Controlling for non-independence in comparative analysis of patterns across populations within species

Graham N. Stone, Sean Nee, Joseph Felsenstein

Research output: Contribution to journalLiterature reviewpeer-review


How do we quantify patterns (such as responses to local selection) sampled across multiple populations within a single species? Key to this question is the extent to which populations within species represent statistically independent data points in our analysis. Comparative analyses across species and higher taxa have long recognized the need to control for the non-independence of species data that arises through patterns of shared common ancestry among them (phylogenetic non-independence), as have quantitative genetic studies of individuals linked by a pedigree. Analyses across populations lacking pedigree information fall in the middle, and not only have to deal with shared common ancestry, but also the impact of exchange of migrants between populations (gene flow). As a result, phenotypes measured in one population are influenced by processes acting on others, and may not be a good guide to either the strength or direction of local selection. Although many studies examine patterns across populations within species, few consider such non-independence. Here, we discuss the sources of non-independence in comparative analysis, and show why the phylogeny-based approaches widely used in cross-species analyses are unlikely to be useful in analyses across populations within species. We outline the approaches (intraspecific contrasts, generalized least squares, generalized linear mixed models and autoregression) that have been used in this context, and explain their specific assumptions. We highlight the power of 'mixed models' in many contexts where problems of non-independence arise, and show that these allow incorporation of both shared common ancestry and gene flow. We suggest what can be done when ideal solutions are inaccessible, highlight the need for incorporation of a wider range of population models in intraspecific comparative methods and call for simulation studies of the error rates associated with alternative approaches.

Original languageEnglish
Pages (from-to)1410-1424
Number of pages15
JournalPhilosophical Transactions of the Royal Society B: Biological Sciences
Issue number1569
Publication statusPublished - 12 May 2011


  • intraspecific
  • comparative method
  • contrasts
  • generalized least squares
  • autoregression


Dive into the research topics of 'Controlling for non-independence in comparative analysis of patterns across populations within species'. Together they form a unique fingerprint.

Cite this