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1. Orthogonal Range Searching in Moderate Dimensions: k-d Trees and Range Trees Strike Back

   https://doi.org/10.1007/s00454-019-00062-5  

   Chan, Timothy M. ( June 2019 , Discrete & Computational Geometry)
2. Identification of Source‐Water Oxygen Isotopes in Trees Toolkit (ISO‐Tool) for Deciphering Historical Water Use by Forest Trees

   https://doi.org/10.1029/2018WR024519  

   Sargeant, Christopher I. ; Singer, Michael Bliss ; Vallet‐Coulomb, Christine ( December 2019 , Water Resources Research)
3. “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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4. Maximum Likelihood Estimation of Species Trees from Gene Trees in the Presence of Ancestral Population Structure

   https://doi.org/10.1093/gbe/evaa022  

   Koch, H ; DeGiorgio, M ( February 2020 , Genome biology and evolution)

   Though large multilocus genomic data sets have led to overall improvements in phylogenetic inference, they have posed the new challenge of addressing conflicting signals across the genome. In particular, ancestral population structure, which has been uncovered in a number of diverse species, can skew gene tree frequencies, thereby hindering the performance of species tree estimators. Here we develop a novel maximum likelihood method, termed TASTI (Taxa with Ancestral structure Species Tree Inference), that can infer phylogenies under such scenarios, and find that it has increasing accuracy with increasing numbers of input gene trees, contrasting with the relatively poor performances of methods not tailored for ancestral structure. Moreover, we propose a supertree approach that allows TASTI to scale computationally with increasing numbers of input taxa. We use genetic simulations to assess TASTI’s performance in the three- and four-taxon settings and demonstrate the application of TASTI on a six-species Afrotropical mosquito data set. Finally, we have implemented TASTI in an open-source software package for ease of use by the scientific community. 

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5. Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-supported Phylogenomic Trees of Nostocalean Cyanobacteria

   Pardo-De la Hoz, C. J. ; Magain, N. ; Piatkowski, B. ; Cornet, L. ; Dal Forno, M. ; Carbone, I. ; Miadlikowska, J. ; Lutzoni, F. ( February 2023 , Systematic biology)