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When the researchers analyzed the Y chromosome data and modeled the typical mutation rate over the centuries, they "recovered a signature of the Greek Contribution to Sicily during the Archaic Period" or between the 8th and 5th centuries BC. Over 800 people native to the areas of Euboea and Corinth, where archaeologists and historians think the first wave of colonizers came from, along with people whose families were native to Sicily and southern Italy, had their DNA sequenced. In particular, they looked for robust gene signatures for Greek contributions to Italy and Sicily, they tested alternative models, and they looked at the relative contributions of males versus females to find out more about the colonizing population.

To counter this, Tofanelli and colleagues used both Y chromosome and mitochondrial DNA analysis and created demographic models to simulate genetic change over time. Tofanelli and colleagues find fault with these studies of Greek colonization primarily because those studies used specific lineages or haplotypes as markers of colonization, and these contemporary genomes may not accurately reflect the genes that were present in ancient populations. Previous DNA analyses have been interpreted to bolster various hypotheses as well.