Mexican Biobank advances population and medical genomics of diverse ancestries.

Latin America continues to be severely underrepresented in genomics research, and fine-scale genetic histories and complex trait architectures remain hidden owing to insufficient data1. To fill this gap, the Mexican Biobank project genotyped 6,057 individuals from 898 rural and urban localities across all 32 states in Mexico at a resolution of 1.8 million genome-wide markers with linked complex trait and disease information creating a valuable nationwide genotype-phenotype database. Here, using ancestry deconvolution and inference of identity-by-descent segments, we inferred ancestral population sizes across Mesoamerican regions over time, unravelling Indigenous, colonial and postcolonial demographic dynamics2-6. We observed variation in runs of homozygosity among genomic regions with different ancestries reflecting distinct demographic histories and, in turn, different distributions of rare deleterious variants. We conducted genome-wide association studies (GWAS) for 22 complex traits and found that several traits are better predicted using the Mexican Biobank GWAS compared to the UK Biobank GWAS7,8. We identified genetic and environmental factors associating with trait variation, such as the length of the genome in runs of homozygosity as a predictor for body mass index, triglycerides, glucose and height. This study provides insights into the genetic histories of individuals in Mexico and dissects their complex trait architectures, both crucial for making precision and preventive medicine initiatives accessible worldwide.

The design of mapping populations: Impacts of geographic scale on genetic architecture and mapping efficacy for defense and immunity.

Genome-wide association studies (GWAS) have yielded tremendous insight into the genetic architecture of trait variation. However, the collections of loci they uncover are far from exhaustive. As many of the complicating factors that confound or limit the efficacy of GWAS are exaggerated over broad geographic scales, a shift toward more analyses using mapping panels sampled from narrow geographic localities ("local" populations) could provide novel, complementary insights. Here, we present an overview of the major complicating factors, review mounting evidence from genomic analyses that these factors are pervasive, and synthesize theoretical and empirical evidence for the power of GWAS in local populations.

A rarefaction approach for measuring population differences in rare and common variation.

In studying allele-frequency variation across populations, it is often convenient to classify an allelic type as "rare," with nonzero frequency less than or equal to a specified threshold, "common," with a frequency above the threshold, or entirely unobserved in a population. When sample sizes differ across populations, however, especially if the threshold separating "rare" and "common" corresponds to a small number of observed copies of an allelic type, discreteness effects can lead a sample from one population to possess substantially more rare allelic types than a sample from another population, even if the two populations have extremely similar underlying allele-frequency distributions across loci. We introduce a rarefaction-based sample-size correction for use in comparing rare and common variation across multiple populations whose sample sizes potentially differ. We use our approach to examine rare and common variation in worldwide human populations, finding that the sample-size correction introduces subtle differences relative to analyses that use the full available sample sizes. We introduce several ways in which the rarefaction approach can be applied: we explore the dependence of allele classifications on subsample sizes, we permit more than two classes of allelic types of nonzero frequency, and we analyze rare and common variation in sliding windows along the genome. The results can assist in clarifying similarities and differences in allele-frequency patterns across populations.

Intestinal microbiota of Nearctic-Neotropical migratory birds vary more over seasons and years than between host species.

Seasonal migration of Nearctic-Neotropical passerine birds may have profound effects on the diversity and abundance of their host-associated microbiota. Migratory birds experience seasonal change in environments and diets throughout the course of the annual cycle that, along with recurrent biological events such as reproduction, may significantly impact their microbiota. In this study, we characterize the intestinal microbiota of four closely related species of migratory Catharus thrushes at three time points of their migratory cycle: during spring migration, on the summer breeding territories and during fall migration. Using observations replicated over 3 years, we determined that microbial community diversity of Catharus thrushes was significantly different across distinct time periods of the annual cycle, whereas community composition was more similar within than across years. Elevated alpha diversity in the summer birds compared to either migratory period indicated that birds may harbour a reduced microbiota during active migration. We also found that community composition of the microbiota did not substantially differ between host species. Finally, we recovered two phyla, Cyanobacteria and Planctomycetota, which are not commonly described from birds, that were in relatively high abundance in specific years. This study contributes to our growing understanding of how microbiota in wild birds vary throughout disparate ecological conditions and reveals potential axes across which an animal's microbial flexibility adapts to variable environments and recurrent biological conditions throughout the annual cycle.

Addressing the challenges of polygenic scores in human genetic research.

The genotyping of millions of human samples has made it possible to evaluate variants across the human genome for their possible association with risks for numerous diseases and other traits by using genome-wide association studies (GWASs). The associations between phenotype and genotype found in GWASs make possible the construction of polygenic scores (PGSs), which aim to predict a trait or disease outcome in an individual on the basis of their genotype (in the disease case, the term polygenic risk score [PRS] is often used). PGSs have shown promise for studying the biology of complex traits and as a tool for evaluating individual disease risks in clinical settings. Although the quantity and quality of data to compute PGSs are increasing, challenges remain in the technical aspects of developing PGSs and in the ethical and social issues that might arise from their use. This ASHG Guidance emphasizes three major themes for researchers working with or interested in the application of PGSs in their own research: (1) developing diverse research cohorts; (2) fostering robustness in the development, application, and interpretation of PGSs; and (3) improving the communication of PGS results and their implications to broad audiences.

Modeling the spatiotemporal spread of beneficial alleles using ancient genomes.

Ancient genome sequencing technologies now provide the opportunity to study natural selection in unprecedented detail. Rather than making inferences from indirect footprints left by selection in present-day genomes, we can directly observe whether a given allele was present or absent in a particular region of the world at almost any period of human history within the last 10,000 years. Methods for studying selection using ancient genomes often rely on partitioning individuals into discrete time periods or regions of the world. However, a complete understanding of natural selection requires more nuanced statistical methods which can explicitly model allele frequency changes in a continuum across space and time. Here we introduce a method for inferring the spread of a beneficial allele across a landscape using two-dimensional partial differential equations. Unlike previous approaches, our framework can handle time-stamped ancient samples, as well as genotype likelihoods and pseudohaploid sequences from low-coverage genomes. We apply the method to a panel of published ancient West Eurasian genomes to produce dynamic maps showcasing the inferred spread of candidate beneficial alleles over time and space. We also provide estimates for the strength of selection and diffusion rate for each of these alleles. Finally, we highlight possible avenues of improvement for accurately tracing the spread of beneficial alleles in more complex scenarios.

Analyzing the genomes of our ancient ancestors can reveal how certain traits spread through the human population over the course of evolution. Mutations that make individuals better equipped to survive their environment are more likely to be passed on to the next generation and become more common. For example, a genetic variant that enables adult people to digest sugars in dairy products has become more common in humans over time. Yet evolution does not only happen across time: it transverses space as well. Modeling the geographic spread of such genetic mutations is challenging using existing methods. To overcome this, Muktupavela et al. developed a new computational method that uses modern and ancient human genomes to study the evolution of specific genetic variants across space and time. The tool can determine where certain variants first emerged, how quickly they spread across geographic areas, and how rapidly they became prevalent in human populations. Muktupavela et al. applied their new method, which was based on a previously published framework, to track the spread of two common genetic variations that have previously been reported to be subject to natural selection: one that allows adult humans to digest dairy products, and another associated with skin pigmentation. They found that the mutation that enabled dairy consumption originated around what is now southwestern Russia or eastern Ukraine. The variation then spread westward, becoming increasingly more common over the course of the Holocene. The mutation related to skin pigmentation emerged further south than the dairy-related variation, and then also spread westward. Massive human migrations during the Neolithic and Bronze Age eras may have helped disperse both variants. The model developed by Muktupavela et al. could help scientists track the geographic spread of other genetic variants in human populations, as well as provide new insights into how humans adapt to changing environmental conditions. Incorporating major events into the model, like mass migrations or glacial retreats, may lead to even more insights.

Population genetic models for the spatial spread of adaptive variants: A review in light of SARS-CoV-2 evolution.

Theoretical population genetics has long studied the arrival and geographic spread of adaptive variants through the analysis of mathematical models of dispersal and natural selection. These models take on a renewed interest in the context of the COVID-19 pandemic, especially given the consequences that novel adaptive variants have had on the course of the pandemic as they have spread through global populations. Here, we review theoretical models for the spatial spread of adaptive variants and identify areas to be improved in future work, toward a better understanding of variants of concern in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) evolution and other contemporary applications. As we describe, characteristics of pandemics such as COVID-19-such as the impact of long-distance travel patterns and the overdispersion of lineages due to superspreading events-suggest new directions for improving upon existing population genetic models.

The background and legacy of Lewontin's apportionment of human genetic diversity.

Lewontin's 1972 article 'The apportionment of human diversity' described a key feature of human genetic diversity that would have profound impacts on conversations regarding genetics and race: the typical genetic locus varies much less between classical human race groupings than one might infer from inspecting the features historically used to define those races, like skin pigmentation. From this, Lewontin concluded: 'Human racial classification … is now seen to be of virtually no genetic or taxonomic significance' (p. 397). Here, 50 years after the paper's publication, the goal is to understand the origins and legacy of the paper. Aided by insights from published papers and interviews with several of Lewontin's contemporaries, I review the 1972 paper, asking about the intellectual background that led to the publication of the paper, the development of its impact, the critiques of the work and the work's application and limitations today. The hope is that by gaining a clearer understanding of the origin and reasoning of the paper, we might dispel various confusions about the result and sharpen an understanding of the enduring value and insight the result provides. This article is part of the theme issue 'Celebrating 50 years since Lewontin's apportionment of human diversity'.

Getting genetic ancestry right for science and society.

We must embrace a multidimensional, continuous view of ancestry and move away from continental ancestry categories.

Ancient genomes from the Himalayas illuminate the genetic history of Tibetans and their Tibeto-Burman speaking neighbors.

Present-day Tibetans have adapted both genetically and culturally to the high altitude environment of the Tibetan Plateau, but fundamental questions about their origins remain unanswered. Recent archaeological and genetic research suggests the presence of an early population on the Plateau within the past 40 thousand years, followed by the arrival of subsequent groups within the past 10 thousand years. Here, we obtain new genome-wide data for 33 ancient individuals from high elevation sites on the southern fringe of the Tibetan Plateau in Nepal, who we show are most closely related to present-day Tibetans. They derive most of their ancestry from groups related to Late Neolithic populations at the northeastern edge of the Tibetan Plateau but also harbor a minor genetic component from a distinct and deep Paleolithic Eurasian ancestry. In contrast to their Tibetan neighbors, present-day non-Tibetan Tibeto-Burman speakers living at mid-elevations along the southern and eastern margins of the Plateau form a genetic cline that reflects a distinct genetic history. Finally, a comparison between ancient and present-day highlanders confirms ongoing positive selection of high altitude adaptive alleles.

Properties of 2-locus genealogies and linkage disequilibrium in temporally structured samples.

Archeogenetics has been revolutionary, revealing insights into demographic history and recent positive selection. However, most studies to date have ignored the nonrandom association of genetic variants at different loci (i.e. linkage disequilibrium). This may be in part because basic properties of linkage disequilibrium in samples from different times are still not well understood. Here, we derive several results for summary statistics of haplotypic variation under a model with time-stratified sampling: (1) The correlation between the number of pairwise differences observed between time-staggered samples (πΔt) in models with and without strict population continuity; (2) The product of the linkage disequilibrium coefficient, D, between ancient and modern samples, which is a measure of haplotypic similarity between modern and ancient samples; and (3) The expected switch rate in the Li and Stephens haplotype copying model. The latter has implications for genotype imputation and phasing in ancient samples with modern reference panels. Overall, these results provide a characterization of how haplotype patterns are affected by sample age, recombination rates, and population sizes. We expect these results will help guide the interpretation and analysis of haplotype data from ancient and modern samples.

Haplotype-based inference of the distribution of fitness effects.

Recent genome sequencing studies with large sample sizes in humans have discovered a vast quantity of low-frequency variants, providing an important source of information to analyze how selection is acting on human genetic variation. In order to estimate the strength of natural selection acting on low-frequency variants, we have developed a likelihood-based method that uses the lengths of pairwise identity-by-state between haplotypes carrying low-frequency variants. We show that in some nonequilibrium populations (such as those that have had recent population expansions) it is possible to distinguish between positive or negative selection acting on a set of variants. With our new framework, one can infer a fixed selection intensity acting on a set of variants at a particular frequency, or a distribution of selection coefficients for standing variants and new mutations. We show an application of our method to the UK10K phased haplotype dataset of individuals.

Indigenous Ancestry and Admixture in the Uruguayan Population.

The Amerindian group known as the Charrúas inhabited Uruguay at the timing of European colonial contact. Even though they were extinguished as an ethnic group as a result of a genocide, Charrúan heritage is part of the Uruguayan identity both culturally and genetically. While mitochondrial DNA studies have shown evidence of Amerindian ancestry in living Uruguayans, here we undertake whole-genome sequencing of 10 Uruguayan individuals with self-declared Charruan heritage. We detect chromosomal segments of Amerindian ancestry supporting the presence of indigenous genetic ancestry in living descendants. Specific haplotypes were found to be enriched in "Charrúas" and rare in the rest of the Amerindian groups studied. Some of these we interpret as the result of positive selection, as we identified selection signatures and they were located mostly within genes related to the infectivity of specific viruses. Historical records describe contacts of the Charrúas with other Amerindians, such as Guaraní, and patterns of genomic similarity observed here concur with genomic similarity between these groups. Less expected, we found a high genomic similarity of the Charrúas to Diaguita from Argentinian and Chile, which could be explained by geographically proximity. Finally, by fitting admixture models of Amerindian and European ancestry for the Uruguayan population, we were able to estimate the timing of the first pulse of admixture between European and Uruguayan indigenous peoples in approximately 1658 and the second migration pulse in 1683. Both dates roughly concurring with the Franciscan missions in 1662 and the foundation of the city of Colonia in 1680 by the Spanish.

Parental relatedness through time revealed by runs of homozygosity in ancient DNA.

Parental relatedness of present-day humans varies substantially across the globe, but little is known about the past. Here we analyze ancient DNA, leveraging that parental relatedness leaves genomic traces in the form of runs of homozygosity. We present an approach to identify such runs in low-coverage ancient DNA data aided by haplotype information from a modern phased reference panel. Simulation and experiments show that this method robustly detects runs of homozygosity longer than 4 centimorgan for ancient individuals with at least 0.3 × coverage. Analyzing genomic data from 1,785 ancient humans who lived in the last 45,000 years, we detect low rates of first cousin or closer unions across most ancient populations. Moreover, we find a marked decay in background parental relatedness co-occurring with or shortly after the advent of sedentary agriculture. We observe this signal, likely linked to increasing local population sizes, across several geographic transects worldwide.

Fast and flexible estimation of effective migration surfaces.

Spatial population genetic data often exhibits 'isolation-by-distance,' where genetic similarity tends to decrease as individuals become more geographically distant. The rate at which genetic similarity decays with distance is often spatially heterogeneous due to variable population processes like genetic drift, gene flow, and natural selection. Petkova et al., 2016 developed a statistical method called Estimating Effective Migration Surfaces (EEMS) for visualizing spatially heterogeneous isolation-by-distance on a geographic map. While EEMS is a powerful tool for depicting spatial population structure, it can suffer from slow runtimes. Here, we develop a related method called Fast Estimation of Effective Migration Surfaces (FEEMS). FEEMS uses a Gaussian Markov Random Field model in a penalized likelihood framework that allows for efficient optimization and output of effective migration surfaces. Further, the efficient optimization facilitates the inference of migration parameters per edge in the graph, rather than per node (as in EEMS). With simulations, we show conditions under which FEEMS can accurately recover effective migration surfaces with complex gene-flow histories, including those with anisotropy. We apply FEEMS to population genetic data from North American gray wolves and show it performs favorably in comparison to EEMS, with solutions obtained orders of magnitude faster. Overall, FEEMS expands the ability of users to quickly visualize and interpret spatial structure in their data.

Public attitudes toward genetic risk scoring in medicine and beyond.

Advances in genomics research have led to the development of polygenic risk scores, which numerically summarize genetic predispositions for a wide array of human outcomes. Initially developed to characterize disease risk, polygenic risk scores can now be calculated for many non-disease traits and social outcomes, with the potential to be used not only in health care but also other institutional domains. In this study, we draw on a nationally-representative survey of U.S. adults to examine three sets of lay attitudes toward the deployment of genetic risk scores in a variety of medical and non-medical domains: 1. abstract belief about whether people should be judged on the basis of genetic predispositions; 2. concrete attitudes about whether various institutions should be permitted to use genetic information; and 3. personal willingness to provide genetic information to various institutions. Results demonstrate two striking differences across these three sets of attitudes. First, despite almost universal agreement that people should not be judged based on genetics, there is support, albeit varied, for institutions being permitted to use genetic information, with support highest for disease outcomes and in reproductive decision-making. We further find significant variation in personal willingness to provide such information, with a majority of respondents expressing willingness to provide information to health care providers and relative finder services, but less than a quarter expressing willingness to do so for an array of other institutions and services. Second, while there are no demographic differences in respondents' abstract beliefs about judging based on genetics, demographic differences emerge in permissibility ratings and personal willingness. Our results should inform debates about the deployment of polygenic scores in domains within and beyond medicine.

A variant-centric perspective on geographic patterns of human allele frequency variation.

A key challenge in human genetics is to understand the geographic distribution of human genetic variation. Often genetic variation is described by showing relationships among populations or individuals, drawing inferences over many variants. Here, we introduce an alternative representation of genetic variation that reveals the relative abundance of different allele frequency patterns. This approach allows viewers to easily see several features of human genetic structure: (1) most variants are rare and geographically localized, (2) variants that are common in a single geographic region are more likely to be shared across the globe than to be private to that region, and (3) where two individuals differ, it is most often due to variants that are found globally, regardless of whether the individuals are from the same region or different regions. Our variant-centric visualization clarifies the geographic patterns of human variation and can help address misconceptions about genetic differentiation among populations.

Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia.

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.

Exploring Population Structure with Admixture Models and Principal Component Analysis.

Population structure is a commonplace feature of genetic variation data, and it has importance in numerous application areas, including evolutionary genetics, conservation genetics, and human genetics. Understanding the structure in a sample is necessary before more sophisticated analyses are undertaken. Here we provide a protocol for running principal component analysis (PCA) and admixture proportion inference-two of the most commonly used approaches in describing population structure. Along with hands-on examples with CEPH-Human Genome Diversity Panel and pragmatic caveats, readers will learn to analyze and visualize population structure on their own data.