Expansion of domesticated goat echoes expansion of early farmers

goat-neolithic

New paper (behind paywall) Ancient goat genomes reveal mosaic domestication in the Fertile Crescent, by Daly et al. Science (2018) 361(6397):85-88.

Interesting excerpts (emphasis mine):

Thus, our data favor a process of Near Eastern animal domestication that is dispersed in space and time, rather than radiating from a central core (3, 11). This resonates with archaeozoological evidence for disparate early management strategies from early Anatolian, Iranian, and Levantine Neolithic sites (12, 13). Interestingly, our finding of divergent goat genomes within the Neolithic echoes genetic investigation of early farmers. Northwestern Anatolian and Iranian human Neolithic genomes are also divergent (14–16), which suggests the sharing of techniques rather than large-scale migrations of populations across Southwest Asia in the period of early domestication. Several crop plants also show evidence of parallel domestication processes in the region (17).

PCA affinity (Fig. 2), supported by qpGraph and outgroup f3 analyses, suggests that modern European goats derive from a source close to the western Neolithic; Far Eastern goats derive from early eastern Neolithic domesticates; and African goats have a contribution from the Levant, but in this case with considerable admixture from the other sources (figs. S11, S16, and S17 and tables S26 and 27). The latter may be in part a result of admixture that is discernible in the same analyses extended to ancient genomes within the Fertile Crescent after the Neolithic (figs. S18 and S19 and tables S20, S27, and S31) when the spread of metallurgy and other developments likely resulted in an expansion of inter-regional trade networks and livestock movement.

goat-middle-east
Maximumlikelihood phylogeny and geographical distributions of ancient mtDNA haplogroups. (A) A phylogeny placing ancient whole mtDNA sequences in the context of known haplogroups. Symbols denoting individuals are colored by clade membership; shape indicates archaeological period (see key). Unlabeled nodes are modern bezoar and outgroup sequence (Nubian ibex) added for reference.We define haplogroup T as the sister branch to the West Caucasian tur (9). (B and C) Geographical distributions of haplogroups show early highly structured diversity in the Neolithic period (B) followed by collapse of structure in succeeding periods (C).We delineate the tiled maps at 7250 to 6950 BP, a period >bracketing both our earliest Chalcolithic sequence (24, Mianroud) and latest Neolithic (6, Aşağı Pınar). Numbered archaeological sites also include Direkli Cave (8), Abu Ghosh (9), ‘Ain Ghazal (10), and Hovk-1 Cave (11) (table S1) (9).

Our results imply a domestication process carried out by humans in dispersed, divergent, but communicating communities across the Fertile Crescent who selected animals in early millennia, including for pigmentation, the most visible of domestic traits.

Related

FADS1 and the timing of human adaptation to agriculture

fads1-farmers

Open access FADS1 and the timing of human adaptation to agriculture, by Sara Mathieson & Iain Mathieson, bioRxiv (2018).

Abstract:

Variation at the FADS1/FADS2 gene cluster is functionally associated with differences in lipid metabolism and is often hypothesized to reflect adaptation to an agricultural diet. Here, we test the evidence for this relationship using both modern and ancient DNA data. We document pre-out-of-Africa selection for both the derived and ancestral FADS1 alleles and show that almost all the inhabitants of Europe carried the ancestral allele until the derived allele was introduced approximately 8,500 years ago by Early Neolithic farming populations. However, we also show that it was not under strong selection in these populations. Further, we find that this allele, and other proposed agricultural adaptations including variants at LCT/MCM6, SLC22A4 and NAT2, were not strongly selected until the Bronze Age, 2,000-4,000 years ago. Similarly, increased copy number variation at the salivary amylase gene AMY1 is not linked to the development of agriculture although in this case, the putative adaptation precedes the agricultural transition. Our analysis shows that selection at the FADS locus was not tightly linked to the development of agriculture. Further, it suggests that the strongest signals of recent human adaptation may not have been driven by the agricultural transition but by more recent changes in environment or by increased efficiency of selection due to increases in effective population size.

Interesting excerpt for the steppe-related expansion:

agricultural-adaptation-allele-frequency
Allele frequency trajectories for other putative agricultural adaptation variants. As in Figure 2C, estimated allele frequency trajectories and selection coefficients in different ancient European populations. Significant selection coefficients are labelled.

In the case of FADS1 and all the other examples we investigated, the proposed agricultural adaption was either not temporally linked with agriculture or showed no evidence of selection in agricultural populations. Instead, most of the variants with any evidence of selection were only strongly selected at some point between the Bronze Age and the present day, that is, in a period starting 2000-4000 BP and continuing until the present. This time period is one in which there is relatively limited ancient DNA data, and so we are unable to determine the timing of selection any more accurately. Future research should address the question of why this recent time period saw the most rapid changes in apparently diet associated genes. One plausible hypothesis is that the change in environment at this time was actually more dramatic than the earlier change associated with agriculture. Another is that effective population sizes were so small before this time that selection did not operate efficiently on variants with small selection coefficients. For example, analysis of present-day genomes from the United Kingdom suggests that effective population size increased by a factor of 100-1000 in the past 4500 years (Browning and Browning 2015). Ancient effective population sizes less that 104 would suggest that those populations would not be able to efficiently select for variants with selection coefficients on the order of 10-4 or smaller. Larger ancient DNA datasets from the past 4,000 years will likely resolve this question.

This complexity of the reasons for selection reminded me of the comment by Narasimhan on lactase persistence expanding with steppe populations into Central Asia (based on data of the paper where he is the first author):

I always thought that to argue for natural selection in humans (viz. skin color, lactase persistence, etc.) was possible for archaic groups over tens of thousands of years, but that more recent selections would be very difficult to prove, in so far as historical population expansions involve more ‘artificial’ (i.e. man-made or man-caused) societal changes.

NOTE. I am probably more inclined to think about regional outbreaks (especially of new diseases) as one of the few potential short-term selection mechanisms in historical societies, because of their potential to create sudden bottlenecks of better fitted survivors.

I think recent works like these are showing a mixed situation, where maybe some traits were strongly selected for environmental reasons; but most of the time they were probably – like, say, Y-DNA haplogroup bottlenecks in Europe after the steppe-related expansions – due mostly to chance.

Human dietary evolution in central Germany, and relationship of Únětice to Corded Ware and Bell Beaker cultures

bronze_age_early_Unetice.

Open access 4000 years of human dietary evolution in central Germany, from the first farmers to the first elites, by Münster et al. PLOS One (2018).

Excerpts (emphasis mine):

This study of human diet between the early stages of the farming lifestyle and the Early Bronze Age in the MES, based on carbon and nitrogen isotope analyses, is amongst the most comprehensive of its kind. Or results show that human dietary behaviour has changed significantly throughout the study period. A distinct increase in the proportion of animal protein in the human diet can be identified over time, a trend which only the people from the BBC did not follow. The results of the stable isotope analyses are consistent with epidemiological data on caries frequency, which indicate the highest proportions of carbohydrates in the human diet in the EN and the lowest in the EBA [19]. These findings may have been due to an increased consumption of either meat or dairy products. Although meat and dairy consumption cannot be distinguished by means of stable isotope data or caries frequency, molecular-genetic analyses of lactase persistence argue against an increased consumption of fresh milk [9]. However, although approximately 70% of the world population has a lactose intolerance, most of them can tolerate dairy foods or lactose-containing foods without developing symptoms [128]. It therefore comes as no surprise that the use of processed milk, i.e. dairy products, appears to have set in early on in the Neolithic period [99]. Unarguably, there was an increasing stabilisation of the supply of meat and secondary animal products throughout the Neolithic. The data dynamics overall argue against an equal availability of animal-derived protein to all sections of the various populations, which attests to early processes of specialisation, individualisation and hierarchisation. Moreover, population-genetic processes are also reflected in the development of human dietary habits. From the 4th millennium BC onwards, groups moved into the MES from the north, sometimes accompanied by violence [6,29], and fundamental demographic changes took place in the FN with the arrival of CWC groups from the north-eastern steppes and the BBC from south-western Europe [6,7]. This former pastoral steppe component, in particular, may have been responsible for the fact that animal-based foodstuffs reached their highest importance in the FN and EBA. Differences in the consumption of animal-derived products between the sexes resulted in significantly lower δ15N values and less access to animal protein in females. Besides behavioural choices as to what food to consume, numerous other nutritional and gender-specific factors must certainly be taken into account when assessing the subsistence and nutritional balance of individuals. In the future, analysis of single amino acids of nitrogen and the compound-specific carbon isotope analysis of lipids and bone mineral may help providing more detailed and nuanced insight on aspects of human diet, such as protein sources in complex foodwebs, nutritional stress and disease [129131]. They should become a standard in isotope studies and applied more often and routinely.

saxony-anhalt-final-neolithic-cultures
Overview of investigated sites and archaeological chronology of Neolithic and Early Bronze Age central Germany. The Stroke Ornamented Culture and Michelsberg Culture are not represented in our sample due to low rate of anthropological findings. Chronology after Schwarz in [29]. https://doi.org/10.1371/journal.pone.0194862.g001

Regarding specifically differences between Corded Ware (CWC) and Bell Beaker (BBC) cultures in Saxony-Anhalt, a region already known to show a resurge of the previous population after the Únětice period:

Based on isotope data from collagen [104], a diet with a high protein content from meat or dairy products has been postulated for CWC groups from south-western Germany, though researchers there were also unable to distinguish between the two sources of protein. The consumption of fresh milk and the consumption of dairy products such as cheese, yoghurt and kefir may also be erroneously dated to the same period and associated with lactase persistence. A newly reported genome-wide SNP dataset from 230 West Eurasians dating from between 6,500 and 300 cal. BC [9] has shown, like earlier studies [105], that no notable increase in lactase persistence in Europe appears to have occurred prior to 2,000 BC. It was and is a fact that milk is not a natural foodstuff for adult consumption, unless one is prepared to negate the numerous symptoms of lactose intolerance, including abdominal pain, bloating, flatulence, diarrhoea, asthma and others. Cultural evolution in conjunction with natural selection has made it possible for us to use milk and its secondary products as a source of protein and energy. Whilst the continuous increase in animal protein in the diet of the Neolithic populations of the MES from the LBK to the Early Bronze Age can undoubtedly partly be traced back to an intensified use of secondary animal products over the course of the Neolithic, it is difficult to estimate how great a contribution this made to the increase in δ15N values. Judging from molecular-genetic data on lactase persistence, however, the consumption of fresh milk, at least, appears to have first begun to have an impact on the protein balance of individuals around 4,000 years ago [9].

NOTE. Regarding lactase persistence, we now know that Ukraine_Eneolithic sample I6561, of haplogroup R1a-Z93 (hence probably related to the later expansion of the Corded Ware culture) is the nearest sample to the population that might have expanded the 13910*T lactase persistence allele in Northern Europe.

neolithic-differences-male-female
Sex-specific differences in stable carbon and nitrogen isotope values in humans. https://doi.org/10.1371/journal.pone.0194862.g004

[After the massive influx of the CWC into central Europe in the FN] The dietary profile once again exhibits an increase in the mean δ15N values, to 10.1 ± 1.0 ‰. The BBC, which spread somewhat later throughout north and central Europe (with the arrival of the CWC jointly making up Event C) and whose origins are presumed to have been in south-western Europe, constitutes an exception, not just from the point of view of genetics. In contrast to the general diachronic trend consisting of raised δ15N values in the cultural groups examined, the BBC exhibited a nutritional decrease in mean δ15N values to 9.7 ± 0.7 ‰. The divergence between the CWC and the BBC to be seen in their funerary rites, despite their chronological and sometimes also territorial coexistence, is thus also visible in their dietary habits. Comparative examinations of CWC sites in southern Germany have shown that their mean δ15N values were, in fact, comparable to those of the CWC in the MES (δ13C: -19.9 ± 0.6 ‰, δ15N: 10.8 ± 0.7 ‰, n = 32), despite exhibiting significant variation between and even within the sites, thus pointing to the diverging subsistence strategies of different communities [104]. The UC, which followed the CWC in the MES, bore close affinities to its forerunner in terms of its population genetics, thus supporting the hypothesis that the BBC only had a minimal genetic impact on the UC [6,7]. The close genetic links between the UC and the CWC, however, are also seen in very similar mean nitrogen values which, at 10.4 ± 0.7 ‰, were the highest in the overall sample. Moreover, a striking aspect in the evaluation of the mean δ15N values over time is a clear tendency towards rising standard deviations (S4 Fig). It is highly likely that this reflects increased social differentiation in society at the end of the Neolithic and in the Early Bronze Age. Socioeconomic advancement led to differences in status within communities and even to the formation of an elite, the differences applying to numerous facets of life, including dietary habits [60].

saxony-anhalt-N-values
Chronological development of the distribution of δ15N-values according to the different archaeological periods. >Numbers of individuals are displayed in parentheses. https://doi.org/10.1371/journal.pone.0194862.g007

I think the overstudied region of Saxony-Anhalt and the Tollense valley region may not be exactly where the Proto-Balto-Slavic homeland actually formed, but they are certainly showing interesting hints to how (and where approximately) it might have happened…

Related:

Iberian prehistoric migrations in Genomics from Neolithic, Chalcolithic, and Bronze Age

iberia-neolithic-bronze-age

New open access paper Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia, by Valdiosera, Günther, Vera-Rodríguez, et al. PNAS (2018) published ahead of print.

Abstract (emphasis mine)

Population genomic studies of ancient human remains have shown how modern-day European population structure has been shaped by a number of prehistoric migrations. The Neolithization of Europe has been associated with large-scale migrations from Anatolia, which was followed by migrations of herders from the Pontic steppe at the onset of the Bronze Age. Southwestern Europe was one of the last parts of the continent reached by these migrations, and modern-day populations from this region show intriguing similarities to the initial Neolithic migrants. Partly due to climatic conditions that are unfavorable for DNA preservation, regional studies on the Mediterranean remain challenging. Here, we present genome-wide sequence data from 13 individuals combined with stable isotope analysis from the north and south of Iberia covering a four-millennial temporal transect (7,500–3,500 BP). Early Iberian farmers and Early Central European farmers exhibit significant genetic differences, suggesting two independent fronts of the Neolithic expansion. The first Neolithic migrants that arrived in Iberia had low levels of genetic diversity, potentially reflecting a small number of individuals; this diversity gradually increased over time from mixing with local hunter-gatherers and potential population expansion. The impact of post-Neolithic migrations on Iberia was much smaller than for the rest of the continent, showing little external influence from the Neolithic to the Bronze Age. Paleodietary reconstruction shows that these populations have a remarkable degree of dietary homogeneity across space and time, suggesting a strong reliance on terrestrial food resources despite changing culture and genetic make-up.

iberia-admixture
(A) f4 statistics testing affinities of prehistoric European farmers to either early Neolithic Iberians or central Europeans, restricting these reference populations to SNP-captured individuals to avoid technical artifacts driving the affinities. The boxplots in A show the distributions of all individual f4 statistics belonging to the respective groups. The signal is not sensitive to the choice of reference populations and is not driven by hunter-gatherer–related admixture (Datasets S4 and S5). (B) Estimates of ancestry proportions in different prehistoric Europeans as well as modern southwestern Europeans. Individuals from regions of Iberia were grouped together for the analysis in A and B to increase sample sizes per group and reduce noise

Conclusion:

We present a comprehensive biomolecular dataset spanning four millennia of prehistory across the whole Iberian Peninsula. Our results highlight the power of archaeogenomic studies focusing on specific regions and covering a temporal transect. The 4,000 y of prehistory in Iberia were shaped by major chronological changes but with little geographic substructure within the Peninsula. The subtle but clear genetic differences between early Neolithic Iberian farmers and early Neolithic central European farmers point toward two independent migrations, potentially originating from two slightly different source populations. These populations followed different routes, one along the Mediterranean coast, giving rise to early Neolithic Iberian farmers, and one via mainland Europe forming early Neolithic central European farmers. This directly links all Neolithic Iberians with the first migrants that arrived with the initial Mediterranean Neolithic wave of expansion. These Iberians mixed with local hunter-gatherers (but maintained farming/pastoral subsistence strategies, i.e., diet), leading to a recovery from the loss of genetic diversity emerging from the initial migration founder bottleneck. Only after the spread of Bell Beaker pottery did steppe-related ancestry arrive in Iberia, where it had smaller contributions to the population compared with the impact that it had in central Europe. This implies that the two prehistoric migrations causing major population turnovers in central Europe had differential effects at the southwestern edge of their distribution: The Neolithic migrations caused substantial changes in the Iberian gene pool (the introduction of agriculture by farmers) (6, 9, 11, 13, 24), whereas the impact of Bronze Age migrations (Yamnaya) was significantly smaller in Iberia than in north-central Europe (24). The post-Neolithic prehistory of Iberia is generally characterized by interactions between residents rather than by migrations from other parts of Europe, resulting in relative genetic continuity, while most other regions were subject to major genetic turnovers after the Neolithic (4, 6, 7, 9, 25, 48). Although Iberian populations represent the furthest wave of Neolithic expansion in the westernmost Mediterranean, the subsequent populations maintain a surprisingly high genetic legacy of the original pioneer farming migrants from the east compared with their central European counterparts. This counterintuitive result emphasizes the importance of in-depth diachronic studies in all parts of the continent.

Related:

Differences in ADMIXTURE between Khvalynsk/Yamna and Sredni Stog/Corded Ware

neolithic-steppe

Looking for differences among steppe cultures in Genomics is like looking for a needle in a haystack.

It means, after all, looking for differences among closely related cultures, such as between South-Western and North-Western Anatolian Neolithic cultures, or among Old European cultures (such as Vinča or Cucuteni–Trypillia), or between Iberian cultures after the arrival of steppe-related populations.

These differences between closely related regions, in all these cases and especially among steppe cultures, even when they are supported by Archaeology and anthropological models of migration (and compatible with linguistic models), are expected to be minimal.

Fortunately, we have phylogeography, which helps us point in the right direction when assessing potential migrations using genomic data.

User Tomenable recently pointed out a curious finding on Anthrogenica, from data available in Mathieson et al (2017): in ADMIXTURE results with K=12, a different ancestral component (in light green in the paper, see below) is traceable from the North Caspian steppe since the Neolithic. This is also partially distinguishable on K=10 and K=11, although not so clearly differentiating among later cultures.

NOTE: Read more on the controversy regarding the ideal number of ancestral populations, the absurd use of ADMIXTURE to solve language questions, and the meaning of cross-validation (CV) values

admixture-khvalynsk-yamna-sredni-stog-cwc
Unsupervised ADMIXTURE plot from k=10 to 12, on a dataset consisting of 1099 present-day individuals and 476 ancient individuals. We show newly reported ancient individuals and some previously published individuals for comparison.

Explanations for this finding might include, as the user points out, a greater contribution of CHG ancestry in the eastern steppe cultures (Khvalynsk/Yamna) compared to the North Pontic steppe (Sredni Stog/Corded Ware), which is probably one of the main genomic differences among both cultures, as I pointed out in the Indo-European demic diffusion model (see accounts on the origins of Khvalynsk and Sredni Stog populations and on contacts between Yamna and the Caucasus, and see below also my sketch of Eurasian genomic history).

Interesting is also the appearance of similar ancestral components later in Vučedol – which probably received admixture from Yamna settlers (see admixture components in West Yamna samples and in the Yamna settler from Bulgaria) – , and later still in the Balkans.

On the other hand, previous ancestral components in outliers from the Balkans seem to be more similar to Sredni Stog samples, giving still more strength to the hypothesis that this common (“steppe”) component expanded westward within the Pontic-Caspian steppe with the spread of Suvorovo-Novodanilovka chiefs.

Problems with this interpretation include:

1) The scarce samples available, the different cultures included, and the CV values of the K populations selected in ADMIXTURE.

2) The lack of data for comparison with Bell Beaker peoples (from Olalde et al. 2017).

3) The sample classified as Latvia_LN/CWC has this component. I have already said before that, given the differences with all other Corded Ware samples, this quite early sample might be an outlier, with Khvalynsk/Yamna population connected directly to the ancestors of this individual, possibly through exogamy (as it is clear from my sketch below). Whether or not this is an outlier among CWC populations in the Baltic, only future samples can tell.

4) Three later individuals from Corded Ware in Germany have the component, in a minimal amount. I would bet – judging by their position in the graphic – that this might be explained through the Esperstedt family. These individuals might have in turn got the contribution directly from the oldest member, who shows what seems (in PCA) like a recent admixture from contemporary steppe cultures (such as the Catacomb culture).

NOTE: See my graphics with interesting members of the Espersted family marked: ADMIXTURE and PCA (outlier).

qgraph-eurasia
Tentative sketch modelling the genetic history of Europe and West Eurasia from ancient populations up to the Neolithic, according to results in recent genetic papers and archaeological models of known migrations.

Again, needle in a haystack… And confirmation bias by me, indeed.

But interesting nonetheless.

EDIT (4 JAN 2017): A reader points out that the interpretation of Unsupervised ADMIXTURE should work backwards (i.e. different contributions into different modern populations), and not based solely on ancestral populations, which seems probably right. So again, confirmation bias (and potentially wrong direction fallacy) by me…

Related:

How to do modern phylogeography: Relationships between clans and genetic kin explain cultural similarities over vast distances

yakut-phylogeography

A preprint paper has been published in BioRxiv, Relationships between clans and genetic kin explain cultural similarities over vast distances: the case of Yakutia, by Zvenigorosky et al (2017).

Abstract:

Archaeological studies sample ancient human populations one site at a time, often limited to a fraction of the regions and periods occupied by a given group. While this bias is known and discussed in the literature, few model populations span areas as large and unforgiving as the Yakuts of Eastern Siberia. We systematically surveyed 31,000 square kilometres in the Sakha Republic (Yakutia) and completed the archaeological study of 174 frozen graves, assembled between the 15th and the 19th century. We analysed genetic data (autosomal genotypes, Y-chromosome haplotypes and mitochondrial haplotypes) for all ancient subjects and confronted it to the study of 190 modern subjects from the same area and the same population. Ancient familial links and paternal clan were identified between graves up to 1500 km apart and we provide new data concerning the origins of the contemporary Yakut population and demonstrate that cultural similarities in the past were linked to (i) the expansion of specific paternal clans, (ii) preferential marriage among the elites and (iii) funeral choices that could constitute a bias in any ancient population study.

Even if you are not interested in the cultural and anthropological evolution of this Turkic-speaking people of the Russian Far Eastern region, the method used is an excellent example of how to use archaeology and genetics (especially Y-DNA and mtDNA data) to obtain meaningful results when investigating ancient populations.

For quite some time, probably since the first renown admixture analyses of ancient DNA samples were published, we have been living under the impression that phylogeography, or simply archaeogenetics as it was called back in the day, is not needed.

Cavalli-Sforza’s assertion that the study of modern populations could offer a clear picture of past population movements is now considered wrong, and the study of Y-DNA and mtDNA haplogroups is today mostly disregarded as of secondary importance, even among geneticists. Whole genomic investigation (and especially admixture analyses) have been leading the new wave of overconfidence in genetic results, tightly joint with the ignorance of its shortcomings (and commercial interests based on desires of ethnic identification), and haplogroups are usually just reported with other, not entirely meaningful aspects of ancient DNA analyses.

While it is undeniable that admixture analyses are offering quite interesting results, they must be carefully balanced against known archaeological and linguistic knowledge. Phylogeography – and especially Y-DNA haplogroup assessment – is quite interesting in investigating kinship and clans in patrilocal communities – i.e. most communities in prehistoric and historic periods, unless proven otherwise.

Luckily enough, there are those researchers who still strive to obtain meaningful information from haplotypes. The article referenced in this post is quite interesting due to its phylogeographic method’s applicability to ancient cultures and peoples.

When some geneticists look at simplistic prehistoric maps, like those depicting Yamna, Afanasevo, Corded Ware, and Bell Beaker cultures together, they forget that 1) cultural regions are selected more or less arbitrarily (we only have certain scattered sites for each of these cultures); 2) economic or population contacts are difficult to ascertain and to represent graphically; and 3) time periods for archaeological sites are important – in fact, they are probably THE most important aspect in assessing how accurate a map (and its “arrows” of migration or exchange) represents reality.

A careful, detailed study like this one, if applied to the Pontic-Caspian steppe, would probably reveal how R1b subclades dominated steppe clans, beginning at least during the Suvorovo-Novodanilovka expansion to the west, and certainly representing the vast majority of lineages during the internal expansion in the Early Yamna period and its later expansion east and west of the steppe…

Featured image from the article, summing up Geography, Archaeology, and Genetics of Yakutia – including Y-DNA and mtDNA haplogroups from ancient populations.

Related:

Indo-European pastoralists healthier than modern populations? Genomic health improving over time

genetic-risk

A new paper has appeared at BioRxiv, The Genomic Health Of Ancient Hominins (2017) by Berence, Cooper and Lachance.

Important results are available at: http://popgen.gatech.edu/ancient-health/.

While the study’s many limitations are obvious to the authors, they still suggest certain interesting possibilities as the most important conclusions:

  • In general, Genetic risk scores (GRS) are similar to present-day individuals
  • Genomic health seems to be improving over time
  • Pastoralists could have been healthier than older and modern populations

Some details and shortcomings of the study (most stated by them, bold is from me) include:

  • Allele selection: only some of the known autosomal disease-associated SNPs were included
  • Discovered disease-associated SNPs are known to be biased toward European diseases
  • Ancient sample selection and genomic quality: only 147 ancient genomes were included, from 449 available, with a conventional cut made at 50% of the focal 3180 disease-associated loci. These samples did not include the same loci. All this can affect whether an individual has high or low GRS (a relationship was found between GRS percentiles and sequencing coverage for ancient samples).
  • Phase 3 of the 1000 Genomes Project was used. However, many disease alleles that segregated in the past remain undiscovered – therefore, GRS for ancient individuals should be considered to be underestimated.
  • Genetic risk scores were calculated for each individual (with different sets of disease-associated loci), hence they were not comparable across individuals. So GRS were standardized as GRS percentiles, with certain assumptions, comparing them to modern individuals
  • Multiple comparisons with all data available, using multiple groups, in the small sample selected: comparisons were made between standardized GRS percentile, sample age (i.e. estimated date), mode of subsistance, and geographic location.
  • Older samples have worse coverage, especially Altai Neandertal, Ust’-Ishim, and Denisovan (which might influence results in hunter-gatherers)
  • Northern ancient individuals (using latitude values) show healthier genomes: but, most ancient individuals are from Eurasia, and samples are heterogeneous.
  • Agriculturalists show a higher genetic risk for dental/periodontal diseases than hunger-gatherers and pastoralists. However, this disease has the smallest number of risk loci (k = 40), so risk in older samples might be underestimated, and pastoralists are the more recent agriculturalist population (most used agriculture as a complementary diet), so it is only natural that selection had an impact over time in this aspect.
  • Pastoralists have the smallest sample size (19 samples) and geographic range, so conclusions about this group are still less trustworthy.
  • Genetic risk percentile ≠ Genomic health ≠ phenotypic health (not deterministic), and also disease-associated alleles in modern populations ≠ same effects in past environments.

To sum up, an interesting approach to studying genomic health with the scarce data available, but too many comparisons, with too many hypotheses being tested, which remind to a brute-force attack on data that can therefore yield statistically significant results anytime, anywhere.