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What Can Ancient DNA Tell Us About Complex Trait Evolution?

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What Can Ancient DNA Tell Us About Complex Trait Evolution? Quantitative Human Paleogenetics: what can ancient DNA tell us about complex trait evolution? Evan K. Irving-Pease1, , Rasa Muktupavela1, Michael Dannemann2, and Fernando Racimo1, 1Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark 2Center for Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, Tartu, Estonia Genetic association data from national biobanks and large-scale age, sex and socioeconomic status (Mostafavi et al., 2020). association studies have provided new prospects for understand- Ancient genomics has yielded considerable insights into nat- ing the genetic evolution of complex traits and diseases in hu- ural selection on large-effect variants (Malaspinas, 2016; De- mans. In turn, genomes from ancient human archaeological re- hasque et al., 2020), and an increasing number of studies are mains are now easier than ever to obtain, and provide a direct also now utilizing ancient genomes to learn about polygenic window into changes in frequencies of trait-associated alleles in adaptation; the process by which natural selection acts on a the past. This has generated a new wave of studies aiming to trait with a large number of genetic loci, leading to changes in analyse the genetic component of traits in historic and prehis- toric times using ancient DNA, and to determine whether any allele frequencies at many sites across the genome. Among such traits were subject to natural selection. In humans, how- these studies, the most commonly inferred complex traits are ever, issues about the portability and robustness of complex trait pigmentation and standing height. inference across different populations are particularly concern- Skin, hair and eye pigmentation are among the least ing when predictions are extended to individuals that died thou- polygenic complex traits; though more than a hundred sands of years ago, and for which little, if any, phenotypic val- pigmentation-associated loci have been found, their heri- idation is possible. In this review, we discuss the advantages of incorporating ancient genomes into studies of trait-associated tability is largely dominated by large-effect common SNPs variants, the need for models that can better accommodate an- (Sturm et al., 2008; Eiberg et al., 2008; Sulem et al., 2007; cient genomes into quantitative genetic frameworks, and the ex- Han et al., 2008; Liu et al., 2015; O’Connor et al., 2019; isting limits to inferences about complex trait evolution, partic- Hider et al., 2013). Additionally, several of these vari- ularly with respect to past populations. ants have signatures of past selective sweeps detectable in present-day genomes (Sabeti et al., 2007; Lao et al., 2007; aDNA | Paleogenetics | GWAS | Polygenic adaptation | Complex traits Pickrell et al., 2009; Rocha, 2020). Nevertheless, genomic Correspondence: [email protected], analyses in previously understudied populations—like sub- [email protected] Saharan African groups—suggest that perhaps hundreds of skin pigmentation alleles of small effect remain to be found 1 - Complex trait genomics and ancient DNA (Martin et al., 2017b). Similarly, recent studies have shown that eye pigmentation is far more polygenic than previous The last decade has seen dramatic advances in our under- thought (Simcoe et al., 2021). Recent quantitative and molec- standing of the genetic architecture of polygenic traitsDRAFT (Viss- ular genomic studies are painting an increasingly complex cher et al., 2017). The advent of genome-wide association picture of the architecture of these traits, featuring more con- studies (GWAS), with large sample sizes and deep phenotyp- siderable roles for epistasis, pleiotropy and small-effect vari- arXiv:2105.02754v2 [q-bio.PE] 13 Jul 2021 ing of individuals, has led to the identification of thousands ants than were previously assumed (for an extensive review of loci associated with complex traits and diseases (Bycroft of skin pigmentation, see Quillen et al.(2019)). et al., 2018; Buniello et al., 2019; MacArthur et al., 2017). Recently, ancient DNA (aDNA) studies have attempted to re- The resulting associations, and their inferred effect sizes, construct pigmentation phenotypes in ancient human popula- have enabled the development of so-called polygenic risk tions, although the extent to which these predictions are ac- scores (PRS), which summarise either the additive genetic curate remains uncertain. These reconstructions have been contribution of single nucleotide polymorphisms (SNPs) to a mostly focused on ancient individuals from Western Eura- quantitative trait (e.g., height), or the increase in probability sia, due to the relatively higher abundance of SNP-phenotype of a binary trait (e.g., major coronary heart disease) (Dud- associations from European-centric studies, and the poor bridge, 2013). For some well-characterised medical traits, portability of gene-trait associations to more distantly re- like cardiovascular disease, the predictive value of PRS has lated populations (Martin et al., 2017a, 2019). For example, led to their adoption in clinical settings (Knowles and Ash- Olalde et al.(2014) queried pigmentation-associated SNPs in ley, 2018); however, the accuracy of PRS remains limited genomes of Mesolithic hunter-gatherer remains from western to populations closely related to the original GWAS cohort and central Eurasia, and suggested that the lighter skin colour (Martin et al., 2019) and can vary within populations due to Irving-Pease et al. | arχiv | July 14, 2021 | 1–12 characteristic of Europeans today was not widely present in tially predicted by genetics; with both measures remaining the continent before the Neolithic. González-Fortes et al. relatively constant between the Mesolithic and Neolithic, and (2017) analysed Mesolithic and Eneolithic genomes from increasing between the Neolithic and Bronze Age. A follow- central Europe, and inferred dark hair, brown eyes and dark up study by Cox et al.(2021) used polygenic scores for height skin pigmentation for the Mesolithic individuals and dark to show that PRS predicts 6.8% of the observed variance in hair, light eyes, and lighter skin pigmentation for an Ene- femur length in ancient skeletons, after controlling for other olithic individual. Similarly, Brace et al.(2019) inferred pig- variables. This is approximately one quarter of the predictive mentation phenotypes for Mesolithic and Neolithic genomes accuracy of PRS in present-day populations; which the au- from western Europe, and reported that the so-called ‘Ched- thors attribute to the low-coverage aDNA data used in their dar Man’, a Mesolithic individual from present-day England, study. Contrastingly, Marciniak et al.(2021) used the discor- had blue/green eyes and dark to black skin, in contrast to later dance between PRS for height, calculated from aDNA, and Neolithic individuals with dark to intermediate skin pigmen- height inferred from the corresponding skeletal remains, to tation. Contrastingly, Günther et al.(2018) found elevated argue that Neolithic individuals were shorter than expected frequencies of light skin pigmentation alleles in individuals due to either poorer nutrition or increased disease burden, rel- from the Scandinavian Mesolithic, suggestive of early envi- ative to hunter-gatherer populations. ronmental adaptation to life at higher latitudes. These re- However, the inference of standing height from skeletal re- constructions have also been carried out in individuals with mains is not without its own problems. Both Cox et al.(2021) no skeletal remains; for example, Jensen et al.(2019) used and Marciniak et al.(2021) used the method developed by pigmentation-associated SNPs to infer the skin, hair and eye Ruff et al.(2012) to estimate stature from skeletal remains. colour of a female individual whose DNA was preserved in a Nevertheless, their respective estimates of stature—based on piece of birch tar ‘chewing gum’. femur length—varied between some of the individuals in- Some aDNA studies have sought to systematically investi- cluded in both studies. Where multiple skeletal elements gate how pigmentation-associated variants were introduced were available for ancient individuals, Marciniak et al.(2021) and evolved in the European continent. Wilde et al.(2014) also produced separate stature estimates from femur, tibia, was one of the first studies to provide aDNA-based evidence humerus and radius length, which varied substantially within that skin, hair, and eye pigmentation-associated alleles have some individuals; highlighting the uncertainty in estimates of been under strong positive selection in Europe over the past stature from skeletal remains. 5,000 years. The first large-scale population genomic studies (Haak et al., 2015; Mathieson et al., 2015; Allentoft et al., 2015) showed that major effect alleles associated with light 2 - Inferring complex traits in archaic ho- eye colour likely rose in frequency in Europe before alleles minids associated with light skin pigmentation. More recently, Ju and Mathieson(2021) argued that the increase in light skin The availability of genome sequences from archaic humans, pigmentation in Europeans was primarily driven by strong se- like Neanderthals and Denisovans, has greatly expanded our lection at a small proportion of pigmentation-associated loci understanding of their demographic history and interactions with large effect sizes. When testing for polygenic adaptation with modern humans (Prüfer et al., 2017, 2014; Meyer et
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