New DNA coalescent models and old population genetics software†

Abstract

The analyses of often large amounts of field and laboratory data depend on computer programs to generate descriptive statistics and to test hypotheses. The algorithms in these programs are often complex and can be understood only with advanced training in mathematics and programming, topics that are beyond the capabilities of most fisheries biologists and empirical population geneticists. The backward looking Kingman coalescent model, based on the classic forward-looking Wright–Fisher model of genetic change, is used in many genetics software programs to generate null distributions against which to test hypotheses. An article in this issue by Niwa et al. shows that the assumption of bifurcations at nodes in the Kingman coalescent model is inappropriate for highly fecund Japanese sardines, which have type III life histories. Species with this life history pattern are better modelled with multiple mergers at the nodes of a coalescent gene genealogy. However, only a few software programs allow analysis with multiple-merger coalescent models. This parameter misspecification produces demographic reconstructions that reach too far into the past and greatly overestimates genetically effective population sizes (the number of individuals actually contributing to the next generation). The results of Niwa et al. underline the need to understand the assumptions and model parameters in the software programs used to analyse DNA sequences.

Genetic analysis reveals historical and contemporary population dynamics in the longfin squid Doryteuthis gahi: implications for cephalopod management and conservation

“…In line with previous studies, the Chilean-Falkland population conformed to equilibrium expectations of a stable population while the Peruvian population exhibited non-equilibrium signatures compatible with population size changes (Ibanez et al, 2012;Ibanez and Poulin, 2014). While non-equilibrium signatures may also be due to locus-specific selection (Grant et al, 2016), similar results for Peruvian samples of D. gigas and O. mimas point to concordant population size changes across species within the Peruvian waters. The timing of these changes can be placed within the post-glacial period which has encompassed considerable changes in HCS productivity (Pardo-Gandarillas et al, 2018).…”

Coalescent Processes with Skewed Offspring Distributions and Nonequilibrium Demography

“…Finally, we apply our approach to mtDNA from Japanese sardine (S. melanostictus) populations. where patterns of sequence variation were shown to be more consistent with sole influence from sweepstake reproductive events, again highlighting the potential mis-inference of growth if reproductive skew is not properly accounted for (Grant et al 2016;Niwa et al 2016).…”

Coalescent Processes with Skewed Offspring Distributions and non-Equilibrium Demography

“…Furthermore, we quantify the bias of coalescent and population growth parameter estimates when mistakenly neglecting population demography or reproductive skew. Finally, we apply our approach to mtDNA from Japanese sardine (Sardinops melanostictus) populations where patterns of sequence variation were shown to be more consistent with sole influence from sweepstake reproductive events, again highlighting the potential mis-inference of growth if reproductive skew is not properly accounted for (Niwa et al 2016;Grant et al 2016).…”