Joint analysis of demography and selection in population genetics: where do we stand and where could we go?

Abstract

Teasing apart the effects of selection and demography on genetic polymorphism remains one of the major challenges in the analysis of population genomic data. The traditional approach has been to assume that demography would leave a genome-wide signature, whereas the effect of selection would be local. In the light of recent genomic surveys of sequence polymorphism, several authors have argued that this approach is questionable based on the evidence of the pervasive role of positive selection and that new approaches are needed. In the first part of this review, we give a few empirical and theoretical examples illustrating the difficulty in teasing apart the effects of selection and demography on genomic polymorphism patterns. In the second part, we review recent efforts to detect recent positive selection. Most available methods still rely on an a priori classification of sites in the genome but there are many promising new approaches. These new methods make use of the latest developments in statistics, explore aspects of the data that had been neglected hitherto or take advantage of the emerging population genomic data. A current and promising approach is based on first estimating demographic and genetic parameters, using, e.g., a likelihood or approximate Bayesian computation framework, focusing on extreme outlier regions, and then using an independent method to confirm these. Finally, especially for species where evidence of natural selection has been limited, more experimental and versatile approaches that contrast populations under varied environmental constraints might be more successful compared with species-wide genome scans in search of specific signatures.

Urbanization shapes the demographic history of a native rodent (the white-footed mouse, Peromyscus leucopus ) in New York City

“…Patterns of genetic variation and population structure reflect past demographic processes [26], and genome-wide SNPs generated from ddRADseq provided enough information to distinguish recent demographic events from past geological processes. Our demographic models estimated divergence times and migration patterns that are consistent with the known geological and historical record of NYC.…”

Disentangling the Roles of History and Local Selection in Shaping Clinal Variation of Allele Frequencies and Gene Expression in Norway Spruce (Picea abies)

“…We then tested for clinal variation in gene expression in a subset of the genes for which clinal variation was detected for SNP allele frequencies. This study offers a clear illustration of the interplay between demographic history and selection in shaping genetic variation and of the intrinsic difficulty in telling the two apart (Li et al 2012). …”

Revisiting the false positive rate in detecting recent positive selection

“…However, it is always difficult to distinguish these footprints from the confounding signatures of demography, such as population size expansion and bottleneck [93,94]. According to our work, the most reliable approach to detect selection, besides functional analysis, may be a genome-wide approach.…”

“…However, it would be a great challenge for all who are working in this field to develop such tests. Recently, the (joint) analysis of demography and selection [25,26,42,90,93,99,100] has become an central issue, and it is believed that we are on the right track. However, researchers should be made aware that simulations have shown that the popularly used SweepFinder is not robust to certain demographics, for example, severe and recent bottlenecks [23].…”