Sequencing the genomes of all species would result in completely congruent phylogenies
Sequencing the genomes of all species would not produce completely congruent phylogenies because biological processes like incomplete lineage sorting, introgression, and rapid radiation naturally generate pervasive gene tree discordance.
The claim posits that sequencing all genomes would result in completely congruent phylogenies. Multiple empirical phylogenomic studies (e.g., papers 0, 1, 3, and 7) demonstrate that gene tree discordance is a pervasive biological reality driven by incomplete lineage sorting, hybridization, horizontal gene flow, and different evolutionary histories across loci and genomic regions. Therefore, genomic sequencing reveals extensive conflict rather than complete congruence, refuting the claim.
Diego F. Morales‐Briones, G. Kadereit, Delphine T. Tefarikis, Michael J Moore, Stephen A. Smith, Samuel F. Brockington, Alfonso Timoneda, Won Yim, J. Cushman, Ya Yang. Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l. 2020. https://doi.org/10.1093/sysbio/syaa066
This study finds high levels of gene tree discordance across genomes of Amaranthaceae due to incomplete lineage sorting, hybridization, and rapid radiation, directly contradicting the idea of completely congruent phylogenies.
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E. A. Myers, R. Rautsaw, M. Borja, Jason Jones, Christoph I. Grünwald, M. Holding, F. Grazziotin, C. Parkinson. Phylogenomic discordance is driven by wide-spread introgression and incomplete lineage sorting during rapid species diversification within rattlesnakes (Viperidae: Crotalus and Sistrurus).. 2024. https://doi.org/10.1093/sysbio/syae018
Genomic data from rattlesnakes reveal that rapid speciation and frequent hybridization lead to widespread phylogenetic discordance, where individual gene trees conflict with the species tree.
Matthew P Greenwood, Thibaut Capblancq, Niklas Wahlberg, Laurence Després. Whole genome data confirm pervasive gene discordance in the evolutionary history of Coenonympha (Nymphalidae) butterflies.. 2024. https://doi.org/10.1016/j.ympev.2024.108222
Whole-genome datasets in Coenonympha butterflies demonstrate that genealogical heterogeneity and gene conflict persist even when extensive genomic data are analyzed.
DeSalle R, Tessler M. Mitochondrial Gene Phylogenetic Incongruencies Are Linked to Chromosomal Position and Function.. 2025. https://doi.org/10.1093/gbe/evaf209
Research across animal mitochondrial genomes demonstrates rampant phylogenetic incongruence among linked genes, illustrating that different genomic regions yield conflicting evolutionary patterns.
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