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The study of structured populations — new hope for a difficult and divided science

Nature Reviews Genetics volume 4, pages 535–543 (2003)Cite this article

Key Points

  • Population genetics can be used to study the history of natural populations. However, it is a difficult science because natural populations have complex geographies and histories.

  • With the advent of DNA-sequence-based data sets drawn from natural populations two main schools of study developed: the phylogeographic approach, which uses the data to estimate the evolutionary tree, or gene tree, then attempts to interpret the history of the populations from which the samples came; and the summary statistics approach, which is an outgrowth of mathematical population genetics and proceeds by mathematically fitting specific population-genetic models to the data.

  • The phylogeographic approach has the advantage of not being constrained by specific models, and lends itself to exploratory types of analysis. However, it is highly dependent on gene-tree estimates, which are often incorrect. This method can be misleading if investigators focus on just a single gene or stretches of tightly-linked sequence, such as mitochondrial DNA, and overlook the large stochastic variance that arises among genes in populations.

  • Summary-statistic approaches can be mathematically sophisticated and provide ways to compare models and assess the sources of variance in the process that gave rise to the data. However, these methods are often highly constrained by the available models and are difficult to apply if investigators have little knowledge of the locations and boundaries of populations in nature. Also, they do not usually take full advantage of all of the information that is available in the data.

  • In recent years, a new family of methods has begun to offer the advantages of the phylogeographic approach, using all of the information in the data and allowing diverse models to be considered, together with the mathematical sophistication of the summary-statistics methods. These are probabilistic methods in which gene trees have a role, but in a framework in which they are used strictly in conjunction with their probability. As these methods continue to develop, they offer the promise of increased flexibility and applicability to a wide range of questions in the history of populations.

Abstract

Natural populations, including those of humans, have complex geographies and histories. Studying how they evolve is difficult, but it is possible with population-based DNA sequence data. However, the study of structured populations is divided by two distinct schools of thought and analysis. The phylogeographic approach is fundamentally graphical and begins with a gene-tree estimate. By contrast, the more traditional approach of using summary statistics is fundamentally mathematical. Both approaches have limitations, but there is promise in newer probabilistic methods that offer the flexibility and data exploitation of the phylogeographic approach in an explicitly model-based mathematical framework.

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Figure 1: Models of population structure.
Figure 2: Contrasting phylogeographic and summary-statistic methods.
Figure 3: The stochastic variance of gene trees.
Figure 4: The isolation-with-migration model.

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Acknowledgements

We are grateful to M. Hare, Y.-J. Won and two anonymous referees for helpful suggestions and corrections. This work was supported in part by a grant from the National Institutes of Health to J.H.

Author information

Authors and Affiliations

  1. Department of Genetics, Rutgers the State University of New Jersey, 604 Allison Road, Piscataway, 08854, New Jersey, USA

    Jody Hey

  2. Department of Ecology and Evolutionary Biology, University of Arizona, 1041 East Lowell Street, BSW 308, Tucson, 85721, Arizona, USA

    Carlos A. Machado

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FURTHER INFORMATION

Batwing

Genetree

GeoDis

LAMARC

MDIV

Glossary

DEMOGRAPHIC HISTORY

The reproductive history of a population or group of populations. This can include population sizes, sex ratios, migration rates, population-splitting events, variation in reproductive rates and times among organisms, as well as variation over time in all of these quantities.

POISSON DISTRIBUTION

A probability distribution that is commonly used to describe the frequency at which similar but independent events can be expected to occur over a given period of time.

GENE EXCHANGE

The process by which genetic material is shared among organisms, which can occur through sexual reproduction or lateral genetic transfer.

GENETIC DRIFT

Random changes in gene frequency in a population that occur when a finite number of progeny are formed by the random sampling of gametes from the parents.

HARDY-WEINBERG

A classical mathematical principle in population genetics that describes the expected frequencies of genotypes for one locus after one generation of random mating if the allele frequencies in the parents are known.

EVOLUTIONARY TREE

A graph or branching diagram that describes the pattern of evolutionary ancestry (historical relationships) among a group of organisms.

GENE TREE

A graph or branching diagram that describes the pattern of ancestry among homologous DNA sequences from different individuals of a population or species.

PHYLOGENETIC TREE

A graph or branching diagram that describes the pattern of ancestry among different species or other taxa.

SYSTEMATICS

A branch of biology that deals with the classification of living organisms on the basis of their evolutionary relationships. This differs from 'taxonomy' as organisms are grouped on the basis of shared ancestry, not just on their similarities (which might or might not correspond to shared evolutionary history).

COALESCENT THEORY

A mathematical approach that models the depths of gene trees for samples that are drawn from one or more closely related populations.

ESTIMATOR

A method for calculating an estimate of a parameter in a model.

SUMMARY STATISTIC

A number that is calculated from a data set, which represents much of the information in the data. For a set of DNA sequences, one commonly used summary statistic is S, which represents the number of variable sites in the sample. Summary statistics are often easier to use to fit models to data than would be the case with the data itself.

OUTGROUP

A sample or group of samples that are included in an evolutionary tree because they are known, or assumed, to connect directly to the root of the tree (that is, to the node of the tree that represents the common ancestor of all samples in the tree).

HOMOPLASY

Identical character states (for example, the same nucleotide base in a DNA sequence) that are not the result of common ancestry (not homologous), but arose independently in different ancestors by parallel or convergent mutations.

LINKAGE BLOCK

A region of DNA that is inherited as a single unit owing to a lack of recombination, such as the mitochondrial DNA of metazoans. The histories of genes that are located in such regions are not independent, and are equally affected by all the selective forces that have acted anywhere in the linkage block.

ALLOPATRIC DIFFERENTIATION

The process of divergence between populations or species that are geographically separated.

INFERENCE KEY

A list of paired rules that are used for diagnosis or identification. Keys are a classic tool for identifying organisms to the species level, on the basis of the presence or absence of specific morphological characters or character states. A similar tool is used in nested-clade analysis to distinguish between different historical scenarios.

HEURISTIC

A method of inference that relies on educated guesses or simplifications that limit the parameter space over which solutions are searched. This approach is not guaranteed to find the correct answer.

STOCHASTIC VARIANCE

In the context of gene histories, this is the variation in gene trees and mutations among unlinked genes that have passed through the same demographic history of populations of organisms.

MONOPHYLY

The property that is attributed to a group of samples in an evolutionary tree that all share the same common ancestor exclusive of other samples in the tree. A set of samples that constitute an entire branch on an evolutionary tree is said to be monophyletic.

F-STATISTICS

A method of summary statistics that was devised by Sewall Wright to describe correlations among alleles that are sampled at different hierarchical levels (individuals, subpopulations and total populations). F-statistics are frequently used to describe the presence of population structure.

SINGLETON MUTATIONS

Polymorphic sites in which a rare base is found in only one of the sampled sequences.

POLYMORPHIC-SITE FREQUENCY DISTRIBUTION

A polymorphic site in a DNA sequence can be described by the frequency of one of its variable bases. The distribution of these values for all the polymorphic sites in a sample can be described using a histogram or bar chart. The shape of the histogram can provide qualitative information on the processes that are involved in the history of the sample.

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Hey, J., Machado, C. The study of structured populations — new hope for a difficult and divided science. Nat Rev Genet 4, 535–543 (2003). https://doi.org/10.1038/nrg1112

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