Predicting the geographic origin of Spanish Cedar (Cedrela odorata L.) based on DNA variation

Abstract

The legality of wood products often depends on their origin, creating a need for forensic tools that verify claims of provenance for wood products. The neotropical tree species Cedrela odorata (Spanish cedar) is economically valuable for its wood and faces threats of overexploitation. We developed a 140 SNP assay for geographic localization of C. odorata specimens. Target capture and short-read sequencing of 46 C. odorata specimens allowed us to identify 140 spatially informative SNPs that differentiate C. odorata specimens by latitude, temperature, and precipitation. We assessed the broad applicability of these SNPs on 356 specimens from eight Cedrela species, three tissue types, and a range of DNA mass inputs. Origin prediction error was evaluated with discrete and continuous spatial assignment methods focusing on C. odorata specimens. Discrete classification with random forests readily differentiated specimens originating in Central America versus South America (5.8% error), while uncertainty increased as specimens were divided into smaller regions. Continuous spatial prediction with SPASIBA showed a median prediction error of 188.7 km. Our results demonstrate that array SNPs and resulting genotypes accurately validate C. odorata geographic origin at the continental scale and show promise for country-level verification, but that finer-scale assignment likely requires denser spatial sampling. Our study underscores the important role of herbaria for developing genomic resources, and joins a growing list of studies that highlight the role of genomic tools for conservation of threatened species.

Spatiotemporal monitoring of the rare northern dragonhead (Dracocephalum ruyschiana, Lamiaceae) — SNP genotyping and environmental niche modeling herbarium specimens

“…As for the DNA stock concentration, the call rate (CR) seemed to be surprisingly little affected by time since collection when comparing modern with historical samples (Figure 2b ); our historical samples obtained a consistently high CR (mean = 99.71%, min = 95.65%, and max = 100%), which was approximately equal to that of the modern samples (mean = 99.89%, min = 94.57%, and max = 100%). In addition, historical materials of both animals and plants have been successfully genotyped using microfluidic SNP arrays (e.g., Finch et al, 2020 ; Johnston et al, 2013 ; Östergren et al, 2021 ). Compared with our results, however, these authors found much higher differences in the CR between historical and modern samples.…”

“…In the present study, we add a historic level to the species monitoring of the flowering plant species, Dracocephalum ruyschiana L. (northern dragonhead; Lamiaceae) by testing a microfluidic‐based SNP genotyping array on old herbarium specimens. This approach has recently been applied by others to historical materials of, for example, tropical tree species and salmon (Finch et al, 2020 ; Johnston et al, 2013 ; Östergren et al, 2021 ).…”

How Wood Identification Technologies Help Ensure Timber Legality in Indonesia

“…In recent years, many genetic approaches have been used to verify the origin and trade routes of protected wildlife species, including elephant ivory (Wasser et al 2004), sturgeon and paddlefish caviar (Ogden et al 2013), tigers (Kitpipit et al 2012), birds (Abe et al 2012), and fishes (Clemento et al 2014). Several marker sets have been developed and tested in plants, namely Gonystylus (Ogden et al 2008), Intsia (Lowe et al 2017), Swietenia (Degen et al 2013), Larix (Blanc-Jolivet et al 2018, and Cedrela (Finch et al 2020;Paredes-Villanueva et al 2020). Lowe and Cross (2011) reported that DNA technology can be broadly applied to trace the origin of timber (Figure 7), and analysis methods continue to become available and improved (Degen et al 2013).…”

SSR individual identification system construction and population genetics analysis for Chamaecyparis formosensis

“…The legality of wood products usually depends on their source 18 . SSR is also often used in genetic diversity and population structure analysis of species 14 , 19 , and can further predict species' geographic provenance and distribution.…”