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- Bergsten, Johannes, et al.
(author)
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The Effect of Geographical Scale of Sampling on DNA Barcoding
- 2012
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In: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 61:5, s. 851-869
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Journal article (peer-reviewed)abstract
- 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 data set 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 recognized species found to be monophyletic, and 5) query identification performance based on 6 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 1 km, to <3.5% for samples up 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 maximize 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.
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2. |
- Ellis, W. Chadwick, et al.
(author)
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Bis phenylene flattened 13-membered tetraamide macrocyclic ligand (TAML) for square planar cobalt(III)
- 2018
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In: Journal of coordination chemistry (Print). - : TAYLOR & FRANCIS LTD. - 0095-8972 .- 1029-0389. ; 71:11-13, s. 1822-1836
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Journal article (peer-reviewed)abstract
- The preparation, characterization, and evaluation of a cobalt(III) complex [CO{(OC)2(o,o'-NC6H4NCO)2CMe2}(OH2)]- with 13-membered tetraamide macrocyclic ligand (TAML) is described. This is a square-planar (X-ray) S=1 paramagnetic (H-1 NMR) compound, which becomes an S=0 diamagnetic octahedral species in excess d(5)-pyridine. Its one-electron oxidation at an electrode is fully reversible with the lowest E-1/2 value (0.66V vs SCE) among all investigated Co-III TAML complexes. The oxidation results in a neutral blue species which is consistent with a Co-III/radical-cation ligand. The ease of oxidation is likely due to the two benzene rings incorporated in the ligand structure (whereas there is just one in many other Co-III TAMLs). The oxidized neutral species are unexpectedly EPR silent, presumably due to the -stacking aggregation. However, they display eight-line hyperfine patterns in the presence of excess of 4-tert-butylpyridine or 4-tert-butyl isonitrile. The EPR spectra are more consistent with the Co-III/radical-cation ligand formulation rather than with a Co-IV complex. Attempts to synthesize a similar vanadium complex under the same conditions as for cobalt using [(VO)-O-V(OCHMe2)(3)] were not successful. TAML-free decavanadate was isolated instead. [GRAPHICS] .
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3. |
- van Es, Michael A, et al.
(author)
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Genome-wide association study identifies 19p13.3 (UNC13A) and 9p21.2 as susceptibility loci for sporadic amyotrophic lateral sclerosis
- 2009
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In: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 41:10, s. 1083-1087
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Journal article (peer-reviewed)abstract
- We conducted a genome-wide association study among 2,323 individuals with sporadic amyotrophic lateral sclerosis (ALS) and 9,013 control subjects and evaluated all SNPs with P < 1.0 x 10(-4) in a second, independent cohort of 2,532 affected individuals and 5,940 controls. Analysis of the genome-wide data revealed genome-wide significance for one SNP, rs12608932, with P = 1.30 x 10(-9). This SNP showed robust replication in the second cohort (P = 1.86 x 10(-6)), and a combined analysis over the two stages yielded P = 2.53 x 10(-14). The rs12608932 SNP is located at 19p13.3 and maps to a haplotype block within the boundaries of UNC13A, which regulates the release of neurotransmitters such as glutamate at neuromuscular synapses. Follow-up of additional SNPs showed genome-wide significance for two further SNPs (rs2814707, with P = 7.45 x 10(-9), and rs3849942, with P = 1.01 x 10(-8)) in the combined analysis of both stages. These SNPs are located at chromosome 9p21.2, in a linkage region for familial ALS with frontotemporal dementia found previously in several large pedigrees.
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