Scotland's universities would lose tuition fees worth £150 million a year from English, Welsh and Northern Irish students if it separates from the rest of the UK as a result of this year's referendum, a UK Government minister has warned.
And universities minister David Willetts said that independence would also put at risk the funding Scottish academics receive for scientific research, as well as the advantages of sharing an integrated science base with researchers in other parts of the United Kingdom.
Scottish scientific institutions received £257 million in funding from UK research councils in 2012/13, which equated to 13% of the total, significantly more than Scotland's 8% share of UK GDP, said Mr Willetts, adding: "That is the scale of the funding that would be at risk if this world-class integrated system were fragmented."
He warned that medical charities like Cancer Research UK would also be likely to focus their funding on institutions in the remaining UK, rather than in an independent Scotland.
EU rules prohibiting states from discriminating on the grounds of nationality mean that Scotland, which does not charge its own students tuition fees, has to do the same for young people from other member states. But the devolved administration can impose fees on students from England, Wales and Northern Ireland because the EU does not regulate for discrimination within member states.
Mr Willetts told the House of Commons Scottish Affairs Committee that independence would make it illegal under EU law to charge fees to students from the remaining UK. And he said that it would be seen as an "incredibly unfriendly" act from an Edinburgh administration which claims to want to maintain co-operation with research institutions after independence.
"To say that French students can come to Scotland without paying fees, but English students do pay fees.... I simply can't see how that is legal," said Mr Willetts.
"We reckon that there are about 20,000 students from the rest of the UK studying in Scotland per year, bringing about £150 million into Scottish higher education. So you would lose £150 million in revenues before you had started. It would be a black hole."
He warned: "You can't put up a new barrier specifically aimed at keeping out students from Manchester at the same time as saying you want to be part of an integrated research area with Manchester."
Mr Willetts said that the UK had a "world class" scientific base which allowed it to maintain specialist research facilities both north and south of the border, with Scotland hosting institutions like the Roslin Institute for animal genetics. But he said this broad base would be fragmented by separation, forcing an independent Scotland to cut back the range of scientific specialisms it could fund.
"Rest-of-UK research councils, in the event of a split, would finance research activities in the rest of the UK," he told the committee.
"We don't by and large finance research activities in France or Germany.
"We would of course collaborate on an international basis whenever possible, but it is hard to see how you could have the rest-of-UK taxpayers and research councils saying `We will pay for this research to be carried out somewhere else'. The rest of the UK would carry on with its research councils and Scotland would not be part of the structure."
Scotland would face an immediate cut in revenues for science because it does so well out of the current UK-wide structure and would have to "face the challenge of what it was going to specialise in with its smaller budget", said Mr Willetts.
Even if efforts were made to continue cross-border scientific integration, they would quickly founder because of diverging policies on issues like academics' pay, pensions and career advancement and taxpayers' unwillingness to fund the research priorities of a foreign country, he claimed.
"It would be a lose-lose situation," said the universities minister. "It wouldn't be something I would relish from the point of view of the rest of the UK. We all gain from being part of a big integrated system where funding is allocated by merit, not geography. That's why we are world class in science and both the rest of the UK and Scotland would lose from separation when it comes to science."