Assessment of phylogenetic approaches to study the timing of recombination cessation on sex chromosomes

The evolution of sex chromosomes is hypothesized to be punctuated by consecutive recombination cessation events, forming “evolutionary strata” that ceased to recombine at different time points. The demarcation of evolutionary strata is often assessed by estimates of the timing of recombination cessation (t (RC)) along the sex chromosomes, commonly inferred from the level of synonymous divergence or with species phylogenies at gametologous (X‐Y or Z‐W) sequence data. However, drift and selection affect sequences unpredictably and introduce uncertainty when inferring t (RC). Here, we assess two alternative phylogenetic approaches to estimate t (RC); (i) the expected likelihood weight (ELW) approach that finds the most likely topology among a set of hypothetical topologies and (ii) the BEAST approach that estimates t (RC) with specified calibration priors on a reference species topology. By using Z and W gametologs of an old and a young evolutionary stratum on the neo‐sex chromosome of Sylvioidea songbirds, we show that the ELW and BEAST approaches yield similar t (RC) estimates, and that both outperform two frequently applied approaches utilizing synonymous substitution rates (dS) and maximum likelihood (ML) trees, respectively. Moreover, we demonstrate that both ELW and BEAST provide more precise t (RC) estimates when sequences of multiple species are included in the analyses.