Science has just published an extensive study on the genetic history of Central Europe. There's a very useful video in the supplementary data summing up the results, so let's start with that.
Above is a screen cap from 40 seconds into the movie showing a gradient map of mitochondrial (mtDNA) affinity between samples from the Corded Ware culture (CWC) from present-day Germany and modern West Eurasians. It suggests that this vast archeological culture, or rather horizon, spread into Central Europe from somewhere in the east. That's because the closest maternal relatives of the Corded Ware samples apparently reside today in Northwestern Russia, Estonia and the Near East.
Now, the last part doesn't really make much sense, because Northwestern Russians and Estonians are less Near Eastern genetically than most other Europeans. However, the result can be explained by the fact that the resolution of the data is actually fairly low. It doesn't discriminate well between European-specific and Near-Eastern-specific lineages from within many of the same mtDNA haplogroups. Complete mt genomes are often necessary for that sort of thing. But the problem is corrected to some extent with the Ward clustering and PCA/procrustes analyses, which show that the Corded Ware mtDNA does indeed cluster in Europe.
So based on this and the other ancient DNA data in the paper, it's clear that the Corded Ware population originated in Eastern Europe, and then migrated west during the late Neolithic (aka. Copper Age). Moreover, its mix of haplogroups and (as per above, in a fairly broad sense) high affinity to the Near East suggest that this was a population of mixed Neolithic Near Eastern and Mesolithic European origin. From the paper:
The CWC is characterized by haplogroups I and U2 (4.6%), which are new maternal elements in Mittelelbe-Saale (Fig. 1C and fig. S3) and appear alongside other Late Neolithic/EBA lineages such as T1 (6.8%) and hunter-gatherer halogroups U4 and U5 (20.5%), whereas Early/Middle Neolithic haplogroups further decrease (45.5%) (Fig. 3). The binomial probability that we missed I and U2 in 211 individuals of preceding cultures is very low (P=0.000). Haplogroup U2 has been reported exclusively from Paleolithic, Mesolithic and Bronze Age samples from Russia (17-19), and PCA and cluster analyses reveal similarities of the CWC to two ancient Kurgan groups of South Siberia (19) and Kazakhstan (20) (Fig. 1, C and D), in which haplogroups I, U2 and T1 are frequent (18.2 to 37.5%) (table S9).
Also, the Corded Ware culture is often credited with the spread of Indo-European languages across much of Northern and Central Europe. Certainly, the data in this paper fit this hypothesis very nicely. Indeed, its eastern origins, time frame of migration into Central Europe, and genetic affinity to Kurgan groups are in line with the mainstream linguistic and archeological hypotheses of a Proto-Indo-European homeland somewhere in Eastern Europe (for instance see here).
However, it seems that a movement of people from the opposite direction, possibly from a staging point in Iberia, and commonly known as the Bell Beakers (BBC), had a greater impact on modern European mtDNA.
Brandt et al. aren't the first to show this, and I showed it too in a recent blog entry titled The Portuguese (or rather Atlantean?) Copper Age conquista of Europe. It's still a mystery where these people came from originally. It most likely wasn't Iberia because Bell Beaker mtDNA is clearly different from that of early Neolithic Iberians, with a much higher frequency of mtDNA H.
There's a video online in which archeologist Kristian Kristiansen suggests that the Proto-Bell Beakers might have initially expanded from the southern Adriatic and Aegean region, and spoke a Proto-Celtic language (see here). That doesn't look very likely based on the PCA below from Brandt et al.
In fact, the Bell Beaker sample doesn't even show much affinity to Basque mtDNA (as per the gradient map above). This is unexpected because Basques are generally thought to be genetic relics of the Bronze Age in Southwestern Europe, and therefore potentially the best living proxies for the Bell Beakers. But I think there are some good reasons for this discrepancy, including the aforementioned low resolution of the data, with which we can only infer general patterns rather than fine scale affinities, and the fact that one of the Bell Beaker datasets was clearly influenced by native Central European admixture. In another study on the genetic history of Central Europe, which used complete mt H genomes, Bell Beaker lineages showed high affinity to those from Basque country and surrounds (see here).
The Brandt et al. data also suggest significant mtDNA continuity in West Slavic regions since the late Neolithic/early Bronze Age, especially in the Czech Republic, but also in Poland. Moreover, the Northeastern European and Kurgan-like structure of the Corded Ware and Unetice (UC) mtDNA gene pools is probably a strong hint that we can expect a lot of these samples to belong to R1a when their Y-chromosomes are tested. In fact, one of the Corded Ware datasets from this study, from a burial site near the town of Eulau, eastern Germany, has already produced an R1a lineage with matches in Gdansk, Poland, and Tambov, Russia (see here).
By the way, the Unetice culture is probably best known for its impressive hoards of weapons and jewellery. One of these hoards included the extraordinary Nebra Sky Disc (pic below courtesy of Wikipedia). Western archeologists and linguists generally consider the Unetice folk as ancestors of Germanics and Celts. But that's starting to look like a very shaky proposition thanks to all of this ancient DNA.
So now we wait for similar studies, but focusing on Y-DNA and full genome sequences, to really flesh out all the details. Perhaps it's wishful thinking on my part, but I don't think we'll have to wait too long. I'll give it another 18 months, tops.
Update 31/10/2013: I totally missed the fact that in figure 1 the Bell Beaker Culture (BBC) sample shows a close relationship to the Neolithic Portuguese (NPO) and Neolithic Basque Country (NBQ) samples. Of course, this is in line with the generally accepted view based on archaeological data that the Bell Beaker folk migrated to Central Europe from present-day Portugal. But it also opens up the possibility that the ancestors of the Bell Beaker folk were already in Iberia during the Neolithic, rather than the Copper Age, as I had suggested here. However, Brandt et al. got this result by combining Neolithic and late Neolithic (Copper Age) Iberian samples. So this issue requires further investigation, including a comprehensive analysis of ancient Y-DNA from Iberia.
Update 20/11/2013: The paper has become freely available in a preview version of Science here, although I have no idea how long the link will work.
Guido Brandt, Wolfgang Haak et al., Ancient DNA Reveals Key Stages in the Formation of Central European Mitochondrial Genetic Diversity, Science 11 October 2013: Vol. 342 no. 6155 pp. 257-261 DOI: 10.1126/science.1241844