Inferring genetic structure of European beech from observations of spectral phenotypes

Abstract

Biodiversity loss presents a growing threat to the global environment and requires systematic and spatially contiguous monitoring. Monitoring of within-species genetic variation, a key factor when assessing biodiversity loss, is laborious and could be complemented by remote observations of phenotypes allowing inferences about genetic variation. We studied genetic and phenotypic variations in the common European beech (Fagus sylvatica L.) derived from whole-genome sequences and spectral phenotypes of more than 200 individuals at 22 sites across the species' natural range. The spectral phenotypes were collected under standardized illumination/observation conditions from the same top-of-canopy leaves used for nuclear DNA extraction. We found that information from spectral phenotypes positively contributes to predictions of genetic structure using environmental variables across the sites in our dataset. We therefore propose that future spaceborne satellites with sufficient spectral and spatial resolution, repeatedly acquiring spectral phenotypes globally across species ranges, improve our ability to rapid and spatially contiguous monitoring of genetic diversity in trees.

Leaf spectroscopy reveals drought response variation inFagus sylvaticasaplings from across the species’ range

“…Visual inspection of the matrix and the PCA indicated the presence of three separate genetic clusters. These corresponded well with a study investigating genetic relatedness based on SNPs among beech trees from many of the same locations as those in this study Czyż et al (2023), although there is not a perfect overlap between the set of locations used by Czyż et al (2023) and those of our study (see Table 1). However, the difference in findings is largely due to the used settings (-mac 5) and the MAF being set to 0.05 in this study.…”

“…However, in an experiment with dozens, hundreds, or even thousands of individuals, as can be the case in ecological studies of species-level, intraspecific and genetic variation, and multiple measurement time points, leaf traits estimated from rapidly acquired spectral data may not only be more practical but also sufficient -or even advantageous, being better able to capture change and support sufficient replication. While the challenge is to meaningfully interpret spectral data, an increasing number of studies, including ours, support this (Cavender-Bares et al, 2016;Czyż et al, 2023;.…”

“…The majority of seed collections were sampled directly from branches of trees located in an area of 10 x 200 meters. However, we also conducted bulk collections from the ground not more than 1 km from a core area of trees used for leaf spectroscopy measurements in Czyż et al (2023). Seeds were placed in labelled containers per collection, and upon arrival, dried in mesh envelopes (1/collection) in closed plastic boxes under a gentle nitrogen flow.…”

“…Grinding was performed using 3 mm glass beads at 30 Hz for three min in a TissueLyser II (Qiagen). Plant DNA was then extracted using the Norgen Plant and Fungi DNA extraction kit (Norgen Biotek, Thorold, Ontario, Canada), and following the manufacturer's protocol with some optimization steps added to minimize RNA contamination and increase lysis, yield, and purity (described in detail in (Czyż et al, 2023)). The quality and quantity of the purified DNA was assessed with Qubit dsDNA HS Assay Kits (Thermo Fisher Scientific), a DS-11+ microvolume spectrophotometer (DeNovix, supplied by Labgene Scientific SA, Châtel-Saint-Denis, Switzerland), and agarose gel electrophoresis.…”