Friday, January 10, 2014


Blackļ¬‚ies comprise 26 genera and some 2200 species, and they are a nuisance. Similarly to the mosquitoes the female requires a bloodmeal for egg maturation but their strategy for getting this from us mammals is a bit more violent. Admittedly, the bites are shallow but they are accomplished by first stretching the skin using teeth on the labrum and then abrading it with the maxillae and mandibles, cutting the skin and rupturing its fine capillaries. Feeding is facilitated by a powerful anticoagulant in the flies' saliva. As the flies are rather tiny one does not feel the process of damaging the skin. The first indication that one was bitten is usually the tickling sensation of blood that flows down the skin. This can be followed by itching and localized swelling. Swelling can be quite pronounced depending on the species and the victim's immune response. The black fly's swarming behavior can make matters worse and any outdoor activities unpleasant or intolerable even if one encounters species that do not require blood meals. Here in Canada black flies built quite a reputation as nicely demonstrated in this song:

Unfortunately the story has a far more serious background as some black fly species serve as vectors for parasites:
The most important human parasites transmitted by blackflies are the nematodes Onchocerca volvulus, the causative agent of river blindness and Mansonella ozzardii, which causes Mansonelliasis or ‘serous cavity filariasis’. In Latin America, blackflies are thought to be responsible for outbreaks of endemic pemphigus foliaceus and to be the aetiological agent of the Altamira haemorrhagic syndrome. Blackflies also transmit pathogens to domestic livestock, resulting in increased mortality, reduced weight, decreased milk production and malnutrition.

A new study not only adds new barcodes for a number of blackfly species to BOLD but perhaps more importantly the authors evaluated the efficacy of various primers for the purpose of DNA barcoding old, pinned museum specimens of blackflies. Of course it is perhaps more desirable to have freshly collected specimens simply because one can easily obtain a full-length barcode fragment from it. However, sometimes museum specimens represent the only available samples for rare or otherwise difficult to acquire species. In addition a barcode from a type specimen could resolve taxonomic uncertainty when putative new species are found. 

Unfortunately, the use of museum specimens to generate DNA Barcodes can be challenging due to factors such as DNA degradation, contamination and uncertainty regarding details of specimen collection and preservation.

The colleagues have utilized primer sets that amplify small overlapping fragments, which can be combined during post hoc analysis to form a full-length or near full-length DNA Barcode. Here are their results copied from the abstract of the study:

We analysed 271 pinned specimens representing two genera and at least 36 species. Due to the age of our material, we targeted overlapping DNA fragments ranging in size from 94 to 407 bp. We were able to recover valid sequences from 215 specimens, of which 18% had 500- to 658-bp barcodes, 36% had 201- to 499-bp barcodes and 46% had 65- to 200-bp barcodes. Our study demonstrates the importance of choosing suitable primers when dealing with older specimens and shows that even very short sequences can be diagnostically informative provided that an appropriate gene region is used.

Sounds a little bit like the good old shotgun sequencing with subsequent contig assembly. Just on a much smaller scale and much more targeted. Sounds like a way to go after all those DNA bearing type specimens in the museums, laborious but perhaps the only way to get a barcode for some species.

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