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Molecular Evolution of the Mitochondrial DNA in Animals
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Molecular Evolution of the Mitochondrial DNA in Animals

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (30 December 2020) | Viewed by 23236

Special Issue Editors

Prof. Dr. Antonio Carapelli

E-Mail Website
Guest Editor
Department of Life Sciences, University of Siena, Via A. Moro 2, 53100 Siena, Italy
Interests: evolution of the basal hexapods; genomics and mitogenomics; molecular phylogeny and biogeography of Collembola species; evolution of the terrestrial invertebrates of Antarctica
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Francesco Nardi

E-Mail Website
Guest Editor
Department of Life Sciences, University of Siena, Via A. Moro 2, 53100 Siena, Italy
Interests: population genetics; mitochondrial genomics; molecular evolution; bioinformatics

Special Issue Information

Dear Colleagues,

The mitochondrial genome (mtDNA) is a compact molecule, usually containing a conserved set of (37) genes, that occurs in multiple copies within the mitochondria of most multicellular organisms. Despite recent progress in the sequencing and analysis of nuclear genomes, mitogenomes still play a crucial role in the study of both non-bilaterian and bilaterian animal evolution, with the greatest impacts in the fields of molecular phylogeny, population genomics, and genome evolution.

The popularity of mitogenomes is largely due to the relatively simple procedure to extract, amplify, and sequence the complete mtDNA from animal tissues, and to the substantial conservation of its gene content, a required feature necessary to compare multiple evolutionary lineages.

This Special Issue of Genes will cover all aspects of biogeography, phylogenetics, and genome evolution in key, as well as less known, taxa based on the comparison of mitochondrial DNA data. Studies on large sets of mtDNA sequences are welcome, as well as meta-analyses on genomic features (e.g., nucleotide composition, codon bias, and gene order) focusing on specific lineages of the animal kingdom. This Special Issue is especially dedicated to collecting new data from researchers that have contributed to the investigation of the systematics, diversity, and molecular evolution of animal lineages using mitogenomic data.

Prof. Antonio Carapelli
Prof. Francesco Nardi
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • mitogenomics
  • systematics
  • phylogenetics
  • phylogeography

Published Papers (6 papers)

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Research

18 pages, 11313 KiB  
Article
Complete Mitochondrial DNA Genome of Nine Species of Sharks and Rays and Their Phylogenetic Placement among Modern Elasmobranchs
by Vasiliki Kousteni, Sofia Mazzoleni, Katerina Vasileiadou and Michail Rovatsos
Genes 2021, 12(3), 324; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12030324 - 24 Feb 2021
Cited by 33 | Viewed by 5388
Abstract
Chondrichthyes occupy a key position in the phylogeny of vertebrates. The complete sequence of the mitochondrial genome (mitogenome) of four species of sharks and five species of rays was obtained by whole genome sequencing (DNA-seq) in the Illumina HiSeq2500 platform. The arrangement and [...] Read more.
Chondrichthyes occupy a key position in the phylogeny of vertebrates. The complete sequence of the mitochondrial genome (mitogenome) of four species of sharks and five species of rays was obtained by whole genome sequencing (DNA-seq) in the Illumina HiSeq2500 platform. The arrangement and features of the genes in the assembled mitogenomes were identical to those found in vertebrates. Both Maximum Likelihood (ML) and Bayesian Inference (BI) analyses were used to reconstruct the phylogenetic relationships among 172 species (including 163 mitogenomes retrieved from GenBank) based on the concatenated dataset of 13 individual protein coding genes. Both ML and BI analyses did not support the “Hypnosqualea” hypothesis and confirmed the monophyly of sharks and rays. The broad notion in shark phylogeny, namely the division of sharks into Galeomorphii and Squalomorphii and the monophyly of the eight shark orders, was also supported. The phylogenetic placement of all nine species sequenced in this study produced high statistical support values. The present study expands our knowledge on the systematics, genetic differentiation, and conservation genetics of the species studied, and contributes to our understanding of the evolutionary history of Chondrichthyes. Full article
(This article belongs to the Special Issue Molecular Evolution of the Mitochondrial DNA in Animals)
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19 pages, 2786 KiB  
Article
Comparative Mitogenomics in Hyalella (Amphipoda: Crustacea)
by Francesco Zapelloni, José A. Jurado-Rivera, Damià Jaume, Carlos Juan and Joan Pons
Genes 2021, 12(2), 292; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12020292 - 19 Feb 2021
Cited by 4 | Viewed by 2868
Abstract
We present the sequencing and comparative analysis of 17 mitochondrial genomes of Nearctic and Neotropical amphipods of the genus Hyalella, most from the Andean Altiplano. The mitogenomes obtained comprised the usual 37 gene-set of the metazoan mitochondrial genome showing a gene rearrangement [...] Read more.
We present the sequencing and comparative analysis of 17 mitochondrial genomes of Nearctic and Neotropical amphipods of the genus Hyalella, most from the Andean Altiplano. The mitogenomes obtained comprised the usual 37 gene-set of the metazoan mitochondrial genome showing a gene rearrangement (a reverse transposition and a reversal) between the North and South American Hyalella mitogenomes. Hyalella mitochondrial genomes show the typical AT-richness and strong nucleotide bias among codon sites and strands of pancrustaceans. Protein-coding sequences are biased towards AT-rich codons, with a preference for leucine and serine amino acids. Numerous base changes (539) were found in tRNA stems, with 103 classified as fully compensatory, 253 hemi-compensatory and the remaining base mismatches and indels. Most compensatory Watson–Crick switches were AU -> GC linked in the same haplotype, whereas most hemi-compensatory changes resulted in wobble GU and a few AC pairs. These results suggest a pairing fitness increase in tRNAs after crossing low fitness valleys. Branch-site level models detected positive selection for several amino acid positions in up to eight mitochondrial genes, with atp6 and nad5 as the genes displaying more sites under selection. Full article
(This article belongs to the Special Issue Molecular Evolution of the Mitochondrial DNA in Animals)
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12 pages, 2040 KiB  
Article
Genetic Diversities and Historical Dynamics of Native Ethiopian Horse Populations (Equus caballus) Inferred from Mitochondrial DNA Polymorphisms
by Kefena Effa, Sonia Rosenbom, Jianlin Han, Tadelle Dessie and Albano Beja-Pereira
Genes 2021, 12(2), 155; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12020155 - 25 Jan 2021
Cited by 3 | Viewed by 4466
Abstract
Matrilineal genetic diversity and relationship were investigated among eight morphologically identified native Ethiopian horse populations using polymorphisms in 46 mtDNA D-loop sequences (454 base pairs). The horse populations identified were Abyssinian, Bale, Borana, Horro, Kafa, Kundido feral horses, Ogaden and Selale. Mitochondrial DNA [...] Read more.
Matrilineal genetic diversity and relationship were investigated among eight morphologically identified native Ethiopian horse populations using polymorphisms in 46 mtDNA D-loop sequences (454 base pairs). The horse populations identified were Abyssinian, Bale, Borana, Horro, Kafa, Kundido feral horses, Ogaden and Selale. Mitochondrial DNA D-loop sequences were characterized by 15 variable sites that defined five different haplotypes. All genetic diversity estimates, including Reynolds’ linearized genetic distance, genetic differentiation (FST) and nucleotide sequence divergence (DA), revealed a low genetic differentiation in native Ethiopian horse populations. However, Kundido feral and Borana domestic horses were slightly diverged from the rest of the Ethiopian horse populations. We also tried to shed some light on the matrilineal genetic root of native Ethiopian horses from a network constructed by combining newly generated haplotypes and reference haplotypes deposited in the GenBank for Eurasian type Turkish Anatolian horses that were used as a genetic conduit between Eurasian and African horse populations. Ninety-two haplotypes were generated from the combined Ethio-Eurasian mtDNA D-loop sequences. A network reconstructed from the combined haplotypes using Median-Joining algorithm showed that haplotypes generated from native Ethiopian horses formed separate clusters. The present result encourages further investigation of the genetic origin of native African horses by retrieving additional mtDNA sequences deposited in the GenBank for African and Eurasian type horses. Full article
(This article belongs to the Special Issue Molecular Evolution of the Mitochondrial DNA in Animals)
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12 pages, 9962 KiB  
Article
Mitochondrial Genome Evolution, Genetic Diversity, and Population Structure in British Water Voles (Arvicola amphibius)
by Corey Kirkland and Marta Farré
Genes 2021, 12(2), 138; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12020138 - 21 Jan 2021
Cited by 3 | Viewed by 2911
Abstract
The European water vole (Arvicola amphibius) is a rodent within the subfamily Arvicolinae. In Britain, water voles have declined rapidly during the last century, making them a conservation priority. The relationship of Arvicola to other genera within Arvicolinae remains debated. Additionally, [...] Read more.
The European water vole (Arvicola amphibius) is a rodent within the subfamily Arvicolinae. In Britain, water voles have declined rapidly during the last century, making them a conservation priority. The relationship of Arvicola to other genera within Arvicolinae remains debated. Additionally, the impact that captive breeding programs in Britain are having on the genetic diversity of water voles is unknown. We use available mitochondrial genomes to construct the phylogeny of species within Arvicolinae, followed by sequencing the mitochondrial DNA control region of 17 individuals from a captive population of water voles in Britain to assess their genetic diversity and population structure. Our study first provides an updated phylogenetic tree of Arvicolinae using the mitochondrial genome of 31 species. Second, our results show considerable genetic diversity in the captive population of water voles, when compared with natural populations in Britain. We confirm the grouping of British water voles into two clades, with all captive individuals found in the English/Welsh clade. Moreover, captive water voles clustered closely with populations in the South East and East of England. The mitochondrial genome provides a useful marker to study the phylogenetics of this rodent clade and in addition, our study provides support for the breeding program at Wildwood Trust and provides a framework for future conservation genetics studies in this species. Full article
(This article belongs to the Special Issue Molecular Evolution of the Mitochondrial DNA in Animals)
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19 pages, 3326 KiB  
Article
Re-Evaluating the Internal Phylogenetic Relationships of Collembola by Means of Mitogenome Data
by Claudio Cucini, Pietro P. Fanciulli, Francesco Frati, Peter Convey, Francesco Nardi and Antonio Carapelli
Genes 2021, 12(1), 44; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12010044 - 30 Dec 2020
Cited by 16 | Viewed by 4256
Abstract
Collembola are an ancient and early diverging lineage of basal hexapods that occur in virtually all terrestrial habitats on Earth. Phylogenetic relationships between the different orders of Collembola are fiercely debated. Despite a range of studies and the application of both morphological and [...] Read more.
Collembola are an ancient and early diverging lineage of basal hexapods that occur in virtually all terrestrial habitats on Earth. Phylogenetic relationships between the different orders of Collembola are fiercely debated. Despite a range of studies and the application of both morphological and genetic approaches (singly or in combination) to assess the evolutionary relationships of major lineages in the group, no consensus has been reached. Several mitogenome sequences have been published for key taxa of the class (and their number is increasing rapidly). Here, we describe two new Antarctic Collembola mitogenomes and compare all complete or semi-complete springtail mitogenome sequences available on GenBank in terms of both gene order and DNA sequence analyses in a genome evolution and molecular phylogenetic framework. With minor exceptions, we confirm the monophyly of Poduromorpha and Symphypleona sensu stricto (the latter placed at the most basal position in the springtail phylogenetic tree), whereas monophyly of Neelipleona and Entomobryomorpha is only supported when a handful of critical taxa in these two lineages are excluded. Finally, we review gene order models observed in the class, as well as the overall mitochondrial nucleotide composition. Full article
(This article belongs to the Special Issue Molecular Evolution of the Mitochondrial DNA in Animals)
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13 pages, 1688 KiB  
Article
Inferring Evolutionary Timescales without Independent Timing Information: An Assessment of “Universal” Insect Rates to Calibrate a Collembola (Hexapoda) Molecular Clock
by Aron D. Katz
Genes 2020, 11(10), 1172; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11101172 - 07 Oct 2020
Cited by 7 | Viewed by 2229
Abstract
Previous estimates of nucleotide substitution rates are routinely applied as secondary or “universal” molecular clock calibrations for estimating evolutionary timescales in groups that lack independent timing information. A major limitation of this approach is that rates can vary considerably among taxonomic groups, but [...] Read more.
Previous estimates of nucleotide substitution rates are routinely applied as secondary or “universal” molecular clock calibrations for estimating evolutionary timescales in groups that lack independent timing information. A major limitation of this approach is that rates can vary considerably among taxonomic groups, but the assumption of rate constancy is rarely evaluated prior to using secondary rate calibrations. Here I evaluate whether an insect mitochondrial DNA clock is appropriate for estimating timescales in Collembola—a group of insect-like arthropods characterized by high levels of cryptic diversity. Relative rates of substitution in cytochrome oxidase subunit 1 (COI) were inferred via Bayesian analysis across a topologically constrained Hexapod phylogeny using a relaxed molecular clock model. Rates for Collembola did not differ significantly from the average rate or from the rates estimated for most other groups (25 of 30), suggesting that (1) their apparent cryptic diversity cannot be explained by accelerated rates of molecular evolution and (2) clocks calibrated using “universal” insect rates may be appropriate for estimating evolutionary timescales in this group. However, of the 31 groups investigated, 10 had rates that deviated significantly from the average (6 higher, 4 lower), underscoring the need for caution and careful consideration when applying secondary insect rate calibrations. Lastly, this study exemplifies a relatively simple approach for evaluating rate constancy within a taxonomic group to determine whether the use of secondary rates are appropriate for molecular clock calibrations. Full article
(This article belongs to the Special Issue Molecular Evolution of the Mitochondrial DNA in Animals)
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