Interpreting phylogenetic conflict: Hybridization in the most speciose genus of lichen-forming fungi.

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Publisher: Elsevier B.V.
Document Type: Report
Length: 413 words

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Keywords Conflict; Incomplete lineage sorting; Introgression; Phylogenetic incongruence; Phylogenomics; Reticulation Highlights * Comprehensive molecular phylogeny of the Holarctic clade of lichen-forming fungi genus Xanthoparmelia. * Despite reconstructing relatively consistent phylogenetic trees, rampant phylogenetic conflict was revealed. * Widespread hybridization was detected among species in the most diverse genus of lichen-forming fungi using three independent tests for hybridization. Abstract While advances in sequencing technologies have been invaluable for understanding evolutionary relationships, increasingly large genomic data sets may result in conflicting evolutionary signals that are often caused by biological processes, including hybridization. Hybridization has been detected in a variety of organisms, influencing evolutionary processes such as generating reproductive barriers and mixing standing genetic variation. Here, we investigate the potential role of hybridization in the diversification of the most speciose genus of lichen-forming fungi, Xanthoparmelia. As Xanthoparmelia is projected to have gone through recent, rapid diversification, this genus is particularly suitable for investigating and interpreting the origins of phylogenomic conflict. Focusing on a clade of Xanthoparmelia largely restricted to the Holarctic region, we used a genome skimming approach to generate 962 single-copy gene regions representing over 2 Mbp of the mycobiont genome. From this genome-scale dataset, we inferred evolutionary relationships using both concatenation and coalescent-based species tree approaches. We also used three independent tests for hybridization. Although different species tree reconstruction methods recovered largely consistent and well-supported trees, there was widespread incongruence among individual gene trees. Despite challenges in differentiating hybridization from ILS in situations of recent rapid radiations, our genome-wide analyses detected multiple potential hybridization events in the Holarctic clade, suggesting one possible source of trait variability in this hyperdiverse genus. This study highlights the value in using a pluralistic approach for characterizing genome-scale conflict, even in groups with well-resolved phylogenies, while highlighting current challenges in detecting the specific impacts of hybridization. Author Affiliation: (a) Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT 84602, USA (b) Field Museum of Natural History, Science & Education, Grainger Bioinformatics Center, 1400 S. DuSable Lake Shore Drive, Chicago, IL 60605, USA (c) Biodiversity Research Center, Academia Sinica, 128 Academia Rd, Section 2, Nankang District, Taipei 11529, Taiwan (d) M. L. Bean Life Science Museum, Brigham Young University, 1115 MLBM, Provo, UT 84602, USA * Corresponding author. Article History: Received 11 June 2021; Revised 6 February 2022; Accepted 13 May 2022 Byline: Rachel Keuler [] (a,*), Jacob Jensen (a), Alejandrina Barcena-Peña (b), Felix Grewe (b), H. Thorsten Lumbsch (b), Jen-Pan Huang (c), Steven D. Leavitt (a,d)

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Gale Document Number: GALE|A708782307