David Bell1,2,3, Qianshi Lin1,2, Wesley K Gerelle1,2, Steve Joya1, Ying Chang1,4, Z Nathan Taylor5, Carl J Rothfels6, Anders Larsson7, Juan Carlos Villarreal8,9, Fay-Wei Li10,11, Lisa Pokorny12,13, Péter Szövényi14, Barbara Crandall-Stotler15, Lisa DeGironimo16, Sandra K Floyd17, David J Beerling18, Michael K Deyholos19, Matt von Konrat20, Shona Ellis1, A Jonathan Shaw21, Tao Chen22, Gane K-S Wong23,24,25, Dennis W Stevenson26, Jeffrey D Palmer5, Sean W Graham1,2. 1. Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada. 2. UBC Botanical Garden and Centre for Plant Research, University of British Columbia, 6804 Marine Drive SW, Vancouver, British Columbia, V6T 1Z4, Canada. 3. Royal Botanic Garden, 20A Inverleith Row, Edinburgh, EH3 5LR, UK. 4. Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA. 5. Department of Biology, Indiana University, Bloomington, Indiana, 47405, USA. 6. University Herbarium and Department of Integrative Biology, University of California Berkeley, Berkeley, California, 94702, USA. 7. Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden. 8. Department of Biology, Université Laval, Québec, G1V 0A6, Canada. 9. Smithsonian Tropical Research Institute, Panama City, Panama. 10. Boyce Thompson Institute, Ithaca, New York, 14853, USA. 11. Plant Biology Section, Cornell University, Ithaca, New York, 14853, USA. 12. Royal Botanic Gardens, Kew, Richmond, TW9 3DS, Surrey, UK. 13. Centre for Plant Biotechnology and Genomics (CBGP, UPM-INIA), 28223, Pozuelo de Alarcón (Madrid), Spain. 14. Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland. 15. School of Biological Sciences, Southern Illinois University, Carbondale, Illinois, 62901, USA. 16. Department of Biology, College of Arts and Science, New York University, New York, New York, 10003, USA. 17. School of Biological Sciences, Monash University, Melbourne, Victoria, 3800, Australia. 18. Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK. 19. Department of Biology, University of British Columbia, Kelowna, British Columbia, V1V 1V7, Canada. 20. Field Museum of Natural History, Chicago, Illinois, 60605, USA. 21. Department of Biology, Duke University, Durham, North Carolina, 27708, USA. 22. Shenzhen Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen, Guangdong, 518004, China. 23. Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada. 24. Department of Medicine, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada. 25. BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China. 26. New York Botanical Garden, Bronx, New York, 10458, USA.
Abstract
PREMISE: Phylogenetic trees of bryophytes provide important evolutionary context for land plants. However, published inferences of overall embryophyte relationships vary considerably. We performed phylogenomic analyses of bryophytes and relatives using both mitochondrial and plastid gene sets, and investigated bryophyte plastome evolution. METHODS: We employed diverse likelihood-based analyses to infer large-scale bryophyte phylogeny for mitochondrial and plastid data sets. We tested for changes in purifying selection in plastid genes of a mycoheterotrophic liverwort (Aneura mirabilis) and a putatively mycoheterotrophic moss (Buxbaumia), and compared 15 bryophyte plastomes for major structural rearrangements. RESULTS: Overall land-plant relationships conflict across analyses, generally weakly. However, an underlying (unrooted) four-taxon tree is consistent across most analyses and published studies. Despite gene coverage patchiness, relationships within mosses, liverworts, and hornworts are largely congruent with previous studies, with plastid results generally better supported. Exclusion of RNA edit sites restores cases of unexpected non-monophyly to monophyly for Takakia and two hornwort genera. Relaxed purifying selection affects multiple plastid genes in mycoheterotrophic Aneura but not Buxbaumia. Plastid genome structure is nearly invariant across bryophytes, but the tufA locus, presumed lost in embryophytes, is unexpectedly retained in several mosses. CONCLUSIONS: A common unrooted tree underlies embryophyte phylogeny, [(liverworts, mosses), (hornworts, vascular plants)]; rooting inconsistency across studies likely reflects substantial distance to algal outgroups. Analyses combining genomic and transcriptomic data may be misled locally for heavily RNA-edited taxa. The Buxbaumia plastome lacks hallmarks of relaxed selection found in mycoheterotrophic Aneura. Autotrophic bryophyte plastomes, including Buxbaumia, hardly vary in overall structure.
PREMISE: Phylogenetic trees of bryophytes provide important evolutionary context for land plants. However, published inferences of overall embryophyte relationships vary considerably. We performed phylogenomic analyses of bryophytes and relatives using both mitochondrial and plastid gene sets, and investigated bryophyte plastome evolution. METHODS: We employed diverse likelihood-based analyses to infer large-scale bryophyte phylogeny for mitochondrial and plastid data sets. We tested for changes in purifying selection in plastid genes of a mycoheterotrophic liverwort (Aneura mirabilis) and a putatively mycoheterotrophic moss (Buxbaumia), and compared 15 bryophyte plastomes for major structural rearrangements. RESULTS: Overall land-plant relationships conflict across analyses, generally weakly. However, an underlying (unrooted) four-taxon tree is consistent across most analyses and published studies. Despite gene coverage patchiness, relationships within mosses, liverworts, and hornworts are largely congruent with previous studies, with plastid results generally better supported. Exclusion of RNA edit sites restores cases of unexpected non-monophyly to monophyly for Takakia and two hornwort genera. Relaxed purifying selection affects multiple plastid genes in mycoheterotrophic Aneura but not Buxbaumia. Plastid genome structure is nearly invariant across bryophytes, but the tufA locus, presumed lost in embryophytes, is unexpectedly retained in several mosses. CONCLUSIONS: A common unrooted tree underlies embryophyte phylogeny, [(liverworts, mosses), (hornworts, vascular plants)]; rooting inconsistency across studies likely reflects substantial distance to algal outgroups. Analyses combining genomic and transcriptomic data may be misled locally for heavily RNA-edited taxa. The Buxbaumia plastome lacks hallmarks of relaxed selection found in mycoheterotrophic Aneura. Autotrophic bryophyte plastomes, including Buxbaumia, hardly vary in overall structure.
Authors: Brogan J Harris; James W Clark; Dominik Schrempf; Gergely J Szöllősi; Philip C J Donoghue; Alistair M Hetherington; Tom A Williams Journal: Nat Ecol Evol Date: 2022-09-29 Impact factor: 19.100
Authors: Bing-Feng Ke; Goang-Jiun Wang; Paulo H Labiak; Germinal Rouhan; Cheng-Wei Chen; Lara D Shepherd; Daniel J Ohlsen; Matthew A M Renner; Kenneth G Karol; Fay-Wei Li; Li-Yaung Kuo Journal: Front Plant Sci Date: 2022-07-13 Impact factor: 6.627
Authors: Sjoerd Woudenberg; Jim Renema; Alexandru M F Tomescu; Bert De Rybel; Dolf Weijers Journal: Plant Physiol Date: 2022-08-29 Impact factor: 8.005