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Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals:...
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Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals: 2024–2025

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: 25 September 2025 | Viewed by 6061

Special Issue Editors

Prof. Dr. Jiayong Zhang

E-Mail Website
Guest Editor
College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
Interests: gene rearrangement; mitochondrial genome; molecular evolution; mitochondrial gene expression
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Jiasheng Hao

E-Mail Website
Guest Editor
College of Life Sciences, Anhui Normal University, Wuhu 241002, China
Interests: insect phylogeny and phylogeography; mitochondrial genome; molecular evolution; molecular clock
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Molecular evolution in animals using nuclear or mitochondrial DNA and mitochondrial genomics have transformed phylogeny of animals in recent decades. Still, there is a lot of work to be done ahead in this research area. The demand for molecular evolution and mitochondrial genomics in animals is rising. At the same time, the mitochondrial gene arrangement in different orders of animals is of great concern. Understanding the molecular evolution in animals, the molecular mechanisms of gene rearrangement in animals, and even the mitochondrial gene expression of animals under different stress will benefit us all. This Special Issue in Genes on “Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals: 2024–2025” will highlight how mitochondrial genomics technologies are paving the way to understand the evolution of animals and the function of mitochondrial gene in animals. The Special Issue will provide an article of recent developments in molecular evolution using nuclear and mitochondrial DNA in animals, or the phylogenetic relationship of animals using mitochondrial genomes, or mitochondrial gene expression of animals under different environmental stresses.

Prof. Dr. Jiayong Zhang
Prof. Dr. Jiasheng Hao
Guest Editors

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Keywords

  • mitochondrial genome
  • gene arrangement
  • phylogenetic relationship
  • mitochondrial gene expression
  • molecular evolution

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Published Papers (9 papers)

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16 pages, 3909 KiB  
Article
Comparative Mitogenomics of Wonder Geckos (Sphaerodactylidae: Teratoscincus Strauch, 1863): Uncovering Evolutionary Insights into Protein-Coding Genes
by Dongqing Zheng, Rongrong Ma, Xianguang Guo and Jun Li
Genes 2025, 16(5), 531; https://doi.org/10.3390/genes16050531 - 29 Apr 2025
Viewed by 195
Abstract
Background: Comparative studies of selection pressures on mitochondrial genomes and protein-coding genes (PCGs) are scarce in the genus Teratoscincus (Strauch, 1863), particularly within Sphaerodactylidae. Given their close evolutionary relationship, Teratoscincus przewalskii (Strauch, 1887) and Teratoscincus roborowskii (Bedriaga, 1906) serve as ideal models for [...] Read more.
Background: Comparative studies of selection pressures on mitochondrial genomes and protein-coding genes (PCGs) are scarce in the genus Teratoscincus (Strauch, 1863), particularly within Sphaerodactylidae. Given their close evolutionary relationship, Teratoscincus przewalskii (Strauch, 1887) and Teratoscincus roborowskii (Bedriaga, 1906) serve as ideal models for the characterization of mitochondrial genome sand analysis of selective pressure in this genus. Methods: In this study, we employed Sanger sequencing to sequence the mitochondrial genome of T. roborowskii (Bedriaga, 1906), and utilized sliding window analysis, selection pressure analysis etc. to compared it with that of its close relative, T. przewalskii (Strauch, 1887). Results: The results contain the genome composition, Ka/Ks values, AT/GC-skew, etc. Selection pressure analysis of PCGs across Teratoscincus (Strauch, 1863) species (including those in GenBank) revealed that most genes evolve slowly, with the exception of ATP8 and ND6, which exhibited faster evolutionary rates. Notably, the ND6 of T. roborowskii (Bedriaga, 1906) demonstrated rapid non-synonymous substitution rates which may contribute to the survival and reproductive success of the species by favoring advantageous mutations. Phylogenetic analysis for the mitochondrial genomes of Sphaerodactylidae, Phyllodactylidae, and Gekkonidae confirmed the distinctiveness of Sphaerodactylidae and the two Teratoscincus (Strauch, 1863) species. Conclusions: This study has advanced the understanding of adaptive evolution in Teratoscincus (Strauch, 1863) mitochondrial genomes, expanded the mitochondrial database of Sphaerodactylidae, and provided insights into the phylogenetic relationships of the genus. Full article
(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals: 2024–2025)
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17 pages, 3068 KiB  
Article
Mitochondrial Genomes of Six Snakes (Lycodon) and Implications for Their Phylogeny
by Fei Zhu, Anqiong Lu and Ke Sun
Genes 2025, 16(5), 493; https://doi.org/10.3390/genes16050493 - 26 Apr 2025
Viewed by 226
Abstract
Background: Colubridae, known to be one of the most species-rich snake families, remains relatively understudied in termshe context of complete mitochondrial genome research. This study provide the first systematic characterization of the mitochondrial genomes of six colubrid species: Lycodon subcinctus, Lycodon rosozonatus [...] Read more.
Background: Colubridae, known to be one of the most species-rich snake families, remains relatively understudied in termshe context of complete mitochondrial genome research. This study provide the first systematic characterization of the mitochondrial genomes of six colubrid species: Lycodon subcinctus, Lycodon rosozonatus, Lycodon fasciatus, Lycodon gongshan, Lycodon futsingensis, and Lycodon aulicus. Method: In this study, mitochondrial genomes were sequenced using Sanger sequencing. The raw data were subjected to quality- filtered withing using Fastp and subsequently assembled into complete mitochondrial genomes via SPAdes. Gene annotation was performed by Tblastn, Genewise (for CDS coding sequences), MiTFi (for transfer RNAs), and Rfam (for ribosomal RNAs). Sequence analyses were conducted with various tools, including MEGA, tRNAscan-SE, DnaSP, MISA, and REPuter. Finally, phylogenetic trees were reconstructed based on 13 protein-coding genes from 14 species. Results:The mitogenomes of these six species ranged from 17,143 to 17,298 bp in length and con-sisted of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and 2 control regions. The nucleotide composition of the Colu-bridae mitogenomes was comparable with an A + T composition ranging from 52.1% to 58.8% except for the trnS1 and trnC. All the tRNAs could fold into a stable secondary structure. The Pi and Ka/Ks values suggested that atp8 was the fastest-evolving gene, while cox1 was the most conserved gene. Bayesian inference and maximum likelihood phylogenetic analyses yielded consistent results, with the six sequenced species clus-tering together with their congeneric species. These findings will provide valuable references for further research on the phylogeny of Colubridae. Full article
(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals: 2024–2025)
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13 pages, 6996 KiB  
Article
Decoding the Mitochondrial Genome of the Tiger Shrimp: Comparative Genomics and Phylogenetic Placement Within Caridean Shrimps
by Zhengfei Wang, Weijie Jiang, Jingxue Ye, Huiwen Wu, Yan Wang and Fei Xiong
Genes 2025, 16(4), 457; https://doi.org/10.3390/genes16040457 - 16 Apr 2025
Viewed by 256
Abstract
Background/Objectives: Freshwater shrimps of the family Atyidae, particularly the hyperdiverse genus Caridina, are keystone decomposers in tropical aquatic ecosystems and valuable aquaculture resources. However, their evolutionary relationships remain unresolved due to conflicting morphological and molecular evidence. Here, we sequenced and characterized the complete [...] Read more.
Background/Objectives: Freshwater shrimps of the family Atyidae, particularly the hyperdiverse genus Caridina, are keystone decomposers in tropical aquatic ecosystems and valuable aquaculture resources. However, their evolutionary relationships remain unresolved due to conflicting morphological and molecular evidence. Here, we sequenced and characterized the complete mitochondrial genome of Caridina mariae (Tiger Shrimp), aiming to (1) elucidate its genomic architecture, and (2) reconstruct a robust phylogeny of Caridea using 155 decapod species to address long-standing taxonomic uncertainties. Methods: Muscle tissue from wild-caught C. mariae (voucher ID: KIZ-2023-001, Guangdong, China) was subjected to Illumina NovaSeq 6000 sequencing (150 bp paired-end). The mitogenome was assembled using MITObim v1.9, annotated via MITOS2, and validated by PCR. Phylogenetic analyses employed 13 protein-coding genes under Bayesian inference (MrBayes v3.2.7; 106 generations, ESS > 200) and maximum likelihood (RAxML v8.2.12; 1000 bootstraps), with Harpiosquilla harpax as the outgroup. The best-fit substitution model (MtZoa + F + I + G4) was selected via jModelTest v2.1.10. Results: The 15,581 bp circular mitogenome encodes 37 genes (13 PCGs, 22 tRNAs, and 2 rRNAs) and an A + T-rich control region (86.7%). Notably, trnS1 lacks the dihydrouracil arm—a rare structural deviation in Decapoda. The 13 PCGs exhibit moderate nucleotide skew (AT = 0.030; GC = −0.214), while nad5, nad4, and nad6 show significant GC-skew. Phylogenomic analyses strongly support (PP = 1.0; BS = 95) a novel sister-group relationship between Halocaridinidae and Typhlatyinae, contradicting prior morphology-based classifications. The monophyly of Penaeoidea, Astacidea, and Caridea was confirmed, but Eryonoidea and Crangonoidea formed an unexpected clade. Conclusions: This study provides the first mitogenomic framework for C. mariae, revealing both conserved features (e.g., PCG content) and lineage-specific innovations (e.g., tRNA truncation). The resolved phylogeny challenges traditional Caridea classifications and highlights convergent adaptation in freshwater lineages. These findings offer molecular tools for the conservation prioritization of threatened Caridina species and underscore the utility of mitogenomics in decapod systematics. Full article
(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals: 2024–2025)
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11 pages, 1330 KiB  
Article
Phylogeny and Specific Determination of Gloydius halys-intermedius Complex Based on Complete Mitochondrial Genes
by Lijie Jin, Zuyao Xia, Ning Liu, Shengyue Hou, Chuandong Lv, Lianyou Tang, Shuguang Feng, Jingsong Shi and Ming Bai
Genes 2025, 16(3), 276; https://doi.org/10.3390/genes16030276 - 25 Feb 2025
Viewed by 444
Abstract
Background: The phylogenetic resolution within the Gloydius halys-intermedius Complex remains debatable due to the following reasons: loci selection in previous studies varied between authors; limited dataset (1−5 mitochondrial or nuclear gene fragments); lack of sampling density; and nodal supports at specific nodes [...] Read more.
Background: The phylogenetic resolution within the Gloydius halys-intermedius Complex remains debatable due to the following reasons: loci selection in previous studies varied between authors; limited dataset (1−5 mitochondrial or nuclear gene fragments); lack of sampling density; and nodal supports at specific nodes remain weak, specifically within Gloydius cognatus, G. halys, and G. stejnegeri. Objectives: To revise the taxonomic and phylogenetic relationships within the G. halys-intermedius Complex, we reconstructed the molecular phylogeny and performed species delimitation based on the complete mitochondrial genomes. Methods: In this study, twelve nomenclatural groups of Gloydius species were involved in the computation of Bayesian phylogenomic inference, five of the twelve nomenclature groups were newly sequenced, while the rest were acquired from the National Center for Biotechnology Information (NCBI). The Bayesian phylogenomic inference was constructed based on 13 mitochondrial protein-coding genes. Species delimitation was performed by two distance-based methods (ABGD and ASAP) and two tree-based methods (GMYC and bPTP). Results: This research resolved the systematic relationship within the G. intermedius Complex with the support of mitogenome-based phylogenomics, while indicating cryptic diversity within the Gloydius halys-intermedius Complex: G. intermedius samples from South Korea show as paraphyletic to the cluster of the samples from northeastern China. Species delimitation results based on four models resemble each other, supporting Gloydius caucasicus, G. cognatus, G. halys, and G. stejnegeri, each representing full species. The species delimitation results of this research also resemble the nomenclatural species based on previous morphometrical results. This research indicates that species delimitation efforts based on the phylogenomic approach would likely resolve complex evolutionary relationships. Full article
(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals: 2024–2025)
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18 pages, 4443 KiB  
Article
Genome-Wide Identification, Gene Duplication, and Expression Pattern of NPC2 Gene Family in Parnassius glacialis
by Zhenyao Zhu, Chengyong Su, Xuejie Guo, Youjie Zhao, Ruie Nie, Bo He and Jiasheng Hao
Genes 2025, 16(3), 249; https://doi.org/10.3390/genes16030249 - 21 Feb 2025
Viewed by 487
Abstract
Background: The Niemann–Pick C2 (NPC2) gene family plays an important role in olfactory communication, immune response, and the recognition of host plants associated with environmental adaptation for insects. Methods: In this study, we conducted a genomic analysis of the structural characteristics [...] Read more.
Background: The Niemann–Pick C2 (NPC2) gene family plays an important role in olfactory communication, immune response, and the recognition of host plants associated with environmental adaptation for insects. Methods: In this study, we conducted a genomic analysis of the structural characteristics and physicochemical properties of the NPC2 genes of eleven butterfly species available, focusing on the alpine Parnassius species, especially Parnassius glacialis, to investigate their duplication and expression patterns. Results: Our results indicate that a significant expansion of NPC2 genes was detected in P. glacialis compared to other butterflies; in addition, the expansion of these unevenly distributed P. glacialis NPC2 chromosome genes was shaped by tandem duplication mediated by transposons. Furthermore, the PgNPC2 genes had relatively higher expression in P. glacialis antennae and other head tissues. These facts were verified by quantitative real-time PCR (qRT-PCR). Conclusions: These findings suggest that the expansion of NPC2 genes may have contributed to the local adaptation of P. glacialis during its dispersal ‘out of the Qinghai–Tibet Plateau’, although further functional tests are needed to confirm their specific role in this adaptive process. Full article
(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals: 2024–2025)
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17 pages, 2352 KiB  
Article
Characterization of the Complete Mitochondrial Genome of Dwarf Form of Purpleback Flying Squid (Sthenoteuthis oualaniensis) and Phylogenetic Analysis of the Family Ommastrephidae
by Wenjuan Duo, Lei Xu, Mohd Johari Mohd Yusof, Yingmin Wang, Seng Beng Ng and Feiyan Du
Genes 2025, 16(2), 226; https://doi.org/10.3390/genes16020226 - 15 Feb 2025
Viewed by 586
Abstract
Background: The Ommastrephidae family of cephalopods is important in marine ecosystems as both predators and prey. Species such as Todarodes pacificus, Illex argentinus, and Dosidicus gigas are economically valuable but are threatened by overfishing and environmental changes. The genus Sthenoteuthis, [...] Read more.
Background: The Ommastrephidae family of cephalopods is important in marine ecosystems as both predators and prey. Species such as Todarodes pacificus, Illex argentinus, and Dosidicus gigas are economically valuable but are threatened by overfishing and environmental changes. The genus Sthenoteuthis, especially S. oualaniensis, shows significant morphological and genetic variation, including medium-sized and dwarf forms found in the South China Sea. Methods: Specimens of S. oualaniensis were collected from the South China Sea, their genomic DNA sequenced, and phylogenetic relationships analyzed using mitochondrial genomes from various Ommastrephidae species. Results: The study presents the complete mitochondrial genome of the dwarf form of S. oualaniensis (20,320 bp) and compares it with the medium-sized form, revealing a typical vertebrate structure with 13 protein-coding genes, 21 tRNA genes, and 2 rRNA genes, along with a strong AT bias. Nucleotide composition analysis shows a 12% genetic divergence between the two forms, suggesting a recent common ancestor and potential cryptic speciation, with all protein-coding genes exhibiting purifying selection based on Ka/Ks ratios below 1. Conclusions: The mitochondrial genome of the dwarf form of S. oualaniensis shows a close evolutionary relationship with the medium-sized form and a 12% genetic divergence, suggesting potential cryptic speciation. These findings underscore the importance of mitochondrial analysis in understanding speciation and guiding future conservation efforts. Full article
(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals: 2024–2025)
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13 pages, 2314 KiB  
Article
Complete Mitochondrial Genomes of Pluvialis fulva and Charadrius dubius with Phylogenetic Analysis of Charadriiformes
by Kuo Sun, Qingxiong Wang, Kun Bian, Feiran Li, Jie Tang, Lijuan Suo, Xiang Hou and Chao Yang
Genes 2024, 15(12), 1642; https://doi.org/10.3390/genes15121642 - 21 Dec 2024
Viewed by 650
Abstract
Background: Plovers (Charadriidae), within the order of Charadriiformes, a group of modern birds distributed worldwide, are a frequent subject of molecular phylogenetic studies. While research on mitochondrial genome (mitogenome) variation within the family Charadriidae, especially intraspecific variation, is limited. Additionally, the monophyly of [...] Read more.
Background: Plovers (Charadriidae), within the order of Charadriiformes, a group of modern birds distributed worldwide, are a frequent subject of molecular phylogenetic studies. While research on mitochondrial genome (mitogenome) variation within the family Charadriidae, especially intraspecific variation, is limited. Additionally, the monophyly of Charadrius and the phylogenetic placement of Pluvialis remain contentious. Nevertheless, recent studies utilizing complete mitogenomes from available databases to construct phylogenetic trees for Charadriidae and Charadriiformes remain scarce. Methods: This study aims to explore mitogenome variation within Charadrius dubius and clarify the phylogenetic placement of Pluvialis fulva. We sequenced the complete mitogenome of six C. dubius and one P. fulva, and all additional available mitogenomes were integrated within Charadriiformes. The average complete mitogenome length of C. dubius is 16,889 bp, and P. fulva is 16,859 bp. Results: Our results support the suggestion that the monophyly of Charadrius and P. fulva is nested within Charadriidae. The phylogenetic analysis of Charadriiformes based on mitogenomes strongly supports the recognition of three major shorebird clades: Charadrii, Lari and Scolopaci, with Lari and Scolopaci identified as sister clades. Conclusions: Our study reinforces the credibility of the inferred evolutionary relationships within Charadriidae and Charadriiformes. Full article
(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals: 2024–2025)
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12 pages, 1906 KiB  
Article
Three Mitochondrial Genomes of Chrysochroinae (Coleoptera, Buprestidae) and Phylogenetic Analyses
by Bowen Ouyang, Xuyan Huang, Yujie Gan, Zhonghua Wei and Aimin Shi
Genes 2024, 15(10), 1336; https://doi.org/10.3390/genes15101336 - 17 Oct 2024
Viewed by 988
Abstract
Three mitochondrial genomes of Chrysochroinae (Buprestidae) were sequenced and analyzed. The mitogenomes of the genera Catoxantha and Nipponobuprestis are first reportedand Chrysochroa opulenta is a first record for China. The complete mitogenomes of Catoxantha luodiana, Nipponobuprestis guangxiensis and Chrysochroa opulenta exhibit striking [...] Read more.
Three mitochondrial genomes of Chrysochroinae (Buprestidae) were sequenced and analyzed. The mitogenomes of the genera Catoxantha and Nipponobuprestis are first reportedand Chrysochroa opulenta is a first record for China. The complete mitogenomes of Catoxantha luodiana, Nipponobuprestis guangxiensis and Chrysochroa opulenta exhibit striking similarities in their lengths and composition. Specifically, their lengths are 15,594 bp, 15,775 bp and 15,587 bp, respectively. Each of these genomes encodes 37 typical mitochondrial genes. The overwhelming majority of protein-coding genes (PCGs) have the typical ATN (ATT, ATA, ATG or ATC) as the start codon and terminate with TAR (TAA or TAG) as the stop codon or an incomplete stop codon T-. Among the three mitogenomes, Leu2, Ser2 and Phe were the most frequently encoded amino acids. In the PCGs, the Ka/Ks ratio of cox1 is the lowest, whereas atp6 has the highest value. This suggests that cox1 can be used as a molecular barcode for species delimitation and phylogeny in Chrysochroinae. The phylogenetic results showed that C. luodiana and two Chrysochroa species formed a clade. Based on the topology of the phylogenetic tree, the genus Catoxantha should be reassigned as a subgenus of Chrysochroa. Full article
(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals: 2024–2025)
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16 pages, 1397 KiB  
Article
Genetic Insights into the Giant Keyhole Limpet (Megathura crenulata), an Eastern Pacific Coastal Endemic: Complete Mitogenome, Phylogenetics, Phylogeography, and Historical Demography
by Brenda Bonett-Calzada, Fausto Valenzuela-Quiñonez, Miguel A. Del Río-Portilla, Natalia J. Bayona-Vásquez, Carmen E. Vargas-Peralta, John R. Hyde and Fabiola Lafarga-De la Cruz
Genes 2024, 15(10), 1303; https://doi.org/10.3390/genes15101303 - 8 Oct 2024
Cited by 1 | Viewed by 1480
Abstract
Background: The giant keyhole limpet Megathura crenulata is a gastropod mollusk (Fissurella superfamily) that is endemic to the eastern Pacific coast from southern California, USA, to Baja California Sur, Mexico. M. crenulata is socioeconomically important as it produces a potent immune-stimulating protein, called [...] Read more.
Background: The giant keyhole limpet Megathura crenulata is a gastropod mollusk (Fissurella superfamily) that is endemic to the eastern Pacific coast from southern California, USA, to Baja California Sur, Mexico. M. crenulata is socioeconomically important as it produces a potent immune-stimulating protein, called Keyhole Limpet Hemocyanin, which is extracted in vivo and utilized for vaccine development. However, ecological studies are scarce and genetic knowledge of the species needs to be improved. Our objectives were to assemble and annotate the mitogenome of M. crenulata, and to assess its phylogenetic relationships with other marine gastropods and to evaluate its population genetic diversity and structure. Methods: Samples were collected for mitogenome assembly (n = 3) spanning its geographic range, Puerto Canoas (PCA) and Punta Eugenia (PEU), Mexico, and California (CAL), USA. Total DNA was extracted from gills sequenced using Illumina paired-end 150-bp-read sequencing. Reads were cleaned, trimmed, assembled de novo, and annotated. In addition, 125 samples from eight locations were analyzed for genetic diversity and structure analysis at the 16s rRNA and COX1 genes. Results: The M. crenulata mitogenomes had lengths of 16,788 bp (PCA) and 16,787 bp (PEU) and were composed of 13 protein-coding regions, 22 tRNAs, two rRNAs, and the D-Loop region. In terms of phylogeographic diversity and structure, we found a panmictic population that has experienced recent demographic expansion with low nucleotide diversity (0.002), high haplotypic diversity (0.915), and low φST (0.047). Conclusions: Genetic insights into the giant keyhole limpet provides tools for its management and conservation by delimiting fishing regions with low genetic diversity and/or genetically discrete units. Full article
(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals: 2024–2025)
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