that halting the introduction of hybridization‐prone exotics and restoring mature and diverse habitats that are resistant to hybrid establishment should be management priorities.

There are several models we use to conceptualize how plants respond to environmental signals through transcriptional regulation. In perhaps the best-understood model, the perception of some environmental signal flows through one or several mechanisms to a master regulator, often a transcription

Populations that have independently evolved reproductive isolation from their ancestors while remaining reproductively cohesive have undergone parallel speciation. A specific type of parallel speciation, known as parallel ecological speciation, is one of several forms of evidence for ecology's role in speciation. In this paper we search the literature for candidate examples of parallel ecological speciation in plants. We use four explicit criteria (independence, isolation, compatibility, and selection) to judge the strength of evidence for each potential case. We find that evidence for parallel ecological speciation in plants is unexpectedly scarce, especially relative to the many well-characterized systems in animals. This does not imply that ecological speciation is uncommon in plants. It only implies that evidence from parallel ecological speciation is rare. Potential explanations for the lack of convincing examples include a lack of rigorous testing and the possibility that plants are less prone to parallel ecological speciation than animals.

Substantial intraspecific variation in life history is rare and potentially a signal of incipient ecological speciation, if variation is driven by geographically heterogenous natural selection. We present the first report of extensive life history polymorphism in Helianthus argophyllus, the silverleaf sunflower, and examine evidence for its evolution by divergent selection. In 18 populations sampled from across the species range and grown in a common garden, most quantitative traits covaried such that individuals could be assigned to two distinct life history syndromes: tall and late flowering with small initial flowerheads, or short and early flowering with larger initial flowerheads. Helianthus argophyllus exhibits regional genetic structure, but this population structure does not closely correspond with patterns of phenotypic variation. The early-flowering syndrome is primarily observed in populations from coastal barrier islands, while populations from the nearby mainland coast, although geographically and genetically close, are primarily late flowering. Additionally, several traits are more differentiated among regions than expected based on neutral genetic divergence (QST > FST ), including the first principal component score corresponding with life history syndrome. This discordance between patterns of phenotypic and genetic variation suggests that divergent selection is driving genetic differences in life history across the species range. If so, the silverleaf sunflower may be in early stages of ecological speciation.

When studying selection during adaptation to novel environments, researchers have often paid little attention to an organism's earliest developmental stages. Despite this lack of attention, early life history traits may be under strong selection during colonization, as the expression of adaptive phenotypes at later points is contingent upon early survival. Moreover, the timing of early developmental transitions can constrain the timing of later transitions, with potentially large effects on fitness. In this issue, Huang et al. (2010) underscore the importance of early life history traits in the adaptation of Arabidopsis thaliana to old-field sites in North America. Using a new population of mapped recombinant inbred lines, the authors examined germination timing and total lifetime fitness of A. thaliana while varying site latitude, dispersal season, and maternal photoperiod. Huang et al. (2010) discovered several Quantitative Trait Loci (QTL) with large effects on fitness that colocalized with QTL for field germination timing and seed dormancy-demonstrating that fitness is genetically associated with these early life history traits, and that these loci are likely under strong selection during adaptation to novel environments. In the epistatic interactions of some loci, recombinant genotypes outperformed parental genotypes, supporting the potentially adaptive role of recombination. This study provides elegant evidence that traits expressed early in an organism's development can play an important role during adaptive evolution.

Genomic studies of speciation often report the presence of highly differentiated genomic regions interspersed within a milieu of weakly diverged loci. The formation of these speciation islands is generally attributed to reduced inter-population gene flow near loci under divergent selection, but few studies have critically evaluated this hypothesis. Here, we report on transcriptome scans among four recently diverged pairs of sunflower (Helianthus) species that vary in the geographical context of speciation. We find that genetic divergence is lower in sympatric and parapatric comparisons, consistent with a role for gene flow in eroding neutral differences. However, genomic islands of divergence are numerous and small in all comparisons, and contrary to expectations, island number and size are not significantly affected by levels of interspecific gene flow. Rather, island formation is strongly associated with reduced recombination rates. Overall, our results indicate that the functional architecture of genomes plays a larger role in shaping genomic divergence than does the geography of speciation.

Like many species, the model plant Arabidopsis thaliana exhibits multiple different life histories in natural environments. We grew mutants impaired in different signaling pathways in field experiments across the species' native European range in order to dissect the mechanisms underlying this variation. Unexpectedly, mutational loss at loci implicated in the cold requirement for flowering had little effect on life history except in late-summer cohorts. A genetically informed photothermal model of progression toward flowering explained most of the observed variation and predicted an abrupt transition from autumn flowering to spring flowering in late-summer germinants. Environmental signals control the timing of this transition, creating a critical window of acute sensitivity to genetic and climatic change that may be common for seasonally regulated life history traits.