1
|
Bogarín D, Pérez-Escobar OA, Karremans AP, Fernández M, Kruizinga J, Pupulin F, Smets E, Gravendeel B. Phylogenetic comparative methods improve the selection of characters for generic delimitations in a hyperdiverse Neotropical orchid clade. Sci Rep 2019; 9:15098. [PMID: 31641165 PMCID: PMC6805863 DOI: 10.1038/s41598-019-51360-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 09/19/2019] [Indexed: 11/28/2022] Open
Abstract
Taxonomic delimitations are challenging because of the convergent and variable nature of phenotypic traits. This is evident in species-rich lineages, where the ancestral and derived states and their gains and losses are difficult to assess. Phylogenetic comparative methods help to evaluate the convergent evolution of a given morphological character, thus enabling the discovery of traits useful for classifications. In this study, we investigate the evolution of selected traits to test for their suitability for generic delimitations in the clade Lepanthes, one of the Neotropical species-richest groups. We evaluated every generic name proposed in the Lepanthes clade producing densely sampled phylogenies with Maximum Parsimony, Maximum Likelihood, and Bayesian approaches. Using Ancestral State Reconstructions, we then assessed 18 phenotypic characters that have been traditionally employed to diagnose genera. We propose the recognition of 14 genera based on solid morphological delimitations. Among the characters assessed, we identified 16 plesiomorphies, 12 homoplastic characters, and seven synapomorphies, the latter of which are reproductive features mostly related to the pollination by pseudocopulation and possibly correlated with rapid diversifications in Lepanthes. Furthermore, the ancestral states of some reproductive characters suggest that these traits are associated with pollination mechanisms alike promoting homoplasy. Our methodological approach enables the discovery of useful traits for generic delimitations in the Lepanthes clade and offers various other testable hypotheses on trait evolution for future research on Pleurothallidinae orchids because the phenotypic variation of some characters evaluated here also occurs in other diverse genera.
Collapse
Affiliation(s)
- Diego Bogarín
- Jardín Botánico Lankester, Universidad de Costa Rica, Cartago, P.O. Box 302-7050, Costa Rica.
- Herbarium UCH, Universidad Autónoma de Chiriquí, David, Chiriquí, Panama.
- Naturalis Biodiversity Center, Endless Forms group, Leiden, The Netherlands.
| | - Oscar A Pérez-Escobar
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Adam P Karremans
- Jardín Botánico Lankester, Universidad de Costa Rica, Cartago, P.O. Box 302-7050, Costa Rica
- Naturalis Biodiversity Center, Endless Forms group, Leiden, The Netherlands
| | - Melania Fernández
- Jardín Botánico Lankester, Universidad de Costa Rica, Cartago, P.O. Box 302-7050, Costa Rica
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Jaco Kruizinga
- Hortus botanicus, Leiden University, Leiden, The Netherlands
| | - Franco Pupulin
- Jardín Botánico Lankester, Universidad de Costa Rica, Cartago, P.O. Box 302-7050, Costa Rica
- Harvard University Herbaria, 22 Divinity Avenue, Cambridge, Massachusetts, USA
- Marie Selby Botanical Gardens, 811 South Palm Avenue, Sarasota, Florida, 34236, USA
| | - Erik Smets
- Naturalis Biodiversity Center, Endless Forms group, Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
- KU Leuven, Ecology, Evolution and Biodiversity Conservation, Leuven, Belgium
| | - Barbara Gravendeel
- Naturalis Biodiversity Center, Endless Forms group, Leiden, The Netherlands
- University of Applied Sciences Leiden, Faculty of Science and Technology, Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| |
Collapse
|
2
|
Jackson LM, Fernando PC, Hanscom JS, Balhoff JP, Mabee PM. Automated Integration of Trees and Traits: A Case Study Using Paired Fin Loss Across Teleost Fishes. Syst Biol 2018; 67:559-575. [PMID: 29325126 PMCID: PMC6005059 DOI: 10.1093/sysbio/syx098] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 12/15/2017] [Accepted: 12/21/2017] [Indexed: 11/24/2022] Open
Abstract
Data synthesis required for large-scale macroevolutionary studies is challenging with the current tools available for integration. Using a classic question regarding the frequency of paired fin loss in teleost fishes as a case study, we sought to create automated methods to facilitate the integration of broad-scale trait data with a sizable species-level phylogeny. Similar to the evolutionary pattern previously described for limbs, pelvic and pectoral fin reduction and loss are thought to have occurred independently multiple times in the evolution of fishes. We developed a bioinformatics pipeline to identify the presence and absence of pectoral and pelvic fins of 12,582 species. To do this, we integrated a synthetic morphological supermatrix of phenotypic data for the pectoral and pelvic fins for teleost fishes from the Phenoscape Knowledgebase (two presence/absence characters for 3047 taxa) with a species-level tree for teleost fishes from the Open Tree of Life project (38,419 species). The integration method detailed herein harnessed a new combined approach by utilizing data based on ontological inference, as well as phylogenetic propagation, to reduce overall data loss. Using inference enabled by ontology-based annotations, missing data were reduced from 98.0% to 85.9%, and further reduced to 34.8% by phylogenetic data propagation. These methods allowed us to extend the data to an additional 11,293 species for a total of 12,582 species with trait data. The pectoral fin appears to have been independently lost in a minimum of 19 lineages and the pelvic fin in 48. Though interpretation is limited by lack of phylogenetic resolution at the species level, it appears that following loss, both pectoral and pelvic fins were regained several (3) to many (14) times respectively. Focused investigation into putative regains of the pectoral fin, all within one clade (Anguilliformes), showed that the pectoral fin was regained at least twice following loss. Overall, this study points to specific teleost clades where strategic phylogenetic resolution and genetic investigation will be necessary to understand the pattern and frequency of pectoral fin reversals.
Collapse
Affiliation(s)
- Laura M Jackson
- Department of Biology, University of South Dakota, 414 East Clark St., Vermillion, SD 57069, USA
| | - Pasan C Fernando
- Department of Biology, University of South Dakota, 414 East Clark St., Vermillion, SD 57069, USA
| | - Josh S Hanscom
- Department of Biology, University of South Dakota, 414 East Clark St., Vermillion, SD 57069, USA
| | - James P Balhoff
- Renaissance Computing Institute, University of North Carolina, 100 Europa Drive Suite 540, Chapel Hill, NC 27517, USA
| | - Paula M Mabee
- Department of Biology, University of South Dakota, 414 East Clark St., Vermillion, SD 57069, USA
| |
Collapse
|