Wednesday, May 18, 2022

Denisovan Remains Found In Laos

Denisovans were an archaic hominin species that was a sister to Neanderthals and admixed with modern humans in Southeast Asia. Previously, Denisovan remains were found in Siberia and Tibet. 

Now, the tooth of a Denisovan female which is at least 131,000 years old, was found in Cobra Cave in Laos. The species identification and gender were based upon morphology and tooth enamel proteins, rather than ancient DNA per se. The presence of Denisovan's in the region was expected based upon Denisovan DNA in Asians and Australians and Papuans. The New York Times discusses the find further.

The paper and its abstract are as follows:

The Pleistocene presence of the genus Homo in continental Southeast Asia is primarily evidenced by a sparse stone tool record and rare human remains. Here we report a Middle Pleistocene hominin specimen from Laos, with the discovery of a molar from the Tam Ngu Hao 2 (Cobra Cave) limestone cave in the Annamite Mountains. The age of the fossil-bearing breccia ranges between 164–131 kyr, based on the Bayesian modelling of luminescence dating of the sedimentary matrix from which it was recovered, U-series dating of an overlying flowstone, and U-series–ESR dating of associated faunal teeth. Analyses of the internal structure of the molar in tandem with palaeoproteomic analyses of the enamel indicate that the tooth derives from a young, likely female, Homo individual. The close morphological affinities with the Xiahe specimen from China indicate that they belong to the same taxon and that Tam Ngu Hao 2 most likely represents a Denisovan.

Fabrice Demeter, et al.,"A Middle Pleistocene Denisovan molar from the Annamite Chain of northern Laos" 13 Nature Communications volume 13, Article number: 2557 (May 17, 2022) (open access).

Tuesday, May 17, 2022

Ancient DNA Insight Into Ashkenazi Jewish Ancestry

Consistent with the paradigm prior to a new preprint, 14th century DNA samples from Ashkenazi Jews show that their ethnogenesis predated this time period and that their Eastern European ancestry was more recent, and hence, more variable in amount, at that time.

Image from here.

The Paper
We report genome-wide data for 33 Ashkenazi Jews (AJ), dated to the 14th century, following a salvage excavation at the medieval Jewish cemetery of Erfurt, Germany. 
The Erfurt individuals are genetically similar to modern AJ and have substantial Southern European ancestry, but they show more variability in Eastern European-related ancestry than modern AJ. A third of the Erfurt individuals carried the same nearly-AJ-specific mitochondrial haplogroup and eight carried pathogenic variants known to affect AJ today
These observations, together with high levels of runs of homozygosity, suggest that the Erfurt community had already experienced the major reduction in size that affected modern AJ. However, the Erfurt bottleneck was more severe, implying substructure in medieval AJ. Together, our results suggest that the AJ founder event and the acquisition of the main sources of ancestry pre-dated the 14th century and highlight late medieval genetic heterogeneity no longer present in modern AJ.
Shaman Waldman, et al., "Genome-wide data from medieval German Jews show that the Ashkenazi founder event pre-dated the 14th century" BioRxiv (May 16, 2022) (Supplementary Material here).

Where Did Ashkenazi Jews Get East Asian Ancestry?

Davidski at Eurogenes, however, pulls some additional insights from the paper. He notes that:
The fact that the authors are using modern-day Russians to model Eastern European-related ancestry in these Ashkenazi ancients from Central Europe tells me that they're somewhat confused.

They did this because some of the Jews harbor significant Slavic ancestry and minor but perceptible East Asian ancestry, and Russians are Slavs who carry some Siberian ancestry, which is closely related to East Asian ancestry. Thus, broadly speaking, in terms of the right mix of DNA, Russians do the job.

However, as per the preprint, based on historical data, these Jews probably sourced their Slavic ancestry from Bohemia, Moravia and/or Silesia, and the Slavic speakers in these regions carry very little, if any, East Asian or Siberian ancestry. I'm sure the authors can verify this claim without too much trouble.

Ergo, it's likely that the Erfurt Jews received their Slavic and East Asian admixtures from different sources, and possibly at different times.

Thus, a new open question in historical genetics and Jewish ethnogenesis is how in some time period prior to the 14th century, Ashkenazi Jews got their small proportion East Asian ancestry.

I would differ with the statement that "Jews probably sourced their Slavic ancestry from Bohemia, Moravia and/or Silesia" which is stronger than the evidence. The Jews with elevated Eastern European ancestry who migrated into this German community in the late 1300s were from these places, but there is very thin evidence regarding the source of the baseline of Eastern European ancestry in this community among non-recent migrants.

Also, data from the Human Origins database (see, e.g. pdf page 16), which doesn't have a Polish sample, shows that Ukrainian, Belorussian, Lithuanian and Estonian gene pools, adjacent or near Poland, have a significant affinity to Han Chinese-like East Asian ancestry (f4 test 0.004 to 0.0045) albeit less than that of Russians, Finns and Mordavians in Russia (f4 test about 0.0052) and the Chuvash in Russian (f4 test about 0.0072) and Finnish Saami (f4 test about 0.008) and also closely tracks ANE ancestry.

A source elsewhere in Eastern Europe is still a possibility, as is a source in Southern Italy, perhaps derived from "barbarian" invaders during the later days of the Roman Empire and the early Middle Ages prior to the Ashkenazi Jewish bottleneck.

Ashkenazi Jewish History 

Wikipedia provides the following summary of the mainstream view of Ashkenazi Jewish history as follows:

A substantial Jewish population emerged in northern Gaul by the Middle Ages, but Jewish communities existed in 465 CE in Brittany, in 524 CE in Valence, and in 533 CE in Orléans. Throughout this period and into the early Middle Ages, some Jews assimilated into the dominant Greek and Latin cultures, mostly through conversion to Christianity. King Dagobert I of the Franks expelled the Jews from his Merovingian kingdom in 629. Jews in former Roman territories faced new challenges as harsher anti-Jewish Church rulings were enforced.

Charlemagne's expansion of the Frankish empire around 800, including northern Italy and Rome, brought on a brief period of stability and unity in Francia. This created opportunities for Jewish merchants to settle again north of the Alps. Charlemagne granted the Jews freedoms similar to those once enjoyed under the Roman Empire. In addition, Jews from southern Italy, fleeing religious persecution, began to move into Central Europe. 
Returning to Frankish lands, many Jewish merchants took up occupations in finance and commerce, including money lending, or usury. (Church legislation banned Christians from lending money in exchange for interest.) 
From Charlemagne's time to the present, Jewish life in northern Europe is well documented. By the 11th century, when Rashi of Troyes wrote his commentaries, Jews in what came to be known as "Ashkenaz" were known for their halakhic learning, and Talmudic studies. They were criticized by Sephardim and other Jewish scholars in Islamic lands for their lack of expertise in Jewish jurisprudence and general ignorance of Hebrew linguistics and literature. 
Yiddish emerged as a result of Judeo-Latin language contact with various High German vernaculars in the medieval period. It is a Germanic language written in Hebrew letters, and heavily influenced by Hebrew and Aramaic, with some elements of Romance and later Slavic languages.

Historical records show evidence of Jewish communities north of the Alps and Pyrenees as early as the 8th and 9th centuries.
By the 11th century, Jewish settlers moving from southern European and Middle Eastern centers (such as Babylonian Jews and Persian Jews) and Maghrebi Jewish traders from North Africa who had contacts with their Ashkenazi brethren and had visited each other from time to time in each's domain appear to have begun to settle in the north, especially along the Rhine, often in response to new economic opportunities and at the invitation of local Christian rulers. Thus [ed. in the 11th century] Baldwin V, Count of Flanders, invited Jacob ben Yekutiel and his fellow Jews to settle in his lands; and soon after the Norman conquest of England, William the Conqueror likewise extended a welcome to continental Jews to take up residence there. Bishop Rüdiger Huzmann [ed. in the 11th century] called on the Jews of Mainz to relocate to Speyer. In all of these decisions, the idea that Jews had the know-how and capacity to jump-start the economy, improve revenues, and enlarge trade seems to have played a prominent role. Typically, Jews relocated close to the markets and churches in town centres, where, though they came under the authority of both royal and ecclesiastical powers, they were accorded administrative autonomy. In the 11th century, both Rabbinic Judaism and the culture of the Babylonian Talmud that underlies it became established in southern Italy and then spread north to Ashkenaz.
Numerous massacres of Jews occurred throughout Europe during the Christian Crusades. Inspired by the preaching of a First Crusade, crusader mobs in France and Germany perpetrated the Rhineland massacres of 1096, devastating Jewish communities along the Rhine River, including the SHuM cities of Speyer, Worms, and Mainz. The cluster of cities contain the earliest Jewish settlements north of the Alps, and played a major role in the formation of Ashkenazi Jewish religious tradition, along with Troyes and Sens in France. Nonetheless, Jewish life in Germany persisted, while some Ashkenazi Jews joined Sephardic Jewry in Spain. 
Expulsions from England (1290), France (1394), and parts of Germany (15th century), gradually pushed Ashkenazi Jewry eastward, to Poland (10th century), Lithuania (10th century), and Russia (12th century). 
Over this period of several hundred years, some have suggested, Jewish economic activity was focused on trade, business management, and financial services, due to several presumed factors: Christian European prohibitions restricting certain activities by Jews, preventing certain financial activities (such as "usurious" loans) between Christians, high rates of literacy, near-universal male education, and ability of merchants to rely upon and trust family members living in different regions and countries.

Text Relevant To East Asian Ancestry In Jews

The text that Davidski is referencing to in the paper notes, in part, that:

Ashkenazi Jews (AJ) emerged as a distinctive ethno-religious cultural group in the Rhineland and Northern France in the 10th century. The AJ population since expanded substantially, both geographically, first to Eastern Europe and recently beyond Europe, and in number, reaching about 10 million today. The AJ population today harbors dozens of recessive pathogenic variants that occur at higher frequency than in any other population, implying that AJ descend from a small set of ancestral founders. This Ashkenazi “founder event” is also manifested by four mitochondrial haplogroups carried by as many as 40% of AJ. More recently, studies found high rates of identical-by-descent (IBD) sharing in AJ, that is, near-identical long haplotypes present in unrelated individuals, a hallmark of founder populations. Quantitative modeling suggested that AJ experienced a sharp reduction in size (a “bottleneck)” in the late Middle Ages and that the (effective) number of founders was in the hundreds

The origins of early Ashkenazi Jews, as well as the history of admixture events that have shaped their gene pool, are subject to debate. In historical research, there are two main hypotheses regarding the identity of the early AJ: either Jews who lived at the Germanic frontiers since late Roman times, or medieval migrants from the established Jewish communities of the Italian peninsula (SI 1). Genetic evidence supports a mixed Middle Eastern (ME) and European (EU) ancestry in AJ. This is based on uniparental markers with origins in either region, as well as autosomal studies showing that AJ have ancestry intermediate between ME and EU populations. Recent modeling suggested that most of the European ancestry in AJ is consistent with Southern European-related sources, and estimated the total proportion of European ancestry in AJ as 50-70%. While the Ashkenazi population is overall highly genetically homogeneous, there are subtle average differences in ancestry between AJ with origins in Eastern vs Western Europe. . . . 

The Erfurt Jewish community existed between the late 11th century to 1454, with a short gap following a 1349 massacre. We report 33 genomes from individuals whose skeletons were extracted in a salvage excavation. Our results demonstrate that Erfurt Ashkenazi Jews (EAJ) are genetically highly similar to modern Ashkenazi Jews (MAJ), implying little gene flow into AJ gene since the 14th century. Further analysis demonstrated that EAJ were more genetically heterogeneous than MAJ, with multidisciplinary evidence supporting the presence of two sub-groups, one of which had higher Eastern European affinity compared to MAJ. The EAJ population shows strong evidence of a recent sharp bottleneck, based on the distribution of mitochondrial haplogroups, high levels of runs of homozygosity, and the presence of AJenriched alleles, including pathogenic variants. 
. . .  
The first Jewish community of Erfurt (pre-1349) was the oldest in Thuringia, and its cemetery also served nearby towns. During the 1349 pogrom, most Jews of Erfurt and nearby communities were murdered or expelled. Jews returned to Erfurt around 1354 to form the second community, which was one of the largest in Germany. The individuals we studied were buried in the south-western part of the medieval Jewish cemetery of Erfurt, which underwent salvage excavations in 2013. 
. . .

An ADMIXTURE analysis demonstrated that EAJ are genetically similar to MAJ, but with higher variance, consistent with the PCA findings. Individuals classified based on the PCA as ErfurtEU had higher EU-related ancestry. The results also revealed a small but consistent East-Asian-related component, especially in the Erfurt-EU group (means of 2.7% and 1.6% in Erfurt-EU and all EAJ, as previously observed. This suggests either a minor gene flow event from East-Asia, as previously attested by mtDNA, or gene flow from Eastern European populations, who carry (at least today) a minor component of this ancestry. 
. . .

[A]ny hypothetical admixture event between AJ and Eastern Europeans in the past ≈20 generations must have been limited to replacing at most 2-4% of the total AJ gene pool (this would correspond to at most 0.2% replacement per generation). 
. . . 

We modeled EAJ as a mixture of the following modern sources: Southern European (South-Italians or North-Italians), Middle Eastern (Druze, Egyptians, Bedouins, Palestinians, Lebanese, Jordanians, or Syrians), and Eastern European (Russians). To avoid bias due to ancient DNA damage, we only used transversions. 
Most of the models with a South-Italian source were plausible (P-value >0.05; Table S7), which would be consistent with historical models pointing to the Italian peninsula as the source for the AJ population. The mean admixture proportions (over all of our plausible models; Table S7) were 68% South-EU, 17% ME, and 15% East-EU (Figure 2A). However, the direct contribution from the Middle East is difficult to estimate given historical ME admixture in Italy [49] (see the Discussion). Indeed, a model with North-Italians as a source (which was only plausible with a Lebanese source; Table S7) had ancestry proportions 44% South-EU, 44% ME, and 12% East-EU (Figure 2A). 
We validated that the results did not qualitatively change when we tested the same models using all available SNPs, a different outgroup population, or fewer SNPs (Table S7, Figure S16). Models with a Western European source (Germans) instead of Russians were not plausible (Table S7), and there was no support for an East-EU-independent contribution of East-Asians (Methods Section 4). Interestingly, Erfurt-ME could be modeled based on Turkish (Sephardi) Jews (97% admixture proportion) and Germans (3%) as sources. 

Figure S12  

Figure S12 shows East Asian ancestry (orange in K=7 charts, yellow in K=8 charts) in various populations. It is present at low levels in modern Ashkenazi Jews, in Russians, and in Erfurt-EU (one of two Eufurt subpopulations notable for higher levels of European ancestry than the other subpopulation Erfurt-ME). This component is absent in Italian, Lebanese (except one individual) and German populations. It is found in some Caucasus and Eastern European samples in the chart as well.

The Erfurt-EU population has a strong affinity of Russia and other places in Eastern Europe indicated by a low z-score, while the Erfurt-ME population has a weak connection to these populations as indicated by a high z-score. The affinity to Russia is strongest, but not that much stronger than Ukraine, Belorussia, and Poland.
This chart shows that the Erfurt-ME population shows a much strong affinity to the populations of the Levant and Arabia than the Erfurt-EU population, and a much weaker affinity to Russia, the Baltic states for which samples are available, and to a slightly lesser extent Poland and Ukraine.

 Figure S16

The Middle Eastern proxy used doesn't impact the ancestry predictions much. The Erfurt-EU population has much more ancestry described as Russian for the Eastern European proxy used in an effort to model them as a mix of Lebanese, Russian and Northern Italian (which unlike Southern Italian lacks Middle Eastern admixture in non-Jews), than Erfurt-ME does, with many Erfurt-ME subpopulation members having no discernible East European ancestry. Thus, East Asian ancestry is not found in Erfurt individuals that lack East European ancestry, ruling out a source in the Italian source population for Ashkenazi Jews, or in the Western European intermediate homeland of Ashkenazi Jews (where there isn't any East Asian ancestry). So, the East Asian ancestry appears to be mediated through East Asian admixture in Eastern Europeans.

Table S7

The two most left charts in Table S7 examine whether Northern Italy or Southern Italy are a better fit for a source population for Erfurt individuals, when in combination with with one of eight possible Middle Eastern populations and a Russian European population. The first, third and fourth looking only at SNPs available in the ancient DNA samples (which have missing data) and the second looks at all SNPS. The third uses the same populations as the first two, but a different outgroup. The far right chart in Table S7 use a German European population rather than a Russian one. A high p-score indicates that this is a more likely possibility, while a low p-score indicates that the combination of source populations is disfavored.

The Lebanese-Southern Italian-Russian combination is favored with or without all SNPs and regardless of outgroup over the alternatives, and the Lebanese-Southern Italian combination is the most favored of the German combinations. The fact that these source populations are preferred favors some narratives of Ashkenazi origins and ethnogenesis over others, although it isn't completely definitive.

Southern European source populations

Across the board, a Southern Italian source for Erfurt Jews (who are basically ancestral to modern Ashkenazi Jews except that their Eastern European/East Asian ancestral component is not yet as homogenous) is strongly preferred over a Northern Italian source, even though a Northern Italian source isn't entirely ruled out in the case of a Lebanese Middle Eastern population and a Russian European population. 

The preference for a Southern Italian source over a Northern Italian source is supported by the historical record.

Middle Eastern source populations

Across the board, a Lebanese Middle Eastern population is favored with Syrian and Bedouin B as runners up, and Druze, Egyptian, Bedouin A, Palestinian and Jordanian comparatively disfavored.  

The data sets which are part of the Human Origins dataset are described here, which notes that Bedouin B has significant North African admixture, with the distinction between Bedouin A and Bedouin B apparently first made in this paper based upon cluster analysis of the paper's Negev Bedouin samples (from the Negev desert in Southern Israel): 
Investigation of surnames identified cluster A as one of the oldest, well established clans in the Negev. On the other hand, cluster B is composed of related tribes, probably from a common founder, that migrated from Gaza to the Negev around 300 years ago. Thus, it seems that clan B, as opposed to clan A, allows interactions with tribes outside the clan.
This result supports the Biblical tradition that puts the ultimate source of people who became Jews in Lebanon, although the Bible states that after Egyptian exile they end up ruling areas that, prior to the 20th century, were inhabited by Palestinians to whom Ashkenazi Jews have a much weaker affinity. 

This data suggests the possibility that Jews in this Iron Age Jewish state had a weak demographic impact on the region that they ruled (and in Egypt where they apparently remained endogamous if indeed their people spend time there as the Book of Exodus claims), and may have been a demographically distinct elite ruling caste that largely relocated away from the region while the people they ruled stayed, upon and before the destruction of the Second Temple in 70 CE and the resulting Jewish diaspora.

Non-Southern European source population

In all cases, a German source population is disfavored, despite the fact that the earliest Ashkenazi Jews were in France and Germany and elsewhere in Western Europe, such as in Flanders Flanders, where they were welcomed until the First Crusade (although these Jews were apparently were strongly endogamous at this time) and despite the fact that Yiddish is a mostly Germanic rather than being a Slavic language. 

Instead, non-Southern Italian ancestry in Ashkenazi Jews is Eastern European rather than Western European, a place where Ashkenazi Jews had started to migrate in the 10th to 12th centuries (both before and after the 11th century period in which Western European leaders were welcoming them) which aligns with the time period of the Ashkenazi population bottleneck. 

The Erfurt-EU subpopulation, which had admixed with Eastern Europeans (mostly by marrying local women) sometime after the 10th century, and then joined the Erfurt community in the late 14th century apparently represented a back migration to the German west. The combined population was quite typical of the population that eventually expanded to form the modern Jews right at the cusp of its post-bottleneck expansion.

It could also be the case that Ashkenazi Jews in Western Europe were not much more endogamous than their Eastern European co-ethnics, but that Ashkenazi Jews with Western European admixture mostly were either killed in the Rhineland massacres of 1096 and subsequent pogroms, or migrated to Moorish Spain to join the Sephardic Jewish population there, with few Western European Ashkenazi Jews actually migrating to Eastern Europe after the 11th-12th centuries. This would have left the lion's share of the surviving Jewish population that did not join the Sephardic Jews in Spain in Eastern Europe. 

Expulsions from England (1290), France (1394), and parts of Germany (15th century) may have had little demographic impact on Jews in Central and Eastern Europe, because most Jews in the areas of Western Europe from which they were ultimately expelled had taken the hint that they were not wanted after numerous pogroms much earlier than these expulsions, or fled to Spain rather than Central and Eastern Europe when they ultimately were expelled.

Multiple lines of evidence suggest that the EAJ population had already experienced a “bottleneck” shared with MAJ: the high frequency of Ashkenazi founder mtDNA haplogroups; and the presence of Ashkenazi-specific pathogenic variants, other AJ-enriched alleles, and long runs of homozygosity. Carriers of the K1a1b1a mtDNA founder haplogroup seem to have descended from an even smaller set of founders. In agreement with previous studies, we date the onset of the expansion in AJ population size to about 20-25 generations ago

Our ancient DNA data allowed us to identify patterns in the history of AJ that would not have been otherwise detectable from modern genetic variation. Specifically, our genetic results suggest that the AJ population was structured during the Middle Ages. Within Erfurt, one group of individuals had an enrichment of Eastern European-related ancestry, while the other had ancestry very close to that of MAJ of Western European origin and modern Sephardi Jews. The two groups also had significantly different levels of enamel δ18O. Medieval AJ may have been structured even beyond Erfurt, based on our inferred demographic model. In contrast, present-day AJ is a remarkably homogeneous population. This suggests that even though the overall sources of ancestry remained very similar between medieval and modern AJ, endogamy and within-AJ mixture since medieval times have contributed to the homogenization of the AJ gene pool. 

We found that a plausible model for the ancestral sources of EAJ include groups related to people in South-Italy (about 70%, who themselves plausibly might harbor Middle East-related ancestry), the Middle East (about 15%), and Eastern Europe (about 15%). Models with North-Italians as a source were also plausible, with an ancestry proportion of about 45% to each of North-Italians and Middle Easterners. The ancestry proportion estimates using North-Italians are closer to previous estimates using modern SNP and sequencing data, but a North-Italian source was less favored by qpAdm. While these results could be consistent with a model where the Middle Eastern ancestry in AJ has not been as large as previously thought, complicating the picture are (i) our inability to identify a satisfactory model for modern AJ; (ii) the historically variable levels of Middle Eastern ancestry in Italy; and (iii) the possible problems when modeling an ancient population with modern sources. 
. . . 
Therefore, the direct contribution of ME sources to AJ ancestry may be higher than estimated. Either way, the substantial Southern European ancestry we inferred adds weight to the evidence that early AJ descended, at least partly, from Italian Jews. The estimate of about 15% Eastern European-related ancestry is consistent with a previous study. 
The identification of this source as Eastern European relies on the f4 results and the qpAdm models; however, this ancestry might derive from a broad area across Central or Eastern Europe, which may accord with recorded migration into Erfurt from Bohemia, Moravia, and Silesia. For an additional discussion on the historical interpretation of these results, see SI 2. 
. . .
4.3. qpAdm

Here too, we used the option "allsnps:YES". The reference populations (right populations) for the qpAdm analyses were: Mbuti, Ami, Basque, Biaka, Bougainville, Chukchi, Eskimo_Naukan, Han, Iranian, Ju_hoan_North, Karitiana, Papuan, Sardinian, She, Ulchi, and Yoruba. Mbuti was used as the outgroup (provided to AdmixTools as the first in the list of reference populations) in all analyses. In robustness tests, we replaced Mbuti with Ami as the outgroup. As in the qpWave analyses, in models with South-Italians we used samples of Sicilian and Italy_South together as one group. In models with ancient Germans, we used samples from [45], not including individuals with elongated skulls or with Southern European ancestry. The ancient Levant (Canaanite) samples included samples from [46] of Bronze-Age Megiddo (Megiddo_MLBA) and the ancient Rome samples included samples from [47] of Late Antiquity (Italy_LA.SG) and Imperial Rome (Italy_Imperial.SG).

For the analyses at the individual level, we used all SNPs, as the coverage of many individuals was already low. To guarantee that using all SNPs did not bias the results, we repeated the analyses at the population level with all SNPs instead of just transversions, and verified that the results remained qualitatively unchanged (Figure S16A). We included first-degree relatives in the individual-level analysis, but omitted the low-coverage individuals (<50k SNPs). For individuals for which the Eastern- EU ancestry proportion was inferred to be negative (Figure 2), we re-ran qpAdm with only Southern-EU and Middle Eastern sources.

To evaluate the potential contribution of East-Asians to the ancestry of EAJ, we tested models where the sources were Lebanese, South-Italians or North-Italians, Russians, and Han Chinese (Han were dropped from the reference populations for this analysis). The models had P-values of 1.9·10^-10 and 1.8·10^-6 with South- and North-Italians, respectively. When the target was Erfurt-EU, the P-values were 7.5·10^-8 and 1.8·10^-4, respectively. Given that the same models for EAJ without Han had plausible P values (Table S7), we conclude that there is no detectable East-Asian ancestry in EAJ.

To quantify the difference in the Eastern European ancestry between MAJ and Erfurt-ME, we used qpAdm to model MAJ as the target of admixture between Erfurt-ME and Russians. We used only transversion SNPs. The model was plausible with P=0.76, with ancestry proportions 87% for Erfurt-ME and 13% for Russians. The model was plausible also with Germans as a source instead of Russians (P=0.74; ancestry proportions 86% for Erfurt-ME and 14% for Germans). To quantify the relation between Erfurt-ME and Sephardi Jews, we used qpAdm to model Erfurt-ME using Turkish Jews and Germans as sources. We again used only transversion SNPs. The model was plausible with P=0.96, with ancestry proportions 97% for Turkish Jews and 3% for Germans. A model with Russians instead of Germans was also plausible (P=0.96; ancestry proportions 96% for Turkish Jews and 4% for Russians). 
. . . 

The information on the origin of Jewish families who migrated to Erfurt comes mainly from records of home rentals from 1354 to 1407. Most persons in these records are mentioned with surnames, which often name the town where they lived before. Information in topographic surnames is limited, as surnames can change, and as the time period when a person has lived in the other town could vary. But in some cases, we have independent sources validating the former place of residence. From 1354, and especially in the 1360s, many families moved to Erfurt whose surnames refer to former places of residence in Bohemia, Moravia, and Silesia. For example, several families came from Breslau (Wrocław) after a pogrom in 1360, some after moving to Wrocław from other Silesian towns. After 1400, there are no known cases of families migrating into Erfurt from the East. Towns in Silesia (present-day Poland) from where families moved into Erfurt include Bunzlau/Bolesławiec (one family, first mentioned in the records in 1383), Liegnitz/Legnica (two related families in 1360), Löwenberg/Lwówek Śląski (one person whose family was originally from Brno), Breslau/Wrocław (one family in 1355/6, more families after 1360), Striegau/Strzegom (one family in 1366), Schweidnitz/Świdńica (one person in 1389), and Glatz/Kłodzko (one family in 1380). Towns in Bohemia and Moravia (present-day Czech Republic) from where families moved into Erfurt include the neighboring towns Braunau/Broumov and Náchod (two families in 1360 or later, who moved through Wrocław), Prag/Praha (one family in 1366), Pilsen/Plzeň (one family in 1365), Eger/Cheb (one family in 1359), and Brünn/Brno (one family in 1363, with a son-in-law in Vienna). We note that one man moved to Erfurt from Poland in 1327 (i.e., in the first community). . . .

Our results provide new evidence for (although do not definitely prove) the theory of AJ origins in Italy, given the good fit of qpAdm models that had Italy as a source, particularly Southern Italy. Southern Italy is one of the very few places in Europe where there is evidence for Jewish demographic and cultural continuity from the late Roman into the early Medieval period and beyond. During this timeframe, the Jewish communities of Southern Italy were at the crossroads of Jewish Mediterranean life. They were in direct contact with the Jewish communities of Byzantine and early Muslim Palestine from whom they received liturgical traditions that they transmitted into Europe and that later turned up in the AJ prayer book. They were also in touch with Jewish communities elsewhere in the Eastern Mediterranean by virtue of the fact that Southern Italy was part of the Byzantine Empire into the late 11th century. 

All the evidence currently available indicates that during the Roman and early Medieval periods Jews were highly integrated in Southern Italy. There is historical evidence that there was at least some gene flow between Jews and non-Jews in Southern Italy, because, in the late Roman and early Medieval periods, imperial and ecclesiastical authorities tried to prevent the practice of intermarriage between Jews and Christians, as well as the phenomenon of conversion of non-Jews to Judaism. When, in due course, highly accomplished and connected Jews from Southern Italy started moving north, they were joined by others from central and northern Italy. For example, the Kalonymus family—a Jewish family from Rome, but with roots in Southern Italy—is known to have had major impact on AJ intellectual life in 10th-century Mainz and Speyer. This was the multilayered migratory legacy that may be reflected in the Southern European genetic ancestry we observed in our models for the genomes of Erfurt Jews. 

Our qpAdm models with a South-Italian source suggested that only a small proportion of EAJ ancestry derived from Middle Eastern populations. This may be interpreted to imply that present-day AJ derive only a small proportion of their ancestry from ancient Judaeans; and if so, most AJ ancestry would owe its origin to European converts. While this is one possible explanation, modern Italians themselves have had much higher proportions of ME admixture since at least European Imperial Roman times and this is especially the case in modern Southern Italy. Thus, an alternative explanation for these observations is that the true ME proportion in AJ is higher than in our fitting model, and that the actual contribution of Italians is not as large as suggested by this analysis. Under this scenario, good qpAdm fits are obtained when using Southern Italians as sources simply because Southern Italians are a modern population that harbors a relatively high proportion of ME ancestry with less impact from additional immigration waves that subsequently affected ME populations and may make modern ME populations relatively poor proxy sources for the ME ancestry in AJ. If this alternative explanation is right, the true ME proportion could be higher than in our fitting models, even higher than the ≈44% for the models using Northern Italians. At present, we believe both types of scenarios are plausible, along with scenarios that involve features of both. Co-analysis of ancient DNA data from the Middle East and the Italian peninsula from the periods of Antiquity and the early Medieval period would make it possible to distinguish them. 

Our genetic data suggest that some Erfurt individuals had elevated levels of European ancestry, likely Eastern European-related. A possible explanation is the documented migration into the second Erfurt Jewish community from Bohemia, Moravia, and Silesia. However, this requires that Jews living in these areas had previously admixed with local non-Jewish populations. Partly supporting this hypothesis may be the presence of names of Slavic origin among medieval Jewish women in Bohemia, particularly as it stands in contrast to naming practices common among Jews in medieval times

Finally, the genetic data suggested a high degree of endogamy in AJ through the last ≈700 years. Historical evidence indicates that the social practice of intermarriage between Jews and Christians was frowned upon by medieval Jewish and Christian authorities. Our genetic results suggest that in practice there was indeed very little gene flow into the Jewish community since this period. 

2.2. Timing demographic events in Ashkenazi history 

Our modeling of shared haplotypes dated the onset of the AJ bottleneck to ≈40-45 generations ago, or approximately about 1000-1200 years ago. This period is well before the time in the late 12th century when the persecution of Jews in the Rhineland became endemic. The appearance of a bottleneck in the early stages of the AJ community formation could reflect the historical evidence that the original AJ settlers comprised only a few dozen families, which were not always welcome and lacked the benefit of a fully developed Jewish community.

Our models dated the onset of expansion of AJ to about 20-25 generations ago, or approximately about 500-700 years ago. This confirms historical research pointing towards a gradual demographic growth within the Jewish community in German lands. The growth is hard to quantify numerically, but, especially from the 1300s onwards, it appears to have been substantial, considering the rapid increase in the number of towns that accommodated Jewish communities. 

In this work, we were unable to reliably estimate the dates of the historical admixture events of AJ in Europe. Our previous work inferred a minor post-bottleneck gene flow event from Eastern Europeans based on a depletion of EU ancestry in IBD segments (as such segments are expected to descend from ancestors who lived during the bottleneck). However, with a model of a prolonged bottleneck (about 20 generations), such a depletion may be observed also if the admixture event had happened late during the bottleneck. Our previous work estimated that admixture between Middle Eastern and European sources in AJ history occurred about 30 generations ago. This date may be associated with the admixture event with Eastern Europeans. Unfortunately, our EAJ genomes did not provide additional insight, as we found that a state-of-the-art tool for admixture time inference (DATES) provided unreliable results under simulations of AJ-like history.

A Case Study In Homogenization of Ancestry

It also highlights a point I've made about Paleoasian ancestry in indigenous population of the Amazon basin, which has a great deal of variation in proportion not only between tribal groups, but within tribal groups, all of which were endogamous with the Amazon basin through the time period of first contact for these tribes which was well after the 1492, and in most cases in the late 19th century or the 20th century.

In Ashkenazi Jews, variability in their proportions of Eastern European and East Asian ancestry vanished in about 700 years (about 24 generations) or less. 

There is simply no way that this variability in ancestry in Amazonian tribal populations could be sustained if it has a 14,000 years old source (in line with the founding population of the Americas), or even a 3,500 year old source (the timing of the Paleo-Eskimo ancestors of the Na-Dene people to the Americas).

Monday, May 16, 2022

Origins Of The First Fertile Crescent Neolithic Farmers

A new paper, Nina Marchi, et al. "The genomic origins of the world's first farmers" Cell (2022) argues based upon analysis of a medium sized sample of ancient hunter-gatherer DNA that early European farmers and early Iranian/Caucasian farmers did share a common genetic hunter-gatherer origins and that two rounds of Western hunter-gatherer introgression of ca. 14-15% each into the Mesolithic hunter-gatherer gene pool ancestral to early European farmers, accounts for the differences between them and early Iranian farmers. 

Bernard's blog explains that:
The results show that contrary to previous studies, hunter-gatherers in the Caucasus and farmers in Europe and Anatolia are all descended from the central meta population. This metapopulation received about 14,200 years ago a contribution (14%) from the western metapopulation. The ancestors of the farmers of Iran did not receive this western contribution. The central and eastern metapopulations diverged about 15,800 years ago.

The ancestors of the European and Anatolian farmers received a second gene flow (15%) from the western meta population about 12,900 years ago. The ancestors of the Caucasian hunter-gatherers did not receive this second contribution. The ancestors of European and Anatolian farmers then underwent a major genetic drift between 12,900 and 9,100 years ago due to a strong reduction in their population.

An Eighth Predicted Decay Channel Of The Higgs Boson?

The CMS experiment at the Large Hadron Collider has searching for a signal of the predicted decay of Higgs bosons to charm anti-charm quark pairs finds results that are not inconsistent with the Standard Model prediction. 

Large backgrounds from multiple sources with significant uncertainties make securing a significant signal difficult, however. 

The money chart from the paper is this one, in which the predicted Higgs to charm decay signal residual after subtracting known backgrounds is shown in red bars in the lower part of the chart and the measurements are shown as crosses:

So, CMS did observe a signal (three bins are exactly what was expected and two show a slightly stronger signal than expected), but not a very strong one, because they don't have enough statistical power from their measurements to expect to see a very strong signal.

Previous results (with the predicted values show as percentage branching fractions) were as follows:

b-quark pairs, 57.7% (observed)
W boson pairs, 21.5% (observed)
gluon pairs, 8.57%
tau-lepton pairs, 6.27% (observed)
c-quark pairs, 2.89% 
Z boson pairs, 2.62% (observed)
photon pairs, 0.227% (observed)
Z boson and a photon, 0.153% (observed)
muon pairs, 0.021 8% (observed)
electron-positron pairs, 0.000 000 5%

The paper and its abstract are as follows:
A search for the standard model Higgs boson decaying to a charm quark-antiquark pair, H →cc¯, produced in association with a leptonically decaying V (W or Z) boson is presented. The search is performed with proton-proton collisions at s√ = 13 TeV collected by the CMS experiment, corresponding to an integrated luminosity of 138 fb−1. Novel charm jet identification and analysis methods using machine learning techniques are employed. 
The analysis is validated by searching for Z →cc¯ in VZ events, leading to its first observation at a hadron collider with a significance of 5.7 standard deviations. 
The observed (expected) upper limit on σ(VH)(H→cc¯) is 0.94 (0.50+0.22−0.15) pb at 95% confidence level (CL), corresponding to 14 (7.6+3.4−2.3) times the standard model prediction. For the Higgs-charm Yukawa coupling modifier, κc, the observed (expected) 95% CL interval is 1.1 <|κC|< 5.5 (|κc|< 3.4), the most stringent constraint to date.
CMS Collaboration, "Search for Higgs boson decay to a charm quark-antiquark pair in proton-proton collisions at s√ = 13 TeV" arXiv:2205.05550 (May 11, 2022) (submitted to Physical Review Letters; Report number: CMS-HIG-21-008, CERN-EP-2022-0811).

Friday, May 6, 2022

Medieval English Diets Even For Elites Had Very Few Animal Products

Analysis in a new paper (here) of the remains of two thousand medieval British people from the pre-Norman Anglo-Saxon era, to determine the makeup of their diets based upon their bone chemistry, show that no one in that era, even elite aristocrats, ate much meat, dairy, or eggs. Many people approached vegan status, based upon what their remains showed that they ate.

This was unexpected, because many food animals were listed on documentation of tribute requirements of royal subjects that survive from that era. If the tributes were authentic and collected, then that means that the feasts that the meats collected at that time for, were infrequent and usually would have included many hundreds of basically ordinary people, and maybe almost everyone in the community.

An author of the paper explains more in a blog post with this money quote: 

We’re looking at kings travelling to massive barbecues hosted by free peasants, people who owned their own farms and sometimes slaves to work on them.

The related papers are:

S. Leggett & T. Lambert, "Food and Power in Early Medieval England: a Lack of (Isotopic) Enrichment", Anglo-Saxon England (2022). 
DOI: 10.1017/S0263675122000072

S. Leggett & T Lambert, "Food and Power in Early Medieval England: Rethinking Feorm", Anglo-Saxon England (2022). 
DOI: 10.1017/S0263675122000084

A Eurasian Stone Age Ancient DNA Megapaper

A new preprint analyzes a huge number of new ancient DNA samples from stone age Eurasia (Hat tip to Razib Khan). Despite its claim "Eurasian" scope, it covers pretty much only Europe and part of Siberia. The paper largely confirms and refines existing paradigms and expectations.

LVN = ancestry maximized in Anatolian farmer populations. WHG = ancestry maximized in western European hunter gatherers. EHG = ancestry maximized in eastern European hunter-gatherers. IRN = ancestry maximized in Iranian Neolithic individuals and Caucasus hunter-gatherers.   


Razib clarifies beyond the abstract that:

New hunter-gatherer cluster with a focus in the eastern Ukraine/Russian border region. Between the Dnieper and Don. . . .

Scandinavia seems to have had several replacements even after the arrival of the early Battle Axe people. This is clear in Y chromosome turnover, from R1a to R1b and finally to mostly I1, the dominant lineage now. They claim that later Viking and Norse ancestry is mostly from the last pulse during the Nordic Bronze Age. . . .

it’s clear that Neolithic ancestry in North/Central/Eastern Europe was from Southeast Europe, while that in Western Europe was from Southwest Europe. . . .

They find the African R1b around Lake Chad in some Ukrainian samples.
The last point confirms my previous analysis of the origins of African Y-DNA R1b, in which I argue that Y-DNA R1b-V88 bearing Chadic people are derived from migrants who originated in the Bug-Dneister culture of Ukraine departing between 5400 BCE and 5200 BCE (this culture is also discussed in the body text of the main paper). 

The pertinent part of the first pdf of Supplemental Materials (at pdf page 42, lines 911-928) states:

Newly reported samples belonging to haplogroup R1b were distributed between two distinct groups depending on whether they formed part of the major European subclade R1b1a1b (R1b-M269). 

Individuals placed outside this subclade were predominantly from Eastern European Mesolithic and Neolithic contexts, and formed part of rare early diverging R1b lineages (Fig. S3b.6). Two Ukrainian individuals belonged to a subclade of R1b1b (R1b-V88) found among present-day Central and North Africans, lending further support5,10 to an ancient Eastern European origin for this clade. 

Haplogroup R1b1a1a (R1b-M73) was frequent among Russian Neolithic individuals. 

Individuals placed within the R1b-M269 clade on the other hand were from Scandinavian Late Neolithic and early Bronze Age contexts (Fig. S3b.6). Interestingly, more fine-scale sub-haplogroup placements of those individuals revealed that Y chromosome lineages distinguished samples from distinct genetic clusters inferred from autosomal IBD sharing (Fig. S3b.6, S3b.7). In particular, individuals associated with the Scandinavian cluster Scandinavia_4200BP_3200BP were all placed within the sub-haplogroup R1b1a1b1a1a1 (R1b-U106), whereas the two Scandinavian males associated with the Western European cluster Europe_4500BP_2000BP were placed within R1b1a1b1a1a2 (R1b-P312) (Fig. S3b.7). 

Figure S3b.6 is as follows and is basically unreadable since even when magnified 500% the resolution isn't fine enough to make it readable, but is presumably referencing the two most basal portions of the circular chart which start in approximately the three o'clock position and evolve counterclockwise. Presumably R1b-V88 is the tree closest to the three o'clock position because it has two samples from the current study in purple/pinkish, while the next tree counterclockwise from it is probably R1b-M73 which has many samples from the study, consistent with the text quoted above.

The footnoted references 5 and 10 to this part of the Supplemental Materials were:

5. Haber, M. et al. "Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations". Am. J. Hum. Genet. 0, (2016). The abstract of this paper states:
Understanding human genetic diversity in Africa is important for interpreting the evolution of all humans, yet vast regions in Africa, such as Chad, remain genetically poorly investigated. Here, we use genotype data from 480 samples from Chad, the Near East, and southern Europe, as well as whole-genome sequencing from 19 of them, to show that many populations today derive their genomes from ancient African-Eurasian admixtures. 
We found evidence of early Eurasian backflow to Africa in people speaking the unclassified isolate Laal language in southern Chad and estimate from linkage-disequilibrium decay that this occurred 4,750–7,200 years ago. It brought to Africa a Y chromosome lineage (R1b-V88) whose closest relatives are widespread in present-day Eurasia; we estimate from sequence data that the Chad R1b-V88 Y chromosomes coalesced 5,700–7,300 years ago. 
This migration could thus have originated among Near Eastern farmers during the African Humid Period. We also found that the previously documented Eurasian backflow into Africa, which occurred ~3,000 years ago and was thought to be mostly limited to East Africa, had a more westward impact affecting populations in northern Chad, such as the Toubou, who have 20%–30% Eurasian ancestry today. 
We observed a decline in heterozygosity in admixed Africans and found that the Eurasian admixture can bias inferences on their coalescent history and confound genetic signals from adaptation and archaic introgression. 


10. Marcus, J. H. et al. "Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia." Nat. Commun. 11, 1–14 (2020) (pertinent Supplemental Information here). The abstract of this paper states:
The island of Sardinia has been of particular interest to geneticists for decades. The current model for Sardinia’s genetic history describes the island as harboring a founder population that was established largely from the Neolithic peoples of southern Europe and remained isolated from later Bronze Age expansions on the mainland. 
To evaluate this model, we generate genome-wide ancient DNA data for 70 individuals from 21 Sardinian archaeological sites spanning the Middle Neolithic through the Medieval period. The earliest individuals show a strong affinity to western Mediterranean Neolithic populations, followed by an extended period of genetic continuity on the island through the Nuragic period (second millennium BCE). Beginning with individuals from Phoenician/Punic sites (first millennium BCE), we observe spatially-varying signals of admixture with sources principally from the eastern and northern Mediterranean. Overall, our analysis sheds light on the genetic history of Sardinia, revealing how relationships to mainland populations shifted over time.

The relevant language in the Supplemental Information states:

The 1240k read capture data allowed us to call several R1b subclades in ancient individuals (see Supp. Fig. 7 for overview of available markers). While R1b-M269 was absent from our sample of ancient Sardinians until the Nuragic period, we detected R1b-V88 equivalent markers in 11 out of 30 ancient Sardinian males from the Middle Neolithic to the Nuragic with Y haplogroup calls. Two ancient individuals carried derived markers of the clade R, but we could not identify more refined subclades due to their very low coverage (Supp. Data 1B). The ancient geographic distribution of R1b-V88 haplogroups is particularly concentrated in the Seulo caves sites and the South of the island (Supp. Data 1B). 
At present, R1b-V88 is prevalent in central Africans, at low frequency in present-day Sardinians, and extremely rare in the rest of Europe58. By inspecting our reference panel of western Eurasian ancient individuals, we identified R1b-V88 markers in 10 mainland European ancient samples (Fig. 8), all dating to before the Steppe expansion (ą 3k years BCE). Two very basal R1b-V88 (with several markers still in the ancestral state) appear in Serbian HGs as old as 9,000 BCE (Fig. 9), which supports a Mesolithic origin of the R1bV88 clade in or near this broad region. The haplotype appears to have become associated with the Mediterranean Neolithic expansion - as it is absent in early and middle Neolithic central Europe, but found in an individual buried at the Els Trocs site in the Pyrenees (modern Aragon, Spain), dated 5,178-5,066 BCE59 and in eleven ancient Sardinians of our sample. Interestingly, markers of the R1b-V88 subclade R1b-V2197, which is at present day found in Sardinians and most African R1b-V88 carriers, are derived only in the Els Trocs individual and two ancient Sardinian individuals (MA89, 3,370-3,110 BCE, MA110 1,220-1,050 BCE) (Fig. 9). MA110 additionally carries derived markers of the R1b-V2197 subclade R1b-V35, which is at present-day almost exclusively found in Sardinians58. 
This configuration suggests that the V88 branch first appeared in eastern Europe, mixed into Early European farmer individuals (after putatively sex-biased admixture60), and then spread with EEF to the western Mediterranean. Individuals carrying an apparently basal V88 haplotype in Mesolithic Balkans and across Neolithic Europe provide evidence against a previously suggested central-west African origin of V88 61. A west Eurasian R1b-V88 origin is further supported by a recent phylogenetic analysis that puts modern Sardinian carrier haplotypes basal to the African R1b-V88 haplotypes 58. The putative coalescence times between the Sardinian and African branches inferred there fall into the Neolithic Subpluvial (“green Sahara”, about 7,000 to 3,000 years BCE). Previous observations of autosomal traces of Holocene admixture with Eurasians for several Chadic populations 62 provide further support for a speculative hypothesis that at least some amounts of EEF ancestry crossed the Sahara southwards. Genetic analysis of Neolithic human remains in the Sahara from the Neolithic Subpluvial would provide key insights into the timing and specific route of R1b-V88 into Africa - and whether this haplogroup was associated with a maritime wave of Cardial Neolithic along Western Mediterranean coasts 63 and subsequent movement across the Sahara 58,64. 
Overall, our analysis provides evidence that R1b-V88 traces back to eastern European Mesolithic hunter gatherers and later spread with the Neolithic expansion into Iberia and Sardinia. These results emphasize that the geographic history of a Y-chromosome haplotype can be complex, and modern day spatial distributions need not reflect the initial spread.

The abstract and paper are as follows:

The transitions from foraging to farming and later to pastoralism in Stone Age Eurasia (c. 11-3 thousand years before present, BP) represent some of the most dramatic lifestyle changes in human evolution. We sequenced 317 genomes of primarily Mesolithic and Neolithic individuals from across Eurasia combined with radiocarbon dates, stable isotope data, and pollen records. 
Genome imputation and co-analysis with previously published shotgun sequencing data resulted in >1600 complete ancient genome sequences offering fine-grained resolution into the Stone Age populations. 
We observe that: 
1) Hunter-gatherer groups were more genetically diverse than previously known, and deeply divergent between western and eastern Eurasia. 
2) We identify hitherto genetically undescribed hunter-gatherers from the Middle Don region that contributed ancestry to the later Yamnaya steppe pastoralists
3) The genetic impact of the Neolithic transition was highly distinct, east and west of a boundary zone extending from the Black Sea to the Baltic. Large-scale shifts in genetic ancestry occurred to the west of this "Great Divide", including an almost complete replacement of hunter-gatherers in Denmark, while no substantial ancestry shifts took place during the same period to the east. This difference is also reflected in genetic relatedness within the populations, decreasing substantially in the west but not in the east where it remained high until c. 4,000 BP; 
4) The second major genetic transformation around 5,000 BP happened at a much faster pace with Steppe-related ancestry reaching most parts of Europe within 1,000-years. Local Neolithic farmers admixed with incoming pastoralists in eastern, western, and southern Europe whereas Scandinavia experienced another near-complete population replacement. Similar dramatic turnover-patterns are evident in western Siberia; 
5) Extensive regional differences in the ancestry components involved in these early events remain visible to this day, even within countries. Neolithic farmer ancestry is highest in southern and eastern England while Steppe-related ancestry is highest in the Celtic populations of Scotland, Wales, and Cornwall (this research has been conducted using the UK Biobank resource); 
6) Shifts in diet, lifestyle and environment introduced new selection pressures involving at least 21 genomic regions. Most such variants were not universally selected across populations but were only advantageous in particular ancestral backgrounds. Contrary to previous claims, we find that selection on the FADS regions, associated with fatty acid metabolism, began before the Neolithisation of Europe. Similarly, the lactase persistence allele started increasing in frequency before the expansion of Steppe-related groups into Europe and has continued to increase up to the present. Along the genetic cline separating Mesolithic hunter-gatherers from Neolithic farmers, we find significant correlations with trait associations related to skin disorders, diet and lifestyle and mental health status, suggesting marked phenotypic differences between these groups with very different lifestyles. 
This work provides new insights into major transformations in recent human evolution, elucidating the complex interplay between selection and admixture that shaped patterns of genetic variation in modern populations.
Morten E. Allentoft, et al., "Population Genomics of Stone Age Eurasia" bioRxiv (May 5, 2022).

Population Replacement in Northern Asia Around The Last Glacial Maximum

A paper in the journal Cell that I missed when it was released a year ago, discussed at the magazine Scienceanalyzes 25 new ancient DNA samples from Russia's Amur region and compares them to existing ancient DNA samples and modern DNA samples in the region.

The paper finds that there was complete population replacement between the pre-Last Glacial Maximum population of Northeast Asia and the modern one ancestral to the current indigenous people of the Amur region that emerged around 19,000 years ago. This population is more closely related to modern East Asians and Native Americans, than to the pre-LGM people of Northeast Asia whose ancient DNA in available. 

These Northern East Asians split about 19,000 years ago from Southern East Asians.

The paper's abstract and citation are as follows:

Northern East Asia was inhabited by modern humans as early as 40 thousand years ago (ka), as demonstrated by the Tianyuan individual. Using genome-wide data obtained from 25 individuals dated to 33.6–3.4 ka from the Amur region, we show that Tianyuan-related ancestry was widespread in northern East Asia before the Last Glacial Maximum (LGM). 
At the close of the LGM stadial, the earliest northern East Asian appeared in the Amur region, and this population is basal to ancient northern East Asians. Human populations in the Amur region have maintained genetic continuity from 14 ka, and these early inhabitants represent the closest East Asian source known for Ancient Paleo-Siberians. 
We also observed that EDAR V370A was likely to have been elevated to high frequency after the LGM, suggesting the possible timing for its selection. This study provides a deep look into the population dynamics of northern East Asia.


Xiaowei Mao, et al., "The deep population history of northern East Asia from the Late Pleistocene to the Holocene" 184(12) Cell 3256-3266 E12 (May 27, 2021)