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Phylogenomics and Molecular Evolution
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Phylogenomics and Molecular Evolution

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

Deadline for manuscript submissions: closed (20 October 2023) | Viewed by 8791

Special Issue Editors

Dr. Artem Nedoluzhko

E-Mail Website
Guest Editor
Paleogenomics Laboratory, European University at Saint-Petersburg, Saint-Petersburg 191187, Russia
Interests: paleogenomics; evolutionary genomics; ancient DNA; museomics; de-extinction; domestication
Dr. Natalia Abramson

E-Mail Website
Guest Editor
Laboratory of Evolutionary Genomics and Paleogenomics, Zoological Institute RAS, Saint-Petersburg 199034, Russia
Interests: paleogenomics; evolutionary genomics; ancient DNA; rodents; phylogeny; Arvicolinae; systematics

Special Issue Information

Dear Colleagues,

Global species diversity is still non-evaluated and the process of describing of new species is ongoing to date. Modern genomic technologies have opened additional opportunities for the study of the phylogeny, population history and demographic structure of many species. Novel methods in this area allow us to carry out many important investigations aimed at molecular systematics and genetic diversity analyses, speciation studies, conservation of species, development of breeding programs to restore endangered species and even de-extinction projects. The development of novel bioinformatics methods allows us to better understand the basics of evolution and describe the traces of speciation using methods of phylogenetic analysis.

This Special Issue is aimed at representing the applicability of modern genomics and bioinformatics methods for understanding the patterns of species evolution and the development of novel practices for molecular systematics and phylogenetics.

For this Special Issue, we therefore invite you to contribute original research and review papers describing the application of DNA sequencing for phylogenetic and systematics analyses, as well as speciation and molecular evolution studies. Novel computational approaches and pipelines for performing such investigations are also welcome.

Dr. Artem Nedoluzhko
Dr. Natalia Abramson
Guest Editors

Manuscript Submission Information

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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

  • phylogeny
  • molecular evolution
  • speciation
  • genetic diversity
  • species adaptation
  • species hybridization

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Published Papers (4 papers)

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Research

23 pages, 43209 KiB  
Article
Assessing the Influence of HGT on the Evolution of Stress Responses in Microbial Communities from Shark Bay, Western Australia
by Emilie J. Skoog, Gregory P. Fournier and Tanja Bosak
Genes 2023, 14(12), 2168; https://doi.org/10.3390/genes14122168 - 1 Dec 2023
Cited by 1 | Viewed by 1719
Abstract
Pustular microbial mats in Shark Bay, Western Australia, are modern analogs of microbial systems that colonized peritidal environments before the evolution of complex life. To understand how these microbial communities evolved to grow and metabolize in the presence of various environmental stresses, the [...] Read more.
Pustular microbial mats in Shark Bay, Western Australia, are modern analogs of microbial systems that colonized peritidal environments before the evolution of complex life. To understand how these microbial communities evolved to grow and metabolize in the presence of various environmental stresses, the horizontal gene transfer (HGT) detection tool, MetaCHIP, was used to identify the horizontal transfer of genes related to stress response in 83 metagenome-assembled genomes from a Shark Bay pustular mat. Subsequently, maximum-likelihood phylogenies were constructed using these genes and their most closely related homologs from other environments in order to determine the likelihood of these HGT events occurring within the pustular mat. Phylogenies of several stress-related genes—including those involved in response to osmotic stress, oxidative stress and arsenic toxicity—indicate a potentially long history of HGT events and are consistent with these transfers occurring outside of modern pustular mats. The phylogeny of a particular osmoprotectant transport gene reveals relatively recent adaptations and suggests interactions between Planctomycetota and Myxococcota within these pustular mats. Overall, HGT phylogenies support a potentially broad distribution in the relative timing of the HGT events of stress-related genes and demonstrate ongoing microbial adaptations and evolution in these pustular mat communities. Full article
(This article belongs to the Special Issue Phylogenomics and Molecular Evolution)
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14 pages, 1720 KiB  
Article
Genetic Diversity of Common Olive (Olea europaea L.) Cultivars from Nikita Botanical Gardens Collection Revealed Using RAD-Seq Method
by Natalia Slobodova, Fedor Sharko, Maria Gladysheva-Azgari, Kristina Petrova, Sergey Tsiupka, Valentina Tsiupka, Eugenia Boulygina, Sergey Rastorguev and Svetlana Tsygankova
Genes 2023, 14(7), 1323; https://doi.org/10.3390/genes14071323 - 23 Jun 2023
Cited by 3 | Viewed by 1490
Abstract
In different countries, interest in the commercial cultivation of the olive has recently greatly increased, which has led to the expansion of its range. The Crimean Peninsula is the northern limit of the common olive (Olea europaea L.) range. A unique collection [...] Read more.
In different countries, interest in the commercial cultivation of the olive has recently greatly increased, which has led to the expansion of its range. The Crimean Peninsula is the northern limit of the common olive (Olea europaea L.) range. A unique collection of common olive’s cultivars and hybrids has been collected in the Nikitsky Botanical Gardens (NBG). The aim of this study was to assess the genetic diversity of 151 samples (total of several biological replicates of 46 olive cultivars including 29 introduced and 11 indigenous genotypes) using the ddRAD sequencing method. Structural analysis showed that the studied samples are divided into ten groups, each of which mainly includes cultivars of the same origin. Cultivars introduced to the Crimean Peninsula from different regions formed separate groups, while local cultivars joined different groups depending on their origin. Cultivars of Crimean origin contain admixtures of mainly Italian and Caucasian cultivars’ genotypes. Our study showed that the significant number of Crimean cultivars contains an admixture of the Italian cultivar “Coreggiolo”. Genetic analysis confirmed the synonymy for the cv. “Otur” and “Nikitskaya 2”, but not for the other four putative synonyms. Our results revealed the genetic diversity of the olive collection of NBG and provided references for future research studies, especially in selection studies for breeding programs. Full article
(This article belongs to the Special Issue Phylogenomics and Molecular Evolution)
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11 pages, 1380 KiB  
Article
The Complete Mitochondrial Genome of Dendrogale murina (Tupaiidae) and Phylogeny of Scandentia
by Tatyana Petrova, Olga Bondareva, Semyon Bodrov, Alexei Abramov and Natalia Abramson
Genes 2023, 14(3), 624; https://doi.org/10.3390/genes14030624 - 1 Mar 2023
Cited by 1 | Viewed by 2215
Abstract
In this paper, we report the complete mitochondrial genome of the northern smooth-tailed treeshrew Dendrogale murina, which was sequenced for the first time using the Illumina next-generation sequencing (NGS) technology. The total length of the mitochondrial genome is 16,844–16,850 bp and encodes [...] Read more.
In this paper, we report the complete mitochondrial genome of the northern smooth-tailed treeshrew Dendrogale murina, which was sequenced for the first time using the Illumina next-generation sequencing (NGS) technology. The total length of the mitochondrial genome is 16,844–16,850 bp and encodes 37 genes, including two ribosomal RNAs (rRNAs) 12S and 16S, 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), and a D-loop in the characteristic arrangement of family Tupaiidae (Mammalia: Scandentia). The overall base composition of the complete mitochondrial DNA is A (33.5%), C (25.5%), G (13.9%), and T (27.1%). Phylogenetic analysis of Scandentia mitochondrial genomes showed a classic pattern, which was revealed previously while using individual phylogenetic markers. The result of the current study is consistent with one based on the latest morphological studies, with the basal position of Ptilocercus and Dendrogale sister to the rest of the Tupaiidae genera. The divergence time of the Dendrogale genus is estimated as Eocene–Oligocene, with the mean value of 35.8 MYA, and the Ptilocercus genus probably separated at about 46.3 MYA. We observe an increase in the age of all nodes within the Scandentia, except for a decrease in the age of separation of Ptilocercus. This result can be explained both by the addition of new mitochondrial genome data in the analysis and the usage of new calibration points from recently published data. Full article
(This article belongs to the Special Issue Phylogenomics and Molecular Evolution)
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15 pages, 7757 KiB  
Article
Genomic Analyses Implicate the Amazon–Orinoco Plume as the Driver of Cryptic Speciation in a Swimming Crab
by Pedro A. Peres, Heather Bracken-Grissom, Laura E. Timm and Fernando L. Mantelatto
Genes 2022, 13(12), 2263; https://doi.org/10.3390/genes13122263 - 1 Dec 2022
Cited by 9 | Viewed by 2290
Abstract
The Amazon–Orinoco plume (AOP) is the world’s largest freshwater and sediment discharge into the ocean. Previous studies limited to mtDNA suggest that the swimming crab Callinectes ornatus Ordway, 1863 exists as two distinct genetic clusters separated by the AOP. However, questions concerning migration, [...] Read more.
The Amazon–Orinoco plume (AOP) is the world’s largest freshwater and sediment discharge into the ocean. Previous studies limited to mtDNA suggest that the swimming crab Callinectes ornatus Ordway, 1863 exists as two distinct genetic clusters separated by the AOP. However, questions concerning migration, diversification time, and species delimitation are unresolved. Densely sampling markers across the genome (SNPs) could elucidate the evolutionary processes within this species. Here, we combined mtDNA data and ddRAD-seq to explore the diversification patterns and processes within the swimming crab C. ornatus. We show great genetic differentiation between groups on the north and south sides of the plume but also signs of hybridization. Demographic modeling indicates the divergence between groups starting around 8 Mya following the AOP’s formation. After a period of isolation, we detect two incidences of secondary contact with stronger migration in concordance with the North Brazil Current flow. Our results suggest speciation with gene flow explained by the interplay among the AOP, oceanographic currents, and long larval dispersal. This work represents the first investigation employing ddRAD-seq in a marine invertebrate species with distribution encompassing the north and south Atlantic and sheds light on the role of the AOP in the diversification of a marine species. Full article
(This article belongs to the Special Issue Phylogenomics and Molecular Evolution)
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