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As tree species vary extensively in genome size, complexity, and resource development, reduced representation methods have been increasingly employed for the generation of population genomic data. By allowing rapid marker discovery and genotyping for thousands of genomic regions in many individuals without requiring genomic resources, restriction site-associated DNA sequencing (RADseq) methods have dramatically improved our ability to bring population genomic perspectives to non-model trees. The rapid recent increase in studies of trees utilizing RADseq suggests that it is likely to become among the most common approaches for generating genome-wide data for a variety of applications. Here we provide a practical review of RADseq and its application to research areas of tree genetics. We briefly review RADseq laboratory methods and consider analytical approaches for assembly, variant calling, and bioinformatic processing. To guide considerations for study design, we use in silico analyses of eight available tree genomes to illustrate how expected marker number and density vary across laboratory approaches and genome sizes, and to consider the ability of RADseq designs to query coding regions. We review the empirical use of RADseq for different research objectives, considering its strengths and limitations. Many studies have used RADseq data to perform genome scans for selection, although limited marker density and linkage disequilibrium will often compromise its utility for such analyses. Regardless of this limitation, RADseq offers a powerful and inexpensive technique for generating genome-wide SNP data that can greatly contribute to research spanning phylogenetic and population genetic inference, linkage mapping, and quantitative genetic parameter estimation for tree genetics.

Population genetic analyses can evaluate how evolutionary processes shape diversity and inform conservation and management of imperiled species. Taimen ( Hucho taimen ), the world’s largest freshwater salmonid, is threatened, endangered, or extirpated across much of its range due to anthropogenic activity including overfishing and habitat degradation. We generated genetic data using high throughput sequencing of reduced representation libraries for taimen from multiple drainages in Mongolia and Russia. Nucleotide diversity estimates were within the range documented in other salmonids, suggesting moderate diversity despite widespread population declines. Similar to other recent studies, our analyses revealed pronounced differentiation among the Arctic (Selenge) and Pacific (Amur and Tugur) drainages, suggesting historical isolation among these systems. However, we found evidence for finer-scale structure within the Pacific drainages, including unexpected differentiation between tributaries and the mainstem of the Tugur River. Differentiation across the Amur and Tugur basins together with coalescent-based demographic modeling suggests the ancestors of Tugur tributary taimen likely diverged in the eastern Amur basin, prior to eventual colonization of the Tugur basin. Our results suggest the potential for differentiation of taimen at different geographic scales, and suggest more thorough geographic and genomic sampling may be needed to inform conservation and management of this iconic salmonid.

Analyses of the factors shaping genetic variation in widespread plant species are important for understanding the evolutionary history and local adaptation and have applied significance for guiding conservation and restoration decisions. Thurber's needlegrass (Achnatherum thurberianum) is a widespread, locally abundant grass that inhabits heterogeneous arid environments of western North America and is of restoration significance. It is a common component of shrubland steppe communities in the Great Basin Desert, where drought, fire, and invasive grasses have degraded natural communities. Using a reduced representation sequencing approach, we generated SNP data at 5677 loci across 246 individuals from 17 A. thurberianum populations spanning five previously delineated seed zones from the western Great Basin. Analyses revealed a pronounced population genetic structure, with individuals forming consistent geographical clusters across a variety of population genetic analyses and spatial scales. Low levels of genetic diversity within populations, as well as high population estimates of linkage disequilibrium and relatedness, were consistent with self‐fertilization as a contributor to population differentiation. Variance partitioning and partial redundancy analysis (pRDA) indicated local adaptation to environment as additionally influencing the spatial distribution of genetic variation. The environmental variables driving these results were similar to those implicated in recent genecological work which inferred local adaptation for seed zone delineation. Our analyses also revealed a complex evolutionary history of A. thurberianum in the Great Basin, where previously delineated seed zones contain distantly related populations. Our results indicate evolutionary history, mating system, and differentiation across distinct geographic and environmental scales have shaped genetic variation in A. thurberianum and illustrate how numerous aspects of population genetic variation might require consideration for restoration planning.

Although translocations can be effective for augmenting and restoring wild populations, they can disrupt native patterns of genetic structure, diversity, and local adaptation, thereby hampering conservation efforts. Managers must weigh potential costs and benefits of choosing well‐differentiated donor individuals that could confer a boost to genetic diversity while avoiding outbreeding depression or ecological mismatch. This decision is more daunting when taxonomy is unclear or debated. For example, bighorn sheep (Ovis canadensis) populations in the United States that have been managed as the “California” lineage (part of the formerly recognized subspecies O. c. californiana) originate from serial translocations sourced from populations in British Columbia, resulting in reduced genetic diversity and elevated risk of inbreeding. After research on skull shape and RFLP analysis of mtDNA failed to find support for that subspecies, some jurisdictions treated the California lineage as part of the Rocky Mountain subspecies (O. c. canadensis) and mixed individuals in subsequent translocations, in part to increase genetic diversity of bottlenecked populations. Yet, detailed genetic data addressing validity of those putative lineages were lacking. We reconstructed the genetic history of bighorn sheep by sampling the major putative subspecies or lineages, focusing on native (remnant) genetic variation, and generating high‐throughput DNA sequencing data ( 15,000–25,000 SNPs). Complementary phylogenetic and population genetic analyses supported the distinctiveness of four bighorn lineages at levels corresponding to subspecies. Our results confirm the genetic identity of the no longer putative California bighorn lineage, answering a question that puzzled geneticists and managers for decades. Moving forward, we recommend that managers (1) maintain the natural variation held in native populations by protecting them from intentional translocations or unintentional mixing with nearby populations; (2) prioritize within‐lineage translocations for population augmentation or repatriation to previously occupied regions; and (3) cautiously consider any translocations that would lead to mixing of distinct evolutionary lineages.

Hybridization is a common process that has broadly impacted the evolution of multicellular eukaryotes; however, how ecological factors influence this process remains poorly understood. Here, we report the findings of a 3-year recapture study of the Bryant’s woodrat (Neotoma bryanti) and desert woodrat (Neotoma lepida), two species that hybridize within a creosote bush (Larrea tridentata) shrubland in Whitewater, CA, USA. We used a genotype-by-sequencing approach to characterize the ancestry distribution of individuals across this hybrid zone coupled with Cormack–Jolly–Seber modeling to describe demography. We identified a high frequency of hybridization at this site with ~40% of individuals possessing admixed ancestry, which is the result of multigenerational backcrossing and advanced hybrid-hybrid crossing. F₁, F₂, and advanced generation hybrids had apparent survival rates similar to parental N. bryanti, while parental and backcross N. lepida had lower apparent survival rates and were far less abundant. Compared to bimodal hybrid zones where hybrids are often rare and selected against, we find that hybrids at Whitewater are common and have comparable survival to the dominant parental species, N. bryanti. The frequency of hybridization at Whitewater is therefore likely limited by the abundance of the less common parental species, N. lepida, rather than selection against hybrids.

Phytochemical variation among plant species is one of the most fascinating and perplexing features of the natural world and has implications for both human health and the functioning of ecosystems. A key area of research on phytochemical variation has focused on insects that feed on plants and the enormous diversity of plant-derived compounds that reduce or deter damage by insects. Empirical studies on the ecology and evolution of these chemically mediated plant–insect interactions have been guided by a long history of theoretical development. However, until recently, such theory was substantially limited by inadequate data, a situation that is rapidly changing as ecologists partner with chemists utilizing the latest technological advances. In this Review, we aim to facilitate the union of ecological theory with modern chemistry by discussing important theoretical frameworks for studying chemical ecology and outlining the steps by which hypotheses on insect–phytochemical interactions can be advanced using current methodologies and statistical approaches. We highlight unique approaches to isolation, synthesis, spectroscopy, metabolomics and genomics relevant to chemical ecology and describe future areas for research that will bring an unprecedented understanding of phytochemical variation. The union of theory in chemical ecology with modern methods in chemistry has enhanced our understanding of phytochemical variation among and within plants. This Review outlines these theoretical frameworks and approaches for hypothesis testing, with a focus on chemically mediated plant–insect interactions.

The decline and loss of species and genetic diversity as a result of anthropogenic change is occurring at an unprecedented rate, reshaping biodiversity and restructuring ecosystems. Population genetic variation is shaped by evolutionary processes and in turn determines the evolutionary potential of natural populations. Facilitated by recent improvements in DNA sequencing technologies, population genomic analyses can resolve patterns of genetic differentiation and evolutionary history, characterize the effects of evolutionary process on genome variation, and facilitate an understanding of how response to environmental variation may underlie local adaptation. Such analyses can inform conservation and restoration by establishing baseline patterns of genetic variation across the landscape, recognizing evolutionary significant units, sourcing propagules for restoration, and predicting species response to changing environmental conditions. Here, I applied high throughput DNA sequencing approaches to characterize the historical, spatial, and environmental factors shaping genetic variation in several systems of conservation and restoration significance. First, I investigated hierarchical genetic structure and evolutionary history of Hucho taimen (taimen, the world’s largest salmonid), listed as vulnerable by the International Union for Conservation of Nature (IUCN), across multiple river basins in Russia and Mongolia. Second, I characterized patterns of emergent population genetic structure of nonnative Oncorhynchus mykiss (rainbow trout) in the Lake Tahoe basin to inform reintroduction of the U.S. Endangered Species Act listed native cutthroat trout Oncorhynchus clarkii henshawi (Lahontan cutthroat trout). Rainbow trout have been widely introduced across the globe, stocked for >50 years into Lake Tahoe, and an understanding of population genetic structure may help inform strategies for successful native species reintroduction. Finally, I quantified spatial genetic structure, identified environmental variables potentially involved in local adaptation, and predicted variation in maladaptation under projected climate change across the range of Pinus muricata, a closed-cone pine occurring in a small number of isolated and disjunct stands along the coast of California, and also listed as vulnerable by the IUCN. Collectively, my research highlights the wide utility of population genomic analyses for taxa of conservation and restoration significance.

Analyses of the factors shaping spatial genetic structure in widespread plant species are important for understanding evolutionary history and local adaptation and have applied significance for guiding conservation and restoration decisions. Thurber needlegrass (Achnatherum thurberianum) is a widespread, locally abundant grass that inhabits heterogeneous arid environments of western North America and is of restoration significance. It is a common component of shrubland steppe communities in the Great Basin Desert, where drought, fire, and invasive grasses have degraded natural communities. Using a reduced representation sequencing approach, we generated SNP data at 5,677 loci across 246 individuals from 17 A. thurberianum populations spanning five previously delineated seed zones from the western Great Basin. Analyses revealed pronounced population genetic structure, with individuals forming consistent geographical clusters across a variety of population genetic analyses and spatial scales. Low levels of genetic diversity within populations, as well as high population estimates of linkage disequilibrium and inbreeding, were consistent with self-fertilization as a contributor to population differentiation. Moreover, variance partitioning and partial RDA indicated local adaptation to the environment as an additional factor influencing the spatial distribution of genetic variation. The environmental variables driving these results were similar to those implicated in recent genecological work which inferred local adaptation in order to delineate seed zones. However, our analyses also reveal a complex evolutionary history of A. thurberanium in the Great Basin, where previously delineated seed zones contain distantly related populations. Overall, our results indicate that numerous factors shape genetic variation in A. thurberianum and that evolutionary history, along with differentiation across distinct geographic and environmental scales, should be considered for conservation and restoration plans. Competing Interest Statement The authors have declared no competing interest.

Although translocations can be effective for augmenting and restoring wild populations, they can disrupt native patterns of genetic structure, diversity, and local adaptation, thereby hampering conservation efforts. Managers must weigh potential costs and benefits of choosing well-differentiated donor individuals that could confer a boost to genetic diversity while avoiding outbreeding depression or ecological mismatch. This decision is more daunting when taxonomy is unclear or debated. For example, bighorn sheep (Ovis canadensis) populations in the United States that have been managed as the “California” lineage (part of the formerly recognized subspecies O. c. californiana) originate from serial translocations sourced from populations in British Columbia, resulting in reduced genetic diversity and elevated risk of inbreeding. After research on skull shape and RFLP analysis of mtDNA failed to find support for that subspecies, some jurisdictions treated the California lineage as part of the Rocky Mountain subspecies (O. c. canadensis) and mixed individuals in subsequent translocations, in part to increase genetic diversity of bottlenecked populations. Yet detailed genetic data addressing validity of those putative lineages were lacking. We reconstructed the genetic history of bighorn sheep by sampling the major putative subspecies or lineages, focusing on native (remnant) genetic variation, and generating high-throughput DNA sequencing data (∼15,000-25,000 SNPs). Complementary phylogenetic and population genetic analyses supported the distinctiveness of four bighorn lineages at levels corresponding to subspecies. Our results confirm the genetic identity of the no longer putative California bighorn lineage, answering a question that puzzled geneticists and managers for decades. Moving forward, we recommend that managers 1) maintain the natural variation held in native populations by protecting them from intentional translocations or unintentional mixing with nearby populations; 2) prioritize withinlineage translocations for population augmentation or repatriation to previously occupied regions; and 3) cautiously consider any translocations that would lead to mixing of distinct evolutionary lineages.