14 research outputs found
Supplementary Figure 2: Strict consensus tree of four most parsimonious trees from complete European dataset of Agabini diving-beetles
Parsimony analysis done in TNT with driven search strategy using tree-fusing and sectorial searches
Data from: The effect of geographical scale of sampling on DNA barcoding
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 >7% for samples within 1km, to 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 <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
Species level CO1 dataset in nexus format for gene-tree dating of European Agabini
Species level CO1 dataset in nexus format for gene-tree dating of European Agabin
Supplementary Figure 1: Neighbour-Joining tree on complete European dataset of Agabini diving-beetles
Produced from PAUP with a Kimura-2-Parameter mode
Supplementary Figure 3: Majority-rule consensus tree from Bayesian analysis on complete European dataset of Agabini diving-beetles
Bayesian analysis done in MrBayes 3.2 with codon-partitioned GTR+I+G model and using a parsimony topology as start tree
Bayesian tree in nexus format European Agabini
Bayesian tree in nexus format European Agabin
43 most parsimonious trees from parsimony analysis in nexus format European Agabini
43 most parsimonious trees from parsimony analysis in nexus format European Agabin
Dated CO1 gene tree in nexus format on species level matrix of European Agabini
Produced from BEAST with codon partitioned GTR+I+G model
Complete CO1 dataset of European Agabini in nexus format
Complete CO1 dataset of European Agabini in nexus forma