ALT EvolCompGen COSI committee | #ISMB2022 @EvolComp COSI & Awards Chairs - Nadia El-Mabrouk - Janani Ravi Track/Abstract Chairs - Edward Braun - Wataru Iwasaki - Giltae Song Area/Proceedings Chairs - Celine Scornavacca - Lars Arvestad Webinars - Erin Molloy - Dannie Durand Other reviewers - Christophe Dessimoz, Xiaofang Jiang, Mattéo Delabre, Louxin Zhang Website/Communications - Aïda Ouangraoua - Maureen Stolzer - Janani Ravi

ALT Talk Title: Phylogenetic network estimation from site patterns using composite likelihood Date: Friday, November 10, 2023. 11am – 12pm Eastern Time (ET) Speaker: Sungsik Kong, University of Wisconsin-Madison Talk Abstract: While phylogenies have been essential in understanding how species evolve, they do not adequately describe some evolutionary processes. For instance, hybridization, a common phenomenon where interbreeding between two species leads to formation of a new species, must be depicted by a phylogenetic network, a structure that modifies a phylogenetic tree by allowing two branches to merge into one, resulting in reticulation. Here, we propose a novel method, PhyNEST (Phylogenetic Network Estimation using SiTe patterns), that estimates level-1 phylogenetic networks directly from sequence alignment. PhyNEST achieves computational efficiency by using composite likelihood as well as accuracy by using the full genomic data to incorporate all sources of variability. To sear

ALT Fig 1. Diagram of the 10 rules organized into 3 groups: foundation rules (Rules 1 to 3), design rules (Rules 4 to 9), and a continuity rule (Rule 10). The overall diagram depicts an arrow from left to right containing all the rules. In the left column, under the first label “Foundation,” there are 3 text boxes in light blue: “1. Vision,” “2. Safe environment,” and “3. Organizing Team.” In the middle column, under the label “Design Rules” there are 6 light green boxes with Rules “4. Counter bias,” “5. Virtual/hybrid,” “6. Accessibility,” “7. Language,” “8. Communication,” “9. Finance.” To the right, below the arrowhead labeled “Continuity,” is the 10th Rule in a light pink box “10. Pass the torch.” https://doi.org/10.1371/journal.pcbi.1010164

ALT Fig 2. Five “Margot the marmot” with colorful scarves. From left to right: a marmot with a dark and light green scarf of the MiR community is looking at her tablet, a marmot with the purple and gray scarf of R-Ladies is stepping on a rock and watches the horizon, a marmot with an orange and purple AfricaR scarf is sitting on a couch watching a film on her laptop with popcorn, a yogi marmot with a rainbow LGBTQIA scarf does the warrior pose on her blue mat, and finally, a marmot with a scarf with the pink, light blue, and white color of the transgender pride flag waves her hand. https://doi.org/10.1371/journal.pcbi.1010164