Abstract Detail

Bryological and Lichenological Section/ABLS

Liu, Yang [1], Cox, Cymon [2], Wang, Wei [3], Goffinet, Bernard [4].

Mitochondrial Phylogenomics of Early Land Plants: Mitigating the Effects of Saturation, Compositional Heterogeneity, and Codon-usage Bias.

Phylogenetic analyses using concatenation of genomic-scale data have been seen as the panacea to resolving the incongruences among inferences from few or single genes. However, phylogenomics may also suffer from systematic errors, due to the, perhaps cumulative, effects of saturation, among-taxa compositional heterogeneity, or codon-usage bias plaguing the individual nucleotide loci that are concatenated. Here we provide an example of how these factors affect the inferences of the phylogeny of early land plants based on mitochondrial genomic data. Mitochondrial sequences evolve slowly in plants and hence are thought to be suitable for resolving deep relationships. We newly assembled mitochondrial genomes from 20 bryophytes, complemented these with 40 other streptophytes, compiling a data matrix of 60 taxa and 41 mitochondrial genes. Homogeneous analyses of the concatenated nucleotide data resolve mosses as sister-group to the remaining land plants. However, the corresponding translated amino acid data support the liverwort lineage in this position. Both results receive weak to moderate support in maximum likelihood analyses, but strong support in Bayesian inferences. Tests of alternative hypotheses using either nucleotide or amino-acid data provide implicit support for the respective optimal topologies. The 3^rd codon positions are more saturated than the 1^st and 2^nd codon positions, and excluding these leads to a topology congruent with that obtained using amino-acid data. Further, we determined that land plant lineages differ in their nucleotide composition, and in their usage of synonymous codon variants. Composition heterogeneous Bayesian analyses employing a non-stationary model that accounts for variation in among-lineage composition, and inferences from degenerated nucleotide data, again recovered liverworts being sister to the remaining land plants. These analyses indicate that the discrepancy between the nucleotide-based and the amino acid-based trees is caused by the lineage specific, parallel compositional bias, or synonymous mutations driving codon-usage bias, as well as saturation in the 3^rd codon positions. While genomic data may generate highly supported phylogenetic trees, these inferences may be artifacts. We suggest that phylogenomic analyses should assess the possible impact of potential biases through comparisons of protein coding gene data and their amino-acids translations, by analyzing data modeling compositional bias, and by excluding nucleotide noisy signals due to saturation or codon-usage bias. We caution against relying on any one presentation of the data (nucleotide or amino acid) or any one type of analysis even of large data sets, no matter how well-supported, without fully exploring the effects of substitution models.

1 - University of Connecticut, Ecology and Evolutionary Biology, 75 North Eagleville road, Storrs, CT, 06269-3043, United States
2 - Universidade do Algarve, CCMAR - Centro de Ciencias do Mar, Campus de Gambelas, Edif. 7, Faro, 8005-139, Portugal
3 - Chinese Academy of Sciences, State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Beijing, 100093, China
4 - University Of Connecticut, Department Of Ecology & Evolutionary Biology, 75 N. Eagleville Road, U-3043, STORRS, CT, 06269-3043, USA

Keywords:
mitochondrion
phylogenomics
land plants
codon bias
GC content
saturation.

Presentation Type: Oral Paper:Papers for Sections
Session: 29
Location: River Fork/Grove
Date: Tuesday, July 29th, 2014
Time: 2:30 PM
Number: 29005
Abstract ID:505
Candidate for Awards:None