Laura P Lagomarsino1,2, Lauren Frankel3, Simon Uribe-Convers2,4, Alexandre Antonelli5,6,7, Nathan Muchhala2. 1. Shirley C. Tucker Herbarium, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA. 2. Department of Biology, University of Missouri-St. Louis, St. Louis, MO, USA. 3. Department of Botany, University of Wisconsin-Madison, Madison, WI, USA. 4. Invitae Corporation, San Francisco, CA, USA. 5. Royal Botanic Gardens, Kew, TW9 3AE, UK. 6. Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, 405 30, Sweden. 7. Department of Plant Science, University of Oxford, Oxford, UK.
Abstract
BACKGROUND AND AIMS: The centropogonid clade (Lobelioideae: Campanulaceae) is an Andean-centred rapid radiation characterized by repeated convergent evolution of morphological traits, including fruit type and pollination syndromes. While previous studies have resolved relationships of lineages with fleshy fruits into subclades, relationships among capsular species remain unresolved. This lack of resolution has impeded reclassification of non-monophyletic genera, whose current taxonomy relies heavily on traits that have undergone convergent evolution. METHODS: Targeted sequence capture using a probe-set recently developed for the centropogonid clade was used to obtain phylogenomic data from DNA extracted from both silica-dried and herbarium leaf tissue. These data were used to infer relationships among species using concatenated and partitioned species tree methods, and to quantify gene tree discordance. KEY RESULTS: While silica-dried leaf tissue resulted in longer assembled sequence data, the inclusion of herbarium samples improved taxonomic representation. Relationships among baccate lineages are similar to those inferred in previous studies, although they differ for lineages within and among capsular clades. We improve the phylogenetic resolution of Siphocampylus, which forms ten groups of closely related species which we informally name. Two subclades of Siphocampylus and two individual species are rogue taxa whose placement differs widely across analyses. Gene tree discordance (including cytonuclear discordance) is rampant. CONCLUSIONS: This first phylogenomic study of the centropogonid clade considerably improves our understanding of relationships in this rapid radiation. Differences across analyses and the possibility of additional lineage discoveries still hamper a solid and stable reclassification. Rapid morphological innovation corresponds with a high degree of phylogenomic complexity, including cytonuclear discordance, nuclear gene tree conflict and well-supported differences between analyses based on different nuclear loci. Together, these results point to a potential role of hemiplasy underlying repeated convergent evolution. This hallmark of rapid radiations is probably present in many other species-rich Andean plant radiations.
BACKGROUND AND AIMS: The centropogonid clade (Lobelioideae: Campanulaceae) is an Andean-centred rapid radiation characterized by repeated convergent evolution of morphological traits, including fruit type and pollination syndromes. While previous studies have resolved relationships of lineages with fleshy fruits into subclades, relationships among capsular species remain unresolved. This lack of resolution has impeded reclassification of non-monophyletic genera, whose current taxonomy relies heavily on traits that have undergone convergent evolution. METHODS: Targeted sequence capture using a probe-set recently developed for the centropogonid clade was used to obtain phylogenomic data from DNA extracted from both silica-dried and herbarium leaf tissue. These data were used to infer relationships among species using concatenated and partitioned species tree methods, and to quantify gene tree discordance. KEY RESULTS: While silica-dried leaf tissue resulted in longer assembled sequence data, the inclusion of herbarium samples improved taxonomic representation. Relationships among baccate lineages are similar to those inferred in previous studies, although they differ for lineages within and among capsular clades. We improve the phylogenetic resolution of Siphocampylus, which forms ten groups of closely related species which we informally name. Two subclades of Siphocampylus and two individual species are rogue taxa whose placement differs widely across analyses. Gene tree discordance (including cytonuclear discordance) is rampant. CONCLUSIONS: This first phylogenomic study of the centropogonid clade considerably improves our understanding of relationships in this rapid radiation. Differences across analyses and the possibility of additional lineage discoveries still hamper a solid and stable reclassification. Rapid morphological innovation corresponds with a high degree of phylogenomic complexity, including cytonuclear discordance, nuclear gene tree conflict and well-supported differences between analyses based on different nuclear loci. Together, these results point to a potential role of hemiplasy underlying repeated convergent evolution. This hallmark of rapid radiations is probably present in many other species-rich Andean plant radiations.
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Authors: Gustavo A Bravo; Alexandre Antonelli; Christine D Bacon; Krzysztof Bartoszek; Mozes P K Blom; Stella Huynh; Graham Jones; L Lacey Knowles; Sangeet Lamichhaney; Thomas Marcussen; Hélène Morlon; Luay K Nakhleh; Bengt Oxelman; Bernard Pfeil; Alexander Schliep; Niklas Wahlberg; Fernanda P Werneck; John Wiedenhoeft; Sandi Willows-Munro; Scott V Edwards Journal: PeerJ Date: 2019-02-14 Impact factor: 2.984
Authors: James Lendemer; Barbara Thiers; Anna K Monfils; Jennifer Zaspel; Elizabeth R Ellwood; Andrew Bentley; Katherine LeVan; John Bates; David Jennings; Dori Contreras; Laura Lagomarsino; Paula Mabee; Linda S Ford; Robert Guralnick; Robert E Gropp; Marcy Revelez; Neil Cobb; Katja Seltmann; M Catherine Aime Journal: Bioscience Date: 2019-11-22 Impact factor: 8.589