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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

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

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Thode, Veronica A. [1, 2] ; Lohmann, Lucia G. [1] ; Sanmartin, Isabel [3]
Total Authors: 3
[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
Total Affiliations: 3
Document type: Journal article
Web of Science Citations: 1

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