Evaluating character partitioning and molecular models in plastid phylogenomics at low taxonomic levels: A case study using Amphilophium (Bignonieae, Bignoniaceae)

Author(s)

Thode, Veronica A. ^{[1, 2]} ; Lohmann, Lucia G. ^[1] ; Sanmartin, Isabel ^[3]

Affiliation

^[1] Univ Sao Paulo, Inst Biociencias, Dept Bot, Rua Matao 277, BR-05508090 Sao Paulo, SP - Brazil

^[2] Univ Fed Rio Grande do Sul, Programa Posgrad Bot, Inst Biociencias, Ave Bento Goncalves 9500, Predio 43433, BR-91501970 Porto Alegre, RS - Brazil

^[3] CSIC, RJB, Plaza Murillo 2, E-28014 Madrid - Spain

• Document type: Journal article
• Source: JOURNAL OF SYSTEMATICS AND EVOLUTION; v. 58, n. 6, SI, p. 1071-1089, NOV 2020.
• Web of Science Citations: 6

Abstract

The accurate analyses of massive amounts of data obtained through next-generation sequencing depend on the selection of appropriate evolutionary models. Many plastid phylogenomic studies typically analyze plastome data as a single partition, or divided by a region, using a concatenate ``supergene{''} approach. The effects of molecular evolutionary models and character partition strategies on plastome-based phylogenies have generally been evaluated at higher taxonomic levels in green plants. Using plastome data from 32 species of Amphilophium, a genus of Neotropical lianas, we explored potential sources of topological incongruence with different plastid genome datasets and approaches. Specifically, we evaluated the effects of compositional heterogeneity, codon usage bias, positive selection, and incomplete lineage sorting as sources of systematic error (i.e., the recovery of well-supported conflicting topologies). We compared different datasets (e.g., non-coding regions, exons, and codon-aligned and translated amino acids) using concatenated approaches under site-heterogeneous and site-homogeneous models, as well as multispecies coalescent (MSC) methods. We found incongruences in recovered phylogenetic relationships, which were mainly located in short internodes. The MSC and concatenated approaches recovered similar topologies. The analysis of GC content and codon usage bias indicated higher substitution rates and AT excess at the third codon positions, and we found evidence of positive selection in 3% of amino acid sites. There were no significant differences among species in site biochemical profiles. We argue that the selection of appropriate partition strategies and evolutionary models is important to increase accuracy in phylogenetic relationships, even when using plastome datasets, which is still the primarily used genome in plant phylogenetics. (AU)

• FAPESP's process: 11/50859-2 - Systematics of the tribe Bignonieae (Bignoniaceae)
• Grantee: Lúcia Garcez Lohmann
• Support Opportunities: Regular Research Grants
• FAPESP's process: 15/26884-8 - Phylogenomics and spatio-temporal evolution of Amphilophium (Bignonieae, Bignoniaceae)
• Grantee: Verônica Aydos Thode
• Support Opportunities: Scholarships abroad - Research Internship - Post-doctor
• FAPESP's process: 13/11706-1 - Phylogegeny, biogeography and diversification in Amphilophium (Bignonieae, Bignoniaceae)
• Grantee: Verônica Aydos Thode
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 12/50260-6 - Structure and evolution of the Amazonian biota and its environment: an integrative approach
• Grantee: Lúcia Garcez Lohmann
• Support Opportunities: BIOTA-FAPESP Program - Thematic Grants