1
|
Cho YG, Kwon K, Rho HS, Min WG, Jeung HD, Hwang UK, Ryu YK, Park A, Hong HK, Shin JS, Yang HS. Insights into the Genetic Connectivity and Climate-Driven Northward Range Expansion of Turbo sazae (Gastropoda: Turbinidae) Along the Eastern Coast of Korea. Animals (Basel) 2025; 15:1321. [PMID: 40362135 PMCID: PMC12070958 DOI: 10.3390/ani15091321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2025] [Revised: 04/30/2025] [Accepted: 05/01/2025] [Indexed: 05/15/2025] Open
Abstract
Turbo sazae, a commercially and ecologically significant marine gastropod traditionally found in Jeju Island and the southern coast of Korea, is experiencing a reported northward expansion into the East Sea, likely influenced by rising seawater temperatures. This study provides preliminary genetic insights into the genetic structure and connectivity of T. sazae populations between Jeju and the East Sea using mitochondrial COI sequences. Samples from 6 geographically distinct locations were analyzed, with three cloned replicates generated to enhance sequence reliability. Genetic diversity, haplotype distribution, and population differentiation were then assessed. Our analysis reveals potential genetic connectivity between Jeju and East Sea populations, possibly driven by larval dispersal via the Kuroshio and Tsushima Currents, highlighted by the predominance of shared haplotype EJ1 (60.0% in Jeju, 50.0% in East Sea). Bayesian phylogenetic analysis estimated the time to the most recent common ancestor (MRCA) between Jeju and East Sea populations at approximately 9.7 to 23.3 million years ago, indicating ancient divergence rather than very recent separation. Pairwise FST values and AMOVA results showed generally low levels of genetic differentiation. Given the small sample sizes and use of a single mitochondrial marker, these findings should be interpreted cautiously as preliminary evidence. Nevertheless, this study highlights the need for continued genetic monitoring of T. sazae populations under climate-driven range shifts and provides a foundation for future research incorporating broader genomic approaches.
Collapse
Affiliation(s)
- Young-Ghan Cho
- Tidal Flat Research Center, National Institute of Fisheries Science, 405 Gangbyeonro, Gunsan 54042, Republic of Korea; (Y.-G.C.); (H.-D.J.); (U.-K.H.)
| | - Kyungman Kwon
- Tropical & Subtropical Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju 63349, Republic of Korea (J.-S.S.)
| | - Hyun Soo Rho
- East Sea Environment Research Center, Korea Institute of Ocean Science and Technology (KIOST), Uljin 36315, Republic of Korea; (H.S.R.); (W.-G.M.)
| | - Won-Gi Min
- East Sea Environment Research Center, Korea Institute of Ocean Science and Technology (KIOST), Uljin 36315, Republic of Korea; (H.S.R.); (W.-G.M.)
| | - Hee-Do Jeung
- Tidal Flat Research Center, National Institute of Fisheries Science, 405 Gangbyeonro, Gunsan 54042, Republic of Korea; (Y.-G.C.); (H.-D.J.); (U.-K.H.)
| | - Un-Ki Hwang
- Tidal Flat Research Center, National Institute of Fisheries Science, 405 Gangbyeonro, Gunsan 54042, Republic of Korea; (Y.-G.C.); (H.-D.J.); (U.-K.H.)
| | - Yong-Kyun Ryu
- Jeju Bio Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju 63349, Republic of Korea; (Y.-K.R.); (A.P.)
| | - Areumi Park
- Jeju Bio Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju 63349, Republic of Korea; (Y.-K.R.); (A.P.)
| | - Hyun-Ki Hong
- Department of Marine Biology and Aquaculture, Gyeongsang National University, Tongyeong 53064, Republic of Korea;
| | - Jong-Seop Shin
- Tropical & Subtropical Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju 63349, Republic of Korea (J.-S.S.)
| | - Hyun-Sung Yang
- Tropical & Subtropical Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju 63349, Republic of Korea (J.-S.S.)
| |
Collapse
|
2
|
Tomizawa Y, Aizawa M, Jouraku A, Sonoda S. Field survey of reproductive modes and sodium channel mutations associated with pyrethroid resistance in Thrips tabaci. JOURNAL OF PESTICIDE SCIENCE 2024; 49:122-129. [PMID: 38882704 PMCID: PMC11176043 DOI: 10.1584/jpestics.d24-009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 04/01/2024] [Indexed: 06/18/2024]
Abstract
Using PCR-Restriction Fragment Length Polymorphism (RFLP) with mitochondrial cytochrome c oxidase subunit I sequences, we examined the reproductive modes of female adults of Thrips tabaci collected at 54 sites across Japan. Results showed the presence of heteroplasmic insects harboring mitochondria associated with arrhenotoky and thelytoky. Using the insects, we also applied PCR-RFLP to examine the genotypes for the amino acid mutation (T929I) site involved in pyrethroid resistance. Findings showed the presence of thelytokous heterozygotes under the circumstance that most arrhenotokous insects are resistant homozygotes, and many thelytokous insects are susceptible homozygotes. These results suggest that, in the field, genetic exchange occurs between insects through of both reproductive modes. A survey of the genotypes for the other amino acid mutations using nucleotide sequencing showed a decline of insects with an M918T and L1014F pair and an increase of insects with M918L. These results suggest the evolutional progression of amino acid mutations associated with pyrethroid resistance in T. tabaci.
Collapse
Affiliation(s)
| | | | - Akiya Jouraku
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization
| | | |
Collapse
|
3
|
Nuryadi H, Mandagi IF, Masengi KWA, Kusumi J, Inomata N, Yamahira K. Evidence for hybridization-driven heteroplasmy maintained across generations in a ricefish endemic to a Wallacean ancient lake. Biol Lett 2024; 20:20230385. [PMID: 38503345 PMCID: PMC10950462 DOI: 10.1098/rsbl.2023.0385] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 02/27/2024] [Indexed: 03/21/2024] Open
Abstract
Heteroplasmy, the presence of multiple mitochondrial DNA (mtDNA) haplotypes within cells of an individual, is caused by mutation or paternal leakage. However, heteroplasmy is usually resolved to homoplasmy within a few generations because of germ-line bottlenecks; therefore, instances of heteroplasmy are limited in nature. Here, we report heteroplasmy in the ricefish species Oryzias matanensis, endemic to Lake Matano, an ancient lake in Sulawesi Island, in which one individual was known to have many heterozygous sites in the mitochondrial NADH dehydrogenase subunit 2 (ND2) gene. In this study, we cloned the ND2 gene for some additional individuals with heterozygous sites and demonstrated that they are truly heteroplasmic. Phylogenetic analysis revealed that the extra haplotype within the heteroplasmic O. matanensis individuals clustered with haplotypes of O. marmoratus, a congeneric species inhabiting adjacent lakes. This indicated that the heteroplasmy originated from paternal leakage due to interspecific hybridization. The extra haplotype was unique and contained two non-synonymous substitutions. These findings demonstrate that this hybridization-driven heteroplasmy was maintained across generations for a long time to the extent that the extra mitochondria evolved within the new host.
Collapse
Affiliation(s)
- Handung Nuryadi
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Ixchel F. Mandagi
- Faculty of Fisheries and Marine Science, Sam Ratulangi University, Manado, Indonesia
| | | | - Junko Kusumi
- Faculty of Social and Cultural Studies, Kyushu University, Fukuoka, Japan
| | - Nobuyuki Inomata
- Department of Environmental Science, Fukuoka Women's University, Fukuoka, Japan
| | - Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| |
Collapse
|
4
|
Martínez-Ríos M, Martín-Torrijos L, Casabella-Herrero G, Tedesco P, Machordom A, Diéguez-Uribeondo J. On the conservation of white-clawed crayfish in the Iberian Peninsula: Unraveling its genetic diversity and structure, and origin. PLoS One 2023; 18:e0292679. [PMID: 37831691 PMCID: PMC10575519 DOI: 10.1371/journal.pone.0292679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
European crayfish species are a clear example of the drastic decline that freshwater species are experiencing. In particular, the native species of the Iberian Peninsula, the white clawed-crayfish (WCC) Austropotamobius pallipes, is listed as "endangered" by the IUCN and included in Annex II of the EU Habitat Directive and requires especially attention. Currently, implemented conservation management strategies require a better understanding of the genetic diversity and phylogeographic patterns, as well as of its evolutionary history. For this purpose, we have generated the largest datasets of two informative ribosomal mitochondrial DNA regions, i.e., cytochrome oxidase subunit I and 16S, from selected populations of the WCC covering its geographical distribution. These datasets allowed us to analyze in detail the (i) genetic diversity and structure of WCC populations, and (ii) divergence times for Iberian populations by testing three evolutionary scenarios with different mtDNA substitution rates (low, intermediate, and high rates). The results indicate high levels of haplotype diversity and a complex geographical structure for WCC in the Iberian Peninsula. The diversity found includes new unique haplotypes from the Iberian Peninsula and reveals that most of the WCC genetic variability is concentrated in the northern and central-eastern regions. Despite the fact that molecular dating analyses provided divergence times that were not statistically supported, the proposed scenarios were congruent with previous studies, which related the origin of these populations with paleogeographic events during the Pleistocene, which suggests an Iberian origin for these WCC. All results generated in this study, indicate that the alternative hypothesis of an introduced origin of the Iberian WCC is highly improbable. The result of this study, therefore, has allowed us to better understand of the genetic diversity, structure patterns, and evolutionary history of the WCC in the Iberian Peninsula, which is crucial for the management and conservation needs of this endangered species.
Collapse
Affiliation(s)
| | | | | | - Perla Tedesco
- Department of Veterinary Medical Sciences Alma Mater Studiorum, University of Bologna, Ozzano dell’Emilia, Italy
| | - Annie Machordom
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
| | | |
Collapse
|
5
|
Suárez Menéndez M, Rivera-León VE, Robbins J, Berube M, Palsbøll PJ. PHFinder: assisted detection of point heteroplasmy in Sanger sequencing chromatograms. PeerJ 2023; 11:e16028. [PMID: 37744223 PMCID: PMC10516101 DOI: 10.7717/peerj.16028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/13/2023] [Indexed: 09/26/2023] Open
Abstract
Heteroplasmy is the presence of two or more organellar genomes (mitochondrial or plastid DNA) in an organism, tissue, cell or organelle. Heteroplasmy can be detected by visual inspection of Sanger sequencing chromatograms, where it appears as multiple peaks of fluorescence at a single nucleotide position. Visual inspection of chromatograms is both consuming and highly subjective, as heteroplasmy is difficult to differentiate from background noise. Few software solutions are available to automate the detection of point heteroplasmies, and those that are available are typically proprietary, lack customization or are unsuitable for automated heteroplasmy assessment in large datasets. Here, we present PHFinder, a Python-based, open-source tool to assist in the detection of point heteroplasmies in large numbers of Sanger chromatograms. PHFinder automatically identifies point heteroplasmies directly from the chromatogram trace data. The program was tested with Sanger sequencing data from 100 humpback whales (Megaptera novaeangliae) tissue samples with known heteroplasmies. PHFinder detected most (90%) of the known heteroplasmies thereby greatly reducing the amount of visual inspection required. PHFinder is flexible and enables explicit specification of key parameters to infer double peaks (i.e., heteroplasmies).
Collapse
Affiliation(s)
- Marcos Suárez Menéndez
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Vania E. Rivera-León
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Jooke Robbins
- Center for Coastal Studies, Provincetown, MA, United States of America
| | - Martine Berube
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
- Center for Coastal Studies, Provincetown, MA, United States of America
| | - Per J. Palsbøll
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
- Center for Coastal Studies, Provincetown, MA, United States of America
| |
Collapse
|
6
|
Li H, Xu J, Wang S, Wang P, Rao W, Hou B, Zhang Y. Genetic Differentiation and Widespread Mitochondrial Heteroplasmy among Geographic Populations of the Gourmet Mushroom Thelephora ganbajun from Yunnan, China. Genes (Basel) 2022; 13:genes13050854. [PMID: 35627240 PMCID: PMC9141859 DOI: 10.3390/genes13050854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/06/2022] [Accepted: 05/08/2022] [Indexed: 11/30/2022] Open
Abstract
The mitochondrial genomes are generally considered non-recombining and homoplasmic in nature. However, our previous study provided the first evidence of extensive and stable mitochondrial heteroplasmy in natural populations of the basidiomycete fungus Thelephora ganbajun from Yunnan province, China. The heteroplasmy was characterized by the presence of two types of introns residing at adjacent but different sites in the cytochrome oxidase subunits I (cox1) gene within an individual strain. However, the frequencies of these two introns among isolates from different geographical populations and the implications for the genetic structure in natural populations have not been investigated. In this study, we analyzed DNA sequence variation at the internal transcribed spacer (ITS) regions of the nuclear ribosomal RNA gene cluster among 489 specimens from 30 geographic locations from Yunnan and compared that variation with distribution patterns of the two signature introns in the cox1 gene that are indicative of heteroplasmy in this species. In our samples, evidence for gene flow, abundant genetic diversity, and genotypic uniqueness among geographic samples in Yunnan were revealed by ITS sequence variation. While there was insignificant positive correlation between geographic distance and genetic differentiation among the geographic samples based on ITS sequences, a moderate significant correlation was found between ITS sequence variation, geographical distance of sampling sites, and distribution patterns of the two heteroplasmic introns in the cox1 gene. Interestingly, there was a significantly negative correlation between the copy numbers of the two co-existing introns. We discussed the implications of our results for a better understanding of the spread of stable mitochondrial heteroplasmy, mito-nuclear interactions, and conservation of this important gourmet mushroom.
Collapse
Affiliation(s)
- Haixia Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650032, China; (H.L.); (J.X.); (S.W.); (P.W.)
- School of Life Science, Yunnan University, Kunming 650032, China; (W.R.); (B.H.)
| | - Jianping Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650032, China; (H.L.); (J.X.); (S.W.); (P.W.)
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Shaojuan Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650032, China; (H.L.); (J.X.); (S.W.); (P.W.)
- School of Life Science, Yunnan University, Kunming 650032, China; (W.R.); (B.H.)
| | - Pengfei Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650032, China; (H.L.); (J.X.); (S.W.); (P.W.)
| | - Wanqin Rao
- School of Life Science, Yunnan University, Kunming 650032, China; (W.R.); (B.H.)
| | - Bin Hou
- School of Life Science, Yunnan University, Kunming 650032, China; (W.R.); (B.H.)
| | - Ying Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650032, China; (H.L.); (J.X.); (S.W.); (P.W.)
- Correspondence:
| |
Collapse
|
7
|
Chow S, Yanagimoto T, Takeyama H. Detection of heteroplasmy and nuclear mitochondrial pseudogenes in the Japanese spiny lobster Panulirus japonicus. Sci Rep 2021; 11:21780. [PMID: 34741113 PMCID: PMC8571370 DOI: 10.1038/s41598-021-01346-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/26/2021] [Indexed: 11/09/2022] Open
Abstract
Partial mtDNA cytochrome oxidase subunit I (COI) fragments and near entire stretch of 12S rDNA (12S) and control region (Dloop) of the Japanese spiny lobster (Panulirus japonicus) (n = 3) were amplified by PCR and used for direct nucleotide sequencing and for clone library-based nucleotide sequence analysis. Nucleotide sequences of a total of 75 clones in COI, 77 in 12S and 92 in Dloop were determined. Haplotypes of the clones matched with those obtained by direct sequencing were determined to be genuine mtDNA sequence of the individual. Phylogenetic analysis revealed several distinct groups of haplotypes in all three regions. Genuine mtDNA sequences were observed to form a group with their closely related variables, and most of these variables may be due to amplification error but a few to be heteroplasmy. Haplotypes determined as nuclear mitochondrial pseudogenes (NUMTs) formed distinct groups. Nucleotide sequence divergence (K2P distance) between genuine haplotypes and NUMTs were substantial (7.169-23.880% for COI, 1.336-23.434% for 12S, and 7.897-71.862% for Dloop). These values were comparable to or smaller than those between species of the genus Panulirus, indicating that integration of mtDNA into the nuclear genome is a continuous and dynamic process throughout pre- and post-speciation events. Double peaks in electropherograms obtained by direct nucleotide sequencing were attributed to common nucleotides shared by multiple NUMTs. Information on the heteroplasmy and NUMTs would be very important for addressing their impact on direct nucleotide sequencing and for quality control of nucleotide sequences obtained.
Collapse
Affiliation(s)
- Seinen Chow
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan.
| | - Takashi Yanagimoto
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Fukuura 2-12-4, Yokohama, Kanagawa, 236-8648, Japan
| | - Haruko Takeyama
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan. .,Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu cho, Shinjuku, Tokyo, 162-8480, Japan. .,Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-0072, Japan.
| |
Collapse
|
8
|
Gut-content analysis in four species, combined with comparative analysis of trophic traits, suggests an araneophagous habit for the entire family Palpimanidae (Araneae). ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00525-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
9
|
mtDNA Heteroplasmy: Origin, Detection, Significance, and Evolutionary Consequences. Life (Basel) 2021; 11:life11070633. [PMID: 34209862 PMCID: PMC8307225 DOI: 10.3390/life11070633] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 06/24/2021] [Indexed: 12/11/2022] Open
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 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.
Collapse
|
10
|
Kakui K, Kano Y. First Complete Mitochondrial Genome of a Tanaidacean Crustacean ( Arctotanais alascensis). Zoolog Sci 2021; 38:267-272. [PMID: 34057352 DOI: 10.2108/zs200167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/03/2021] [Indexed: 11/17/2022]
Abstract
We present a complete mitochondrial genomic sequence for the tanaidacean Arctotanais alascensis (Richardson, 1899); this is the first complete mitogenome reported from the order Tanaidacea. The mitogenome is 13,988 bp long and contains 13 protein coding and two ribosomal RNA genes (as is typical for animal mitogenomes), and 21 of 22 transfer RNAs; we did not detect an isoleucine transfer RNA (trnI) gene. The gene order differed markedly from the hypothetical ground pattern for Pancrustacea; only four clusters (trnM + nad2; trnC + trnY + cox1 + trnL2 + cox2; trnD + atp8 + atp6 + cox3; trnH + nad4 + nad4l) ancestrally present were retained. In a malacostracan phylogenetic tree reconstructed from mitogenome data, basal relationships were marginally supported or incongruent with the traditional morphology-based classification and the latest phylogenetic reconstructions from large transcriptomic datasets. Relationships involving more recent divergences were better supported in our tree, suggesting that complete mitogenome sequences are more suitable for phylogenetic analyses within malacostracan orders, presumably including Tanaidacea.
Collapse
Affiliation(s)
- Keiichi Kakui
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan,
| | - Yasunori Kano
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa 277-8564, Japan
| |
Collapse
|
11
|
Pereira RJ, Ruiz‐Ruano FJ, Thomas CJ, Pérez‐Ruiz M, Jiménez‐Bartolomé M, Liu S, Torre J, Bella JL. Mind the
numt
: Finding informative mitochondrial markers in a giant grasshopper genome. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12446] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ricardo J. Pereira
- Division of Evolutionary Biology Faculty of Biology II Ludwig‐ Maximilians‐Universität München Planegg‐Martinsried Germany
| | - Francisco J. Ruiz‐Ruano
- Department of Genetics University of Granada Granada Spain
- Department of Ecology and Genetics – Evolutionary Biology Evolutionary Biology Centre (EBC) Uppsala University Uppsala Sweden
- Department of Organismal Biology – Systematic Biology Evolutionary Biology Centre (EBC) Uppsala University Uppsala Sweden
| | - Callum J.E. Thomas
- Division of Evolutionary Biology Faculty of Biology II Ludwig‐ Maximilians‐Universität München Planegg‐Martinsried Germany
| | - Mar Pérez‐Ruiz
- Departamento de Biología (Genética) Facultad de Ciencias Universidad Autónoma de Madrid Madrid Spain
| | - Miguel Jiménez‐Bartolomé
- Departamento de Biología (Genética) Facultad de Ciencias Universidad Autónoma de Madrid Madrid Spain
| | - Shanlin Liu
- Department of Entomology College of Plant Protection China Agricultural University Beijing China
| | - Joaquina Torre
- Departamento de Biología (Genética) Facultad de Ciencias Universidad Autónoma de Madrid Madrid Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC‐UAM) Universidad Autónoma de Madrid Madrid Spain
| | - José L. Bella
- Departamento de Biología (Genética) Facultad de Ciencias Universidad Autónoma de Madrid Madrid Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC‐UAM) Universidad Autónoma de Madrid Madrid Spain
| |
Collapse
|
12
|
Towarnicki SG, Ballard JWO. Towards understanding the evolutionary dynamics of mtDNA. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:355-364. [PMID: 33026269 DOI: 10.1080/24701394.2020.1830076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Historically, mtDNA was considered a selectively neutral marker that was useful for estimating the population genetic history of the maternal lineage. Over time there has been an increasing appreciation of mtDNA and mitochondria in maintaining cellular and organismal health. Beyond energy production, mtDNA and mitochondria have critical cellular roles in signalling. Here we briefly review the structure of mtDNA and the role of the mitochondrion in energy production. We then discuss the predictions that can be obtained from quaternary structure modelling and focus on mitochondrial complex I. Complex I is the primary entry point for electrons into the electron transport system is the largest respiratory complex of the chain and produces about 40% of the proton flux used to synthesize ATP. A focus of the review is Drosophila's utility as a model organism to study the selective advantage of specific mutations. However, we note that the incorporation of insights from a multitude of systems is necessary to fully understand the range of roles that mtDNA has in organismal fitness. We speculate that dietary changes can illicit stress responses that influence the selective advantage of specific mtDNA mutations and cause spatial and temporal fluctuations in the frequencies of mutations. We conclude that developing our understanding of the roles mtDNA has in determining organismal fitness will enable increased evolutionary insight and propose we can no longer assume it is evolving as a strictly neutral marker without testing this hypothesis.
Collapse
Affiliation(s)
- Samuel G Towarnicki
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
| | - J William O Ballard
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
| |
Collapse
|
13
|
Ricardo PC, Françoso E, Arias MC. Mitochondrial DNA intra-individual variation in a bumblebee species: A challenge for evolutionary studies and molecular identification. Mitochondrion 2020; 53:243-254. [PMID: 32569843 DOI: 10.1016/j.mito.2020.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 04/28/2020] [Accepted: 06/15/2020] [Indexed: 10/24/2022]
Abstract
Mitochondrial DNA (mtDNA) regions have been widely used as molecular markers in evolutionary studies and species identification. However, the presence of heteroplasmy and NUMTs may represent obstacles. Heteroplasmy is a state where an organism has different mitochondrial haplotypes. NUMTs are nuclear pseudogenes originating from mtDNA sequences transferred to nuclear DNA. Evidences of heteroplasmy were already verified in the bumblebee Bombus morio in an earlier study. The present work investigated in more detail the presence of intra-individual haplotypes variation in this species. Heteroplasmy was detected in individuals from all the ten sampled locations, with an average of six heteroplasmic haplotypes per individual. In addition, some of these heteroplasmic haplotypes were shared among individuals from different locations, suggesting the existence of stable heteroplasmy in B. morio. These results demonstrated that heteroplasmy is likely to affect inferences based on mtDNA analysis, especially in phylogenetic, phylogeographic and population genetics studies. In addition, NUMTs were also detected. These sequences showed divergence of 2.7% to 12% in relation to the mitochondrial haplotypes. These levels of divergence could mislead conclusions in evolutionary studies and affect species identification through DNA barcoding.
Collapse
Affiliation(s)
- Paulo Cseri Ricardo
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Elaine Françoso
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Maria Cristina Arias
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
| |
Collapse
|