Stochastic Safety Radius on UPGMA by Ruriko Yoshida, Lillian Paul, Peter Nesbitt

“…Since we use equidistant trees as gene trees for phylogenomic analyses under the multi-species coalescent model and since an input distance matrix computed from an alignment of each gene in a genome is estimated via the maximum likelihood estimators, it is important to conduct a robust analysis on UPGMA. …”
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Visualizing incompatibilities in phylogenetic trees using consensus outlines by Daniel H. Huson, Daniel H. Huson, Banu Cetinkaya, Banu Cetinkaya

“…We demonstrate its usage and explore how it compares to other methods on a Bayesian phylogenetic analysis of languages using data from a published database and on multiple gene trees from a published study on water lilies.…”
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Species delineation and hybrid identification using diagnostic nuclear markers for Mediterranean groupers Epinephelus marginatus and Mycteroperca rubra by Song He, Michel Bariche, Lucía Pombo-Ayora, Michael L. Berumen

“…The discordance of the phylogenetic gene trees of the mitochondrial and nuclear markers indicates that E. marginatus and M. rubra are potential parent species of a hybrid individual in our samples. …”
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Identification of an aquaculture poriferan “Pest with Potential” and its phylogenetic implications by Adrian Galitz, Steve de C. Cook, Merrick Ekins, John N. A. Hooper, Peter T. Naumann, Nicole J. de Voogd, Muhammad Abdul Wahab, Gert Wörheide, Dirk Erpenbeck

“…We reconstructed ribosomal gene trees and determined this species as Lendenfeldia chondrodes (De Laubenfels, 1954) (Phyllospongiinae), distant to Collospongia auris, and corroborated by skeletal features. …”
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Unexpected diversity in the host-generalist oribatid mite Paraleius leontonychus (Oribatida, Scheloribatidae) phoretic on Palearctic bark beetles by Sylvia Schäffer, Stephan Koblmüller

“…In the present study, phylogenetic analyses of one mitochondrial and two nuclear genes identified six well supported, fairly divergent clades within P. leontonychus which we consider to represent distinct species based on molecular species delimitation methods and largely congruent clustering in mitochondrial and nuclear gene trees. These species do not tend to be strictly host specific and might occur syntopically. …”
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The species coalescent indicates possible bat and pangolin origins of the COVID-19 pandemic by Jialin Yang, Michael Skaro, Jiani Chen, Duna Zhan, Leke Lyu, Skylar Gay, Ahmed Kandeil, Mohamed A. Ali, Ghazi Kayali, Kateryna Stoianova, Pensheng Ji, Magdy Alabady, Justin Bahl, Liang Liu, Jonathan Arnold

“…Abstract A consensus species tree is reconstructed from 11 gene trees for human, bat, and pangolin beta coronaviruses from samples taken early in the pandemic (prior to April 1, 2020). …”
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Patterns of gene evolution following duplications and speciations in vertebrates by Kyle T. David, Jamie R. Oaks, Kenneth M. Halanych

“…Methods To provide an empirical assessment of ortholog/paralog evolution, we estimated ratios of nonsynonymous to synonymous substitutions (ω = dN/dS) for 251,044 lineages in 6,244 gene trees across 77 vertebrate taxa. Results Overall, we found ω to be more similar between lineages descended from speciation events (p < 0.001) than lineages descended from duplication events, providing strong support for the Ortholog Conjecture. …”
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Evolution of ascariasis in humans and pigs: a multi-disciplinary approach by Odile Loreille, Françoise Bouchet

“…While nuclear DNA markers decisively separate the two populations, mitochondrial sequences reveal that three major haplotypes are found in A. suum and in A. lumbricoides, indicating either occasional hybridization, causing introgression of gene trees, or retention of polymorphism dating back to the original ancestral species. …”
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From famine to feast? Selecting nuclear DNA sequence loci for plant species-level phylogeny reconstruction. by Hughest, C, Eastwood, R, Bailey, C

“…We show that for plants, the rapid accumulation of DNA characters at higher taxonomic levels has not been matched by conventional sequence loci at the species level, leaving a lack of well-resolved gene trees that is hindering investigations of many fundamental questions in plant evolutionary biology. …”

Evolution and phylogeography of Culex pipiens densovirus by Altinli, M, Lequime, S, Courcelle, M, François, S, Justy, F, Gosselin-Grenet, A-S, Ogliastro, M, Weill, M, Sicard, M

“…The incongruence of the different gene trees for some samples suggested the possibility of recombination events between strains from different clades. …”

High rates of recombination in otitis media isolates of non-typeable Haemophilus influenzae. by Cody, A, Field, D, Feil, E, Stringer, S, Deadman, M, Tsolaki, A, Gratz, B, Bouchet, V, Goldstein, R, Hood, D, Moxon, E

“…We found mosaic sequences, linkage equilibrium between loci and a lack of congruence between gene trees. These high rates were not confined to LPS genes since evidence for similar amounts of recombination was also found in eight housekeeping genes in a subset of the same 25 isolates. …”

Molecular and Morphological Assessment of <i>Septoria</i> Species Associated with Ornamental Plants in Yunnan Province, China by Yuan-Yan An, Monika C. Dayarathne, Xiang-Yu Zeng, Alan J. L. Phillips, Kevin D. Hyde, Yong Wang

“…Based on single-gene and multi-gene analyses of five gene loci (<i>tef1</i>, <i>rpb2</i>, <i>tub2</i>, ITS, and <i>LSU</i>) and four gene regions (without <i>LSU</i>), these strains were found to belong to three independent phylogenetic lineages representing five species, including four novel taxa, and one new record for China. Five single gene trees were also provided to evaluate the effectiveness of each gene for discriminating the species, as a result of which <i>tub2</i> was found to have the most suitable DNA barcode for rapid identification. …”
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Transcriptome-based phylogenomic analysis reveals evidence of ancient hybridization events in the Mepraia genus (Hemiptera: Reduviidae: Triatominae) by Tiago Belintani, Tiago Belintani, Carlos Congrains, Carlos Congrains, Heloisa Pinotti, Samira Chahad-Ehlers, Reinaldo A. de Brito, Jader Oliveira, Daniel Frias-Lasserre, Felipe Mendes Fontes, João Aristeu da Rosa

“…Our transcriptomes were used to robustly infer the phylogenetic relationships, employing multi-species coalescent and supermatrix approaches, as well as to investigate the occurrence of introgression.Results and discussionThe inferred phylogenies support the monophyly of the three described taxa and infer divergence times, although gene trees display high levels of discordance. Our results indicate widespread introgression among Mepraia lineages. …”
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Positive selection in cytochrome P450 genes is associated with gonad phenotype and mating strategy in social bees by Denyse Cavalcante Lago, Luísa Czamanski Nora, Martin Hasselmann, Klaus Hartfelder

“…Two of these encode cytochrome P450 proteins, and their gene trees indicated a lineage-specific evolution in the genus Apis, indicating that cytochrome P450 genes may be involved in the evolutionary association of polyandry and the exaggerated gonad phenotype in social bees.…”
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A phylogeny of the evening primrose family (Onagraceae) using a target enrichment approach with 303 nuclear loci by Rick P. Overson, Matthew G. Johnson, Lindsey L. Bechen, Sylvia P. Kinosian, Norman A. Douglas, Jeremie B. Fant, Peter C. Hoch, Rachel A. Levin, Michael J. Moore, Robert A. Raguso, Warren L. Wagner, Krissa A. Skogen, Norman J. Wickett

“…Deep splits within the family are strongly supported, whereas relationships among closely related genera and species are characterized by extensive conflict among individual gene trees. Conclusions This phylogenetic resource will augment current research projects focused throughout the family in genomics, ecology, coevolutionary dynamics, biogeography, and the evolution of characters driving diversification in the family.…”
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Multilocus phylogeny of the parasitic wasps in the tribe Euphorini (Hymenoptera: Braconidae) with revised generic classifications by Yuanmeng Miles Zhang, Julia Stigenberg, Jacqueline Hope Meyer, Barbara Jo-Anne Sharanowski

“…Methods Using a combination of three genes (COI, 28S, and CAD) and 80 taxa collected worldwide, we conducted Bayesian inference using MrBayes, and maximum likelihood analyses using RAxML and IQ-Tree on individual gene trees as well as the concatenated dataset. Results The monophyly of the tribe Euphorini and the two genera Peristenus and Leiophron were confirmed using maximum likelihood and Bayesian inference. …”
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Evolution of Three-Finger Toxin Genes in Neotropical Colubrine Snakes (Colubridae) by Kristy Srodawa, Peter A. Cerda, Alison R. Davis Rabosky, Jenna M. Crowe-Riddell

“…By reconstructing the gene trees of 3FTxs, we found evidence of putative novel heterodimers in the sequences of <i>Chironius multiventris</i> and <i>Oxybelis aeneus</i>, revealing an instance of parallel evolution of this structural change in 3FTxs among rear-fanged colubrine snakes. …”
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SINE-Based Phylogenomics Reveal Extensive Introgression and Incomplete Lineage Sorting in <i>Myotis</i> by Jennifer M. Korstian, Nicole S. Paulat, Roy N. Platt, Richard D. Stevens, David A. Ray

“…With nearly one-third of individual Ves gene trees discordant with the overall species tree, phylogenetic conflict appears to be rampant in this genus. …”
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Comparative analysis of organellar genomes between diploid and tetraploid Chrysanthemum indicum with its relatives by Huihui Liu, Zhuangwei Hou, Lei Xu, Qing Ma, Min Wei, Luke R. Tembrock, Shuo Zhang, Shuo Zhang, Zhiqiang Wu, Zhiqiang Wu

“…Finally, differences observed between mitogenome and plastome gene trees may be the result of the difference in the rate of sequence evolution between genes in these two genomes. …”
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Molecular Phylogeny and Evolution of the <i>Tuerkayana</i> (Decapoda: Brachyura: Gecarcinidae) Genus Based on Whole Mitochondrial Genome Sequences by Zhengfei Wang, Yuqing Zheng, Xinyue Zhao, Xinyi Xu, Zhiwen Xu, Chong Cui

“…Furthermore, two single gene trees based on <i>cox1</i> and <i>16SrRNA</i> separately within interspecies of Gecarcinidae were reconstructed, providing molecular evidence for <i>Tuerkayana</i> and further clarifying the division of genera in Gecarcinidae. …”
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