Analysis of DNA sequence variation within marine species using Beta-coalescents

TL;DR

This paper applies advanced coalescent inference methods to marine species DNA data, exploring whether Beta coalescents better model their genealogies, which impacts mutation rate and common ancestor time estimates.

Contribution

It introduces the application of Beta coalescent models to marine species DNA data, addressing the suitability of multiple-merger genealogies over Kingman's coalescent.

Findings

Evidence supporting Beta coalescents for some marine species

Implications for mutation rate and common ancestor time estimation

Potential for more accurate modeling of reproductive behaviors

Abstract

We apply recently developed inference methods based on general coalescent processes to DNA sequence data obtained from various marine species. Several of these species are believed to exhibit so-called shallow gene genealogies, potentially due to extreme reproductive behaviour, e.g. via Hedgecock's "reproduction sweepstakes". Besides the data analysis, in particular the inference of mutation rates and the estimation of the (real) time to the most recent common ancestor, we briefly address the question whether the genealogies might be adequately described by so-called Beta coalescents (as opposed to Kingman's coalescent), allowing multiple mergers of genealogies. The choice of the underlying coalescent model for the genealogy has drastic implications for the estimation of the above quantities, in particular the real-time embedding of the genealogy.