Abstract
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 data sets 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 that are among 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 data sets for phylogenetics, divergence time estimation, and inference of introgression, and we propose a strategy to optimize 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. [Aves; incomplete lineage sorting; introgression; PE-ddRAD-Seq; phylogenomics; radiations; shearwaters; UCEs.]
Highlights
Estimation and inference of introgression, and we propose a strategy to optimise RAD-Seq data for phylogenetic analyses
Our results demonstrate the power of integrating ultraconserved elements (UCEs) and RAD markers for resolving the phylogenetic relationships of a group of pelagic seabirds characterised by rapid diversification events that have confounded previous phylogenetic studies
Using a higher number of taxa and loci than these previous studies, we show the advantages of integrating PE-ddRAD-Seq and UCE data to infer the phylogenetic relationships of a challenging group, the shearwaters, across a range of timescales using concatenation and coalescent approaches
Summary
Estimation and inference of introgression, and we propose a strategy to optimise RAD-Seq data for phylogenetic analyses. Several methodological approaches have been developed that simultaneously account for both ILS and gene flow when reconstructing the evolutionary history of a clade (Solís-Lemus et al 2017; Wen et al 2018) The footprints of these processes on sequence data can, vary between different phylogenomic markers at different phylogenetic scales depending on factors such as their evolutionary rates or the type of selection that they experience (Martin and Jiggins 2017; Knowles et al 2018). RAD-Seq and UCEs have been compared in terms of divergence time estimation using fossil-calibrated molecular-clock models and have been shown to accurately estimate divergence times at recent timescales (Collins and Hrbek 2018) Integrating these two approaches may provide a powerful tool for disentangling the roles of ILS and introgression in rapid diversification events; empirical studies to test this assumption are generally lacking. Hybridisation can be common at the species level (Mallet 2005) and birds show relatively high levels, with 16.4% of the species having been documented to hybridise in nature (Ottenburghs et al 2015)
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