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Molecular Phylogenetics and Mitochondrial Evolution
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Molecular Phylogenetics and Mitochondrial Evolution

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Evolutionary Biology".

Deadline for manuscript submissions: closed (10 June 2021) | Viewed by 43796

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editors

Prof. Dr. Andrea Luchetti

E-Mail Website
Guest Editor
MoZoo Lab, Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Via Selmi, 3, 40126 Bologna BO, Italy
Interests: arthropoda; genomics; phylogenetic analysis; genetic diversity; molecular ecology; molecular evolution; molecular phylogenetics; phylogeography; DNA barcoding; hybridization; molecular taxonomy; nucleic acids; transposable elements; retrotransposons; zoology
Special Issues, Collections and Topics in MDPI journals
Dr. Federico Plazzi

E-Mail Website
Guest Editor
MoZoo Lab, Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Via Selmi, 3, 40126 Bologna BO, Italy
Interests: evolutionary biology; systematics; biodiversity; zoology; molecular biology; phylogenetic analysis; phylogenetics; genetics; sncRNA; miRNA; mitochondrial biology; bivalve molluscs; biology teaching and learning

Special Issue Information

Dear Colleagues,

Is mitochondrial phylogenetics trustworthy? In fact, mitochondrial genes are long-time phylogenetic markers: they are widely used to infer evolutionary trees across all eukaryotic realms, making cox1, rrnL, and their kin possibly the most popular genes in the world. They were initially chosen because of some key features that they were supposed to share universally.

In recent years, an increasing body of knowledge has shown several exceptions, including evidence of recombination, noncanonical ways of mitochondrial inheritance, strong selective constraints on some mitochondrial regions, and complex interactions with the nuclear genome. Conversely, massive sequencing technologies brought phylogeny into the -omics era, and the use of ESTs and transcriptomes is now common in phylogenetics, often unveiling discrepancies between the signal massively retrieved from nuclear sources and the signal carried by weird organellar chromosomes.

Although the drawbacks of mitochondrial phylogenetics have come to light and mitochondrial inferences have been questioned in front of their nuclear counterparts, the use of mitochondrial markers is nevertheless still widespread in the scientific community, and research on mitochondrial evolution, idiosyncrasies, and vagaries has emerged as a stimulating field per se. This Special Issue aims to unravel different topics on mitochondrial evolution, with special emphasis on their implications on phylogenetic reconstruction.

Prof. Dr. Andrea Luchetti
Dr. Federico Plazzi
Guest Editors

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Keywords

  • mitochondrial genome
  • tree reconstruction
  • phylogenetics
  • phylogenomics
  • phylotranscriptomics
  • mitochondrial evolution
  • mitochondrial inheritance
  • phylogenetic signal
  • selective constraints

Published Papers (15 papers)

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3 pages, 186 KiB  
Editorial
Molecular Phylogenetics and Mitochondrial Evolution
by Andrea Luchetti and Federico Plazzi
Life 2022, 12(1), 4; https://0-doi-org.brum.beds.ac.uk/10.3390/life12010004 - 21 Dec 2021
Cited by 2 | Viewed by 2213
Abstract
The myth of a “typical” mitochondrial genome (mtDNA) is a rock-hard belief in the field of genetics, at least for the animal kingdom [...] Full article
(This article belongs to the Special Issue Molecular Phylogenetics and Mitochondrial Evolution)
19 pages, 3329 KiB  
Article
Mitochondrial Genomic Landscape: A Portrait of the Mitochondrial Genome 40 Years after the First Complete Sequence
by Alessandro Formaggioni, Andrea Luchetti and Federico Plazzi
Life 2021, 11(7), 663; https://0-doi-org.brum.beds.ac.uk/10.3390/life11070663 - 06 Jul 2021
Cited by 15 | Viewed by 3846
Abstract
Notwithstanding the initial claims of general conservation, mitochondrial genomes are a largely heterogeneous set of organellar chromosomes which displays a bewildering diversity in terms of structure, architecture, gene content, and functionality. The mitochondrial genome is typically described as a single chromosome, yet many [...] Read more.
Notwithstanding the initial claims of general conservation, mitochondrial genomes are a largely heterogeneous set of organellar chromosomes which displays a bewildering diversity in terms of structure, architecture, gene content, and functionality. The mitochondrial genome is typically described as a single chromosome, yet many examples of multipartite genomes have been found (for example, among sponges and diplonemeans); the mitochondrial genome is typically depicted as circular, yet many linear genomes are known (for example, among jellyfish, alveolates, and apicomplexans); the chromosome is normally said to be “small”, yet there is a huge variation between the smallest and the largest known genomes (found, for example, in ctenophores and vascular plants, respectively); even the gene content is highly unconserved, ranging from the 13 oxidative phosphorylation-related enzymatic subunits encoded by animal mitochondria to the wider set of mitochondrial genes found in jakobids. In the present paper, we compile and describe a large database of 27,873 mitochondrial genomes currently available in GenBank, encompassing the whole eukaryotic domain. We discuss the major features of mitochondrial molecular diversity, with special reference to nucleotide composition and compositional biases; moreover, the database is made publicly available for future analyses on the MoZoo Lab GitHub page. Full article
(This article belongs to the Special Issue Molecular Phylogenetics and Mitochondrial Evolution)
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16 pages, 5401 KiB  
Article
Looking at the Nudibranch Family Myrrhinidae (Gastropoda, Heterobranchia) from a Mitochondrial ‘2D Folding Structure’ Point of View
by Giulia Furfaro and Paolo Mariottini
Life 2021, 11(6), 583; https://0-doi-org.brum.beds.ac.uk/10.3390/life11060583 - 18 Jun 2021
Cited by 3 | Viewed by 2145
Abstract
Integrative taxonomy is an evolving field of multidisciplinary studies often utilised to elucidate phylogenetic reconstructions that were poorly understood in the past. The systematics of many taxa have been resolved by combining data from different research approaches, i.e., molecular, ecological, behavioural, morphological and [...] Read more.
Integrative taxonomy is an evolving field of multidisciplinary studies often utilised to elucidate phylogenetic reconstructions that were poorly understood in the past. The systematics of many taxa have been resolved by combining data from different research approaches, i.e., molecular, ecological, behavioural, morphological and chemical. Regarding molecular analysis, there is currently a search for new genetic markers that could be diagnostic at different taxonomic levels and that can be added to the canonical ones. In marine Heterobranchia, the most widely used mitochondrial markers, COI and 16S, are usually analysed by comparing the primary sequence. The 16S rRNA molecule can be folded into a 2D secondary structure that has been poorly exploited in the past study of heterobranchs, despite 2D molecular analyses being sources of possible diagnostic characters. Comparison of the results from the phylogenetic analyses of a concatenated (the nuclear H3 and the mitochondrial COI and 16S markers) dataset (including 30 species belonging to eight accepted genera) and from the 2D folding structure analyses of the 16S rRNA from the type species of the genera investigated demonstrated the diagnostic power of this RNA molecule to reveal the systematics of four genera belonging to the family Myrrhinidae (Gastropoda, Heterobranchia). The “molecular morphological” approach to the 16S rRNA revealed to be a powerful tool to delimit at both species and genus taxonomic levels and to be a useful way of recovering information that is usually lost in phylogenetic analyses. While the validity of the genera Godiva, Hermissenda and Phyllodesmium are confirmed, a new genus is necessary and introduced for Dondice banyulensis, Nemesis gen. nov. and the monospecific genus Nanuca is here synonymised with Dondice, with Nanuca sebastiani transferred into Dondice as Dondice sebastiani comb. nov. Full article
(This article belongs to the Special Issue Molecular Phylogenetics and Mitochondrial Evolution)
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2 pages, 199 KiB  
Communication
Nemesignis, a Replacement Name for Nemesis Furfaro & Mariottini, 2021 (Mollusca, Gastropoda, Myrrhinidae), Preoccupied by Nemesis Risso, 1826 (Crustacea, Copepoda)
by Giulia Furfaro and Paolo Mariottini
Life 2021, 11(8), 809; https://0-doi-org.brum.beds.ac.uk/10.3390/life11080809 - 10 Aug 2021
Cited by 3 | Viewed by 1815
Abstract
The genus Nemesis Furfaro & Mariottini, 2021, was recently introduced for an independent lineage of aeolid nudibranchs, and Dondice banyulensis Portmann & Sandmeier, 1960, established as its type species. Anyway, the presence of a senior homonym, Nemesis Risso, 1826, was evidently missed. In [...] Read more.
The genus Nemesis Furfaro & Mariottini, 2021, was recently introduced for an independent lineage of aeolid nudibranchs, and Dondice banyulensis Portmann & Sandmeier, 1960, established as its type species. Anyway, the presence of a senior homonym, Nemesis Risso, 1826, was evidently missed. In fact, in 1826, Risso established this genus for a group of Copepoda (Arthropoda, Crustacea) and according to the Principle of Priority (ICZN) only the senior homonym may be used as a valid name. Therefore, a new replacement name is here proposed. Furthermore, the genus name Nanuca Er. Marcus, 1957, has priority over Dondice Er. Marcus, 1958 and consequently, the species in this clade should be classified under Nanuca, mostly as new combinations. Full article
(This article belongs to the Special Issue Molecular Phylogenetics and Mitochondrial Evolution)
11 pages, 2528 KiB  
Article
Mitochondrial DNA Analysis Clarifies Taxonomic Status of the Northernmost Snow Sheep (Ovis nivicola) Population
by Arsen V. Dotsev, Elisabeth Kunz, Veronika R. Kharzinova, Innokentiy M. Okhlopkov, Feng-Hua Lv, Meng-Hua Li, Andrey N. Rodionov, Alexey V. Shakhin, Taras P. Sipko, Dmitry G. Medvedev, Elena A. Gladyr, Vugar A. Bagirov, Gottfried Brem, Ivica Medugorac and Natalia A. Zinovieva
Life 2021, 11(3), 252; https://0-doi-org.brum.beds.ac.uk/10.3390/life11030252 - 18 Mar 2021
Cited by 6 | Viewed by 3145
Abstract
Currently, the intraspecific taxonomy of snow sheep (Ovis nivicola) is controversial and needs to be specified using DNA molecular genetic markers. In our previous work using whole-genome single nucleotide polymorphism (SNP) analysis, we found that the population inhabiting Kharaulakh Ridge was [...] Read more.
Currently, the intraspecific taxonomy of snow sheep (Ovis nivicola) is controversial and needs to be specified using DNA molecular genetic markers. In our previous work using whole-genome single nucleotide polymorphism (SNP) analysis, we found that the population inhabiting Kharaulakh Ridge was genetically different from the other populations of Yakut subspecies to which it was usually referred. Here, our study was aimed at the clarification of taxonomic status of Kharaulakh snow sheep using mitochondrial cytochrome b gene. A total of 87 specimens from five different geographic locations of Yakut snow sheep as well as 20 specimens of other recognized subspecies were included in this study. We identified 19 haplotypes, two of which belonged to the population from Kharaulakh Ridge. Median-joining network and Bayesian tree analyses revealed that Kharaulakh population clustered separately from all the other Yakut snow sheep. The divergence time between Kharaulakh population and Yakut snow sheep was estimated as 0.48 ± 0.19 MYA. Thus, the study of the mtDNA cytb sequences confirmed the results of genome-wide SNP analysis. Taking into account the high degree of divergence of Kharaulakh snow sheep from other groups, identified by both nuclear and mitochondrial DNA markers, we propose to classify the Kharaulakh population as a separate subspecies. Full article
(This article belongs to the Special Issue Molecular Phylogenetics and Mitochondrial Evolution)
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16 pages, 1849 KiB  
Article
Unique Mitochondrial Single Nucleotide Polymorphisms Demonstrate Resolution Potential to Discriminate Theileria parva Vaccine and Buffalo-Derived Strains
by Micky M. Mwamuye, Isaiah Obara, Khawla Elati, David Odongo, Mohammed A. Bakheit, Frans Jongejan and Ard M. Nijhof
Life 2020, 10(12), 334; https://doi.org/10.3390/life10120334 - 08 Dec 2020
Cited by 4 | Viewed by 2343
Abstract
Distinct pathogenic and epidemiological features underlie different Theileria parva strains resulting in different clinical manifestations of East Coast Fever and Corridor Disease in susceptible cattle. Unclear delineation of these strains limits the control of these diseases in endemic areas. Hence, an accurate characterization [...] Read more.
Distinct pathogenic and epidemiological features underlie different Theileria parva strains resulting in different clinical manifestations of East Coast Fever and Corridor Disease in susceptible cattle. Unclear delineation of these strains limits the control of these diseases in endemic areas. Hence, an accurate characterization of strains can improve the treatment and prevention approaches as well as investigate their origin. Here, we describe a set of single nucleotide polymorphisms (SNPs) based on 13 near-complete mitogenomes of T. parva strains originating from East and Southern Africa, including the live vaccine stock strains. We identified 11 SNPs that are non-preferentially distributed within the coding and non-coding regions, all of which are synonymous except for two within the cytochrome b gene of buffalo-derived strains. Our analysis ascertains haplotype-specific mutations that segregate the different vaccine and the buffalo-derived strains except T. parva-Muguga and Serengeti-transformed strains suggesting a shared lineage between the latter two vaccine strains. Phylogenetic analyses including the mitogenomes of other Theileria species: T. annulata, T. taurotragi, and T. lestoquardi, with the latter two sequenced in this study for the first time, were congruent with nuclear-encoded genes. Importantly, we describe seven T. parva haplotypes characterized by synonymous SNPs and parsimony-informative characters with the other three transforming species mitogenomes. We anticipate that tracking T. parva mitochondrial haplotypes from this study will provide insight into the parasite’s epidemiological dynamics and underpin current control efforts. Full article
(This article belongs to the Special Issue Molecular Phylogenetics and Mitochondrial Evolution)
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23 pages, 2433 KiB  
Article
The Patterns and Puzzles of Genetic Diversity of Endangered Freshwater Mussel Unio crassus Philipsson, 1788 Populations from Vistula and Neman Drainages (Eastern Central Europe)
by Adrianna Kilikowska, Monika Mioduchowska, Anna Wysocka, Agnieszka Kaczmarczyk-Ziemba, Joanna Rychlińska, Katarzyna Zając, Tadeusz Zając, Povilas Ivinskis and Jerzy Sell
Life 2020, 10(7), 119; https://0-doi-org.brum.beds.ac.uk/10.3390/life10070119 - 21 Jul 2020
Cited by 7 | Viewed by 3242
Abstract
Mussels of the family Unionidae are important components of freshwater ecosystems. Alarmingly, the International Union for Conservation of Nature and Natural Resources Red List of Threatened Species identifies almost 200 unionid species as extinct, endangered, or threatened. Their decline is the result of [...] Read more.
Mussels of the family Unionidae are important components of freshwater ecosystems. Alarmingly, the International Union for Conservation of Nature and Natural Resources Red List of Threatened Species identifies almost 200 unionid species as extinct, endangered, or threatened. Their decline is the result of human impact on freshwater habitats, and the decrease of host fish populations. The Thick Shelled River Mussel Unio crassus Philipsson, 1788 is one of the examples that has been reported to show a dramatic decline of populations. Hierarchical organization of riverine systems is supposed to reflect the genetic structure of populations inhabiting them. The main goal of this study was an assessment of the U. crassus genetic diversity in river ecosystems using hierarchical analysis. Different molecular markers, the nuclear ribosomal internal transcribed spacer ITS region, and mitochondrial DNA genes (cox1 and ndh1), were used to examine the distribution of U. crassus among-population genetic variation at multiple spatial scales (within rivers, among rivers within drainages, and between drainages of the Neman and Vistula rivers). We found high genetic structure between both drainages suggesting that in the case of the analyzed U. crassus populations we were dealing with at least two different genetic units. Only about 4% of the mtDNA variation was due to differences among populations within drainages. However, comparison of population differentiation within drainages for mtDNA also showed some genetic structure among populations within the Vistula drainage. Only one haplotype was shared among all Polish populations whereas the remainder were unique for each population despite the hydrological connection. Interestingly, some haplotypes were present in both drainages. In the case of U. crassus populations under study, the Mantel test revealed a relatively strong relationship between genetic and geographical distances. However, in detail, the pattern of genetic diversity seems to be much more complicated. Therefore, we suggest that the observed pattern of U. crassus genetic diversity distribution is shaped by both historical and current factors i.e. different routes of post glacial colonization and history of drainage systems, historical gene flow, and more recent habitat fragmentation due to anthropogenic factors. Full article
(This article belongs to the Special Issue Molecular Phylogenetics and Mitochondrial Evolution)
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12 pages, 10764 KiB  
Article
One in a Million: Genetic Diversity and Conservation of the Reference Crassostrea angulata Population in Europe from the Sado Estuary (Portugal)
by Stefania Chiesa, Livia Lucentini, Paula Chainho, Federico Plazzi, Maria Manuel Angélico, Francisco Ruano, Rosa Freitas and José Lino Costa
Life 2021, 11(11), 1173; https://0-doi-org.brum.beds.ac.uk/10.3390/life11111173 - 03 Nov 2021
Cited by 2 | Viewed by 1615
Abstract
The production of cupped oysters is an important component of European aquaculture. Most of the production relies on the cultivation of the Pacific oyster Crassostrea gigas, although the Portuguese oyster Crassostrea angulata represents a valuable product with both cultural and economic relevance, [...] Read more.
The production of cupped oysters is an important component of European aquaculture. Most of the production relies on the cultivation of the Pacific oyster Crassostrea gigas, although the Portuguese oyster Crassostrea angulata represents a valuable product with both cultural and economic relevance, especially in Portugal. The authors of the present study investigated the genetic diversity of Portuguese oyster populations of the Sado estuary, both from natural oyster beds and aquaculture facilities, through cox1 gene fragment sequencing. Then, a comparison with a wide dataset of cupped oyster sequences obtained from GenBank (up to now the widest available dataset in literature for the Portuguese oyster) was performed. Genetic data obtained from this work confirmed that the Pacific oyster does not occur in the natural oyster beds of the Sado estuary but showed that the species occasionally occurs in the oyster hatcheries. Moreover, the results showed that despite the founder effect and the bottleneck events that the Sado populations have experienced, they still exhibit high haplotype diversity. Risks are arising for the conservation of the Portuguese oyster reference populations of the Sado estuary due to the occurrence of the Pacific oyster in the local hatcheries. Therefore, researchers, local authorities, and oyster producers should work together to avoid the loss of this valuable resource. Full article
(This article belongs to the Special Issue Molecular Phylogenetics and Mitochondrial Evolution)
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15 pages, 19719 KiB  
Article
Molecular Correlation between Larval, Deutonymph and Adult Stages of the Water Mite Arrenurus (Micruracarus) Novus
by Pedro María Alarcón-Elbal, Ricardo García-Jiménez, María Luisa Peláez, Jose Luis Horreo and Antonio G. Valdecasas
Life 2020, 10(7), 108; https://0-doi-org.brum.beds.ac.uk/10.3390/life10070108 - 09 Jul 2020
Cited by 3 | Viewed by 2703
Abstract
The systematics of many groups of organisms has been based on the adult stage. Morphological transformations that occur during development from the embryonic to the adult stage make it difficult (or impossible) to identify a juvenile (larval) stage in some species. Hydrachnidia (Acari, [...] Read more.
The systematics of many groups of organisms has been based on the adult stage. Morphological transformations that occur during development from the embryonic to the adult stage make it difficult (or impossible) to identify a juvenile (larval) stage in some species. Hydrachnidia (Acari, Actinotrichida, which inhabit mainly continental waters) are characterized by three main active stages—larval, deutonymph and adult—with intermediate dormant stages. Deutonymphs and adults may be identified through diagnostic morphological characters. Larvae that have not been tracked directly from a gravid female are difficult to identify to the species level. In this work, we compared the morphology of five water mite larvae and obtained the molecular sequences of that found on a pupa of the common mosquito Culex (Culex) pipiens with the sequences of 51 adults diagnosed as Arrenurus species and identified the undescribed larvae as Arrenurus (Micruracarus) novus. Further corroborating this finding, adult A. novus was found thriving in the same mosquito habitat. We established the identity of adult and deutonymph A. novus by morphology and by correlating COI and cytB sequences of the water mites at the larval, deutonymph and adult (both male and female) life stages in a particular case of ‘reverse taxonomy’. In addition, we constructed the Arrenuridae phylogeny based on mitochondrial DNA, which supports the idea that three Arrenurus subgenera are ‘natural’: Arrenurus, Megaluracarus and Micruracarus, and the somewhat arbitrary distinction of the species assigned to the subgenus Truncaturus. Full article
(This article belongs to the Special Issue Molecular Phylogenetics and Mitochondrial Evolution)
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11 pages, 1908 KiB  
Article
Inferring the Phylogenetic Positions of Two Fig Wasp Subfamilies of Epichrysomallinae and Sycophaginae Using Transcriptomes and Mitochondrial Data
by Dan Zhao, Zhaozhe Xin, Hongxia Hou, Yi Zhou, Jianxia Wang, Jinhua Xiao and Dawei Huang
Life 2021, 11(1), 40; https://0-doi-org.brum.beds.ac.uk/10.3390/life11010040 - 11 Jan 2021
Cited by 3 | Viewed by 1927
Abstract
Fig wasps are a group of insects (Hymenoptera: Chalcidoidea) that live in the compact syconia of fig trees (Moraceae: Ficus). Accurate classification and phylogenetic results are very important for studies of fig wasps, but the taxonomic statuses of some fig wasps, especially [...] Read more.
Fig wasps are a group of insects (Hymenoptera: Chalcidoidea) that live in the compact syconia of fig trees (Moraceae: Ficus). Accurate classification and phylogenetic results are very important for studies of fig wasps, but the taxonomic statuses of some fig wasps, especially the non-pollinating subfamilies are difficult to determine, such as Epichrysomallinae and Sycophaginae. To resolve the taxonomic statuses of Epichrysomallinae and Sycophaginae, we obtained transcriptomes and mitochondrial genome (mitogenome) data for four species of fig wasps. These newly added data were combined with the data of 13 wasps (data on 11 fig wasp species were from our laboratory and two wasp species were download from NCBI). Based on the transcriptome and genome data, we obtained 145 single-copy orthologous (SCO) genes in 17 wasp species, and based on mitogenome data, we obtained 13 mitochondrial protein-coding genes (PCGs) for each of the 17 wasp species. Ultimately, we used 145 SCO genes, 13 mitochondrial PCGs and combined SCO genes and mitochondrial genes data to reconstruct the phylogenies of fig wasps using both maximum likelihood (ML) and Bayesian inference (BI) analyses. Our results suggest that both Epichrysomallinae and Sycophaginae are more closely related to Agaonidae with a high statistical support. Full article
(This article belongs to the Special Issue Molecular Phylogenetics and Mitochondrial Evolution)
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17 pages, 5829 KiB  
Article
Chronological Incongruences between Mitochondrial and Nuclear Phylogenies of Aedes Mosquitoes
by Nicola Zadra, Annapaola Rizzoli and Omar Rota-Stabelli
Life 2021, 11(3), 181; https://0-doi-org.brum.beds.ac.uk/10.3390/life11030181 - 25 Feb 2021
Cited by 12 | Viewed by 3078
Abstract
One-third of all mosquitoes belong to the Aedini, a tribe comprising common vectors of viral zoonoses such as Aedes aegypti and Aedes albopictus. To improve our understanding of their evolution, we present an updated multigene estimate of Aedini phylogeny and divergence, focusing [...] Read more.
One-third of all mosquitoes belong to the Aedini, a tribe comprising common vectors of viral zoonoses such as Aedes aegypti and Aedes albopictus. To improve our understanding of their evolution, we present an updated multigene estimate of Aedini phylogeny and divergence, focusing on the disentanglement between nuclear and mitochondrial phylogenetic signals. We first show that there are some phylogenetic discrepancies between nuclear and mitochondrial markers which may be caused by wrong taxa assignment in samples collections or by some stochastic effect due to small gene samples. We indeed show that the concatenated dataset is model and framework dependent, indicating a general paucity of signal. Our Bayesian calibrated divergence estimates point toward a mosquito radiation in the mid-Jurassic and an Aedes radiation from the mid-Cretaceous on. We observe, however a strong chronological incongruence between mitochondrial and nuclear data, the latter providing divergence times within the Aedini significantly younger than the former. We show that this incongruence is consistent over different datasets and taxon sampling and that may be explained by either peculiar evolutionary event such as different levels of saturation in certain lineages or a past history of hybridization throughout the genus. Overall, our updated picture of Aedini phylogeny, reveal a strong nuclear-mitochondrial incongruence which may be of help in setting the research agenda for future phylogenomic studies of Aedini mosquitoes. Full article
(This article belongs to the Special Issue Molecular Phylogenetics and Mitochondrial Evolution)
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15 pages, 2629 KiB  
Article
Improving Phylogenetic Signals of Mitochondrial Genes Using a New Method of Codon Degeneration
by Xuhua Xia
Life 2020, 10(9), 171; https://0-doi-org.brum.beds.ac.uk/10.3390/life10090171 - 30 Aug 2020
Cited by 1 | Viewed by 2437
Abstract
Recovering deep phylogeny is challenging with animal mitochondrial genes because of their rapid evolution. Codon degeneration decreases the phylogenetic noise and bias by aiming to achieve two objectives: (1) alleviate the bias associated with nucleotide composition, which may lead to homoplasy and long-branch [...] Read more.
Recovering deep phylogeny is challenging with animal mitochondrial genes because of their rapid evolution. Codon degeneration decreases the phylogenetic noise and bias by aiming to achieve two objectives: (1) alleviate the bias associated with nucleotide composition, which may lead to homoplasy and long-branch attraction, and (2) reduce differences in the phylogenetic results between nucleotide-based and amino acid (AA)-based analyses. The discrepancy between nucleotide-based analysis and AA-based analysis is partially caused by some synonymous codons that differ more from each other at the nucleotide level than from some nonsynonymous codons, e.g., Leu codon TTR in the standard genetic code is more similar to Phe codon TTY than to synonymous CTN codons. Thus, nucleotide similarity conflicts with AA similarity. There are many such examples involving other codon families in various mitochondrial genetic codes. Proper codon degeneration will make synonymous codons more similar to each other at the nucleotide level than they are to nonsynonymous codons. Here, I illustrate a “principled” codon degeneration method that achieves these objectives. The method was applied to resolving the mammalian basal lineage and phylogenetic position of rheas among ratites. The codon degeneration method was implemented in the user-friendly and freely available DAMBE software for all known genetic codes (genetic codes 1 to 33). Full article
(This article belongs to the Special Issue Molecular Phylogenetics and Mitochondrial Evolution)
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19 pages, 2501 KiB  
Article
The Mitochondrial Genome of a Plant Fungal Pathogen Pseudocercospora fijiensis (Mycosphaerellaceae), Comparative Analysis and Diversification Times of the Sigatoka Disease Complex Using Fossil Calibrated Phylogenies
by Juliana E. Arcila-Galvis, Rafael E. Arango, Javier M. Torres-Bonilla and Tatiana Arias
Life 2021, 11(3), 215; https://0-doi-org.brum.beds.ac.uk/10.3390/life11030215 - 09 Mar 2021
Cited by 6 | Viewed by 2814
Abstract
Mycosphaerellaceae is a highly diverse fungal family containing a variety of pathogens affecting many economically important crops. Mitochondria play a crucial role in fungal metabolism and in the study of fungal evolution. This study aims to: (i) describe the mitochondrial genome of Pseudocercospora [...] Read more.
Mycosphaerellaceae is a highly diverse fungal family containing a variety of pathogens affecting many economically important crops. Mitochondria play a crucial role in fungal metabolism and in the study of fungal evolution. This study aims to: (i) describe the mitochondrial genome of Pseudocercospora fijiensis, and (ii) compare it with closely related species (Sphaerulina musiva, S. populicola, P. musae and P. eumusae) available online, paying particular attention to the Sigatoka disease’s complex causal agents. The mitochondrial genome of P. fijiensis is a circular molecule of 74,089 bp containing typical genes coding for the 14 proteins related to oxidative phosphorylation, 2 rRNA genes and a set of 38 tRNAs. P. fijiensis mitogenome has two truncated cox1 copies, and bicistronic transcription of nad2-nad3 and atp6-atp8 confirmed experimentally. Comparative analysis revealed high variability in size and gene order among selected Mycosphaerellaceae mitogenomes likely to be due to rearrangements caused by mobile intron invasion. Using fossil calibrated Bayesian phylogenies, we found later diversification times for Mycosphaerellaceae (66.6 MYA) and the Sigatoka disease complex causal agents, compared to previous strict molecular clock studies. An early divergent Pseudocercospora fijiensis split from the sister species P. musae + P. eumusae 13.31 MYA while their sister group, the sister species P. eumusae and P. musae, split from their shared common ancestor in the late Miocene 8.22 MYA. This newly dated phylogeny suggests that species belonging to the Sigatoka disease complex originated after wild relatives of domesticated bananas (section Eumusae; 27.9 MYA). During this time frame, mitochondrial genomes expanded significantly, possibly due to invasions of introns into different electron transport chain genes. Full article
(This article belongs to the Special Issue Molecular Phylogenetics and Mitochondrial Evolution)
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13 pages, 3197 KiB  
Article
The Mitochondrial Genome of the Sea Anemone Stichodactyla haddoni Reveals Catalytic Introns, Insertion-Like Element, and Unexpected Phylogeny
by Steinar Daae Johansen, Sylvia I. Chi, Arseny Dubin and Tor Erik Jørgensen
Life 2021, 11(5), 402; https://0-doi-org.brum.beds.ac.uk/10.3390/life11050402 - 28 Apr 2021
Cited by 5 | Viewed by 3220
Abstract
A hallmark of sea anemone mitochondrial genomes (mitogenomes) is the presence of complex catalytic group I introns. Here, we report the complete mitogenome and corresponding transcriptome of the carpet sea anemone Stichodactyla haddoni (family Stichodactylidae). The mitogenome is vertebrate-like in size, organization, and [...] Read more.
A hallmark of sea anemone mitochondrial genomes (mitogenomes) is the presence of complex catalytic group I introns. Here, we report the complete mitogenome and corresponding transcriptome of the carpet sea anemone Stichodactyla haddoni (family Stichodactylidae). The mitogenome is vertebrate-like in size, organization, and gene content. Two mitochondrial genes encoding NADH dehydrogenase subunit 5 (ND5) and cytochrome c oxidase subunit I (COI) are interrupted with complex group I introns, and one of the introns (ND5-717) harbors two conventional mitochondrial genes (ND1 and ND3) within its sequence. All the mitochondrial genes, including the group I introns, are expressed at the RNA level. Nonconventional and optional mitochondrial genes are present in the mitogenome of S. haddoni. One of these gene codes for a COI-884 intron homing endonuclease and is organized in-frame with the upstream COI exon. The insertion-like orfA is expressed as RNA and translocated in the mitogenome as compared with other sea anemones. Phylogenetic analyses based on complete nucleotide and derived protein sequences indicate that S. haddoni is embedded within the family Actiniidae, a finding that challenges current taxonomy. Full article
(This article belongs to the Special Issue Molecular Phylogenetics and Mitochondrial Evolution)
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Review
mtDNA Heteroplasmy: Origin, Detection, Significance, and Evolutionary Consequences
by Maria-Eleni Parakatselaki and Emmanuel D. Ladoukakis
Life 2021, 11(7), 633; https://0-doi-org.brum.beds.ac.uk/10.3390/life11070633 - 29 Jun 2021
Cited by 35 | Viewed by 4657
Abstract
Mitochondrial DNA (mtDNA) is predominately uniparentally transmitted. This results in organisms with a single type of mtDNA (homoplasmy), but two or more mtDNA haplotypes have been observed in low frequency in several species (heteroplasmy). In this review, we aim to highlight several aspects [...] Read more.
Mitochondrial DNA (mtDNA) is predominately uniparentally transmitted. This results in organisms with a single type of mtDNA (homoplasmy), but two or more mtDNA haplotypes have been observed in low frequency in several species (heteroplasmy). In this review, we aim to highlight several aspects of heteroplasmy regarding its origin and its significance on mtDNA function and evolution, which has been progressively recognized in the last several years. Heteroplasmic organisms commonly occur through somatic mutations during an individual’s lifetime. They also occur due to leakage of paternal mtDNA, which rarely happens during fertilization. Alternatively, heteroplasmy can be potentially inherited maternally if an egg is already heteroplasmic. Recent advances in sequencing techniques have increased the ability to detect and quantify heteroplasmy and have revealed that mitochondrial DNA copies in the nucleus (NUMTs) can imitate true heteroplasmy. Heteroplasmy can have significant evolutionary consequences on the survival of mtDNA from the accumulation of deleterious mutations and for its coevolution with the nuclear genome. Particularly in humans, heteroplasmy plays an important role in the emergence of mitochondrial diseases and determines the success of the mitochondrial replacement therapy, a recent method that has been developed to cure mitochondrial diseases. Full article
(This article belongs to the Special Issue Molecular Phylogenetics and Mitochondrial Evolution)
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