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Evolutionary and Conservation Genetics: 2nd Edition

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

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 12728

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Dr. Daria Sanna

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Guest Editor

Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
Interests: evolutionary genetics; conservation genetics; population genetics; molecular taxonomy; phylogenetics; phylogeography
Special Issues, Collections and Topics in MDPI journals

Dr. Fabio Scarpa

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Department of Biomedical Science, University of Sassari, 07100 Sassari, Italy
Interests: genetics; genomics; phylodynamics; bioinformatics; biostatistics; population genetics; one health
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

During the last two years of the COVID-19 pandemic, the entire world has witnessed how evolution and genetics dynamics can affect human health. Now more than any previous time, it is evident that the role of scientific research in all fields has become of great importance by increasing our knowledge on every kind of organism (from viruses to mammals and plants) and biological phenomenon. In this context, evolutionary genetics can shed further light on the evolutionary mechanisms that shape organisms’ development and diffusion.

In addition, genetic variation represents the giant upon whose shoulders we find the basis of conservation genetics. This specific field of research derives from population and evolutionary genetics and focuses on the study of threats to every species.

For these reasons, this Special Issue aims to combine the contributions of research groups working all over the world in the fields of phylodynamics, evolutionary genetics, population genetics, DNA barcoding, conservation genetics, molecular epidemiology, and molecular taxonomy, with the aim of collating a group of original papers that highlight the importance of studying the genetic variability of organisms for the protection of all species.

The first volume of this Special Issue was a great success. Now, we invite you to publish in the second volume. (https://www.mdpi.com/journal/life/special_issues/Evolutionary_Conservation)

Dr. Daria Sanna
Dr. Fabio Scarpa
Guest Editors

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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. Life 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

evolutionary genetics
population genetics
conservation genetics
phylogeography
phylogenetics
phylodynamics
molecular taxonomy

Related Special Issue

Evolutionary and Conservation Genetics in Life (9 articles)

Published Papers (10 papers)

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Research

14 pages, 2845 KiB

Open AccessArticle

Haematococcus lacustris Carotenogensis: A Historical Event of Primary to Secondary Adaptations to Earth’s Oxygenation

by Cui Lan Qu, Hui Jin, Bing Zhang, Wei Jian Chen, Yang Zhang, Yuan Yuan Xu, Rui Wang and Yong Min Lao

Life 2024, 14(5), 576; https://doi.org/10.3390/life14050576 - 30 Apr 2024

Viewed by 340

Abstract

(1) Background: Oxygen has exerted a great effect in shaping the environment and driving biological diversity in Earth’s history. Green lineage has evolved primary and secondary carotenoid biosynthetic systems to adapt to Earth’s oxygenation, e.g., Haematococcus lacustris, which accumulates the highest amount of secondary astaxanthin under stresses. The two systems are controlled by lycopene ε-cyclase (LCYE) and β-cyclase (LCYB), which leave an important trace in Earth’s oxygenation. (2) Objectives: This work intends to disclose the underlying molecular evolutionary mechanism of Earth’s oxygenation in shaping green algal carotenogensis with a special focus on lycopene cyclases. (3) Methods: The two kinds of cyclases were analyzed by site-directed mutagenesis, phylogeny, divergence time and functional divergence. (4) Results: Green lineage LCYEs appeared at ~1.5 Ga after the first significant appearance and accumulation of atmospheric oxygen, the so-called Great Oxygenation Event (GOE), from which LCYBs diverged by gene duplication. Bacterial β-bicyclases evolved from β-monocyclase. Enhanced catalytic activity accompanied evolutionary transformation from ε-/β-monocyclase to β-bicyclase. Strong positive selection occurred in green lineage LCYEs after the GOE and in algal LCYBs during the second oxidation, the Neoproterozoic Oxygenation Event (NOE). Positively selected sites in the catalytic cavities of the enzymes controlled the mono-/bicyclase activity, respectively. Carotenoid profiling revealed that oxidative adaptation has been wildly preserved in evolution. (5) Conclusions: the functionalization of the two enzymes is a result of primary to secondary adaptations to Earth’s oxygenation. Full article

(This article belongs to the Special Issue Evolutionary and Conservation Genetics: 2nd Edition)

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12 pages, 1459 KiB

Open AccessArticle

Phylogeographic Reconstruction to Trace the Source Population of Asian Giant Hornet Caught in Nanaimo in Canada and Blaine in the USA

by Alexa Freeman and Xuhua Xia

Life 2024, 14(3), 283; https://doi.org/10.3390/life14030283 - 20 Feb 2024

Viewed by 960

Abstract

The Asian giant hornet, Vespa mandarinia, is an invasive species that could potentially destroy the local honeybee industry in North America. It has been observed to nest in the coastal regions of British Columbia in Canada and Washington State in the USA. What is the source population of the immigrant hornets? The identification of the source population can shed light not only on the route of immigration but also on the similarity between the native habitat and the potential new habitat in the Pacific Northwest. We analyzed mitochondrial COX1 sequences of specimens sampled from multiple populations in China, the Republic of Korea, Japan, and the Russian Far East. V. mandarinia exhibits phylogeographic patterns, forming monophyletic clades for 16 specimens from China, six specimens from the Republic of Korea, and two specimens from Japan. The two mitochondrial COX1 sequences from Nanaimo, British Columbia, are identical to the two sequences from Japan. The COX1 sequence from Blaine, Washington State, clustered with those from the Republic of Korea and is identical to one sequence from the Republic of Korea. Our geophylogeny, which allows visualization of genetic variation over time and space, provides evolutionary insights on the evolution and speciation of three closely related vespine species (V. tropica, V. soror, and V. mandarinia), with the speciation events associated with the expansion of the distribution to the north. Full article

(This article belongs to the Special Issue Evolutionary and Conservation Genetics: 2nd Edition)

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16 pages, 2245 KiB

Open AccessArticle

Stress Induced Activation of LTR Retrotransposons in the Drosophila melanogaster Genome

by Polina A. Milyaeva, Inna V. Kukushkina, Alexander I. Kim and Lidia N. Nefedova

Life 2023, 13(12), 2272; https://doi.org/10.3390/life13122272 - 28 Nov 2023

Cited by 1 | Viewed by 945

Abstract

Background: Retrotransposons with long terminal repeats (LTR retrotransposons) are widespread in all groups of eukaryotes and are often both the cause of new mutations and the source of new sequences. Apart from their high activity in generative and differentiation-stage tissues, LTR retrotransposons also become more active in response to different stressors. The precise causes of LTR retrotransposons’ activation in response to stress, however, have not yet been thoroughly investigated. Methods: We used RT-PCR to investigate the transcriptional profile of LTR retrotransposons and piRNA clusters in response to oxidative and chronic heat stresses. We used Oxford Nanopore sequencing to investigate the genomic environment of new insertions of the retrotransposons. We used bioinformatics methods to find the stress-induced transcription factor binding sites in LTR retrotransposons. Results: We studied the transposition activity and transcription level of LTR retrotransposons in response to oxidative and chronic heat stress and assessed the contribution of various factors that can affect the increase in their expression under stress conditions: the state of the piRNA-interference system, the influence of the genomic environment on individual copies, and the presence of the stress-induced transcription factor binding sites in retrotransposon sequences. Conclusions: The main reason for the activation of LTR retrotransposons under stress conditions is the presence of transcription factor binding sites in their regulatory sequences, which are triggered in response to stress and are necessary for tissue regeneration processes. Stress-induced transposable element activation can function as a trigger mechanism, triggering multiple signal pathways and resulting in a polyvariant cell response. Full article

(This article belongs to the Special Issue Evolutionary and Conservation Genetics: 2nd Edition)

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18 pages, 3838 KiB

Open AccessArticle

Assessing Drought Tolerance in a Large Number of Upland Cotton Plants (Gossypium hirsutum L.) under Different Irrigation Regimes at the Seedling Stage

by Sadettin Çelik

Life 2023, 13(10), 2067; https://doi.org/10.3390/life13102067 - 16 Oct 2023

Cited by 2 | Viewed by 967

Abstract

The cotton plant is important since it provides raw materials for various industry branches. Even though cotton is generally drought-tolerant, it is affected negatively by long-term drought stress. The trial was conducted according to the applied experimental design as a completely randomized design (CRD) with three replications to determine a panel of 93 cotton genotypes’ genotypic responses against drought under controlled conditions in 2022. All genotypes were watered with 80 mL⁻¹ of water (100% irrigation, field capacity) until three true leaves appeared, and then water stress was applied at a limited irrigation of 75% (60 mL⁻¹), 50% (40 mL⁻¹), and 25% (20 mL⁻¹) of the field capacity. After the trial terminated at 52 days, the cv. G56, G44, G5, and G86 in RL; G1, G56, G44, G86, G51, and G88 in RFW; advanced line G5, followed by the cv. G56, advanced line G44, G75, and the cv. G90 in RDW; G44, followed by G86, the cv. G56, and elite lines G13 and G5 in NLRs were observed as drought-tolerant genotypes, respectively, while G35, G15, G26, G67, and G56 in SL; G15, G52, G60, G31, and G68 in SFW; G35, G52, G57, G41, and G60 in SDW show the highest drought tolerance means, respectively. In conclusion, the commercial varieties with high means in roots, namely G86, G56, G88, and G90, and the genotypes G67, G20, G60, and G57 showing tolerance in shoots, are suggested to be potential parent plants for developing cotton varieties resistant to drought. Using the cultivars found tolerant in the current study as parents in a drought-tolerant variety development marker-assisted selection (MAS) plant breeding program will increase the chance of success in reaching the target after genetic diversity analyses are performed. On the other hand, it is highly recommended to continue the plant breeding program with the G44, G30, G19, G1, G5, G75, G35, G15, G52, G29, and G76 genotypes, which show high tolerance in both root and shoot systems. Full article

(This article belongs to the Special Issue Evolutionary and Conservation Genetics: 2nd Edition)

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21 pages, 10712 KiB

Open AccessArticle

Speciation on the Roof of the World: Parallel Fast Evolution of Cryptic Mole Vole Species in the Pamir-Alay—Tien Shan Region

by Aleksey Bogdanov, Valentina Tambovtseva, Sergey Matveevsky and Irina Bakloushinskaya

Life 2023, 13(8), 1751; https://doi.org/10.3390/life13081751 - 16 Aug 2023

Cited by 2 | Viewed by 998

Abstract

Speciation is not always accompanied by morphological changes; numerous cryptic closely related species were revealed using genetic methods. In natural populations of Ellobius tancrei (2n = 54–30) and E. alaicus (2n = 52–48) of the Pamir-Alay and Tien Shan, the chromosomal variability due to Robertsonian translocations has been revealed. Here, by comprehensive genetic analysis (karyological analyses as well as sequencing of mitochondrial genes, cytb and COI, and nuclear genes, XIST and IRBP) of E. alaicus and E. tancrei samples from the Inner Tien Shan, the Alay Valley, and the Pamir-Alay, we demonstrated fast and independent diversification of these species. We described an incompletely consistent polymorphism of the mitochondrial and nuclear markers, which arose presumably because of habitat fragmentation in the highlands, rapid karyotype changes, and hybridization of different intraspecific varieties and species. The most intriguing results are a low level of genetic distances calculated from mitochondrial and nuclear genes between some phylogenetic lines of E. tancrei and E. alaicus, as well significant species-specific chromosome variability in both species. The chromosomal rearrangements are what most clearly define species specificity and provide further diversification. The “mosaicism” and inconsistency in polymorphism patterns are evidence of rapid speciation in these mammals. Full article

(This article belongs to the Special Issue Evolutionary and Conservation Genetics: 2nd Edition)

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14 pages, 3549 KiB

Open AccessArticle

Characterization of Two Transposable Elements and an Ultra-Conserved Element Isolated in the Genome of Zootoca vivipara (Squamata, Lacertidae)

by Marcello Mezzasalma, Teresa Capriglione, Larissa Kupriyanova, Gaetano Odierna, Maria Michela Pallotta, Agnese Petraccioli, Orfeo Picariello and Fabio M. Guarino

Life 2023, 13(3), 637; https://doi.org/10.3390/life13030637 - 24 Feb 2023

Cited by 1 | Viewed by 1326

Abstract

Transposable elements (TEs) constitute a considerable fraction of eukaryote genomes representing a major source of genetic variability. We describe two DNA sequences isolated in the lizard Zootoca vivipara, here named Zv516 and Zv817. Both sequences are single-copy nuclear sequences, including a truncation of two transposable elements (TEs), SINE Squam1 in Zv516 and a Tc1/Mariner-like DNA transposon in Zv817. FISH analyses with Zv516 showed the occurrence of interspersed signals of the SINE Squam1 sequence on all chromosomes of Z. vivipara and quantitative dot blot indicated that this TE is present with about 4700 copies in the Z. vivipara genome. FISH and dot blot with Zv817 did not produce clear hybridization signals. Bioinformatic analysis showed the presence of active SINE Squam 1 copies in the genome of different lacertids, in different mRNAs, and intronic and coding regions of various genes. The Tc1/Mariner-like DNA transposon occurs in all reptiles, excluding Sphenodon and Archosauria. Zv817 includes a trait of 284 bp, representing an amniote ultra-conserved element (UCE). Using amniote UCE homologous sequences from available whole genome sequences of major amniote taxonomic groups, we performed a phylogenetic analysis which retrieved Prototheria as the sister group of Metatheria and Eutheria. Within diapsids, Testudines are the sister group to Aves + Crocodylia (Archosauria), and Sphenodon is the sister group to Squamata. Furthermore, large trait regions flanking the UCE are conserved at family level. Full article

(This article belongs to the Special Issue Evolutionary and Conservation Genetics: 2nd Edition)

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17 pages, 16856 KiB

Open AccessArticle

The First Analysis of Synaptonemal Complexes in Jawless Vertebrates: Chromosome Synapsis and Transcription Reactivation at Meiotic Prophase I in the Lamprey Lampetra fluviatilis (Petromyzontiformes, Cyclostomata)

by Sergey Matveevsky, Nikolay Tropin, Aleksandr Kucheryavyy and Oxana Kolomiets

Life 2023, 13(2), 501; https://doi.org/10.3390/life13020501 - 11 Feb 2023

Cited by 1 | Viewed by 1539

Abstract

Transcription is known to be substage-specific in meiotic prophase I. If transcription is reactivated in the mid pachytene stage in mammals when synapsis is completed, then this process is observed in the zygotene stage in insects. The process of transcriptional reactivation has been studied in a small number of different taxa of invertebrates and vertebrates. Here, for the first time, we investigate synapsis and transcription in prophase I in the European river lamprey Lampetra fluviatilis (Petromyzontiformes, Cyclostomata), which is representative of jawless vertebrates that diverged from the main branch of vertebrates between 535 and 462 million years ago. We found that not all chromosomes complete synapsis in telomeric regions. Rounded structures were detected in chromatin and in some synaptonemal complexes, but their nature could not be determined conclusively. An analysis of RNA polymerase II distribution led to the conclusion that transcriptional reactivation in lamprey prophase I is not associated with the completion of chromosome synapsis. Monomethylated histone H3K4 is localized in meiotic chromatin throughout prophase I, and this pattern has not been previously detected in animals. Thus, the findings made it possible to identify synaptic and epigenetic patterns specific to this group and to expand knowledge about chromatin epigenetics in prophase I. Full article

(This article belongs to the Special Issue Evolutionary and Conservation Genetics: 2nd Edition)

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18 pages, 2949 KiB

Open AccessArticle

Mitochondriomics of Clarias Fishes (Siluriformes: Clariidae) with a New Assembly of Clarias camerunensis: Insights into the Genetic Characterization and Diversification

by Piyumi S. De Alwis, Shantanu Kundu, Fantong Zealous Gietbong, Muhammad Hilman Fu’adil Amin, Soo-Rin Lee, Hyun-Woo Kim and Ah Ran Kim

Life 2023, 13(2), 482; https://doi.org/10.3390/life13020482 - 9 Feb 2023

Cited by 5 | Viewed by 2103

Abstract

The mitogenome of an endemic catfish Clarias camerunensis was determined from the Cameroon water. This circular mitogenome was 16,511 bp in length and comprised 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a single AT-rich control region. The heavy strand accommodates 28 genes, whereas the light strand is constituted by ND6 and eight transfer RNA (tRNA) genes. The C. camerunensis mitochondrial genome is AT biased (56.89%), as showcased in other Clarias species. The comparative analyses revealed that most of the Clarias species have 6 overlapping and 11 intergenic spacer regions. Most of the PCGs were initiated and terminated with the ATG start codon and TAA stop codon, respectively. The tRNAs of C. camerunensis folded into the distinctive cloverleaf secondary structure, except trnS1. The placement of the conserved domains in the control region was similar in all the Clarias species with highly variable nucleotides in CSB-I. Both maximum likelihood and Bayesian-based matrilineal phylogenies distinctly separated all Clarias species into five clades on the basis of their known distributions (South China, Sundaland, Indochina, India, and Africa). The TimeTree analysis revealed that the two major clades (Indo-Africa and Asia) of Clarias species might have diverged during the Paleogene (≈28.66 MYA). Our findings revealed the separation of Indian species (C. dussumieri) and African species (C. camerunensis and Clarias gariepinus) took place during the Paleogene, as well as the South Chinese species (Clarias fuscus) and Sundaland species (Clarias batrachus) splits from the Indochinese species (Clarias macrocephalus) during the Neogene through independent colonization. This pattern of biotic relationships highlights the influence of topography and geological events in determining the evolutionary history of Clarias species. The enrichment of mitogenomic data and multiple nuclear loci from their native range or type locality will confirm the true diversification of Clarias species in African and Asian countries. Full article

(This article belongs to the Special Issue Evolutionary and Conservation Genetics: 2nd Edition)

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16 pages, 19187 KiB

Open AccessArticle

Genetic Variability and Admixture Zones in the Italian Populations of Turkey Oak (Quercus cerris L.)

by Bruno Bertolasi, Luisa Zago, Lorenzo Gui, Piero Cossu, Isabella Vanetti, Silvio Rizzi, Marta Cavallini, Gianluca Lombardo and Giorgio Binelli

Life 2023, 13(1), 18; https://doi.org/10.3390/life13010018 - 21 Dec 2022

Cited by 2 | Viewed by 1707

Abstract

The Turkey oak (Quercus cerris L.) is widely distributed in Italy, where it is the ecologically dominant oak on sandy and acidic soil. In this work, we analysed 23 natural populations by means of eight SSR (microsatellite) markers, to obtain the first synthetic map of genetic variability for this species and to study its dispersion during the Holocene, due to the possibility that at least one refugium during the Last Glacial Maximum was in Italy. The analyses showed a good amount of genetic variability together with fair differentiation between populations, as indicated by F_ST = 0.059. A Bayesian analysis of the amount of admixture among populations revealed the presence of four putative gene pools of origin and a rough subdivision of the populations according to their geographic location, as confirmed by the spatial analysis. No evidence for the existence of putative refugial populations was found; however, this study paves the way for the planning of conservation strategies also with regard to the relationship between Turkey oak and other oak species in Italy. Full article

(This article belongs to the Special Issue Evolutionary and Conservation Genetics: 2nd Edition)

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13 pages, 2428 KiB

Open AccessArticle

Prokaryotic Diversity of Ruminal Content and Its Relationship with Methane Emissions in Cattle from Kazakhstan

by Aida Daugaliyeva, Saule Daugaliyeva, Alexander Ashanin, Chiara Beltramo, Latipa Mamyrova, Zinagul Yessembekova and Simone Peletto

Life 2022, 12(11), 1911; https://doi.org/10.3390/life12111911 - 17 Nov 2022

Cited by 2 | Viewed by 1045

Abstract

In this study, we analyzed the microbial composition of the rumen contents of cattle from Kazakhstan. Specifically, samples of the liquid and solid fractions of the rumen were collected to determine the quantitative and qualitative composition of methanogenic archaea. Cattle were six steers receiving hay-concentrate feeding. Methane emission was determined by repeated measurements for each animal. Rumen samples were then taken from fistulas and analyzed using 16S metabarcoding via Next-Generation Sequencing (NGS). The difference between the rumen fractions was investigated, resulting in differential distribution of the families Streptococccaceae, Lactobacillaceae, Desulfobulbaceae, and Succinivibrionaceae, which were more abundant in the liquid fraction, while Thalassospiraceae showed a higher presence in the solid fraction. These differences can be explained by the fact that fibrolytic bacteria are associated with the solid fraction compared to the liquid. A relationship between methane emission and methanogenic microbiota was also observed. Steers producing more methane showed microbiota richer in methanogens; specifically, most Mathanobacteriaceae resided in the liquid fraction and solid fraction of animals 1 and 6, respectively. The same animals carried most of the Methanobrevibacter and Methanosphaera genera. On the contrary, animals 2, 3, and 5 hosted a lower amount of methanogens, which also agreed with the data on methane emissions. In conclusion, this study demonstrated a relationship between methane emission and the content of methanogenic archaea in different rumen fractions collected from cattle in Kazakhstan. As a result of the studies, it was found that the solid fraction of the rumen contained more genera of methanogens than the liquid fraction of the rumen. These results prove that taking rumen contents through a fistula is more useful than taking it through a probe. The presented data may be of interest to scientists from all over the world engaged in similar research in a comparative aspect. Full article

(This article belongs to the Special Issue Evolutionary and Conservation Genetics: 2nd Edition)

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