Key Points
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High-throughput sequencing is enabling massively large catalogues of DNA sequence variation to be collected in geographically diverse human populations. Such data sets contain considerable information about human history but are complex and require careful analysis.
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Quality control and exploratory data analyses are critical in analyses of large-scale sequencing data sets and help to identify features of the data that may complicate downstream inferences.
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Functional and comparative genomics data (such as sequence conservation, chromatin immunoprecipitation followed by sequencing (ChIP–seq) and DNase I hypersensitivity) can be leveraged to mitigate the confounding effect of natural selection when inferring demographic models.
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A large number of flexible and sophisticated methods have been developed that allow specific and detailed demographic inferences to be made. The appropriate method to use depends on the specific hypothesis or question being asked, and the underlying assumptions of a given method should be carefully considered.
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As sample sizes become increasingly large, inferences about specific aspects of breeding structure and demography may be possible. However, these methods are still in their infancy and require substantial theoretical and methodological development.
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The increasing availability of ancient DNA from modern and archaic humans provides exciting new possibilities to refine parameters of human evolutionary history, although new methodological development is needed to fully realize the potential of these data.
Abstract
The genomes of contemporary humans contain considerable information about the history of our species. Although the general contours of human evolutionary history have been defined with increasing resolution throughout the past several decades, the continuing deluge of massively large sequencing data sets presents new opportunities and challenges for understanding human evolutionary history. Here, we review the signatures that demographic history imparts on patterns of DNA sequence variation, statistical methods that have been developed to leverage information contained in genome-scale data sets and insights gleaned from these studies. We also discuss the importance of using exploratory analyses to assess data quality, the strengths and limitations of commonly used population genomics methods, and factors that confound population genomics inferences.
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Acknowledgements
The author would like to acknowledge Kelley Harris for helpful discussions regarding SMC-based approaches.
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J.M.A. is a paid consultant of Glenview Capital. J.G.S. declares no competing interests.
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Issues in inferring absolute dates (PDF 141 kb)
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Lambda coalescents (PDF 139 kb)
Glossary
- Exploratory data analyses
-
(EDA). The initial stages of 'digging into' a data set, usually by plotting low-dimensional summaries of the data.
- Likelihoods
-
The probabilities of the data given various models and their parameters, thought of as functions of those parameters. The parameter values that maximize the probability of the data in each model are called maximum likelihood estimates.
- Eigenvectors
-
Vectors that, when multiplied by a given matrix, still point in the same direction.
- Covariance matrix
-
An n×n matrix describing the covariance between each pair in a sample of size n.
- Panmictic population
-
A group of individuals among whom random mating occurs.
- Linkage disequilibrium
-
(LD). Nonrandom association between alleles at physically distinct genomic loci. Over time, this will be broken down by recombination.
- Coalescence times
-
The times in the past when genomic regions shared a common genetic ancestor.
- Isolation by distance
-
Genetic differentiation between individuals induced by geographic separation. Individuals that are closer geographically will be closer genetically.
- Overfitting
-
By adding more parameters to a model, it will begin to model the noise in the observed data, rather than the true underlying mechanism of data generation. Overfit models will generalize poorly to new data sets.
- Cross-validation error
-
The error in predicting the structure of a held-out portion of the data, when a model is trained on a subset of the whole data set. Minimizing cross-validation error is an effective way to choose parameters and hyperparameters.
- Ancestral recombination graphs
-
Graph structures representing the genealogical history of a sample with a recombining genome. In addition to coalescence events (which bring two lineages together and therefore reduce the number of lineages in the graph), recombination events cause splits to occur, which increases the number of lineages in the graph.
- Hidden Markov model
-
(HMM). A statistical model in which a set of underlying hidden states are assumed to follow Markov chain dynamics and induce a set of observed states.
- Reference panel
-
A large number of individuals, related to samples of interest, for which some quality is known (for example, allelic phase).
- Effective population size
-
The size that a theoretical population evolving under a Wright–Fisher model would need to be in order to match aspects of the observed genetic data.
- Poisson process
-
A stochastic process in which new events occur at a constant rate per unit of time. Often used to model mutation.
- Identity by descent
-
(IBD). Whether a genomic region has descended from an ancestor unchanged. A genomic region in two (or more) individuals is identical by descent if it is inherited from a common ancestor without being broken up by recombination. Some authors require IBD segments to also be identical by state, that is, to also have no mutations in the region.
- Identity by state
-
(IBS). Whether a genomic region has the same sequence as the corresponding region in another individual. A genomic region in two (or more) individuals is identical by state if it contains no mutations that distinguish the two individuals. Note that a region of IBS is not necessarily also identical by descent.
- SMC'
-
A modification to the sequential Markov coalescent (SMC) that allows for hidden recombination events that do not change the local genealogy.
- Conditionally sampled alleles
-
Alleles that are sampled from a population given that a set of reference alleles is already in hand.
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Schraiber, J., Akey, J. Methods and models for unravelling human evolutionary history. Nat Rev Genet 16, 727–740 (2015). https://doi.org/10.1038/nrg4005
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DOI: https://doi.org/10.1038/nrg4005
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