Loren H. Rieseberg's research while affiliated with University of British Columbia - Vancouver and other places

Publications (714)

Article
Full-text available
Sunflowers of the genus Helianthus are models for hybridization research and contain three of the best studied examples of homoploid hybrid speciation. To understand the broader picture of hybridization within the annual sunflowers, we used whole genome resequencing to conduct a phylogenomic analysis and test for gene flow between lineages. We find...
Article
Similar traits and functions commonly evolve in nature. Here, we explore patterns of replicated evolution across the plant kingdom and discuss the processes responsible for such patterns. We begin this review by defining replicated evolution and the theoretical, genetic, and ecological concepts that help explain it. We then focus our attention on e...
Article
Full-text available
Genomic studies often attempt to link natural genetic variation with important phenotypic variation. To succeed, robust and reliable phenotypic data, as well as curated genomic assemblies, are required. Wild sunflowers, originally from North America, are adapted to diverse and often extreme environments and have historically been a widely used mode...
Article
Conspecific populations living in adjacent but contrasting microenvironments represent excellent systems for studying natural selection. These systems are valuable because gene flow is expected to force genetic homogeneity except at loci experiencing divergent selection. A history of reciprocal transplant and common garden studies in such systems,...
Preprint
Full-text available
Sunflowers of the genus Helianthus are models for hybridization research and contain three of the best studied examples of homoploid hybrid speciation. To understand the broader picture of hybridization within the annual sunflowers, we used whole genome resequencing to conduct a phylogenomic analysis and test for gene flow between lineages. We find...
Preprint
Full-text available
Yellow starthistle (Centaurea solstitialis) is a highly invasive species that has been a model system for the potential contribution of evolution to invader traits. Here, we report the construction of a chromosome-scale reference genome for C. solstitialis using a combination of PacBio HiFi and Dovetail Omni-C technologies, and functional gene anno...
Article
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Over the course of history, humans have moved crops from their regions of origin to new locations across the world. The social, cultural and economic drivers of these movements have generated differences not only between current distributions of crops and their climatic origins, but also between crop distributions and climate suitability for their...
Article
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We assembled the 9.8 Gbp genome of western redcedar (WRC, Thuja plicata ), an ecologically and economically important conifer species of the Cupressaceae. The genome assembly, derived from a uniquely inbred tree produced through five generations of self-fertilization (selfing), was determined to be 86% complete by BUSCO analysis - one of the most c...
Preprint
Full-text available
We assembled the 9.8 Gbp genome of western redcedar (WRC, Thuja plicata ), an ecologically and economically important conifer species of the Cupressaceae. The genome assembly, derived from a uniquely inbred tree produced through five generations of self-fertilization (selfing), was determined to be 86% complete by BUSCO analysis - one of the most c...
Article
Full-text available
Invasive species are a key driver of the global biodiversity crisis, but the drivers of invasiveness, including the role of pathogens, remain debated. We investigated the genomic basis of invasiveness in Ambrosia artemisiifolia (common ragweed), introduced to Europe in the late 19th century, by resequencing 655 ragweed genomes, including 308 herbar...
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Species introduced through human-related activities beyond their native range, termed alien species, have various impacts worldwide. The IUCN Environmental Impact Classification for Alien Taxa (EICAT) is a global standard to assess negative impacts of alien species on native biodiversity. Alien species can also positively affect biodiversity (for i...
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Biological invasions offer a unique opportunity to investigate evolution over contemporary time‐scales. Rapid adaptation to local climates during range expansion can be a major determinant of invasion success, yet fundamental questions remain about its genetic basis. This study sought to investigate the genetic basis of climate adaptation in invasi...
Article
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Speciation is the process by which barriers to gene flow evolve between populations. Although we now know that speciation is largely driven by natural selection, knowledge of the agents of selection and the genetic and genomic mechanisms that facilitate divergence is required for a satisfactory theory of speciation. In this essay, we highlight thre...
Article
Diaporthe gulyae and D. helianthi cause Phomopsis stem canker of sunflower (Helianthus annuus L.) in the United States. Since Phomopsis stem canker did not gain importance until the disease epidemic in 2010, limited studies were conducted to understand the genetic basis of sunflower resistance to D. gulyae and D. helianthi. The objectives of this s...
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Extreme events, such as those caused by climate change, economic or geopolitical shocks, and pest or disease epidemics, threaten global food security. The complexity of causation, as well as the myriad ways that an event, or a sequence of events, creates cascading and systemic impacts, poses significant challenges to food systems research and polic...
Article
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The repeated, rapid and often pronounced patterns of evolutionary divergence observed in insular plants, or the ‘plant island syndrome’, include changes in leaf phenotypes, growth, as well as the acquisition of a perennial lifestyle. Here, we sequence and describe the genome of the critically endangered, Galápagos-endemic species Scalesia atractylo...
Preprint
Crop wild relatives represent valuable sources of alleles for crop improvement, including adaptation to climate change and emerging diseases. However, introgressions from wild relatives might have deleterious effects on desirable traits, including yield, due to linkage drag. Here we comprehensively analyzed the genomic and phenotypic impacts of wil...
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To what extent is evolution repeatable? Little is known about whether the evolution of hybrids is more (or less) repeatable than non‐hybrids. We used field experimental evolution in annual sunflowers (Helianthus) in Texas to ask the extent to which hybrid evolution is repeatable across environments compared to non‐hybrid controls. We created hybrid...
Article
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Seed and breeding zones are traditionally delineated based on local adaptation of phenotypic traits associated with climate variables, an approach requiring long‐term field experiments. In this study, we applied a landscape genomics approach to delineate seed and breeding zones for lodgepole pine. We used gradient forest (GF) model to select enviro...
Article
Full-text available
Recombination is critical both for accelerating adaptation and purging deleterious mutations. Chromosomal inversions can act as recombination modifiers that suppress local recombination in heterozygotes and thus, under some conditions, are predicted to accumulate such mutations. In this study, we investigated patterns of recombination, transposable...
Article
Full-text available
Introduction Numerous crops have transitioned to hybrid seed production to increase yields and yield stability through heterosis. However, the molecular mechanisms underlying heterosis and its stability across environments are not yet fully understood. Objectives This study aimed to (1) elucidate the genetic and molecular mechanisms underlying het...
Preprint
Full-text available
Adaptation is the central feature and leading explanation for the evolutionary diversification of life. Adaptation is also notoriously difficult to study in nature, owing to its complexity and logistically prohibitive timescale. We leverage extensive contemporary and historical collections of Ambrosia artemisiifolia —an aggressively invasive weed a...
Preprint
Full-text available
Biological invasions offer a unique opportunity to investigate evolution over contemporary time-scales. Rapid adaptation to local climates during range expansion can be a major determinant of invasion success, yet fundamental questions remain about its genetic basis. This study sought to investigate the genetic basis of climate adaptation in invasi...
Article
Population genomic analysis of hybrid zones is instrumental to our understanding of the evolution of reproductive isolation. Many temperate hybrid zones are formed by the secondary contact between two parental populations that have undergone postglacial range expansion. Here, we show that explicitly accounting for historical parental isolation foll...
Preprint
Full-text available
While invasive species are a key driver of the global biodiversity crisis, the drivers of invasiveness remain debated. To investigate the genomic basis of invasiveness in plants, we use the invasive weed Ambrosia artemisiifolia , introduced to Europe in the late 19 th century, resequencing 655 ragweed genomes, including 308 herbarium specimens coll...
Preprint
Full-text available
Oceanic archipelagos comprise multiple disparate environments over small geographic areas and are isolated from other biotas. These conditions have led to some of the most spectacular adaptive radiations, which have been key to our understanding of evolution, and offer a unique chance to characterise the genomic basis underlying rapid and pronounce...
Article
Full-text available
Variation in floral displays, both between and within species, has been long known to be shaped by the mutualistic interactions that plants establish with their pollinators. However, increasing evidence suggests that abiotic selection pressures influence floral diversity as well. Here, we analyse the genetic and environmental factors that underlie...
Preprint
Recombination is critical both for accelerating adaptation and for the purging of deleterious mutations. Chromosomal inversions can act as recombination modifiers that suppress local recombination and, thus, are predicted to accumulate such mutations. In this study, we investigated patterns of recombination, transposable element abundance and codin...
Article
Full-text available
Background and aims: The Arctic tundra, with its extreme temperatures and short growing season, is evolutionarily young and harbors one of the most species-poor floras on Earth. Arctic species often show little phenotypic and genetic divergence across circumpolar ranges. However, strong intraspecific postzygotic reproductive isolation (RI) in term...
Article
Full-text available
The emerging field of invasion genetics examines the genetic causes and consequences of biological invasions, but few study systems are available that integrate deep ecological knowledge with genomic tools. Here we report on the de novo assembly and annotation of a genome for the biennial herb Alliaria petiolata (M. Bieb.) Cavara & Grande (Brassica...
Article
Genome-scale studies have revealed divergent mRNA splicing patterns between closely related species or populations. However, it is unclear whether splicing differentiation is a simple byproduct of population divergence, or whether it also acts as a mechanism for reproductive isolation. We examined mRNA splicing in wild domesticated sunflower hybrid...
Article
Full-text available
We assembled a dual-layered biological network to study the roles of Resistance Gene Analogs (RGAs) in the resistance of sugarcane upon infection by the biotrophic fungus causing smut disease. Based on sugarcane-Arabidopsis orthology, the modeling used metabolic and protein-protein interaction data from A. thaliana (from KEGG and BioGRID databases)...
Chapter
Hybridisation between genetically divergent populations may lead to the formation of new evolutionary lineages. This may occur via duplication of a hybrid's chromosome complement (allopolyploid speciation) or by stabilisation of a fertile hybrid segregant (homoploid hybrid speciation). Although more common in plants, both modes of hybrid speciation...
Preprint
Full-text available
Variation in floral displays, both between and within species, has been long known to be shaped by the mutualistic interactions that plants establish with their pollinators. However, increasing evidence suggests that abiotic selection pressures influence floral diversity as well. Here we analyze the genetic and environmental factors that underlie p...
Article
The origins of geographic races in wide-ranging species are poorly understood. In Texas, the texanus subspecies of Helianthus annuus has long been thought to have acquired its defining phenotypic traits via introgression from a local congener, H. debilis, but previous tests of this hypothesis were inconclusive. Here we explore the origins of H. a....
Article
Full-text available
Mutations that provide environment-dependent selective advantages drive adaptive divergence among species. Many phenotypic differences among related species are more likely to result from gene expression divergence rather than from non-synonymous mutations. In this regard, cis-regulatory mutations play an important part in generating functionally s...
Preprint
Full-text available
Mutations that provide environment dependent selective advantages drive adaptive divergence among species. Many phenotypic differences among related species are more likely to result from gene expression divergence rather than from non-synonymous mutations. In this regard, cis-regulatory mutations play an important part in generating functionally s...
Preprint
Full-text available
The selection of new crops and the migration of crop areas are two key strategies for agriculture to cope with climate change and ensure food security in the coming years. However, both rely on the assumption that climate is a major factor determining crop distributions worldwide. Here, we show that the current global distributions of nine of twelv...
Preprint
Full-text available
Sunflower seeds (technically achenes) are characterized by a wide spectrum of sizes, shapes, and colors. These traits are genetically correlated with the branching plant architecture loci, which were introgressed into restorer lines to facilitate efficient hybrid production. To break this genetic correlation between branching and seed traits, high...
Preprint
Full-text available
The selection of new crops and the migration of crop areas are two key strategies for agriculture to cope with climate change and ensure food security in the coming years. However, both rely on the assumption that climate is a major factor determining crop distributions worldwide. Here, we show that the current global distributions of nine of twelv...
Article
Full-text available
Significance Temperate trees originating from warmer localities usually grow faster and acclimate to winter later than trees of the same species from colder localities. However, when trees are selected for faster growth, are climatically adaptive genes and traits affected? Our research demonstrates a simple, sensitive, broadly applicable, and elusi...
Preprint
Full-text available
The emerging field of invasion genetics examines the genetic causes and consequences of biological invasions, but few study systems are available that integrate deep ecological knowledge with genomic tools. Here we report on the de novo assembly and annotation of a genome for the biennial herb Alliaria petiolata (M. Bieb.) Cavara & Grande (Brassica...
Article
Full-text available
Invasive species represent excellent opportunities to study the evolutionary potential of traits important to success in novel environments. Although some ecologically important traits have been identified in invasive species, little is typically known about the genetic mechanisms that underlie invasion success in non-model species. Here, we use a...
Article
Full-text available
Approximately 10% of agricultural land is subject to periodic flooding, which reduces the growth, survivorship, and yield of most crops, reinforcing the need to understand and enhance flooding resistance in our crops. Here, we generated RNA-Seq data from leaf and root tissue of domesticated sunflower to explore differences in gene expression and al...
Article
Biological invasions are accelerating, and invasive species can have large economic impacts as well as severe consequences for biodiversity. During invasions, species can interact, potentially resulting in hybridization. Here, we examined two Cakile species, C. edentula and C. maritima (Brassicaceae), that co‐occur and may hybridize during range ex...
Preprint
Full-text available
Hybridization is widely acknowledged as an important mechanism of acquiring adaptive variation. In Texas, the sunflower Helianthus annuus subsp. texanus is thought to have acquired herbivore resistance and morphological traits via introgression from a local congener, H. debilis . Here we test this hypothesis using whole genome sequencing data from...
Article
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Compared to those of their parents, are the traits of first-generation (F1) hybrids typically intermediate, biased toward one parent, or mismatched for alternative parental phenotypes? To address this empirical gap, we compiled data from 233 crosses in which traits were measured in a common environment for two parent taxa and their F1 hybrids. We f...
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Trade-offs between performance and tolerance of abiotic and biotic stress have been proposed to explain both the success of invasive species and frequently observed size differences between native and introduced populations. Canada thistle seeds collected from across the introduced North American and the native European range were grown in benign a...
Chapter
Sunflowers are well-established model organisms in evolutionary biology; studies of them have made important contributions to our understanding of hybridization as an evolutionarily constructive process. Here, after introducing earlier foundational work, we review recent population genomics studies in this group. We discuss the origin of sunflowers...
Article
Full-text available
The Arctic is one of the most extreme terrestrial environments on the planet. Here we present the first chromosome‐scale genome assembly of a plant adapted to the high Arctic, Draba nivalis (Brassicaceae), an attractive model species for studying plant adaptation to the stresses imposed by this harsh environment. We used an iterative scaffolding st...
Preprint
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Alternative spicing is an integral part of gene expression in multicellular organisms that allows for diverse mRNA transcripts and proteins to be produced from a single gene. However, most existing analyses have focused on macro-evolution, with only limited research on splice site evolution over shorter term, micro-evolutionary time scales. Here we...
Article
Full-text available
Species often include multiple ecotypes that are adapted to different environments¹. However, it is unclear how ecotypes arise and how their distinctive combinations of adaptive alleles are maintained despite hybridization with non-adapted populations2,3,4. Here, by resequencing 1,506 wild sunflowers from 3 species (Helianthus annuus, Helianthus pe...
Preprint
Full-text available
Conspecific populations living in adjacent, but contrasting, microenvironments represent excellent systems for studying natural selection. These systems are valuable because gene flow maintains genetic homogeneity except at loci experiencing strong, divergent selection. A history of reciprocal transplant and common garden studies in such systems, a...
Article
Full-text available
Over the past 70 years, the world has witnessed extraordinary growth in crop productivity, enabled by a suite of technological advances, including higher yielding crop varieties, improved farm management, synthetic agrochemicals, and agricultural mechanization. While this “Green Revolution” intensified crop production, and is credited with reducing...
Article
Full-text available
The efficient management and distribution of experimental data from pre‐breeding projects is important to ensure uptake of valuable germplasm into breeding and research programmes. Being able to access and share this data in standard formats is essential in this process. The adoption of a common informatics platform for crops which may have limited...
Article
Both models and case studies suggest that chromosomal inversions can facilitate adaptation and speciation in the presence of gene flow by suppressing recombination between locally adapted alleles. Until recently, however, it has been laborious and time‐consuming to identify and genotype inversions in natural populations. Here we apply RAD sequencin...
Article
Full-text available
Modern breeding of sunflower ( Helianthus annuus L .), which started 100 years ago, increased the number and the diversity of cultivated forms. In addition, for more than 50 years, wild sunflower and other Helianthus species have been collected in North America where they all originated. Collections of both cultivated and wild forms are maintained...
Article
Full-text available
Chromosomal inversions have the potential to play an important role in evolution by reducing recombination between favorable combinations of alleles. Until recently, however, most evidence for their likely importance derived from dipteran flies, whose giant larval salivary chromosomes aided early cytogenetic studies. The widespread application of n...
Article
Full-text available
Mapping the chromosomal rearrangements between species can inform our understanding of genome evolution, reproductive isolation, and speciation. Here we present a novel algorithm for identifying regions of synteny in pairs of genetic maps, which is implemented in the accompanying R package, syntR. The syntR algorithm performs as well as previous ad...
Article
Full-text available
Resolving the origin of endangered taxa is an essential component of conservation. This information can be used to guide efforts of bolstering genetic diversity, and also enables species recovery and future evolutionary studies. Here, we used low-coverage whole genome sequencing to clarify the origin of Helianthus schweinitzii, an endangered tetrap...
Preprint
Full-text available
Both models and case studies suggest that chromosomal inversions can facilitate adaptation and speciation in the presence of gene flow by suppressing recombination between locally adapted alleles. Until recently, however, it has been laborious and time-consuming to identify and genotype inversions in natural populations. Here we apply RAD sequencin...
Article
Widespread mating between species creates mosaic genomes in Heliconius butterflies