Using environmental and geographic data to optimize ex situ collections and preserve evolutionary potential

Abstract

Maintenance of biodiversity through seed banks and botanical gardens, where the wealth of species' genetic variation may be preserved ex situ, is a major goal of conservation. However, challenges can persist in optimizing ex situ collections if trade-offs exist among cost, effort, and conserving species evolutionary potential, particularly when genetic data are not available. We evaluated the genetic consequences of population preservation informed by geographic (isolation by distance [IBD]) and environmental (isolation by environment [IBE]) distance for ex situ collections for which population provenance is available. We used 19 genetic and genomic data sets from 15 plant species to assess the proportion of population genetic differentiation explained by geographic and environmental factors and to simulate ex situ collections prioritizing source populations based on pairwise geographic distance, environmental distance, or both. Specifically, we tested the impact prioritizing sampling based on these distances may have on the capture of neutral, functional, or putatively adaptive genetic diversity and differentiation. Individually, IBD and IBE explained limited population genetic differences across all 3 genetic marker classes (IBD, 10-16%; IBE, 1-5.5%). Together, they explained a substantial proportion of population genetic differences for functional (45%) and adaptive (71%) variation. Simulated ex situ collections revealed that inclusion of IBD, IBE, or both increased allelic diversity and genetic differentiation captured among populations, particularly for loci that may be important for adaptation. Thus, prioritizing population collections based on environmental and geographic distance data can optimize genetic variation captured ex situ. For the vast majority of plant species for which there is no genetic information, these data are invaluable to conservation because they can guide preservation of genetic variation needed to maintain evolutionary potential within collections.

Reduced representation sequencing to understand the evolutionary history of Torrey pine (Pinus torreyana Parry) with implications for rare species conservation

“…Conservation biology aims to preserve rare species and determine the appropriate management strategies necessary for long-term persistence and maintenance of evolutionary potential (Di Santo & Hamilton, 2020; Ralls et al, 2018; Swarts, Sinclair, Krauss, & Dixon, 2009; Young, Brown, & Zich, 1999). Rare species may have reduced effective population sizes (Ne), impeding populations’ ability to adapt to change (e.g., Ne < 1000) or increasing probability of inbreeding (e.g., Ne < 100) (Frankham, Bradshaw, & Brook, 2014), ultimately increasing the risk of local extirpation.…”

Testing for evolutionary change in restoration: a genomic comparison betweenex situ, native and commercial seed sources ofHelianthus maximiliani

“…Ex situ seed collections aim to preserve extant genetic variation that may be incorporated into restoration or breeding programs in the future (Hamilton 1994, Li & Pritchard 2009). Both commercial and ex situ seed collections aim to maximize genetic diversity while maintaining locally adaptive genetic variation across space and time (DiSanto & Hamilton 2020). Consequently, genomic comparisons between contemporary wild populations, commercially produced material, and ex situ conservation collections provide an ideal means to evaluate evolution of seed material maintained for conservation and restoration (Robichauxet al 1997, Schoen & Brown 1993, Taft et al 2020).…”

“…Sampling effects can generate substantial genomic differences across seed sources with potential lasting impacts to conservation goals and restoration outcomes (DiSanto & Hamilton 2020, Diwan et al 1995, Franco et al 2005, Hamilton 1994). The genomic effects of sampling correspond to those found following population bottlenecks, including a reduction in effective population sizes (N e ) (Leberg 1992, Wright 1938), making this a useful metric to compare across populations when quantifying the effects of sampling.…”

Seed morphological traits as a tool to quantify variation maintained inex situcollections: a case study inPinus torreyana(Parry)

“…However, the cost and logistical constraints associated with seed collection pose a significant challenge. Given this challenge, identifying means to optimize ex situ sampling efforts are needed (Hoban and Schlarbaum, 2014;Di Santo and Hamilton, 2020). One approach may be to use the distribution of trait variation existing within contemporary ex situ collections as a proxy for quantifying standing genetic variation within and among populations.…”

“…However, the cost and logistical constraints associated with seed collection pose a significant challenge. Given this challenge, means are needed to optimize ex situ sampling efforts (Hoban and Schlarbaum 2014; Di Santo and Hamilton 2020).…”