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1. “Correcting” Gene Trees to be More Like Species Trees Frequently Increases Topological Error

   https://doi.org/10.1093/gbe/evad094  

   Yan, Zhi; Ogilvie, Huw A; Nakhleh, Luay (June 2023, Genome Biology and Evolution)

   Holland, Barbara (Ed.)

   Abstract The evolutionary histories of individual loci in a genome can be estimated independently, but this approach is error-prone due to the limited amount of sequence data available for each gene, which has led to the development of a diverse array of gene tree error correction methods which reduce the distance to the species tree. We investigate the performance of two representatives of these methods: TRACTION and TreeFix. We found that gene tree error correction frequently increases the level of error in gene tree topologies by “correcting” them to be closer to the species tree, even when the true gene and species trees are discordant. We confirm that full Bayesian inference of the gene trees under the multispecies coalescent model is more accurate than independent inference. Future gene tree correction approaches and methods should incorporate an adequately realistic model of evolution instead of relying on oversimplified heuristics. 

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2. Phylogenomic Analysis of the Parrots of the World Distinguishes Artifactual from Biological Sources of Gene Tree Discordance

   https://doi.org/10.1093/sysbio/syac055  

   Smith, Brian Tilston; Merwin, Jon; Provost, Kaiya L.; Thom, Gregory; Brumfield, Robb T.; Ferreira, Mateus; Mauck, III, William M.; Moyle, Robert G.; Wright, Timothy F.; Joseph, Leo; et al (August 2022, Systematic Biology)

   Abstract Gene tree discordance is expected in phylogenomic trees and biological processes are often invoked to explain it. However, heterogeneous levels of phylogenetic signal among individuals within data sets may cause artifactual sources of topological discordance. We examined how the information content in tips and subclades impacts topological discordance in the parrots (Order: Psittaciformes), a diverse and highly threatened clade of nearly 400 species. Using ultraconserved elements from 96% of the clade’s species-level diversity, we estimated concatenated and species trees for 382 ingroup taxa. We found that discordance among tree topologies was most common at nodes dating between the late Miocene and Pliocene, and often at the taxonomic level of the genus. Accordingly, we used two metrics to characterize information content in tips and assess the degree to which conflict between trees was being driven by lower-quality samples. Most instances of topological conflict and nonmonophyletic genera in the species tree could be objectively identified using these metrics. For subclades still discordant after tip-based filtering, we used a machine learning approach to determine whether phylogenetic signal or noise was the more important predictor of metrics supporting the alternative topologies. We found that when signal favored one of the topologies, the noise was the most important variable in poorly performing models that favored the alternative topology. In sum, we show that artifactual sources of gene tree discordance, which are likely a common phenomenon in many data sets, can be distinguished from biological sources by quantifying the information content in each tip and modeling which factors support each topology. [Historical DNA; machine learning; museomics; Psittaciformes; species tree.] 

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3. Phylogenomic comparative methods: Accurate evolutionary inferences in the presence of gene tree discordance

   https://doi.org/10.1073/pnas.2220389120  

   Hibbins, Mark S; Breithaupt, Lara C; Hahn, Matthew W (May 2023, Proceedings of the National Academy of Sciences)

   Phylogenetic comparative methods have long been a mainstay of evolutionary biology, allowing for the study of trait evolution across species while accounting for their common ancestry. These analyses typically assume a single, bifurcating phylogenetic tree describing the shared history among species. However, modern phylogenomic analyses have shown that genomes are often composed of mosaic histories that can disagree both with the species tree and with each other—so-called discordant gene trees. These gene trees describe shared histories that are not captured by the species tree, and therefore that are unaccounted for in classic comparative approaches. The application of standard comparative methods to species histories containing discordance leads to incorrect inferences about the timing, direction, and rate of evolution. Here, we develop two approaches for incorporating gene tree histories into comparative methods: one that constructs an updated phylogenetic variance–covariance matrix from gene trees, and another that applies Felsenstein's pruning algorithm over a set of gene trees to calculate trait histories and likelihoods. Using simulation, we demonstrate that our approaches generate much more accurate estimates of tree-wide rates of trait evolution than standard methods. We apply our methods to two clades of the wild tomato genusSolanumwith varying rates of discordance, demonstrating the contribution of gene tree discordance to variation in a set of floral traits. Our approaches have the potential to be applied to a broad range of classic inference problems in phylogenetics, including ancestral state reconstruction and the inference of lineage-specific rate shifts. 

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4. Mitonuclear discordance results from incomplete lineage sorting, with no detectable evidence for gene flow, in a rapid radiation of Todiramphus kingfishers

   https://doi.org/10.1111/mec.17080  

   DeRaad, Devon A.; McCullough, Jenna M.; DeCicco, Lucas H.; Hime, Paul M.; Joseph, Leo; Andersen, Michael J.; Moyle, Robert G. (July 2023, Molecular Ecology)

   Abstract Many organisms possess multiple discrete genomes (i.e. nuclear and organellar), which are inherited separately and may have unique and even conflicting evolutionary histories. Phylogenetic reconstructions from these discrete genomes can yield different patterns of relatedness, a phenomenon known as cytonuclear discordance. In many animals, mitonuclear discordance (i.e. discordant evolutionary histories between the nuclear and mitochondrial genomes) has been widely documented, but its causes are often considered idiosyncratic and inscrutable. We show that a case of mitonuclear discordance inTodiramphuskingfishers can be explained by extensive genome‐wide incomplete lineage sorting (ILS), likely a result of the explosive diversification history of this genus. For these kingfishers, quartet frequencies reveal that the nuclear genome is dominated by discordant topologies, with none of the internal branches in our consensus nuclear tree recovered in >50% of genome‐wide gene trees. Meanwhile, a lack of inter‐species shared ancestry, non‐significant pairwise tests for gene flow, and little evidence for meaningful migration edges between species, leads to the conclusion that gene flow cannot explain the mitonuclear discordance we observe. This lack of evidence for gene flow combined with evidence for extensive genome‐wide gene tree discordance, a hallmark of ILS, leads us to conclude that the mitonuclear discordance we observe likely results from ILS, specifically deep coalescence of the mitochondrial genome. Based on this case study, we hypothesize that similar demographic histories in other ‘great speciator’ taxa across the Indo‐Pacific likely predispose these groups to high levels of ILS and high likelihoods of mitonuclear discordance. 

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5. Exploring Conflicts in Whole Genome Phylogenetics: A Case Study Within Manakins (Aves: Pipridae)

   https://doi.org/10.1093/sysbio/syac062  

   Zhao, Min; Kurtis, Sarah M; White, Noor D; Moncrieff, Andre E; Leite, Rafael N; Brumfield, Robb T; Braun, Edward L; Kimball, Rebecca T (December 2022, Systematic Biology)

   Ruane, Sara (Ed.)

   Abstract Some phylogenetic problems remain unresolved even when large amounts of sequence data are analyzed and methods that accommodate processes such as incomplete lineage sorting are employed. In addition to investigating biological sources of phylogenetic incongruence, it is also important to reduce noise in the phylogenomic dataset by using appropriate filtering approach that addresses gene tree estimation errors. We present the results of a case study in manakins, focusing on the very difficult clade comprising the genera Antilophia and Chiroxiphia. Previous studies suggest that Antilophia is nested within Chiroxiphia, though relationships among Antilophia+Chiroxiphia species have been highly unstable. We extracted more than 11,000 loci (ultra-conserved elements and introns) from whole genomes and conducted analyses using concatenation and multispecies coalescent methods. Topologies resulting from analyses using all loci differed depending on the data type and analytical method, with 2 clades (Antilophia+Chiroxiphia and Manacus+Pipra+Machaeopterus) in the manakin tree showing incongruent results. We hypothesized that gene trees that conflicted with a long coalescent branch (e.g., the branch uniting Antilophia+Chiroxiphia) might be enriched for cases of gene tree estimation error, so we conducted analyses that either constrained those gene trees to include monophyly of Antilophia+Chiroxiphia or excluded these loci. While constraining trees reduced some incongruence, excluding the trees led to completely congruent species trees, regardless of the data type or model of sequence evolution used. We found that a suite of gene metrics (most importantly the number of informative sites and likelihood of intralocus recombination) collectively explained the loci that resulted in non-monophyly of Antilophia+Chiroxiphia. We also found evidence for introgression that may have contributed to the discordant topologies we observe in Antilophia+Chiroxiphia and led to deviations from expectations given the multispecies coalescent model. Our study highlights the importance of identifying factors that can obscure phylogenetic signal when dealing with recalcitrant phylogenetic problems, such as gene tree estimation error, incomplete lineage sorting, and reticulation events. [Birds; c-gene; data type; gene estimation error; model fit; multispecies coalescent; phylogenomics; reticulation] 

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