MtOrt: an empirical mitochondrial amino acid substitution model for evolutionary studies of Orthoptera insects

Abstract

Background: Amino acid substitution models play an important role in inferring phylogenies from proteins. Although different amino acid substitution models have been proposed, only a few were estimated from mitochondrial protein sequences for specific taxa such as the mtArt model for Arthropoda. The increasing of mitochondrial genome data from broad Orthoptera taxa provides an opportunity to estimate the Orthopteraspecific mitochondrial amino acid empirical model. Results: We sequenced complete mitochondrial genomes of 54 Orthoptera species, and estimated an amino acid substitution model (named mtOrt) by maximum likelihood method based on the 283 complete mitochondrial genomes available currently. The results indicated that there are obvious differences between mtOrt and the existing models, and the new model can better fit the Orthoptera mitochondrial protein datasets. Moreover, topologies of trees constructed using mtOrt and existing models are frequently different. MtOrt does indeed have an impact on likelihood improvement as well as tree topologies. The comparisons between the topologies of trees constructed using mtOrt and existing models show that the new model outperforms the existing models in inferring phylogenies from Orthoptera mitochondrial protein data. Conclusions: The new mitochondrial amino acid substitution model of Orthoptera shows obvious differences from the existing models, and outperforms the existing models in inferring phylogenies from Orthoptera mitochondrial protein sequences.

Consequences of Substitution Model Selection on Protein Ancestral Sequence Reconstruction

“…As indicated in the Introduction, protein ASR is frequently applied in diverse fields such as paleoenzymology and biotechnology (e.g., Perez-Jimenez et al 2011 ; Holinski et al 2017 ) and the reconstructed molecules should be as realistic as possible to display reliable biological properties. The observed patterns of amino acid substitution are the consequence of diverse selection constrains (i.e., selection on the protein function and stability; Lorenzo-Redondo et al 2014 ; Arenas et al 2016 ; Duchene et al 2016 ; Echave et al 2016 ; Kirchner et al 2017 ; Geoghegan and Holmes 2018 ; Jimenez-Santos et al 2018 ; Moshe and Pupko 2019 ) that can differ among taxonomic levels ( Duchene et al 2016 ; Chang et al 2020 ), protein families ( Rios et al 2015 ; Del Amparo and Arenas 2022 ), and even within protein families ( Del Amparo and Arenas 2022 ). Here we show that these different selection processes, mimicked with different substitution models, should be taken into consideration to more accurately reconstruct ancestral proteins.…”

Mitochondrial genomes of eight Scelimeninae species (Orthoptera) and their phylogenetic implications within Tetrigoidea

“…Complete mitogenomes have been shown to provide more highly supported results than single or multiple mitochondrial genes ( Yuan et al, 2016 ; Liu et al, 2019 ). Until recently, only 18 mitogenome sequences of Tetrigidae have been submitted to the GenBank ( ; last visited on July 30, 2020) ( Xiao et al, 2012 ; Lin et al, 2017 ; Sun et al, 2017 ; Yang et al, 2017 ; Chang et al, 2020 ). Therefore, more mitogenomes of Tetrigidae are required for a comprehensive phylogenetic analysis, and before a full picture of the mitogenome for Tetrigidae can be depicted.…”

The Complete Mitogenomes of Three Grasshopper Species with Special Notes on the Phylogenetic Positions of Some Related Genera

“…Reconstructing a robust phylogeny will promote our understanding of the interesting biology and evolutionary patterns within this family, such as character and behaviour evolution [ 2 , 3 , 4 , 5 ]. In recent years, an increasing number of studies have been carried out based on molecular evidence to resolve phylogenetic problems at different taxonomic scales of Acrididae [ 6 , 7 , 8 , 9 , 10 ], and the complete mitogenome data has demonstrated great potential in this field [ 3 , 4 , 5 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 ]. Therefore, studies of the mitogenome for various purposes have always been a hot topic [ 4 ].…”

“…Similar problems are also explicit in the genera Emeiacris , Choroedocus , Conophymacris, and Xiangelilacris . Emeiacris is recognized as a member of the subfamily Oxyinae in OSF [ 32 ], but was placed in the subfamily Melanoplinae by Li and Xia [ 33 ], and Mao et al [ 34 ], and this was always supported by molecular evidences [ 24 , 25 , 27 ]. Choroedocus is currently placed in the subfamily Catantopinae in OSF [ 32 ], but was obviously regarded as a member of the subfamily Eyprepocnemidinae in nearly all published literatures.…”