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I sent my CV to a Professor regarding a PhD position. He asked me to send the name of three referees. I could have sent him the names, but here is an issue.

I have worked in Germany for 2 years as a research assistant and then I moved to my home country and worked here for almost 4 years and published papers in reputed journals. Logically I think I should include the names of my current supervisors or the supervisors I have published works with.

But the professor (I am applying to) is originally from Germany, currently residing in Canada. He asked me to include three referees from Germany. Is there any specific reason that he asked specifically for references from that country? Also, how do professors usually communicate? Do they call or send emails? Are they more comfortable if they are from the same country?

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We aren't in a position to address the question of why this professor made this specific request. However, on a more general level:

You don't specify where your home country is; let's suppose it's Ruritania. Why wouldn't a professor want references from your Ruritanian colleagues?

  • Reference-writing culture and purpose differs around the world. In US/Canada/Northern Europe/etc, an academic reference is expected to be a fairly detailed appraisal of your strengths and performance. Unfortunately referees from some parts of the world do not appreciate this, and submit attestations about a candidate's personal character or family circumstances. This damages their application, as there are effectively no meaningful references. Perhaps the professor knows, or fears, that Ruritanian professors do not write helpful letters.
  • Good references usually include information about how the writer perceives the candidate relative to others: "One of the most innovative researchers I have ever worked with", "Consistently ranking in the top 5 in her undergraduate class", etc. Of course, this is only meaningful if the reader is familiar with the comparators. If I have never encountered anyone else from Ruritania, how do I interpret such statements? I simply have no point of reference.
  • The concept of academic references relies on the fact that the writer stands to damage their professional reputation if they recommend someone who turns out to be a flop. For this to be a meaningful cost, the writer's professional circle has to intersect sufficiently with the recipient's professional circle. If nobody I know has any Ruritanian connections, why shouldn't a Ruritanian professor lie through his teeth in order to get rid of a troublesome postdoc?
  • Edited to add: The way in which academia operates varies around the globe. It is conceivable that the characteristics that are desirable in the Ruritanian system are undesireable somewhere else. Again, it is helpful to understand the perspective from which referees are writing.

As for communication, most academics prefer to communicate (at least initially) by email. However, a phonecall may sometimes be made for references, to allow transfer of information without generating any paper trail.

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