The rate of global climate change is projected to outpace the ability of many natural populations and species to adapt. Assisted migration (AM), which is defined as the managed movement of climate‐adapted individuals within or outside the species ranges, is a conservation option to improve species' adaptive capacity and facilitate persistence. Although conservation biologists have long been using genetic tools to increase or maintain diversity of natural populations, genomic techniques could add extra benefit in AM that include selectively neutral and adaptive regions of the genome. In this review, we first propose a framework along with detailed procedures to aid collaboration among scientists, agencies, and local and regional managers during the decision‐making process of genomics‐guided AM. We then summarize the genomic approaches for applying AM, followed by a literature search of existing incorporation of genomics in AM across taxa. Our literature search initially identified 729 publications, but after filtering returned only 50 empirical studies that were either directly applied or considered genomics in AM related to climate change across taxa of plants, terrestrial animals, and aquatic animals; 42 studies were in plants. This demonstrated limited application of genomic methods in AM in organisms other than plants, so we provide further case studies as two examples to demonstrate the negative impact of climate change on non‐model species and how genomics could be applied in AM. With the rapidly developing sequencing technology and accumulating genomic data, we expect to see more successful applications of genomics in AM, and more broadly, in the conservation of biodiversity.

• Premise of the study: Hybridization has played an important role in the evolution and ecological adaptation of diploid and polyploid plants. Artemisia tridentata (Asteraceae) tetraploids are extremely widespread and of great ecological importance. These tetraploids are often taxonomically identified as A. tridentata subsp. wyomingensis or as autotetraploids of diploid subspecies tridentata and vaseyana. Few details are available as to how these tetraploids are formed or how they are related to diploid subspecies.• Methods: We used amplicon sequencing to assess phylogenetic relationships among three recognized subspecies: tridentata, vaseyana, and wyomingensis. DNA sequence data from putative genes were pyrosequenced and assembled from 329 samples. Nucleotide diversity and putative haplotypes were estimated from the high‐read coverage. Phylogenies were constructed from Bayesian coalescence and neighbor‐net network analyses.• Key results: Analyses support distinct diploid subspecies of tridentata and vaseyana in spite of known hybridization in ecotones. Nucleotide diversity estimates of populations compared to the total diversity indicate the relationships are predominately driven by a small proportion of the amplicons. Tetraploids, including subspecies wyomingensis, are polyphyletic occurring within and between diploid subspecies groups.• Conclusions: Artemisia tridentata is a species comprising phylogenetically distinct diploid progenitors and a tetraploid complex with varying degrees of phylogenetic and morphological affinities to the diploid subspecies. These analyses suggest tetraploids are formed locally or regionally from diploid tridentata and vaseyana populations via autotetraploidy, followed by introgression between tetraploid groups. Understanding the phylogenetic vs. ecological relationships of A. tridentata subspecies will have bearing on how to restore these desert ecosystems.

Background: Big sagebrush (Artemisia tridentata) is one of the most widely distributed and ecologically important shrub species in western North America. This species serves as a critical habitat and food resource for many animals and invertebrates. Habitat loss due to a combination of disturbances followed by establishment of invasive plant species is a serious threat to big sagebrush ecosystem sustainability. Lack of genomic data has limited our understanding of the evolutionary history and ecological adaptation in this species. Here, we report on the sequencing of expressed sequence tags (ESTs) and detection of single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers in subspecies of big sagebrush.Results: cDNA ofA. tridentatasspp.tridentataandvaseyanawere normalized and sequenced using the 454 GS FLX Titanium pyrosequencing technology. Assembly of the reads resulted in 20,357 contig consensus sequences in ssp.tridentataand 20,250 contigs in ssp.vaseyana. A BLASTx search against the non-redundant (NR) protein database using 29,541 consensus sequences obtained from a combined assembly resulted in 21,436 sequences with significant blast alignments (≤ 1e^-15). A total of 20,952 SNPs and 119 polymorphic SSRs were detected between the two subspecies. SNPs were validated through various methods including sequence capture. Validation of SNPs in different individuals uncovered a high level of nucleotide variation in EST sequences. EST sequences of a third, tetraploid subspecies (ssp.wyomingensis) obtained by Illumina sequencing were mapped to the consensus sequences of the combined 454 EST assembly. Approximately one-third of the SNPs between sspp.tridentataandvaseyanaidentified in the combined assembly were also polymorphic within the two geographically distant ssp.wyomingensissamples.Conclusion: We have produced a large EST dataset forArtemisia tridentata, which contains a large sample of the big sagebrush leaf transcriptome. SNP mapping among the three subspecies suggest the origin of ssp.wyomingensisvia mixed ancestry. A large number of SNP and SSR markers provide the foundation for future research to address questions in big sagebrush evolution, ecological genetics, and conservation using genomic approaches.

Genetic resources have to be managed appropriately to mitigate the impact of climate change. For many wildland plants, conservation will require knowledge of the climatic factors affecting intraspecific genetic variation to minimize maladaptation. Knowledge of the interaction between traits and climate can focus management resources on vulnerable populations, provide guidance for seed transfer, and enhance fitness and resilience under changing climates. In this study, traits of big sagebrush (Artemisia tridentata) were examined among common gardens located in different climates. We focus on two subspecies,wyomingensisandtridentata, that occupy the most imperiled warm‐dry spectrum of the sagebrush biome. Populations collected across the sagebrush biome were recorded for flower phenology and survival. Mixed‐effects models examined each trait to evaluate genetic variation, environmental effects, and adaptive breadth of populations. Climate variables derived from population‐source locations were significantly associated with these traits (P < 0.0001), explaining 31% and 11% of the flower phenology and survival variation, respectively. To illustrate our model and assess variability in prediction, we examine fixed and focal point seed transfer approaches to map contemporary and climate model ensemble projections in two different regions of the sagebrush biome. A comparison of seed transfer areas predicts that populations from warmer climates become more prevalent, replacing colder‐adapted populations by mid‐century. However, these warm‐adapted populations are often located along the trailing edge, margins of the species range predicted to be lost due to a contraction of the climatic niche. Management efforts should focus on the collection and conservation of vulnerable populations and prudent seed transfer to colder regions where these populations are projected to occur by mid‐century. Our models provide the foundation to develop an empirical, climate‐based seed transfer system for current and future restoration of big sagebrush.