DNA barcodes for ecology, evolution, and conservation

Kress, W. John; García‐Robledo, Carlos; Uriarte, María; Erickson, David L.

doi:10.1016/j.tree.2014.10.008

Cited by 440 publications

(366 citation statements)

References 95 publications

(134 reference statements)

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“…Our focus was to develop a genotyping tool specifically for predominant white oaks of the North Americas. Given the difficulties of phylogenetic inference in forest trees and oaks in particular, our targeted barcode is not an appropriate tool for community phylogenetics or biodiversity discovery (Kress, García‐Robledo, Uriarte, & Erickson, 2015; Kress et al., 2009) or inferring phylogenetic relationships among large numbers of individuals within diverse clades (The Global Carex Group et al., 2016). It is, however, appropriate to investigations of species identity and hybridization among white oaks of eastern North American deciduous forests.…”

Section: Discussionmentioning

confidence: 99%

A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting

Fitzek

Delcamp

Guichoux

et al. 2018

Ecology and Evolution

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DNA barcoding has proved difficult in a number of woody plant genera, including the ecologically important oak genus Quercus. In this study, we utilized restrictionsite‐associated DNA sequencing (RAD‐seq) to develop an economical single nucleotide polymorphism (SNP) DNA barcoding system that suffices to distinguish eight common, sympatric eastern North American white oak species. Two de novo clustering pipelines, PyRAD and Stacks, were used in combination with postclustering bioinformatic tools to generate a list of 291 potential SNPs, 80 of which were included in a barcoding toolkit that is easily implemented using MassARRAY mass spectrometry technology. As a proof‐of‐concept, we used the genotyping toolkit to infer potential hybridization between North American white oaks transplanted outside of their native range (Q. michauxii, Q. montana, Q muehlenbergii/Q. prinoides, and Q. stellata) into a horticultural collection surrounded by natural forests of locally native trees (Q. alba and Q. macrocarpa) in the living collection at The Morton Arboretum (Lisle, IL, USA). Phylogenetic and clustering analyses suggested low rates of hybridization between cultivated and native species, with the exception of one Q. michauxii mother tree, the acorns of which exhibited high admixture from either Q. alba or Q. stellata and Q. macrocarpa, and a hybrid between Q. stellata that appears to have backcrossed almost exclusively to Q. alba. Together, RAD‐seq and MassARRAY technologies allow for efficient development and implementation of a multispecies barcode for one of the more challenging forest tree genera.

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Section: Discussionmentioning

confidence: 99%

A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting

Fitzek

Delcamp

Guichoux

et al. 2018

Ecology and Evolution

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“…2003a; Kress et al. 2014). DNA barcoding is generally presented as a means to automate the recognition of previously defined taxa, and a 648‐base pair region of the cytochrome c oxidase subunit one (COX1) gene has proven highly effective in correctly distinguishing among metazoan species (Hebert et al.…”

Section: Introductionmentioning

confidence: 99%

Mitonuclear coevolution as the genesis of speciation and the mitochondrial DNA barcode gap

Hill

2016

Ecology and Evolution

149

178

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Mitochondrial genes are widely used in taxonomy and systematics because high mutation rates lead to rapid sequence divergence and because such changes have long been assumed to be neutral with respect to function. In particular, the nucleotide sequence of the mitochondrial gene cytochrome c oxidase subunit 1 has been established as a highly effective DNA barcode for diagnosing the species boundaries of animals. Rarely considered in discussions of mitochondrial evolution in the context of systematics, speciation, or DNA barcodes, however, is the genomic architecture of the eukaryotes: Mitochondrial and nuclear genes must function in tight coordination to produce the complexes of the electron transport chain and enable cellular respiration. Coadaptation of these interacting gene products is essential for organism function. I extend the hypothesis that mitonuclear interactions are integral to the process of speciation. To maintain mitonuclear coadaptation, nuclear genes, which code for proteins in mitochondria that cofunction with the products of mitochondrial genes, must coevolve with rapidly changing mitochondrial genes. Mitonuclear coevolution in isolated populations leads to speciation because population‐specific mitonuclear coadaptations create between‐population mitonuclear incompatibilities and hence barriers to gene flow between populations. In addition, selection for adaptive divergence of products of mitochondrial genes, particularly in response to climate or altitude, can lead to rapid fixation of novel mitochondrial genotypes between populations and consequently to disruption in gene flow between populations as the initiating step in animal speciation. By this model, the defining characteristic of a metazoan species is a coadapted mitonuclear genotype that is incompatible with the coadapted mitochondrial and nuclear genotype of any other population.

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“…For instance, the species concept is very elusive for the microbial world, where the strain/isolate definition might be more practically helpful to allow exhaustive description of phenotypic features (Ahn, Chai, and Pan 2014;Caro-Quintero and Konstantinidis 2012). This can be potentially addressed through specific and progressively advanced molecular methods such as DNA barcoding and metagenomics (Gilbert and Dupont 2011;Kress et al 2015;Shokralla et al 2014;Simon and Daniel 2011).…”

Section: Major Challenges For the Global Implementation Of Ebvsmentioning

confidence: 99%

“…It also includes molecular biodiversity data (e.g. barcoding, meta-barcoding and metagenomic approaches based on next-generation sequencing technologies and bioinformatic data analysis) which increasingly allow species or strain identification at a high rate and accuracy, even in the most remote and extreme ecosystems (Gilbert and Dupont 2011;Kress et al 2015;Shokralla et al 2014;Simon and Daniel 2011). Workshop 3 will be centred on the EBV class 'Species traits' which can include phenology, plant functional traits, animal body mass, natal dispersal distances or migratory behaviour (Pereira et al 2013).…”

Section: Scientific Content and Workhops Of Globis-bmentioning

confidence: 99%

Towards global interoperability for supporting biodiversity research on essential biodiversity variables (EBVs)

et al. 2015

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General rightsIt is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulationsIf you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: http://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. Essential biodiversity variables (EBVs) have been proposed by the Group on Earth Observations Biodiversity Observation Network (GEO BON) to identify a minimum set of essential measurements that are required for studying, monitoring and reporting biodiversity and ecosystem change. Despite the initial conceptualisation, however, the practical implementation of EBVs remains challenging. There is much discussion about the concept and implementation of EBVs: which variables are meaningful; which data are needed and available; at which spatial, temporal and topical scales can EBVs be calculated; and how sensitive are EBVs to variations in underlying data? To advance scientific progress in implementing EBVs we propose that both scientists and research infrastructure operators need to cooperate globally to serve and process the essential large datasets for calculating EBVs. We introduce GLOBIS-B (GLOBal Infrastructures for Supporting Biodiversity research), a global cooperation funded by the Horizon 2020 research and innovation framework programme of the European Commission. The main aim of GLOBIS-B is to bring together biodiversity scientists, global research infrastructure operators and legal interoperability experts to identify the research needs and infrastructure services underpinning the concept of EBVs. The project will facilitate the multi-lateral cooperation of biodiversity research infrastructures worldwide and identify the required primary data, analysis tools, methodologies and legal and technical bottlenecks to develop an agenda for research and infrastructure development to compute EBVs. This requires development of standards, protocols and workflows that are 'self-documenting' and openly shared to allow the discovery and analysis of data across large spatial extents and different temporal resolutions. The interoperability of existing biodiversity research infrastructures will be crucial for integrating the necessary biodiversity data to calculate EBVs, and to advance our ability to assess progress towards the Aichi targets for 2020 of the Convention on Biological Diversity (CBD).

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DNA barcodes for ecology, evolution, and conservation

Cited by 440 publications

References 95 publications

A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting

A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting

Mitonuclear coevolution as the genesis of speciation and the mitochondrial DNA barcode gap

Towards global interoperability for supporting biodiversity research on essential biodiversity variables (EBVs)

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