DOI: 10.5061/dryad.2rg92p5v
title: Data from: The effect of geographical scale of sampling on DNA barcoding

description: Eight years after DNA barcoding was formally proposed on a large scale,
 CO1 sequences are rapidly accumulating from around the world. While
 studies to date have mostly targeted local or regional species
 assemblages, the recent launch of the global iBOL project (International
 Barcode of Life), highlights the need to understand the effects of
 geographical scale on Barcoding’s goals. Sampling has been central in the
 debate on DNA Barcoding, but the effect of the geographical scale of
 sampling has not yet been thoroughly and explicitly tested with empirical
 data. Here we present a CO1 dataset of aquatic predaceous diving beetles
 of the tribe Agabini, sampled throughout Europe, and use it to investigate
 how the geographic scale of sampling affects 1) the estimated
 intraspecific variation of species, 2) the genetic distance to the most
 closely related heterospecific, 3) the ratio of intraspecific and
 interspecific variation, 4) the frequency of taxonomically recognised
 species found to be monophyletic, and 5) query identification performance
 based on six different species assignment methods. Intraspecific variation
 was significantly correlated with the geographical scale of sampling
 (R-square=0.7), and more than half of the species with 10 or more sampled
 individuals (N=29) showed higher intraspecific variation than 1% sequence
 divergence. In contrast the distance to the closest heterospecific showed
 a significant decrease with increasing geographical scale of sampling. The
 average genetic distance dropped from &gt;7% for samples within 1km,
 to &lt;3.5% for samples up to &gt;6000 km apart. Over a third of
 the species were not monophyletic, and the proportion increased through
 locally, nationally, regionally and continentally restricted subsets of
 the data. The success of identifying queries decreased with increasing
 spatial scale of sampling; liberal methods declined from 100% to around
 90% whereas strict methods dropped to below 50% at continental scales. The
 proportion of query identifications considered uncertain (more than one
 species &lt;1% distance from query) escalated from zero at local, to
 50% at continental scale. Finally, by resampling the most widely sampled
 species we show that even if samples are collected to maximise the
 geographical coverage, up to 70 individuals are required to sample 95% of
 intraspecific variation. The results show that the geographical scale of
 sampling has a critical impact on the global application of DNA barcoding.
 Scale-effects result from the relative importance of different processes
 determining the composition of regional species assemblages (dispersal and
 ecological assembly) and global clades (demography, speciation and
 extinction). The incorporation of geographical information, where
 available, will be required to obtain identification rates at global
 scales equivalent to those in regional barcoding studies. Our result hence
 provides an impetus for both smarter barcoding tools and sprouting
 national barcoding initiatives – smaller geographical scales deliver
 higher accuracy.
description: Supplementary Figure 1:
 Neighbour-Joining tree on complete European dataset of Agabini
 diving-beetlesProduced from PAUP with
 a Kimura-2-Parameter modelSuppl_Fig_1_NJ_tree.pdfSupplementary Figure 2: Strict consensus tree of four most parsimonious trees from complete European dataset of Agabini diving-beetlesParsimony analysis done in TNT with driven search strategy using tree-fusing and sectorial searches.Suppl_Fig_2_parsimony_tree.pdfSupplementary Figure 3: Majority-rule consensus tree from Bayesian analysis on complete European dataset of Agabini diving-beetlesBayesian analysis done in MrBayes 3.2 with codon-partitioned GTR+I+G model and using a parsimony topology as start tree.Suppl_Fig_3_Bayesian_tree.pdfNeighbour joining tree in nexus format European AgabiniNJ_tree.nexBayesian tree in nexus format European Agabinibayesian_tree.nex43 most parsimonious trees from parsimony analysis in nexus format European Agabini43MPT.nexDated CO1 gene tree in nexus format on species level matrix of European AgabiniProduced from BEAST with codon partitioned GTR+I+G model.beast_chronogram.nexSpecies level CO1 dataset in nexus format for gene-tree dating of European AgabiniAgabini_CO1_species_level_for_dating.nexComplete European Agabini dataset in tab-delimited text format with CO1 sequences, species names, unique ID, geographic origin and coordinatesTab-delimited text file with the following fields; BMNH number Family Subfamily Genus Species Name State Country Lat_dec Lon_dec CO1_sequence DNA.Plate DNA.Plate.WellAgabini_data_w_lat_and_lon.txtComplete CO1 dataset of European Agabini in nexus formatAgabini_CO1_sequences.nex