Molecular Population Genetics

Abstract

Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data.

Population Genomics on the Fly: Recent Advances in Drosophila

“…In heterogametic males (XY), X-linked mutations are hemizygous and therefore directly exposed to selection, whereas new recessive autosomal mutations are masked from expression in heterozygotes individuals. Moreover, the effective recombination rate is ~1.8-fold greater on the X compared to autosomes [194], which reduces Hill-Robertson interference and increases the efficiency of selection. The increased selection in hemizygous males together with the higher efficiency of selection due to the increased recombination may act synergistically to account for the "faster-X evolution", which is generally supported by genomic data collected in Drosophila populations (reviewed in [255]).…”

A comprehensive overview of the developmental basis and adaptive significance of a textbook polymorphism: head asymmetry in the cichlid fish Perissodus microlepis

“…Some studies observed phylogeographic structure among P. microlepis populations (Koblmüller et al, 2009;Lee et al, 2010;Raffini et al, 2017); however, the effects of this population subdivision and demographic history on the phenotypic and genetic bases of head asymmetry have not been fully investigated. Neutral population processes such as mutation, gene flow and genetic drift can play an important role in phenotypic/genetic diversity and hence adaptation, especially for polygenic traits (reviewed in Hedrick, 2011;Yeaman, 2015;Bernatchez, 2016;Casillas & Barbadilla, 2017, examples in cichlids: Koblmüller et al, 2011Husemann, 2013;Sefc et al, 2017). Particularly, hybridization have a relevant impact on intra-and interspecific divergence (reviewed in Schwenk et al, 2008;Abbott et al, 2013), as seen in cichlids (e.g., Nichols et al, 2015;Kautt et al, 2016;Meier et al, 2017;Irissari et al, in press).…”

A faster and more accurate algorithm for calculating population genetics statistics requiring sums of Stirling numbers of the first kind

“…The dominant paradigm in population genetics is based on a comparison of observed data with parameters derived from a theoretical model [1,2]. Specifically for DNA sequences, many techniques have been developed to test for extreme relationships between average sequence diversity (number of DNA differences between individuals) and the number alleles (distinct DNA sequences in the population).…”