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Delineating closely related species with DNA barcodes for routine biological monitoring

Carew, Melissa E., Hoffmann, Ary A.
Freshwater biology 2015 v.60 no.8 pp. 1545-1560
Chironomidae, DNA barcoding, cytochrome b, genes, monitoring, monophyly, nucleotide sequences, pollution, salt tolerance, zinc
DNA barcoding has proven useful for identifying species, and there is increasing interest in this approach to determine species compositions for routine biological monitoring. Generally, DNA barcodes applied to taxa used for monitoring are clearly linked to species, but where taxa are closely related separation using DNA barcodes can be ambiguous. This raises challenges for monitoring, especially if closely related taxa are not recognised as separate species and these species have different environmental responses. Here we examine whether separation of closely related taxa with DNA barcodes is supported by other gene sequences and whether morphological and environmental differences occur among related species that cannot be easily separated. We selected six Chironomidae genera where initial neighbour‐joining analysis of DNA barcodes produced monophyletic groups supported by high bootstraps (>95%), but groups were separated by low nucleotide divergence of 3–7%. Taxon separation based on DNA barcodes and mitochondrial cytochrome b (CytB) gene sequences were compared to delineations based on nuclear sequences from the carbomoylphosphate synthase‐like gene region 1 (CAD1) and the zinc metalloproteinase (ZMP) gene. Species delineations with DNA barcodes were not always the same as those defined with nuclear sequences, morphological variation or differences in pollution and salinity tolerance. Morphological differences and some environmental differences were often in agreement with taxon separation based on nuclear CAD1 (and ZMP) sequences rather than DNA barcodes (and CytB variation). This study suggests that nuclear sequence data when used in combination with DNA barcodes can help separate closely related taxa into groups useful for routine biological monitoring.