The genomic era has been transformative for many fields, including our understanding of the phylogenetic relationships between organisms. The wide availability of whole-genome sequences practically eliminated data availability as a limiting factor for inferring phylogenetic trees, providing hundreds to thousands of loci for analyses, leading to molecular phylogenetics gradually being replaced by phylogenomics. The new era has also brought new challenges: systematic errors (resulting from, e.g., model violation) can be more pronounced in phylogenomic datasets and can lead to strongly supported incorrect relationships, creating significant incongruence among studies. Here, we review common practices, technical and biological challenges of phylogenomic analyses, with examples illustrated from fungi. We compare major approaches of phylogenetic inference, and illustrate the advantages conferred and challenges presented in phylogenomic case studies across the fungal tree of life, including cases where genome-scale data could conclusively resolve contentious relationships, and others that remain challenging despite the flood of genomic data.
Keywords: Concatenation; Incongruence; Model violation; Phylogenomics; Signal-to-noise ratio; Tree of life.
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