@article {Bravo, title = {Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics}, journal = {PeerJ}, volume = {7}, year = {2019}, pages = {e6399}, abstract = {Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are}, doi = {10.7717/peerj.6399}, url = {https://peerj.com/articles/6399.pdf}, author = {Bravo, Gustavo A and Antonelli, Alexandre and Bacon, Christine D and Bartoszek, Krzysztof and Blom, Mozes P K and Huynh, Stella and Jones, Graham and Knowles, L Lacey and Lamichhaney, Sangeet and Marcussen, Thomas and Morlon, H{\'e}l{\`e}ne and Nakhleh, Luay K and Oxelman, Bengt and Pfeil, Bernard and Schliep, Alexander and Wahlberg, Niklas and Werneck, Fernanda P and Wiedenhoeft, John and Willows-Munro, Sandi and Edwards, Scott V.} }