Haplogroup H39 - Description
H39 is a mitochondrial DNA haplogroup defined by the mutation A > G at position 16299 on the HVR1 region of the mitochondria (represented as “A16299G”); this lineage split from macro-haplogroup H approximately 10,000 years ago, probably in Anatolia or otherwise in the general area of West Asia. Due to the conspicuous absence of haplogroup H in Europe during the Mesolithic and its sudden appearance in association with farming populations, we can assume that H39 arrived in Europe in the Neolithic with groups carrying Early European Farmer ancestry, mixing with local hunter-gatherer populations to varying degrees. There are three major downstream branches of H39 on the FamilyTreeDNA Haplotree: H39a (defined by mutations G709A and C16169T), H39b (defined by mutation T5892C), and H39c (C13362T). H39a is the largest subclade of H39, with the vast majority testers who are positive for this branch listing their earliest known maternal ancestors being from the British Isles and Scandinavia. H39b is a smaller branch that has a distinct British Isles shift in its distribution, but also contains a Swedish kit. H39c is a distinctly Fennoscandian branch with all of its downstream testers listing earliest known maternal ancestors from Finland and Sweden. YFull identifies two other branches named H39d (defined by mutation A2755G) and H39e (defined by mutation T3398C), both of which combined only consist of a few kits; this project includes kits that fall under H39d and H39e under "DNA Results". 

H39 - Origins and Spread
The oldest H39+ sample we currently have in the ancient DNA record is BICS4, dated to c. 5050 B.C.; this individual, found in Bicske, Hungary, was a male who belonged to the early phase of the Sopot Culture, a Neolithic archaeological culture that was present in Slavonia, Croatia, and Hungary c. 5500-c. 3800 B.C. BICS4 also carried the Y-chromosome E1b-L618, and individuals associated with this culture are notable for their very high levels of Early European Farmer ancestry, carrying low levels of Western Hunter-Gatherer ancestry (ranging from 2-12%). This early H39 sample helps to anchor the area of focus for the origins of H39 around the Transdanubian Mountains, pointing to the area stretching from the northern Dinaric Alps to the Carpathians being responsible for the first dispersal of H39 during the Neolithic.

Following BICS4, we come across several H39+ samples at the Links of Noltland, a large prehistoric settlement in Westray, Orkney, Scotland; the samples in question (KD047, KD048, KD049, KD050) date to the Middle Bronze Age (c. 1400-1700 B.C.) and aside from KD050 and KD047 (who were siblings), these H39+ individuals had different branches, pointing to a distant relationship between the people at the site rather than a recent one. While there is strong persistence of Y-DNA from the Neolithic up to the Iron Age (i.e., the Y-chromosomes of the men were of Western Hunter-Gatherer origin), the mtDNA lineages were remarkably varied, pointing to female exogamy being the rule of thumb for the communities that existed on Orkney. Dulias et al. (2022), “Ancient DNA at the edge of the world: Continental immigration and the persistence of Neolithic male lineages in Bronze Age Orkney” notes an association with northern Europe for modern H39 in connection with the samples at the Links of Noltland: “The age and geographic distribution of the clusters to which most of the BA LoN lineages belonged suggest that most of them were not inherited from the local Neolithic but arrived later. Many are associated in ancient DNA studies with continental Corded Ware Culture, BBC, or BA populations (SI Appendix, Section S5). For example, T2a1b1 is seen in the German Corded Ware, whereas T2b21 matches German and Czech BBC lineages. While H39 and K1c2 lineages have not been seen in published ancient DNA data, the modern lineages are restricted to northern Europe and date to ∼3000 BC and 2600 BC, respectively, again suggesting a source in the Corded Ware expansion across northern Europe at 2500 to 3000 BC.” The presence of the H39+ individual at Bicske predates the tentative 3000 B.C. dating for H39 offered by Dulias et al. (2022), pushing the date of H39 back at least to ~5100 B.C. – this suggests that the Corded Ware Culture absorbed and propagated H39 after mixing with the women of farmer populations in northern-central Europe, especially those of the Funnelbeaker Culture and Globular Amphora Culture.

We also find a genetically southern H39+ sample at a Gothic burial site in the mid to late 5th century AD at Hács, Hács-Béndekpuszta, Somogy, Hungary. Judging from the autosomal profile of HACS5, it seems that some diverged subclades of H39 that are not under branches such as H39a, H39b, H39c, etc. might have stayed in the area around the Carpathian Mountains in very low frequency – HACS5 was buried with a copy of Wulfilas’ Gothic translation of the Bible, but based on his Y-DNA and autosomal profile looks to have been an assimilated Daco-Thracian man accompanying the Goths on their journey westward from the territory of the Chernyakhov culture (located in modern-day Romania, Ukraine, and Moldova). Free Dacians are known to have been part of the ethnic composition of the Chernyakhov Culture and mixed with the Goths (alongside groups such as the Sarmatians), so it is unsurprising to see a Daco-Thracian man in a relatively prestigious burial context. Despite the gap in chronology, it is tempting to connect this to the broad Northern Balkanic-Danubian point of origin for the earliest instance of H39, especially considering the fact Neolithic European farming communities in and around the Balkans and Carpathians contributed substantially to the genetic profile of Daco-Thracians, in addition to contributing lineages such as E1b-V13 (downstream of L618, which was carried by the earliest H39 sample we have so far).

Extant H39, however, looks to have thrived in various communities in northern Europe, and the Migration Period looks to have helped bring some H39 to the British Isles especially. One such sample is S6, Grave 1943, a woman buried in Skovgaarde, Zealand, Denmark dated to c. 200-270 AD. According to Melchior et al. (2008), "Rare mtDNA Haplogroups and Genetic Differences in Rich and Poor Danish Iron-Age Villages", S6 was part of an elite burial site which the authors connect to the migration of the Danes out of southern Sweden and into Zealand, expelling the Heruli from their former territory and introducing new maternal lineages that are not found in the local population. Only a couple hundred years later we see another Migration Period H39 sample named BUK029, buried at the Buckland Anglo-Saxon cemetery in Dover, Kent, England. BUK029 was a woman in her 20s-30s buried between 560-570 AD; her burial stands out because she displays a very northern genetic profile and was buried with Frankish and some Frisian grave goods, indicating that this woman had a great degree of wealth and perhaps came from abroad (Frisia?) to settle in Kent.

All these factors point to H39 as a lineage which propagated in Northern Europe, first with its assimilation by the Corded Ware Culture and then moving at various points among different Bronze Age communities in the north. Although not a dominant lineage by any means, H39 has an uptick in aDNA samples during the Migration Period, and branches H39a and H39c seem to have especially thrived in this context judging from their modern distribution pattern. We do find H39* samples in places such as Bulgaria, Spain, and Poland on FamilyTreeDNA and YFull, perhaps pointing to the survival of very diverged H39* lineages among other communities to the south. Regardless of these diverged H39* lineages, Northern Europe looks to be responsible for the largest share of surviving H39 and its propagation into the modern period, and ancient populations connected to the north will probably continue to provide new ancient H39+ samples in the future.