If you know that birds survive the phenomenon of 'moult' (e.g. partial or complete replacement of the feathers of a bird), why should they not survive the removal of three feathers? 

I think that the issue is not whether the birds survive per se (as Marcel pointed out, birds moult naturally), but more about the timing of the plucking.  Moulting occurs during the moulting season (obviously!), when many birds tend to be less mobile and will often remain in the vicinity of reliable food resources.  If feathers are removed (un-naturally) at a time when the birds are migrating or chick rearing etc, then there is the potential for the added energetic costs of reduced flight capabilities to affect their (and their offspring's) fitness and surival.  So, I would say that you need to think about both the timing of the sampling and the position and function of the feathers that you are removing.  With a highly endangered species, you don't want to risk having any adverse effects.  Do you need to remove a whole feather?  For some of the sampling I have been involved in (for isotopic analysis), we just removed small sections of the feathers rather than the whole thing.  I don't know about DNA sampling, but presumably, with modern methods it is not nesessary to collect large samples these days?  

If already exposed to the stressors of catching, handling, and presumably ringing (and having the rings), the marginal effect of plucking a few contour feathers should be negligible

I work 4 years with individually marked population of the Bluethroat (Luscinia svecica), and in the first stages of investigations used contour feathers as a source of DNA. Another variant of sampling DNA were buccal swabs. We work during nesting period, and now I know exactly, that plucking 3 contour feathers (2 from the tail and 1 secondary) effecting neither survival nor reproductive success for this species. But for our needs (microsatellite analysis of parentage) buccal swabs provide better material, and now we use almost only this method of sampling

Thanks for the replies.  Feathers are to be taken from adult birds and fledglings to assess feather quality, so it would appear that taking a whole feather is required.

The comment on buccal sampling is important--that sounds like the solution to many blood free DNA sample collections and would minimize harm. Does anyone have further comments on that?  what does the buccal swab get put into?

Feathers provide DNA on the proximal tip of the shaft, that which was in the skin.  BUT the bigger and newer the feather, the better from the point of good dna.  I have not done the extractions myself, but have been told by the persons working with feather dna extraction that small contour feathers (as opposed to tail feathers and secondaries or primaries) often just don't provide enough material.  Contour feathers are indeed dropped here and there with preening and such, and if one clipped them off leaving the base, I think it could be worse than plucking if it messed up the replacement process. 

May be its off-topic, because the author of this question explained, that he is interested in feather quality, not in DNA-source. But I can add some comments about buccal sampling. First of all, our work is not pioneer in using buccal swabs for small birds, for example:

1) Handel CM, Pajot LM, Talbot SL, Sage GK (2006) Use of buccal swabs for sampling DNA from nestling and adult birds. Wildlife Society Bulletin, 34, 1094–1100.

2) H. Arima and N.Ohnishi. (2006) Usefulness of avian buccal cells for molecular sexing. Ornithol Sci 5: 139–143

As for our study, I'm not sure, that it's an universal method: it needs to be validated in the cases of long DNA fragments, for example. Another problem is that buccal epithelium is external environment for the individual. We know cases, when DNA of parents contaminate nestlings sample.

As for methods, we use phenol-chloroform extraction, so we store swabs in the buffer solution, which is used on the first stage of extraction.

Olga, if you have an issue with bucal contamination, what about ussing a capillary tube for getting a fluid sample from inside the cloaca?

Fernando, thanks for your comment, but I gave an example of contamination just for showing non-universal buccal epithelium as a source of DNA. For our study it's not a problem, because our task is to detect extra-pare parentage, so, the contamination by social parents DNA not affects the results. In addition, we looked for the most easy and non-invasive method, which allow to receive a lot of samples from nestlings from 3 days old. So, using of buccal swabs became the best variant.

We have been working in our group with large wing and tail feathers plucked to small birds. These are probably much more valuable to the birds than the small contour feathers, which made me think that first-hand data on the impacts of plucking large feathers could be relevant to this discussion. Our favourite model species has been the blackcap (body mass ca. 15 g). Depending on our specific goals, we plucked the two fifth rectrices (the second most external tail feathers), or one innermost primary plus one fifth rectrix. These are important feathers (ok, we chose the ones that should have the least aerodynamic impact when removed), yet we never observed any obvious detrimental effect of feather plucking on birds’ flight. We even plucked the feathers produced in different moult seasons to some birds recaptured in different years, which shows that plucking didn’t harm feather follicles and birds that had been plucked feathers could maintain feather properties in subsequent moults (see De la Hera et al. 2009. Repeatable length and mass but not growth rate of individual feathers between moults in a passerine bird. Acta Ornithologica 44: 95-99). After reading the comments by ResearchGate colleagues, I had a quick look to our data of birds captured in winter, which were plucked feathers well outside the moult season. A very simple chi-square analysis of the contingency table with variables “sampled for feathers on first capture” (Yes/No) and “recaptured later on” (Yes/No) gives a clearly non-significant result (P = 0.98 with n = 777). Obviously this is a very preliminay results that doesn’t control for the many factors that may affect the probability of recapture of each bird. But given the small effect and the big sample size, I don’t think that the most depurated survival analysis would detect any mortality associated with feather plucking.

Although plucking large feathers may have more subtle effects if it seriously impairs flight performance or energetic balance (for a recent example see Cantarero et al. 2014. Males respond to female begging signals of need: a handicapping experiment in the pied flycatcher, Ficedula hypoleuca. Animal Behaviour 94: 167-173), birds can probably afford losing one or two of these feathers with little or no fitness cost. Therefore, by comparison, the impact of plucking three small contour feathers must be less than negligible as said by other colleagues.