Range-wide assessment of a SNP panel for individualization and geolocalization of bigleaf maple (Acer macrophyllum Pursh)

Illegal logging is a worldwide problem that degrades ecosystems, and even low-risk markets like the United States report ~1000 significant hardwood timber theft cases per year. Due to its high value, bigleaf maple (Acer macrophyllum Pursh) is a common target of timber theft in western North America....

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Autores principales:	Richard C. Cronn, Kristen N. Finch, Laura L. Hauck, Meaghan Parker-Forney, Brook G. Milligan, Jenélle Dowling, Adventure Scientists
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Timber poaching Bigleaf maple Acer macrophyllum Agena MassARRAY® Ecology QH540-549.5 Veterinary medicine SF600-1100
Acceso en línea:	https://doaj.org/article/da5e70bb7cb848eda828c29f5f315384
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spelling	oai:doaj.org-article:da5e70bb7cb848eda828c29f5f3153842021-11-12T04:49:14ZRange-wide assessment of a SNP panel for individualization and geolocalization of bigleaf maple (Acer macrophyllum Pursh)2666-937410.1016/j.fsiae.2021.100033https://doaj.org/article/da5e70bb7cb848eda828c29f5f3153842021-11-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S2666937421000329https://doaj.org/toc/2666-9374Illegal logging is a worldwide problem that degrades ecosystems, and even low-risk markets like the United States report ~1000 significant hardwood timber theft cases per year. Due to its high value, bigleaf maple (Acer macrophyllum Pursh) is a common target of timber theft in western North America. Using samples from Washington, USA, a single nucleotide polymorphism [SNP] assay was recently developed to facilitate timber poaching investigations in this species based on the single base extension Agena MassARRAY® genotyping system and 133 loci. Our study expands earlier evaluations to include the full 2000 km latitudinal range of bigleaf maple, using 1142 samples collected from California, USA to British Columbia, CAN. Populations in this study are equivalent to level 3 ecoregions, with sample sizes ranging from 28 (California Coast) to 191 (Washington Coast). Wood-derived DNA concentrations between 0.24 and 6 ng/μL yielded SNP call rates >92%, and DNA concentrations within this range did not influence genotyping call rates. DNA from different tissues showed a weak but significant difference in call rate, with DNA from wood showing a slightly higher call rate than leaves (99.4% vs 97.9%, respectively). Analysis of 108 sample replicates showed that missing genotypes occurred at 0.165% of all loci, and that allelic drop-outs and drop-ins each occurred at frequencies of 0.022% and 0.032%, respectively. Population-specific genotype profile probabilities for Pacific Northwest ecoregions were lower than 1.9×10−33; profile probabilities are higher (less powerful) in Californian trees due to lower variability across these SNP loci. Conversely, the geographic origin of trees from Southern Californian ecoregions could be predicted with lower error (8.5–11.7%) than trees from the Pacific Northwest (36–80%), based on random forest classification. This study provides a rich database for forensic individualization of bigleaf maple across its complete range in western North America.Richard C. CronnKristen N. FinchLaura L. HauckMeaghan Parker-ForneyBrook G. MilliganJenélle DowlingAdventure ScientistsElsevierarticleTimber poachingBigleaf mapleAcer macrophyllumAgena MassARRAY®EcologyQH540-549.5Veterinary medicineSF600-1100ENForensic Science International: Animals and Environments, Vol 1, Iss , Pp 100033- (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Timber poaching Bigleaf maple Acer macrophyllum Agena MassARRAY® Ecology QH540-549.5 Veterinary medicine SF600-1100
spellingShingle	Timber poaching Bigleaf maple Acer macrophyllum Agena MassARRAY® Ecology QH540-549.5 Veterinary medicine SF600-1100 Richard C. Cronn Kristen N. Finch Laura L. Hauck Meaghan Parker-Forney Brook G. Milligan Jenélle Dowling Adventure Scientists Range-wide assessment of a SNP panel for individualization and geolocalization of bigleaf maple (Acer macrophyllum Pursh)
description	Illegal logging is a worldwide problem that degrades ecosystems, and even low-risk markets like the United States report ~1000 significant hardwood timber theft cases per year. Due to its high value, bigleaf maple (Acer macrophyllum Pursh) is a common target of timber theft in western North America. Using samples from Washington, USA, a single nucleotide polymorphism [SNP] assay was recently developed to facilitate timber poaching investigations in this species based on the single base extension Agena MassARRAY® genotyping system and 133 loci. Our study expands earlier evaluations to include the full 2000 km latitudinal range of bigleaf maple, using 1142 samples collected from California, USA to British Columbia, CAN. Populations in this study are equivalent to level 3 ecoregions, with sample sizes ranging from 28 (California Coast) to 191 (Washington Coast). Wood-derived DNA concentrations between 0.24 and 6 ng/μL yielded SNP call rates >92%, and DNA concentrations within this range did not influence genotyping call rates. DNA from different tissues showed a weak but significant difference in call rate, with DNA from wood showing a slightly higher call rate than leaves (99.4% vs 97.9%, respectively). Analysis of 108 sample replicates showed that missing genotypes occurred at 0.165% of all loci, and that allelic drop-outs and drop-ins each occurred at frequencies of 0.022% and 0.032%, respectively. Population-specific genotype profile probabilities for Pacific Northwest ecoregions were lower than 1.9×10−33; profile probabilities are higher (less powerful) in Californian trees due to lower variability across these SNP loci. Conversely, the geographic origin of trees from Southern Californian ecoregions could be predicted with lower error (8.5–11.7%) than trees from the Pacific Northwest (36–80%), based on random forest classification. This study provides a rich database for forensic individualization of bigleaf maple across its complete range in western North America.
format	article
author	Richard C. Cronn Kristen N. Finch Laura L. Hauck Meaghan Parker-Forney Brook G. Milligan Jenélle Dowling Adventure Scientists
author_facet	Richard C. Cronn Kristen N. Finch Laura L. Hauck Meaghan Parker-Forney Brook G. Milligan Jenélle Dowling Adventure Scientists
author_sort	Richard C. Cronn
title	Range-wide assessment of a SNP panel for individualization and geolocalization of bigleaf maple (Acer macrophyllum Pursh)
title_short	Range-wide assessment of a SNP panel for individualization and geolocalization of bigleaf maple (Acer macrophyllum Pursh)
title_full	Range-wide assessment of a SNP panel for individualization and geolocalization of bigleaf maple (Acer macrophyllum Pursh)
title_fullStr	Range-wide assessment of a SNP panel for individualization and geolocalization of bigleaf maple (Acer macrophyllum Pursh)
title_full_unstemmed	Range-wide assessment of a SNP panel for individualization and geolocalization of bigleaf maple (Acer macrophyllum Pursh)
title_sort	range-wide assessment of a snp panel for individualization and geolocalization of bigleaf maple (acer macrophyllum pursh)
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/da5e70bb7cb848eda828c29f5f315384
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Range-wide assessment of a SNP panel for individualization and geolocalization of bigleaf maple (Acer macrophyllum Pursh)

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