Harnessing landscape genomics to identify future climate resilient genotypes in a desert annual

Abstract

Local adaptation features critically in shaping species responses to changing environments, complicating efforts to revegetate degraded areas. Rapid climate change poses an additional challenge that could reduce fitness of even locally sourced seeds in restoration. Predictive restoration strategies that apply seeds with favourable adaptations to future climate may promote long‐term resilience. Landscape genomics is increasingly used to assess spatial patterns in local adaption and may represent a cost‐efficient approach for identifying future‐adapted genotypes. To demonstrate such an approach, we genotyped 760 plants from 64 Mojave Desert populations of the desert annual Plantago ovata. Genome scans on 5,960 SNPs identified 184 potentially adaptive loci related to climate and satellite vegetation metrics. Causal modelling indicated that variation in potentially adaptive loci was not confounded by isolation by distance or isolation by habitat resistance. A generalized dissimilarity model (GDM) attributed spatial turnover in potentially adaptive loci to temperature, precipitation and NDVI amplitude, a measure of vegetation green‐up potential. By integrating a species distribution model (SDM), we find evidence that summer maximum temperature may both constrain the range of P. ovata and drive adaptive divergence in populations exposed to higher temperatures. Within the species’ current range, warm‐adapted genotypes are predicted to experience a fivefold expansion in climate niche by midcentury and could harbour key adaptations to cope with future climate. We recommend eight seed transfer zones and project each zone into its relative position in future climate. Prioritizing seed collection efforts on genotypes with expanding future habitat represents a promising strategy for restoration practitioners to address rapidly changing climates.

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

“…While whole genome resequencing can be costly when applied to large numbers of individuals, reduced representation approaches (e.g., GBS, RADseq; Andrews et al, 2016;Parchman et al, 2018) can rapidly and inexpensively assay tens of thousands of genetic variants in a large number of individuals without relying on prior genomic resources. These approaches have shown utility for describing fine-scale population structure and evolutionary history relevant to evolutionary potential in changing environments (Massatti, Doherty, et al, 2018;Shryock et al, 2021), and for characterizing the genetic context and consequences of restoration efforts (Bragg et al, 2020;Dittberner et al, 2019;Jahner et al, 2019;Williams et al, 2014). Reduced representation sequencing has also increasingly been used to analyze the genomic signature and environmental drivers of local adaptation in non-model organisms (Hendricks et al, 2018;Savolainen et al, 2013) or in the context of restoration (Flanagan et al, 2018;Harrisson et al, 2014;Hoffmann et al, 2015).…”

“…Genetic differentiation among populations can reflect independent evolutionary histories across variable ecological contexts, and genetic diversity itself is often used as a proxy for evolutionary potential which can predict population viability or restoration outcomes (e.g., Reynolds et al, 2012;Wernberg et al, 2018). To date, most inferences regarding local adaptation for restoration have used phenotypic data from common gardens (Baughman et al, 2019;Kawecki & Ebert, 2004;Langlet, 1971), but more recent efforts have used DNA sequencing data for this purpose (e.g., Massatti & Knowles, 2020;Shryock et al, 2017Shryock et al, , 2021. High throughput sequencing has improved the ability to characterize the finescale genetic structure of populations (e.g., Larroque et al, 2019;Novembre et al, 2008;Wang et al, 2013), to describe the genetic signatures of adaptation (Cao et al, 2011;Li et al, 2018;McKown et al, 2014), and to link environmental variation to evolutionary processes (Forester et al, 2016;Storfer et al, 2018).…”

New developments in the field of genomic technologies and their relevance to conservation management

“…Genomic knowledge of specific genes can not only be used to identify specific variants of interest (e.g. Shryock et al 2021) but the genetic code can also be altered by targeted changes of an organism's genome, also known as genome editing (see glossary). This approach encompasses a wide variety of tools using site-specific enzymes.…”

How to increase the supply of native seed to improve restoration success: the US native seed development process

“…Newer technologies, such as next‐generation sequencing genetic techniques, may also support the creation of seed transfer zones that not only match species' patterns of adaptation to present and future landscapes (e.g. Shryock et al 2020), but can protect natural patterns of genetic diversity (Massatti & Knowles 2020).…”