Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

Author(s):Show less -

Alejandra Serna-Sanchez, Maria ^{[1, 2]} ; Perez-Escobar, Oscar A. ^[3] ; Bogarin, Diego ^{[4, 5]} ; Torres-Jimenez, Maria Fernanda ^[6] ; Catalina Alvarez-Yela, Astrid ^[7] ; Arcila-Galvis, Juliana E. ^[1] ; Hall, Climbie F. ^[8] ; de Barros, Fabio ^[8] ; Pinheiro, Fabio ^[9] ; Dodsworth, Steven ^[10] ; Chase, Mark W. ^[3] ; Antonelli, Alexandre ^{[3, 6, 11]} ; Arias, Tatiana ^{[1, 7, 12]}

Affiliation:Show less -

^[1] Corp Invest Biol CIB, Lab Biol Comparat, Cra 72 78 B 141, Medellin - Colombia

^[2] EAFIT Univ, Biodivers Evolut & Conservat, Cra 49, 7 Sur 50, Medellin - Colombia

^[3] Royal Bot Gardens Kew, London TW9 3AE - England

^[4] Univ Costa Rica, Jardin Bot Lankester, POB 302-7050, Cartago - Costa Rica

^[5] Nat Biodivers Ctr, Endless Forms Grp, POB 9517, NL-2300 RA Leiden - Netherlands

^[6] Univ Gothenburg, Gothenburg Global Biodivers Ctr, Dept Biol & Environm Sci, S-40530 Gothenburg - Sweden

^[7] Ecoparque Yarumos Edificio BIOS, Ctr Bioinformat & Biol Computat BIOS, Manizales - Colombia

^[8] Nucleo Pesquisa Orquidario Estado, Inst Bot, Postal 68041, BR-04045972 Sao Paulo, SP - Brazil

^[9] Univ Estadual Campinas, Dept Biol Vegetal, Inst Biol, BR-13083862 Campinas, SP - Brazil

^[10] Univ Bedfordshire, Sch Life Sci, Univ Sq, Luton LU1 3JU, Beds - England

^[11] Univ Oxford, Dept Plant Sci, South Pk Rd, Oxford - England

^[12] Tecnol Antioquia, Calle 78B 72A-220, Medellin - Colombia

• Document type: Journal article
• Source: SCIENTIFIC REPORTS; v. 11, n. 1 MAR 25 2021.
• Web of Science Citations: 2

Abstract

Recent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth-death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies. (AU)

• FAPESP's process: 13/19124-1 - Phylogenetic systematics, cytogenetics and taxonomic revision of the genus Koellensteinia Rchb. f. (Orchidaceae)
• Grantee: Climbiê Ferreira Hall
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate
• FAPESP's process: 11/08308-9 - Phylogeny, taxonomic revision and cytogenetics of the genus Koellensteinia Rchb.f. (Orchidaceae)
• Grantee: Climbiê Ferreira Hall
• Support Opportunities: Scholarships in Brazil - Doctorate