Another one-third of African mtDNA haplogroups observed in Europe are considerably older, possibly arriving in Europe about 11,000 years ago, which was before herding and farming (the Neolithic revolution) arrived in Europe. Alternately, these mtDNA lineages may have merely been present in Southeastern European or West Asian sources of Neolithic migrants to Europe and arrived in Europe as part of those populations.
None of these mtDNA haplogroups are likely to have been present in Europe prior to the Epipaleolithic period.
Genome Research DOI: 10.1002/ajpa.22052
Reconstructing ancient mitochondrial DNA links between Africa and Europe
María Cerezo et al.
Mitochondrial DNA (mtDNA) lineages of macro-haplogroup L (excluding the derived L3 branches M and N) represent the majority of the typical sub-Saharan mtDNA variability. In Europe, these mtDNAs account for less than 1% of the total but, when analyzed at the level of control region, they show no signals of having evolved within the European continent, an observation that is compatible with a recent arrival from the African continent. To further evaluate this issue, we analyzed 69 mitochondrial genomes belonging to various L sublineages from a wide range of European populations. Phylogeographic analyses showed that ∼65% of the European L lineages most likely arrived in rather recent historical times, including the Romanization period, the Arab conquest of the Iberian Peninsula and Sicily, and during the period of the Atlantic slave trade. However, the remaining 35% of L mtDNAs form European-specific subclades, revealing that there was gene flow from sub-Saharan Africa toward Europe as early as 11,000 yr ago.
From here (with emphasis from me rather than the source). There are also Supplemental Materials.
The mtDNA mutation rate dating system used is more reliable as a measure of relative dates than it is of absolute dates. There are serious disputed regarding the calibration of these dates, although they do have a decent record of being correct at an order of magnitude level, at least. An estimated age of 3,000 years is probably not really 30,000 years, and visa versa. Dates based on mtDNA mutations seem to be more reliable than dates based on Y-DNA mutations, where fundamental irregularities have been demonstrated.
For example, the data strongly disfavor an interpretation that any of these lineages arrived in Europe or Asia during the Out of Africa migration from Africa of proto-Eurasians, even given all of the caveats that apply to mtDNA mutation rate based dates. The only mtDNA L3 haplogroup (all Eurasian mtDNA haplogroups derived from mtDNA subhaplogroup L3) for which an age of arrival in Europe could be estimated, L3d1b1a, was estimated to be 2,200 to 5,100 years old (most likely 3,600 years old), and is not particularly basal in the mtDNA L3 phylogeny.
The mtDNA data only trace matriline descent, and do not show all sources of a person's ancestry, although, all other things being equal, at a population level they are likely to be fairly representative of the mtDNA mix in a reasonable decent sized source population.
The study had a sample size of 69, with most coming from Southern Europe. The potentially European origin lineages were L1b1a8 and L1b1a12 (possibly Iberian rooted), and L2a1k (with one example in the Czech Republic and another from Slovakia).
According to Wikipedia discussing the geographical roots of the lineage that includes the possibly European Iberian lineages: "Haplogroup L1b is most frequent in West Africa specially in Senegal at 17-20%, and among Nigerian Igbo, Mauritanians, El Hierro, Gran Canarians, Akan people, Algerians, the Lemba, and Egyptians."
A prehistoric migration of women who could be the source of these mtDNA lineages to Spain across the Straits of Gibraltar (which has been the route of other prehistoric migrations documented with genetic evidence) is not too much of a stretch to imagine.
Similarly, per Wikipedia, discussing the geographical roots of the lineage that include the possibly Czechoslovakian lineage:
The wide distribution of L2a and diversity makes identifying a geographical origin difficult. The main puzzle is the almost ubiquitous Haplogroup L2a, which may have spread East and West along the Sahel Corridor in North Africa after the Last Glacial Maximum, or the origins of these expansions may lie earlier, at the beginnings of the Later Stone Age, ∼40,000 years ago.
In East Africa L2a was found 15% in Nile Valley- Nubia, 5% of Egyptians, 14% of Cushite speakers, 15% of Semitic Amhara people, 10% of Gurage, 6% of Tigray-Tigrinya people, 13% of Ethiopians and 5% of Yemenis.
Haplogroup L2a also appears in North Africa, with the highest frequency 20% Tuareg, Fulani (14%). Found also among some Algeria Arabs, it is found at 10% among Moroccan Arabs, some Moroccan Berbers and Tunisian Berbers. . .
[L2a1] is observed in West Africa among the Malinke, Wolof, and others; in North Africa among the Maure/Moor, Hausa, Fulbe, and others; in Central Africa among the Bamileke, Fali, and others; in South Africa among the Khoisan family including the Khwe and Bantu speakers; and in East Africa among the Kikuyu from Kenya. Closely related variants are observed among the Tuareg in North Africa and West Africa and among the East African Dinka and Somali People. . . . All Ethiopian L2 lineages can be seen as derived from the two subclades L2a1 and L2b.
How these lineages could end up in a quite differentiated form in Czechoslovakia in prehistoric times is any one's guess, although it is notable that many of the populations that share related lineages were historically nomadic.
It is also possible that L1b1a8, L1b1a12, and L2a1k are simply low frequency African lineages whose more recent African roots have not been discerned in Africa to due to sampling issues in Africa, or due to misfortunes that befell the source population in Africa during the historic era. In this scenario there may have been differentiation within the putatively European lineage within African populations, and a migration of multiple women who were members of this already differentiated African populations that has not been sampled in Africa to Europe could create the false appearance of European a rooting of these lineages. Given that every single African mtDNA subhaplogroup in Europe was analyzed that likelihood that something of this nature could have cropped up in the analysis due to African sampling related issues (where sampling strategies are often limited by practical and geopolitical considerations) is considerable.
The methods used in this paper are more useful in convincingly establishing that a migration of people with a particular mtDNA lineages to Europe was recent than it is in convincingly establishing that people with a particular mtDNA lineage arrived in Europe prior to the historic era.
Also pertinent is a recent paper summarizing the main points that argue for North African influences on the South Iberian Neolithic. To the extent that other lines of evidence support North African interaction with Southern Iberia about 8,000 years ago, attributing mtDNA lineages L1b1a8 and L1b1a12 in Europe to this event, which is within the mtDNA mutation date confidence interval in the mtDNA paper, makes a fair amount of sense.
Of course, this still does little to explain why there are two, fairly divergent permutations of mtDNA haplogroup L2a1k in modern Czechoslovakia that look like they've been in Europe since the Epipaleolithic.
On one hand, the fewer outliers there are, the more acceptable it is to propose that something really weird made them happen.
On the other hand, it is hard to see how a 14,000 year old mtDNA lineage would survive, but just barely, over that kind of time frame beginning so close to the founder population. You'd expect an mtDNA lineage that has survived so long to either have been wiped out, or to have grown to make up a larger percentage of the total sample and greater geographic range, in the course of fourteen thousand years. The hypothesis that a lineage like that which is still in the population, but appears only twice in the entire mtDNA catalog of Europe, has really been in Europe that long stinks a little from the point of view of statistical intuition.