Ancestry variation in hybrid zones can reflect the causes and genetic basis of reproductive isolation and result in novel phenotypic variation with the potential for extended ecological effects. Junipers (Juniperus) are foundational tree species in many semi-arid landscapes of western North America and often hybridize in zones of secondary contact. Such hybridization can be ecologically significant in foundational tree species, due to the strong genetic control and ecological consequences of plant chemistry. We generated genetic and phytochemical data to analyze hybridization among Juniperus grandis, Juniperus occidentalis, and Juniperus osteosperma in western Nevada and the impact of hybridization on plant chemistry. We used population genomic data [9,125 single-nucleotide polymorphisms (SNPs), 326 individuals, and 25 populations] to quantify patterns of genetic variation across populations and species and to characterize ancestry variation in hybrids. Although populations within species showed little genetic differentiation, the parental species formed distinct, monophyletic lineages with clear phenotypic and ecological differences. Hybrids occupied intermediate environments, contained ancestry from all three parents, and were mainly F1 or backcross hybrids. Phytochemical data (gas chromatography-mass spectrometry; 163 terpenoid compounds) were likewise analyzed to understand the consequences of hybridization for plant chemistry. The parental species and hybrids displayed distinct phytochemical profiles; hybrids had higher chemical diversity overall, and hybrid terpenoid concentrations were often intermediate or exceeded the range of all the parental species. Our results illustrate that geography and environment shape hybrid ancestry for a syngameon involving three Juniperus species, and that admixture generates novel phytochemical variation likely to have ecological consequences.

Investigations into the genetic basis of color polymorphism have played a key role in our understanding of genetic architecture and the evolution of mating systems. Sulfur butterflies (Colias) have been models in this field, but also contain unsolved puzzles with respect to species boundaries and hybridization. We surveyed genomic variation across 5 years in a location where phenotypic intermediates between Colias eurytheme and C. eriphyle are observed, but ancestry variation of potential hybrids has not been quantified. Our results reveal individuals with hybrid ancestry roughly in proportion to the frequency of individuals of intermediate phenotype recorded in the wild. Individuals with hybrid ancestry were predominantly those with intermediate morphologies, but morphologically intermediate individuals were not always of hybrid origin, which raises alternative possibilities for the origin and maintenance of color variation in the system. Genomic regions differentiated between species are largely located on the Z chromosome, and we find more candidates on autosomes than in another Colias contact zone. The dynamics of hybridization in this system are highly variable through time, suggesting fertile avenues for future study into the maintenance of species boundaries in the face of temporally variable, climatically influenced, and pervasive hybridization.

ABSTRACT 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.

Understanding the evolutionary processes underlying range-wide genomic variation is critical to designing effective conservation and restoration strategies. Evaluating the influence of connectivity, demographic change and environmental adaptation for threatened species can be invaluable to proactive conservation of evolutionary potential. In this study, we assessed genomic variation across the range of Fraxinus latifolia, a foundational riparian tree native to western North America recently exposed to the invasive emerald ash borer (Agrilus planipennis; EAB). Over 1000 individuals from 61 populations were sequenced using reduced representation (ddRAD-seq) across the species' range. Strong population structure was evident along a latitudinal gradient, with population connectivity largely maintained along central valley river systems, and a centre of genetic diversity coinciding with major river systems central to the species' range. Despite evidence of connectivity, estimates of nucleotide diversity and effective population size were low across all populations, suggesting the patchy distribution of F. latifolia populations may impact its long-term evolutionary potential. Range-wide estimates of genomic offset, which indicate genomic change required to adjust to future climate projections, were greatest in the eastern and lowest in the southern portions of the species' range, suggesting the regional distribution of genomic variation may impact evolutionary potential longer-term. To preserve evolutionary capacity across populations needed for the development of breeding and restoration programmes, prioritising conservation of range-wide genomic diversity will provide a foundation for long-term species management.

Structural elements are widespread across genomes, but their complexity and role in repeatedly driving local adaptation remain unclear. In this work, we use phased genome assemblies to show that adaptive divergence in cryptic color pattern in a stick insect is repeatedly underlain by structural variation, but not a simple chromosomal inversion. We found that color pattern in populations of stick insects on two mountains is associated with translocations that have also been inverted. These translocations differ in size and origin on each mountain, but they overlap partially and involve some of the same gene regions. Moreover, this structural variation is subject to divergent selection and arose without introgression between species. Our results show how the origin of structural variation provides a mechanism for repeated bouts of adaptation.

Assessing the evolutionary potential of rare species with limited migration amidst ongoing climate change requires an understanding of patterns of genetic variation and local adaptation. In contrast to the large distributions and population sizes of most pines, Pinus muricata (bishop pine) occurs in a few isolated populations along coastal western North America and is listed as threatened by the IUCN. To quantify how current genetic variation is influenced by distribution and environment, we generated reduced representation DNA sequencing data for most extant populations of P. muricata (12 locations, 7828 loci). We assessed geographic variation in differentiation and diversity and used genetic-environment association (GEA) analyses to characterise the contribution of environmental variables to local adaptation and genetic structure. Based on these inferences, we quantified genomic offset as a relative estimate of potential maladaptation under mild (SSP1-2.6) and severe (SSP5-8.5) climate change scenarios across 2041-2060 and 2081-2100. Despite occurring in small, isolated populations, genetic diversity was not low in P. muricata. Population differentiation was, however, defined across a hierarchy of spatial scales, with stands generally forming genetically identifiable groups across latitude and environments. GEA analyses implicated temperature- and soil-related variables as most strongly contributing to local adaptation. Estimates of maladaptation to future climate varied non-linearly with latitude, increased with severity of projections and over time, and were predicted by increases in annual temperature. Our results suggest that isolation and local adaptation have shaped genetic variation among disjunct populations and that these factors may shape maladaptation risk under projected climate change.

Species with shared geographic history may show coevolution that reduces niche overlap and improves resource capture. Thus, plant communities assembled from sympatric source populations (shared locations) are predicted to be more productive and invasion resistant than those from allopatric sources (different locations), even with identical species composition. Using four native plant species from 15 environmentally similar locations across a broad region, we compared ecosystem function among communities assembled from allopatric or sympatric sources. Consistent with predictions of niche differentiation in co-occurring native plants, we observed more negative native plant-plant interactions in allopatric-sourced communities, and more positive interactions in sympatric-sourced communities. However, this did not translate into the predicted community-level outcomes. Unexpectedly, allopatric-sourced communities outperformed sympatric ones in all responses, with 34-42% more inflorescences, 17% higher survival, 21% longer growing season, 29-72% greater size, and after invasion, 70% less invader biomass. Two impactful native species grew larger and reproduced more when grown with allopatric neighbours, leading to greater invasion suppression, though the mechanism for this response is unknown. These findings challenge assumptions about the universal advantages of maintaining shared origins for community function and have broad implications for understanding plant competition and community assembly, as well as restoration of invaded ecosystems.

Many widespread plant taxa of western North America have diversified into phenotypically and genetically divergent lineages due to complex biogeographic histories across heterogeneous landscapes. Mosaic hybrid zones can form when geographically co-occurring, yet environmentally distinct, lineages cross-pollinate and form hybrids that occupy unique environmental niches absent of a geographic cline. This expands the total environmental space across which parental and hybrid individuals grow, resulting in larger, less fragmented geographic distributions. Here, we highlight hybridization mosaics across three study systems containing taxa critical to widespread plant communities in western North America: Ericameria nauseosa, Artemisia tridentata, and Sphaeralcea fendleri. The systems contain diverged taxa that co-occur across the landscape and hybridize readily. Hybridization among taxa has facilitated niche expansion into intermediate environments consistent with unique combinations of adaptive genetic variation, creating more continuity within each study system-study systems occupy ~820 to 270,000 km2 more geographic area by virtue of hybridization. Furthermore, hybrids are predicted to play important roles in future climates, as they may occupy 8 to 475% larger distributions compared to present. Convergent patterns signal mosaic hybridization as an underappreciated mechanism with broad ecological and evolutionary ramifications. Leveraging mosaic hybridization may assist the creation of restoration management plans that aim to mitigate the deleterious effects of habitat fragmentation on ecosystems in the context of climate change.

The formation of new species often involves the correlated divergence of multiple traits and genetic regions. However, the mechanisms by which such trait covariation builds up remain poorly understood. In this context, we consider two non-exclusive hypotheses. First, genetic covariance between traits can cause divergent selection on one trait to promote population divergence in correlated traits (a genetic covariation hypothesis). Second, correlated environmental pressures can generate selection on multiple traits, facilitating the evolution of trait complexes (an environmental covariation hypothesis). Here, we test these hypotheses using cryptic colouration (controlled by a likely incipient supergene) and chemical traits (i.e., cuticular hydrocarbons, CHCs) involved in desiccation resistance and mate choice in Timema cristinae stick insects. We first demonstrate that population divergence in colour-pattern is correlated with divergence in some (but not all) CHC traits. We show that correlated population divergence is unlikely to be explained by genetic covariation, as our analyses using genotyping-by-sequencing data reveal weak within-population genetic covariance between colour-pattern and CHC traits. In contrast, we find that correlated geographic variation in climate and host plant likely generates selection jointly on colour-pattern and some CHC traits. This supports the environmental covariation hypothesis, likely via the effects of two correlated environmental axes selecting on different traits. Finally, we provide evidence that misalignment between natural and sexual selection also contributes to patterns of correlated trait divergence. Our results shed light on transitions between phases of speciation by showing that environmental factors can promote population divergence in trait complexes, even without strong genetic covariance.

While 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 much-needed boost to genetic diversity while avoiding outbreeding depression or ecological mismatch. This decision is more daunting when taxonomy is unclear or debated: 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 several 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 (20 populations, ~15,000-25,000 SNPs). Complementary phylogenetic and population genetic analyses supported the distinctiveness of at least four bighorn sheep lineages at levels corresponding to subspecies, including California bighorn sheep. Additionally, analyses revealed hierarchical genetic structure within some lineages that correspond with major biogeographical regions. 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. ### Competing Interest Statement The authors have declared no competing interest.

The extent to which evolution is repeatable remains debated. Here, we study changes over time in the frequency of cryptic color-pattern morphs in 10 replicate long-term field studies of a stick insect, each spanning at least a decade (across 30 years of total data). We find predictable “up-and-down” fluctuations in stripe frequency in all populations, representing repeatable evolutionary dynamics based on standing genetic variation. A field experiment demonstrates that these fluctuations involve negative frequency-dependent natural selection (NFDS). These fluctuations rely on demographic and selective variability that pushes populations away from equilibrium, such that they can reliably move back toward it via NFDS. Last, we show that the origin of new cryptic forms is associated with multiple structural genomic variants such that which mutations arise affects evolution at larger temporal scales. Thus, evolution from existing variation is predictable and repeatable, but mutation adds complexity even for traits evolving deterministically under natural selection.

Declines in biodiversity generated by anthropogenic stressors at both species and population levels can alter emergent processes instrumental to ecosystem function and resilience. As such, understanding the role of biodiversity in ecosystem function and its response to climate perturbation is increasingly important, especially in tropical systems where responses to changes in biodiversity are less predictable and more challenging to assess experimentally. Using large-scale transplant experiments conducted at five neotropical sites, we documented the impacts of changes in intraspecific and interspecific plant richness in the genus Piper on insect herbivory, insect richness, and ecosystem resilience to perturbations in water availability. We found that reductions of both intraspecific and interspecific Piper diversity had measurable and site-specific effects on herbivory, herbivorous insect richness, and plant mortality. The responses of these ecosystem-relevant processes to reduced intraspecific Piper richness were often similar in magnitude to the effects of reduced interspecific richness. Increased water availability reduced herbivory by 4.2% overall, and the response of herbivorous insect richness and herbivory to water availability were altered by both intra- and interspecific richness in a site-dependent manner. Our results underscore the role of intraspecific and interspecific richness as foundations of ecosystem function and the importance of community and location-specific contingencies in controlling function in complex tropical systems.

Hybridization with introduced or invasive species is a major threat and driver of population declines in native salmonids. The rainbow trout ( Oncorhynchus mykiss ) is a major introduced and invasive species, often establishing entrenched naturalized populations. Here, we characterize population genetic variation of naturalized rainbow trout in a subset of Lake Tahoe tributaries to assess potential homing of rainbow trout to specific streams for spawning, thereby informing native Lahontan cutthroat trout ( Oncorhynchus clarkii henshawi ) reintroduction. Diploid, reproductively viable rainbow trout of commonly raised hatchery strains were stocked into Lake Tahoe from the late 1800s until the early 2000s by California and Nevada fish and wildlife agencies. Since 2007, however, triploid individuals comprise the bulk of rainbow trout planted. Despite dispersal from stocking locations across regions, our analyses revealed variation in population differentiation among tributaries, with individuals from spatially proximate streams clustering across multiple population genetic analyses. Although subtle, we detected evidence for genetic differentiation among tributaries from the southern, western, and northern regions, including surprising structure involving a single tributary. These results illustrate the extent of differentiation within and among streams and could inform possibilities for and implications of rainbow trout removal and Lahontan cutthroat trout reintroduction into its historical habitat.

Widely distributed plants of western North America experience divergent selection across environmental gradients, have complex histories shaped by biogeographic barriers and distributional shifts and often illustrate continuums of reproductive isolation. Rubber rabbitbrush (Ericameria nauseosa) is a foundational shrub species that occurs across diverse environments of western North America. Its remarkable phenotypic diversity is currently ascribed to two subspecies—Ericameria nauseosa nauseosa and Ericameria nauseosa consimilis—and 22 named varieties. To understand how genetic variation is partitioned across subspecies, varieties, and environments, we used high throughput sequencing of reduced representation libraries. We found clear evidence for divergence between the two subspecies, despite largely sympatric distributions. Numerous locations exhibiting admixed ancestry were not geographically localized but were widely distributed across a mosaic hybrid zone. The occurrence of hybrid and subspecific ancestries was strongly predicted by environmental variables as well as the proximity to major ecotones between ecoregions. Although this repeatability illustrates the importance of environmental factors in shaping reproductive isolation, variability in the prevalence of hybridization also indicates these factors likely differ across ecological contexts. There was mixed evidence for the evolutionary cohesiveness of varieties, but several genetically distinct and narrow endemic varieties exhibited admixed subspecific ancestries, hinting at the possibility for transgressive hybridization to contribute to phenotypic novelty and the colonization of new environments in E. nauseosa.

Abstract The extent to which evolution is repeatable is central to understanding the role of determinism and chance in the history of life, with implications for basic and applied science 1–5 . Real-time studies of evolutionary dynamics in replicated laboratory populations have revealed repeatable evolution by natural selection, but also a role for chance mutation 6–11 . In contrast to the laboratory, replicated, long-term studies of real-time evolution in the wild are rare. Such studies are required to help establish general principles of evolution and to compliment those based on the fossil record 5 , but are challenging to implement because time cannot simply be sped up with more effort. Here we demonstrate repeatable evolutionary changes in the frequency of cryptic color-pattern morphs of a stick-insect, using three decades of field data and 10 replicate studies that each study span at least a decade. We find predictable ‘up-and-down’ fluctuations in stripe frequency in all populations and demonstrate experimentally that these involve negative frequency-dependent selection (NFDS). Adding complexity, these fluctuations rely on demographic and selective variability that pushes populations away from equilibrium, such that they reliably move back towards it via NFDS. Finally, we show with genomic analyses that contingency in which mutations arise also affects crypsis at larger temporal and phylogenetic scales. Thus, evolution from existing variation is repeatable, but mutation adds complexity even for traits evolving deterministically under natural selection. The findings highlight how evolution can be better understood by the joint effects of selection and mutation than by either process in isolation.

Abstract The extent to which evolution is repeatable is central to understanding the role of determinism and chance in the history of life, with implications for basic and applied science 1–5. Real-time studies of evolutionary dynamics in replicated laboratory populations have revealed repeatable evolution by natural selection, but also a role for chance mutation 6–11. In contrast to the laboratory, replicated, long-term studies of real-time evolution in the wild are rare. Such studies are required to help establish general principles of evolution and to compliment those based on the fossil record5, but are challenging to implement because time cannot simply be sped up with more effort. Here we demonstrate repeatable evolutionary changes in the frequency of cryptic color-pattern morphs of a stick-insect, using three decades of field data and 10 replicate studies that each study span at least a decade. We find predictable ‘up-and-down’ fluctuations in stripe frequency in all populations and demonstrate experimentally that these involve negative frequency-dependent selection (NFDS). Adding complexity, these fluctuations rely on demographic and selective variability that pushes populations away from equilibrium, such that they reliably move back towards it via NFDS. Finally, we show with genomic analyses that contingency in which mutations arise also affects crypsis at larger temporal and phylogenetic scales. Thus, evolution from existing variation is repeatable, but mutation adds complexity even for traits evolving deterministically under natural selection. The findings highlight how evolution can be better understood by the joint effects of selection and mutation than by either process in isolation.

A history of species co-occurrence in plant communities is hypothesized to lead to greater niche differentiation, more efficient resource partitioning, and more productive, resistant communities as a result of evolution in response to biotic interactions. A similar question can be asked of co-occurring populations: do individual species or community responses differ when communities are founded with plants sharing a history of population co-occurrence (sympatric) or originating from different locations (allopatric)? Using shrub, grass, and forb species from six locations in the western Great Basin, North America, we compared establishment, productivity, reproduction, phenology, and resistance to invaders for experimental communities with either sympatric or allopatric population associations. Each community type was planted with six taxa in outdoor mesocosms, measured over three growing seasons, and invaded with the annual grass Bromus tectorum in the final season. For most populations, the allopatric or sympatric status of neighbors was not important. However, in some cases, it was beneficial for some species from some locations to be planted with allopatric neighbors, while others benefited from sympatric neighbors, and some of these responses had large effects. For instance, the Elymus population that benefited the most from allopatry grew 50% larger with allopatric neighbors than in single origin mesocosms. This response affected invasion resistance, as B. tectorum biomass was strongly affected by productivity and phenology of Elymus spp., as well as Poa secunda. Our results demonstrate that, while community composition can affect plant performance in semi-arid plant communities, assembling communities from sympatric populations is not sufficient to ensure high productivity and invasion resistance. Instead, we observed an idiosyncratic interaction between sampling effects and evolutionary history, with the potential for seed source of individual populations to have community-level effects.

Genome re-arrangements such as chromosomal inversions are often involved in adaptation. As such, they experience natural selection, which can erode genetic variation. Thus, whether and how inversions can remain polymorphic for extended periods of time remains debated. Here we combine genomics, experiments, and evolutionary modeling to elucidate the processes maintaining an inversion polymorphism associated with the use of a challenging host plant (Redwood trees) in Timema stick insects. We show that the inversion is maintained by a combination of processes, finding roles for life-history trade-offs, heterozygote advantage, local adaptation to different hosts, and gene flow. We use models to show how such multi-layered regimes of balancing selection and gene flow provide resilience to help buffer populations against the loss of genetic variation, maintaining the potential for future evolution. We further show that the inversion polymorphism has persisted for millions of years and is not a result of recent introgression. We thus find that rather than being a nuisance, the complex interplay of evolutionary processes provides a mechanism for the long-term maintenance of genetic variation.

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.