Genomic and common garden approaches yield complementary results for quantifying environmental drivers of local adaptation in rubber rabbitbrush, a foundational Great Basin shrub

Faske, Trevor M.; Agneray, Alison C.; Jahner, Joshua P.; Sheta, Lana M.; Leger, Elizabeth A.

doi:10.1111/eva.13323

Cited by 10 publications

(12 citation statements)

References 228 publications

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“…Pseudoroegneria spicata (St. Clair et al 2013;Massatti et al 2018) and Artemisia tridentata Richardson & Chaney 2018). These datasets can lead to genetic-environment analyses that synthesize genomic, trait, and environmental data, providing a comprehensive assessment of adaptive genetic variation and how the environment shapes these patterns (Temunovi c et al 2020;Faske et al 2021). As the set of species with genetic information grows, restoration programs will benefit by having more tools to meet restoration targets, such as plant communities with genetically appropriate restoration materials that ultimately support pollinator health relationships within ecosystems (Bucharova et al 2021).…”

Section: Discussionmentioning

confidence: 99%

“…mitigate the influence of invasive species. In addition, these data can guide seed collecting efforts by illuminating how adaptive genetic variation correlates to environmental gradients (Shryock et al 2015;Faske et al 2021) and by providing baseline information on how species are demographically connected (e.g. through migration) across their ranges (Massatti et al 2018); these biological characteristics of species are critical to consider as seed sources are selected for development into new NPMs using different strategies (e.g.…”

Section: Introductionmentioning

confidence: 99%

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Assessing population genomic structure and polyploidy: a crucial step for native plant restoration

Richardson

Massatti

Islam‐Faridi

et al. 2022

Restoration Ecology

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Establishing an effective restoration program requires baseline genetic information to make sound decisions for seed increase and transfer. For many plants this information is lacking, especially among native forbs that are critical for pollinator health. Erigeron speciosus is a widespread, perennial forb occupying montane environments in the western United States and Canada. This species is important in fostering pollinator diversity. Our study examines the population genetic patterns across the species range using reduced‐representation sequencing and surveys for genome duplication using flow cytometry and cytology. These genomic tools provide critical information for seed increase and seed transfer, necessary for restoration programs. Population genetic differentiation (FST) average was 0.13 and ranged from 0.05 to 0.24 among 23 collection sites. Model‐based Bayesian clustering supported a model with collection sites grouped into two populations, occupying distinct geographic regions of this species range. A genetic distance‐based neighbor‐joining tree also supported this division. Flow cytometry of 53 samples from 17 populations had 2C values that ranged from 1.7 to 3.6 pg with a mean 2C value of 2.3 pg. Putative triploids were found in two individuals from one collection site. The spatial distribution of genetic structure supports regionally based taxonomic descriptions of two varieties: speciosus in the North and macranthus in the South. This assessment of genetic structure and genome duplication describes an effective approach in developing baseline genetic information for restoration species, especially those species that may harbor complex taxonomy and polyploidy.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Assessing population genomic structure and polyploidy: a crucial step for native plant restoration

Richardson

Massatti

Islam‐Faridi

et al. 2022

Restoration Ecology

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“…We collected leaf material from 17 localities in the western Great Basin during the Fall of 2017 from a range of 20 to 39 plants per location (Figure 1a, Table 1). We sampled these locations because they hosted multiple native species that could potentially serve as restoration seed sources for this region; collections of other species from these locations are being used for additional restoration genetic studies (e.g., Agneray et al, 2022; Faske et al, 2021). Although A. thurberianum can hybridize with A. hymenoides , hybrids are easily distinguishable ( A. thurberianum has elongated ligules and pilose awns and the hybrids have a deciduous awn and relatively short ligules; Barkworth et al, 2007) and were not encountered in our sampling locations.…”

Section: Methodsmentioning

confidence: 99%

“…Climate environmental variables for each site were obtained from the PRISM database (https://prism.nacse.org) using the "get_ prism_normals" function from the R prism library (Hart et al, 2015) with a data range from 1981 to 2010 and an 800 m × 800 m resolution. Following Faske et al (2021), we converted monthly normals to estimates of potential evapotranspiration, actual evapotranspiration, soil water balance and climatic water deficit, which have been shown to effectively predict aspects of spatial and distributional variation across sagebrush steppe plant communities (Barga et al, 2018). Elevation data was acquired from the R library elevatr v 0.2.0 (Hollister & Shah, 2017).…”

Section: Influence Of Environmental Variation On Spatial Genetic Vari...mentioning

confidence: 99%

Fine‐scale spatial genetic structure in a locally abundant native bunchgrass (Achnatherum thurberianum) including distinct lineages revealed within seed transfer zones

Osuna‐Mascaró

Agneray

Galland

et al. 2023

Evolutionary Applications

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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.

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“…Sites were primarily mid-elevation, sagebrush steppe communities, with average annual precipitation between 237 and 384 mm and elevation ranging from 1395 to 2055 m (Appendix S1: Table S1; PRISM Climate Group, 2004). While it is not possible to know the duration of occupancy for each species in each site, or the degree of gene flow among populations for each species, genetic analyses for several species from these sites (Faske et al, 2021;Osuna-Mascar o et al, 2023) suggest moderate to strong isolation, and the opportunity for independent evolution, for even the most proximate populations (e.g., Peavine and Patagonia; Figure 1). We bulk-collected mature seeds for each species in each location from a minimum of 50 individual plants, with a minimum of 1 m separating individuals, between 1 June and 15 December of 2015.…”

Section: Species Selection and Seed Collectionmentioning

confidence: 99%

Does a history of population co‐occurrence predict plant performance, community productivity, or invasion resistance?

Agneray

Forister

Leger

2023

Ecology

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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.

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Genomic and common garden approaches yield complementary results for quantifying environmental drivers of local adaptation in rubber rabbitbrush, a foundational Great Basin shrub

Abstract: This is an open access article under the terms of the Creat ive Commo ns Attri bution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 10 publications

References 228 publications

Assessing population genomic structure and polyploidy: a crucial step for native plant restoration

Assessing population genomic structure and polyploidy: a crucial step for native plant restoration

Fine‐scale spatial genetic structure in a locally abundant native bunchgrass (Achnatherum thurberianum) including distinct lineages revealed within seed transfer zones

Does a history of population co‐occurrence predict plant performance, community productivity, or invasion resistance?

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