Abstract
BackgroundNew polymorphism datasets from heterochroneous data have arisen thanks to recent advances in experimental and microbial molecular evolution, and the sequencing of ancient DNA (aDNA). However, classical tools for population genetics analyses do not take into account heterochrony between subsets, despite potential bias on neutrality and population structure tests. Here, we characterize the extent of such possible biases using serial coalescent simulations.Methodology/Principal FindingsWe first use a coalescent framework to generate datasets assuming no or different levels of heterochrony and contrast most classical population genetic statistics. We show that even weak levels of heterochrony (∼10% of the average depth of a standard population tree) affect the distribution of polymorphism substantially, leading to overestimate the level of polymorphism θ, to star like trees, with an excess of rare mutations and a deficit of linkage disequilibrium, which are the hallmark of e.g. population expansion (possibly after a drastic bottleneck). Substantial departures of the tests are detected in the opposite direction for more heterochroneous and equilibrated datasets, with balanced trees mimicking in particular population contraction, balancing selection, and population differentiation. We therefore introduce simple corrections to classical estimators of polymorphism and of the genetic distance between populations, in order to remove heterochrony-driven bias. Finally, we show that these effects do occur on real aDNA datasets, taking advantage of the currently available sequence data for Cave Bears (Ursus spelaeus), for which large mtDNA haplotypes have been reported over a substantial time period (22–130 thousand years ago (KYA)).Conclusions/SignificanceConsidering serial sampling changed the conclusion of several tests, indicating that neglecting heterochrony could provide significant support for false past history of populations and inappropriate conservation decisions. We therefore argue for systematically considering heterochroneous models when analyzing heterochroneous samples covering a large time scale.
Highlights
Most present population genetics analyses rely on coalescent theory, representing the genetic history of a random set of gene copies with genealogical trees where nodes represent coalescent events, that is when two evolutionary lines of descent reach a common ancestor [1] (Figure 1A; see Table 1 for a summary of notations)
This sampling theory allows an efficient treatment of data and overall good predictions for the outcome of evolution on a set of gene copies in population(s) under specific demographic and migration scenarios. It is most used within the framework of the classical population genetics Wright-Fisher model (WF) [2] and one of several implicit assumptions is that all individuals are sampled at the same time
This is reasonable for most datasets sampled on extant species since (1) polymorphism arises from mutations occurring along the total size of genealogies and (2) the number of generations covered across the sample is low with regard to the total depth of the genealogy that lasts on average 2 Ne generations for mitochondrial DNA with Ne, the effective size of the population considered, assumed to be large in the coalescent framework
Summary
Most present population genetics analyses rely on coalescent theory, representing the genetic history of a random set of gene copies with genealogical trees where nodes represent coalescent events, that is when two evolutionary lines of descent reach a common ancestor [1] (Figure 1A; see Table 1 for a summary of notations) This sampling theory allows an efficient treatment of data and overall good predictions for the outcome of evolution on a set of gene copies in population(s) under specific demographic and migration scenarios. It is most used within the framework of the classical population genetics Wright-Fisher model (WF) [2] (hereafter ‘‘standard’’) and one of several implicit assumptions is that all individuals are sampled at the same time (hereafter ‘‘contemporaneous’’). We characterize the extent of such possible biases using serial coalescent simulations
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