The number of mtDNA samples from Neolithic/Chalcolithic Europe(roughly 5500-3000 BC) has grown to over 500. The principal locations the samples come from are Germany, Spain, and Hungary.
I've been studying European mtDNA from this era for two years. What has been blatantly obvious to me is that since the Neolithic/Chalcolithic the frequencies of mHGs in Europe have changed pretty dramatically. mHG K and T2 are about half as popular as they once were. In contrast mHG H is about twice as popular as it once was.
Data from Germany, Spain, and Hungary all tell the same story. Here are a few states to demonstrate this change....
Frequency of Haplogroup H, K, T2, N1a1a
Early Neo Germany/Hungary: 20%, 18.7%, 25.4%, 9.4%
Early Neo Spain: 17%, 30%, 12.7%, 0.8%
Middle Neo/Chal Germany: 26.5%, 16.5%, 14%, 4.6%
Chalcolithic Spain: 23%, 22%, 4.3%, 0%
Modern Spain: 35%, 6.5%, 4%, 0%
Modern Poland: 45.2%, 3.4%, 9.4%, 0%
mHG frequencies in Spain and Germany/Hungary weren't identical back then and mHG frequencies among Europeans aren't identical today, but consistent mHG frequency trends exist in each era no matter the location in Europe.
What caused mHG frequencies in Europe to change?
If my life depended on it I would guess natural selection is the answer. I would guess that certain mHGs affected post-Neolithic European women's' mitochrondrial DNA in ways which helped them have more daughters than women of other mHGs. I don't believe migration from a population with scary high frequencies of H and scary low frequencies of K and T2 is the answer. Genome-wide DNA from Pre-Historic Europe tell us migration into Europe after the Neolithic came primary from the Pontic Caspien Steppe which had pretty low frequencies of H. I discussed how migration from the Pontic Caspien Steppe affected European mtDNA here.
Neolithic and Chalcolithic European mtDNA belongs (95%+++!)exclusively, exclusively to what today are European-specific haplogroups. So they are important ancestors of modern European mtDNA without a doubt. Genome-wide DNA is consistent with the idea they're an ancestor of modern Europeans, actually it suggests they're the most important ancestor. Haplogroup H was unfrequent in Neolithic/Chalcolithic Iberia but about 90% of it was European-specific H1 and H3. Any theories that European specific mHGs, like H1, arrived from an unknown source are invalidated by ancient mtDNA. Ancient European belonged to the same mHGs bug at different frequencies.