N1a became particularly prominent in this debate when a team led by Wolfgang Haak analyzed skeletons from Linear Pottery Culture sites.

Seven of these ancient individuals were found to belong to haplogroup N1a[5][6] A separate study analyzed 22 skeletons from European hunter-gatherer sites dated 13400-2300 BC.

[7] Haak's team concludes that "the transition to farming in central Europe was accompanied by a substantial influx of people from outside the region.

"[7] However, they note that haplogroup frequencies in modern Europeans are substantially different from early farming and late hunter-gatherer populations.

Critics of these studies claim that the LBK N1a specimens could have derived from local communities established in Europe before the introduction of farming.

Ammerman's team voiced concern due to some of the LBK specimens coming from communities several hundred years after farming was first established in the region;[8] a rebuttal was given.

[1] Deguilloux's team agreed with Haak's conclusion on a genetic discontinuity between ancient and modern Europeans.

[10] Seven of 42 skeletons from Linear Pottery Culture (Linearbandkeramik) sites were found to be members of the N1a haplogroup (see Neolithic European).

[12] One of thirteen skeletons analyzed from a medieval cemetery dated 1250-1450 AD in Denmark was found to be a member of subclade N1a1a.

[13] The N1 subclade has also been found in various other fossils that were analysed for ancient DNA, including specimens associated with the Starčevo (N1a1a1, Alsónyék-Bátaszék, Mérnöki telep, 1/3 or 33%), Linearbandkeramik (N1a1a1a3, Szemely-Hegyes, 1/1 or 100%; N1a1b/N1a1a3/N1a1a1a2/N1a1a1/N1a1a1a, Halberstadt-Sonntagsfeld, 6/22 or ~27%), Alföld Linear Pottery (N1a1a1, Hejőkürt-Lidl, 1/2 or 50%), Transdanubian Late Neolithic (N1a1a1a, Apc-Berekalja, 1/1 or 100%), Protoboleráz (N1a1a1a3, Abony, Turjányos-dűlő, 1/4 or 25%), Iberia Early Neolithic cultures (N1a1a1, Els Trocs, 1/4 or 25%),[14] Rinaldone-Gaudo Eneolithic cultures (N1a1a1a3, Monte San Biagio, 1/1 or 100%).

[24] Analysis of modern Siberian populations revealed a 1.2% prevalence in Altaians, 0.2% in the Buryats,[25] and 0.9% in the Khanty people.

[27] N1a is concentrated among Afro-Asiatic-speaking populations in Northeast Africa, occurring in Eritrea, Ethiopia, Kenya, Tanzania, Somalia and Sudan.

[30] This phylogenetic tree of haplogroup N1a subclades is based on the paper by Mannis van Oven and Manfred Kayser Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation[2] and subsequent published research.