Supplementary information for integrating sequence capture and restriction-site associated DNA sequencing to resolve recent radiations of Pelagic seabirds

The diversification of modern birds has been shaped by a number of
radiations. Rapid diversification events make reconstructing the
evolutionary relationships among taxa challenging due to the convoluted
effects of incomplete lineage sorting (ILS) and introgression.
Phylogenomic datasets have the potential to detect patterns of
phylogenetic incongruence, and to address their causes. However, the
footprints of ILS and introgression on sequence data can vary between
different phylogenomic markers at different phylogenetic scales depending
on factors such as their evolutionary rates or their selection pressures.
We show that combining phylogenomic markers that evolve at different
rates, such as paired-end double-digest restriction site-associated DNA
(PE-ddRAD) and ultraconserved elements (UCEs), allows a comprehensive
exploration of the causes of phylogenetic discordance associated with
short internodes at different timescales. We used thousands of UCE and
PE-ddRAD markers to produce the first well-resolved phylogeny of
shearwaters, a group of medium-sized pelagic seabirds amongst the most
phylogenetically controversial and endangered bird groups. We found that
phylogenomic conflict was mainly derived from high levels of ILS due to
rapid speciation events. We also documented a case of introgression,
despite the high philopatry of shearwaters to their breeding sites, which
typically limits gene flow. We integrated state-of-the-art concatenated
and coalescent-based approaches to expand on previous comparisons of UCE
and RAD-Seq datasets for phylogenetics, divergence time estimation and
inference of introgression, and we propose a strategy to optimise RAD-Seq
data for phylogenetic analyses. Our results highlight the usefulness of
combining phylogenomic markers evolving at different rates to understand
the causes of phylogenetic discordance at different timescales.