Scientists from Dublin and Belfast have looked deep into Ireland’s early history to discover a still-familiar pattern of migration: of stone age settlers with origins in the Fertile Crescent, and bronze age economic migrants who began a journey somewhere in eastern Europe.

The evidence has lain for more than 5,000 years in the bones of a woman farmer unearthed from a tomb in Ballynahatty, near Belfast, and in the remains of three men who lived between 3,000 and 4,000 years ago and were buried on Rathlin Island in County Antrim.

Scientists at Trinity College Dublin used a technique called whole-genome analysis to “read” not the unique characteristics of each individual, but a wider history of ancestral migration and settlement in the DNA from all four bodies.

Facebook Twitter Pinterest A reconstruction of the Ballynahatty Neolithic skull by Elizabeth Black. Her genes tell us she had black hair and brown eyes. Photograph: Barrie Hartwell

They confirm a picture that has been emerging for decades from archaeological studies. Migrant communities did not compete with the original Irish. They became the Irish.

The ancestors of the Stone Age farmers began their journey in the Bible lands, where agriculture first began, and arrived in Ireland perhaps via the southern Mediterranean. They brought with them cattle, cereals, ceramics and a tendency to black hair and brown eyes.

These settlers were followed by people, initially from the Pontic steppe of southern Russia, who knew how to mine for copper and work with gold, and who carried the genetic variant for a blood disorder called haemochromatosis, a hereditary genetic condition so common in Ireland that it is sometimes called Celtic disease.

These people also brought with them the inherited variation that permits the digestion of milk in maturity – much of the world becomes intolerant to the milk sugar lactose after infancy – and they may even have brought the language that became what is now Irish. Some of them, too, had blue eyes.

Facebook Twitter Pinterest Geneticists from Trinity College Dublin, and archaeologists from Queens University Belfast, speak about their discoveries.

“There was a great wave of genome change that swept into Europe from above the Black Sea into Bronze Age Europe and we now know it washed all the way to the shores of its most westerly island,” said Dan Bradley, professor of population genetics at Trinity College Dublin.

“And this degree of genetic change invites the possibility of other associated changes, perhaps even the introduction of language ancestral to western Celtic tongues.”

The Dublin team and colleagues from Queens University Belfast report in the Proceedings of the National Academy of Sciences that the two great changes in European prehistory – the emergence of agriculture and the advance of metallurgy – were not just culture shifts: they came with new blood. An earlier population of hunter gatherers was successively overwhelmed by new arrivals. And in Ireland, these new settlers began to define a nation.

“These findings,” the authors say, “suggest the establishment of central attributes of the Irish genome 4,000 years ago.”

Working from the principle that any human DNA tells a story not just of individual identity but of ten thousand years of ancestry, researchers have begun to piece together the entire story of Homo sapiens. The story is incomplete, and under constant revision, but the outline of the settlement of Europe and Asia told by DNA confirms and illuminates the archaeological evidence.

Modern humans arrived in the British Isles relatively late after the end of the Ice Age. Evidence of early settlement in Ireland is sketchy and indirect: in 2013, researchers looked at the DNA of the Irish banded wood snail and identified it as closely related to the species found in the French Pyrenees. The best explanation so far is that these snails may have arrived 8,000 years ago as the leftovers from the packed lunch, so to speak, of a much earlier community of European traders or migrants. Nobody can say who these people may have been, or why they arrived with a taste for escargots.

But the latest study throws more light on the birth of a nation. All three dead men from Rathlin Island carried what is now the most common type of Irish Y chromosome, inherited only from male forebears.

“It is clear that this project has demonstrated what a powerful tool ancient DNA analysis can provide in answering questions which have long perplexed academics regarding the origins of the Irish,” said Eileen Murphy, who lectures in osteoarchaeology at Queen’s in Belfast.

And Lara Cassidy, a researcher in genetics at Trinity College Dublin and another co-author, said “Genetic affinity is strongest between Bronze Age genomes and modern Irish, Scottish and Welsh, suggesting establishment of central attributes of the insular Celtic genome 4,000 years ago.”