ArticlePeerJ2019
Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics.
Article in PeerJ, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers, 1 of them a synthesis that pooled it.
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Who cites it
60 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Evolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary.Frontiers in genetics · 2019Pooled it
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- Evaluating UCE Data Adequacy and Integrating Uncertainty in a Comprehensive Phylogeny of Ants.Systematic biology · 2025Article
- Phylogenomics of Marine Angelfishes: Diagnosing Sources of Systematic Discordance for an Iconic Reef Fish Family (F: Pomacanthidae).Systematic biology · 2025Article
- PickMe: Sample Selection for Species Tree Reconstruction using Coalescent Weighted Quartets.Systematic biology · 2025Article
- Phylogenomic and Population Genomic Analyses of Ultraconserved Elements Reveal Deep Coalescence and Introgression Shaped Diversification Patterns in Lamprologine Cichlids of the Congo River.Systematic biology · 2025Article
- Thrushes in Love: Extensive Gene Flow, With Differential Resistance and Selection, Obscures and Reveals the Evolutionary History of a Songbird Clade.Molecular ecology · 2025Article
- Museomics unravels cryptic diversity in an endemic group of New Guinean songbirds.Biology letters · 2025Article
- Comparative Analysis of Mitogenomic and Nuclear Gene Data Reveals Phylogenetic Implications, Divergence Times, and Historical Biogeography in the Subfamily Pyrginae (Lepidoptera: Hesperiidae).Ecology and evolution · 2025Article
- Phylogenomics reveals the slow-burning fuse of diatom evolution.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Genetic traceability, conservation effectiveness, and selection signatures analysis based on ancestral information: a case study of Beijing-You chicken.BMC genomics · 2025Article
- Comparative analysis of the mitochondrial genomes of the soft-shelled turtles Palea steindachneri and Pelodiscus axenaria and phylogenetic implications for Trionychia.Scientific reports · 2025Article
- CamITree: a streamlined software for phylogenetic analysis of viral and mitochondrial genomes.BMC bioinformatics · 2025Article
- Phylogenomic resolution of lampreys reveals the recent evolution of an ancient vertebrate lineage.Proceedings. Biological sciences · 2025Article
- Practical Guidance and Workflows for Identifying Fast Evolving Non-Coding Genomic Elements Using PhyloAcc.Integrative and comparative biology · 2024Article
- The Meaning and Measure of Concordance Factors in Phylogenomics.Molecular biology and evolution · 2024Review
- Article
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Authors and funding
20 authors.
Funding
No grant is acknowledged in the PubMed record.
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 made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.
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