Forensic validation of a SNP and INDEL panel for individualisation of timber from bigleaf maple (Acer macrophyllum Pursch)

Abstract

Illegal logging is one of the largest illicit trades in the world, with high profits and generally low risks of detection and prosecution. Timber identification presents problems for law enforcement as traditionally used forensic methods such as wood anatomy and dendrochronology are often unable to confidently match wood evidence to the remains of illegally felled trees. Here we have developed and validated a set of genetic markers for individualisation in bigleaf maple (Acer macrophyllum), a high value timber species often felled illegally in the USA. Using 128 single nucleotide polymorphisms and three insertion/deletion markers developed through massively parallel sequencing, 394 individuals were genotyped on the MassARRAY® iPLEX™ platform (Agena Bio-science™, San Diego, USA) to produce a population reference database for the species. We demonstrate that the resulting DNA assay is reliable, species specific, effective at low DNA concentrations (< 1 ng/μL) and suitable for application to timber samples. The P ID for the most common profile, calculated using an overall dataset level F ST -correction factor, was 1.785 × 10 −25 and P ID-SIB across all individuals (treated as a single population) was 2.496 × 10 -22 . The further development of forensic identification assays for timber species has the potential to deliver robust tools for improved detection and prosecution of illegal logging crimes as well as for the verification of legality in reputable supply chains.

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

“…Thirty-five to 72% of wood sourced in 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). Laws are in place to protect economically valuable tree species from overexploitation and promote sustainable practices (e.g., U.S. Lacey Act [2008]; European Union timber regulation [2010]; Australian Illegal Logging Prohibition Act [2012]; Japanese Clean Wood Act [2017]), but these remain difficult to enforce because of the sheer scale of illegal logging, and the challenge of identifying protected species and their countries of origin, especially after wood is transported from the site of harvest, processed, and enters commercial markets (Dormontt et al 2015(Dormontt et al , 2020Wiedenhoeft et al 2019).…”

“…Cedrela odorata and closely allied species will likely require multiple techniques for validation of taxonomy and origin because its wood lacks the anatomical features required for discrimination among species (Gasson 2011), and variation in wood chemistry does not vary in a manner that is geographically predictive (Paredes-Villanueva et al 2018). While methods for DNA extraction and recovery from wood are improving (Dumolin-Lapègue et al 1999;Asif and Cannon 2005;Rachmayanti et al 2006;Tnah et al 2012;Jiao et al 2012Jiao et al , 2018Yu et al 2017;Dormontt et al 2020), genetic markers of short length, such as single nucleotide polymorphisms (SNPs), are increasingly being used in wildlife forensics because they are suitable for low concentration, degraded DNA extracts (Ogden et al 2009). Here, we evaluate the power of SNPs to resolve geographic origin of C. odorata across much of its range in Central America and western South America.…”

Massively parallel sequencing is unlocking the potential of environmental trace evidence

“…Often species identification of a plant fragment is not sufficient to indicate provenance or substantiate a link between a suspect, victim or crime scene due to a high prevalence of that species within the region. While population genetics using microsatellites or SNPs can be used to distinguish between different populations of the same plant species, and has been successfully applied to the illegal timber trade [106,107], extensive assay development is required for each species of interest which is costly and not ideal in forensic practice where a broad range of species are encountered across different cases. Furthermore, plants in close proximity at the scales encountered in casework, may be very similar genetically and thus cannot be resolved using such DNA techniques.…”

Wildlife crime in Australia

“…Assigning a sample to a particular discrete population is becoming increasingly important and more frequently requested [ 39 ]. High profile examples include the determination of poaching hotspots and common areas where illegal logging [ 40 ] or poaching of elephant occurs [ 11 , 36 ]. Population assignment has been used largely for investigative purposes and is currently in the early stages of validation.…”