If the species in question is/are covered by national legislation, then the collectors should have requested and received permission from the relevant government agency to collect specimens.  If the specimens were transported by any means outside of the country in which they were collected (including tissue samples), then the researchers would have had to apply for CITES licences through the national CITES-competent agency.   In all cases, the publications should cite somewhere in the text that they hold appropriate licences for the collection of samples.  However, whether the agency they dealt with is sufficiently competent to assess whether sampling could be detrimental to the species or indeed if they researchers are sufficiently professional is an entirely different matter.  

To answer the question: the number of specimens of each species formed (also concerns not only endangered species) by the quota appointed by local authority (like Nature Agency or something like this) and at the end confirmed by Government ofthe country of species origin.

Depending to the relation to International RED Data Book/Local status and/or CITES it is restricted for collecting or not (CITES I).

Dear John,

Thank you very much for your helpful answer. The publications including large number of collected specimens belonging to some endangered specimens have cited permission from local agencies. After reading your answer I have checked into this  and I have the sad feeling that these are cases that correspond to "an entirely different matter" following your answer. I will check the situation again and try to approach the respective local authorities.

Thanks again, Gloria

Dear Mikhall,

Thank you very much for your helpful answer. I am looking into this matter now, especially CITES.

Thanks again,

Gloria

Yes, Gloria, the CITES rules (in general principles) was developed long ago and also need great changes in this ever-changing world...

It is sad to evident some species restricted to export but nearly fully eaten or used for medicine by locals who did it without any problems and restrictions. Even such anigmatic species like giant salamander Andrias davidianus which established a mass breeding farm program in its country (China) are now nearly extinct from most of its range... :( That CITES doesn't works in many cases nowadays and shall be reviewed and renewed.

Thank you very much Mikhall. It is tragic that many species are in danger all over the world and it is difficult to call attention on many of them, especially when they are not of direct interest for human beings. In the same way that now journals request that authors follow certain rules in the killing of animals used in research, probably it would be helpful if similar rules are requested by editors and reviewers of scientific journals when dealing with manuscripts including endangered species.