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.
Highlights
Biodiversity loss is of global concern, and is due in part to deforestation and high consumer demand for wood and wood products (Nellemann 2012; Elias 2012; van Zonneveld et al 2018)
We identified single nucleotide polymorphisms (SNPs) showing the highest differentiation in allele frequencies (FST) (Weir and Cockerham 1984) for groups based on latitude (LAT; decimal degrees), mean annual temperature (MAT; °C × 10), and annual precipitation (AP; mm)
We demonstrated that SNPs have the power to at least partially resolve the geographic origin of C. odorata across much of its range in Central America and western South America, and we present results from discrete classification of geographic origin with random forests (Breiman 2001) and continuous spatial prediction with SPASIBA (Guillot et al 2016)
Summary
Biodiversity loss is of global concern, and is due in part to deforestation and high consumer demand for wood and wood products (Nellemann 2012; Elias 2012; van Zonneveld et al 2018). Forests of Central and South America (or “neotropical” forests) face the largest threat because they support the most terrestrial biodiversity, with an estimated 16,000 tree species contained within the Amazon rainforest alone (Pennington et al 2015; Pennington and Lavin 2016; Dick and Pennington 2019). Extended author information available on the last page of the article the Amazon is thought to be acquired from illegal logging (Saunders and Reeve 2014), and illegal logging accounts for 50–90% of forestry activities across tropical forests globally (Hoare 2015; Sheikh et al 2019). Spanish cedar (Cedrela odorata L.; Meliaceae) and congeners are among the most valuable neotropical
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