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Ruiz-García M, Escobar-Armel P, Martínez-Agüero M, Gaviria M, Álvarez D, Pinedo M, Shostell JM. Are There Barriers Separating the Pink River Dolphin Populations ( Inia boliviensis, Iniidae, Cetacea) within the Mamoré-Iténez River Basins (Bolivia)? An Analysis of Its Genetic Structure by Means of Mitochondrial and Nuclear DNA Markers. Genes (Basel) 2024; 15:1012. [PMID: 39202372 DOI: 10.3390/genes15081012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/27/2024] [Accepted: 07/28/2024] [Indexed: 09/03/2024] Open
Abstract
The pink river dolphin, or bufeo, is one of the dolphins which lives in the rivers of the Orinoco and Amazon basins in South America. The Bolivian bufeo population is considered a differentiated species (Inia boliviensis) from the Amazon and Orinoco species (Inia geoffrensis). Until now, no study has completed an extensive population genetics analysis of the bufeo in Bolivian rivers. We analyzed 82 bufeos from different rivers from the Mamoré and Iténez (Guaporé) river basins for the mt control region (CR), nuclear microsatellites, and DQB-1 gene sequences to determine if the inner rapids of these Bolivian river basins have some influence on the genetic structure of this species. The first relevant result was that the genetic diversity for CR, and the microsatellites were substantially lower in the Bolivian bufeos than in the dolphins studied in other areas of the Amazon and Orinoco. However, the DQB-1 gene sequences yielded similar genetic diversity to those found in other areas. The second relevant result is the existence of some significant genetic heterogeneity among the bufeo populations within Bolivia, although in a small degree, but this differentiation is independent of the inner rapids of the Bolivian rivers we sampled. The third relevant result was the existence of significant isolation by distance for the CR, but not for microsatellites and DQB-1 gene sequences. This was related to differential gene flow capacity of females (philopatric) and males (less philopatric and more migrants) and, possibly, to different selective patterns affecting the molecular markers studied. The fourth relevant result was related to diverse demographic changes of these bufeos. At least two or three bottleneck events and one or two population expansions have occurred in the Bolivian bufeo population. The major part of these events occurred during the Pleistocene.
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Affiliation(s)
- Manuel Ruiz-García
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7A No 43-82, Bogotá 110311, DC, Colombia
| | - Pablo Escobar-Armel
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7A No 43-82, Bogotá 110311, DC, Colombia
| | - María Martínez-Agüero
- Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá 111321, DC, Colombia
| | - Magda Gaviria
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7A No 43-82, Bogotá 110311, DC, Colombia
| | - Diana Álvarez
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7A No 43-82, Bogotá 110311, DC, Colombia
| | - Myreya Pinedo
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7A No 43-82, Bogotá 110311, DC, Colombia
| | - Joseph Mark Shostell
- Math, Science and Technology Department, University of Minnesota Crookston, Crookston, MN 56716, USA
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Nitsch L, Lareau CA, Ludwig LS. Mitochondrial genetics through the lens of single-cell multi-omics. Nat Genet 2024; 56:1355-1365. [PMID: 38951641 PMCID: PMC11260401 DOI: 10.1038/s41588-024-01794-8] [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: 09/17/2023] [Accepted: 05/09/2024] [Indexed: 07/03/2024]
Abstract
Mitochondria carry their own genetic information encoding for a subset of protein-coding genes and translational machinery essential for cellular respiration and metabolism. Despite its small size, the mitochondrial genome, its natural genetic variation and molecular phenotypes have been challenging to study using bulk sequencing approaches, due to its variation in cellular copy number, non-Mendelian modes of inheritance and propensity for mutations. Here we highlight emerging strategies designed to capture mitochondrial genetic variation across individual cells for lineage tracing and studying mitochondrial genetics in primary human cells and clinical specimens. We review recent advances surrounding single-cell mitochondrial genome sequencing and its integration with functional genomic readouts, including leveraging somatic mitochondrial DNA mutations as clonal markers that can resolve cellular population dynamics in complex human tissues. Finally, we discuss how single-cell whole mitochondrial genome sequencing approaches can be utilized to investigate mitochondrial genetics and its contribution to cellular heterogeneity and disease.
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Affiliation(s)
- Lena Nitsch
- Berlin Institute of Health at Charité Universitätsmedizin Berlin, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Caleb A Lareau
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Leif S Ludwig
- Berlin Institute of Health at Charité Universitätsmedizin Berlin, Berlin, Germany.
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany.
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Henkel R. Leukocytospermia and/or Bacteriospermia: Impact on Male Infertility. J Clin Med 2024; 13:2841. [PMID: 38792382 PMCID: PMC11122306 DOI: 10.3390/jcm13102841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Infertility is a globally underestimated public health concern affecting almost 190 million people, i.e., about 17.5% of people during their lifetime, while the prevalence of male factor infertility is about 7%. Among numerous other causes, the prevalence of male genital tract infections reportedly ranges between 10% and 35%. Leukocytospermia is found in 30% of infertile men and up to 20% in fertile men. Bacterial infections cause an inflammatory response attracting leukocytes, which produce reactive oxygen species (ROS) and release cytokines, both of which can cause damage to sperm, rendering them dysfunctional. Although leukocytospermia and bacteriospermia are both clinical conditions that can negatively affect male fertility, there is still debate about their impact on assisted reproduction outcomes and management. According to World Health Organization (WHO) guidelines, leukocytes should be determined by means of the Endtz test or with monoclonal antibodies against CD15, CD68 or CD22. The cut-off value proposed by the WHO is 1 × 106 peroxidase-positive cells/mL. For bacteria, Gram staining and semen culture are regarded as the "gold standard", while modern techniques such as PCR and next-generation sequencing (NGS) are allowing clinicians to detect a wider range of pathogens. Whereas the WHO manual does not specify a specific value as a cut-off for bacterial contamination, several studies consider semen samples with more than 103 colony-forming units (cfu)/mL as bacteriospermic. The pathogenic mechanisms leading to sperm dysfunction include direct interaction of bacteria with the male germ cells, bacterial release of spermatotoxic substances, induction of pro-inflammatory cytokines and ROS, all of which lead to oxidative stress. Clinically, bacterial infections, including "silent" infections, are treatable, with antibiotics being the treatment of choice. Yet, non-steroidal antiphlogistics or antioxidants should also be considered to alleviate inflammatory lesions and improve semen quality. In an assisted reproduction set up, sperm separation techniques significantly reduce the bacterial load in the semen. Nonetheless, contamination of the semen sample with skin commensals should be prevented by applying relevant hygiene techniques. In patients where leukocytospermia is detected, the causes (e.g. infection, inflammation, varicocele, smoking, etc.) of the leukocyte infiltration have to be identified and addressed with antibiotics, anti-inflammatories or antioxidants in cases where high oxidative stress levels are detected. However, no specific strategy is available for the management of leukocytospermia. Therefore, the relationship between bacteriospermia and leukocytospermia as well as their specific impact on functional sperm parameters and reproductive outcome variables such as fertilization or clinical pregnancy must be further investigated. The aim of this narrative review is to provide an update on the current knowledge on leukocytospermia and bacteriospermia and their impact on male fertility.
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Affiliation(s)
- Ralf Henkel
- LogixX Pharma Ltd., Merlin House, Brunel Road, Theale, Reading RG7 4AB, UK;
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0HS, UK
- Department of Medical Bioscience, University of the Western Cape, Bellville 7535, South Africa
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Sandberg TOM, Yahalomi D, Bracha N, Haddas-Sasson M, Pupko T, Atkinson SD, Bartholomew JL, Zhang JY, Huchon D. Evolution of myxozoan mitochondrial genomes: insights from myxobolids. BMC Genomics 2024; 25:388. [PMID: 38649808 PMCID: PMC11034133 DOI: 10.1186/s12864-024-10254-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Myxozoa is a class of cnidarian parasites that encompasses over 2,400 species. Phylogenetic relationships among myxozoans remain highly debated, owing to both a lack of informative morphological characters and a shortage of molecular markers. Mitochondrial (mt) genomes are a common marker in phylogeny and biogeography. However, only five complete myxozoan mt genomes have been sequenced: four belonging to two closely related genera, Enteromyxum and Kudoa, and one from the genus Myxobolus. Interestingly, while cytochrome oxidase genes could be identified in Enteromyxum and Kudoa, no such genes were found in Myxobolus squamalis, and another member of the Myxobolidae (Henneguya salminicola) was found to have lost its entire mt genome. To evaluate the utility of mt genomes to reconstruct myxozoan relationships and to understand if the loss of cytochrome oxidase genes is a characteristic of myxobolids, we sequenced the mt genome of five myxozoans (Myxobolus wulii, M. honghuensis, M. shantungensis, Thelohanellus kitauei and, Sphaeromyxa zaharoni) using Illumina and Oxford Nanopore platforms. RESULTS Unlike Enteromyxum, which possesses a partitioned mt genome, the five mt genomes were encoded on single circular chromosomes. An mt plasmid was found in M. wulii, as described previously in Kudoa iwatai. In all new myxozoan genomes, five protein-coding genes (cob, cox1, cox2, nad1, and nad5) and two rRNAs (rnl and rns) were recognized, but no tRNA. We found that Myxobolus and Thelohanellus species shared unidentified reading frames, supporting the view that these mt open reading frames are functional. Our phylogenetic reconstructions based on the five conserved mt genes agree with previously published trees based on the 18S rRNA gene. CONCLUSIONS Our results suggest that the loss of cytochrome oxidase genes is not a characteristic of all myxobolids, the ancestral myxozoan mt genome was likely encoded on a single circular chromosome, and mt plasmids exist in a few lineages. Our findings indicate that myxozoan mt sequences are poor markers for reconstructing myxozoan phylogenetic relationships because of their fast-evolutionary rates and the abundance of repeated elements, which complicates assembly.
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Affiliation(s)
| | - Dayana Yahalomi
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Noam Bracha
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Michal Haddas-Sasson
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Tal Pupko
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Stephen D Atkinson
- Department of Microbiology, Oregon State University, 97331, Corvallis, OR, USA
| | - Jerri L Bartholomew
- Department of Microbiology, Oregon State University, 97331, Corvallis, OR, USA
| | - Jin Yong Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Dorothée Huchon
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel.
- The Steinhardt Museum of Natural History and National Research Center, Tel Aviv University, 6997801, Tel Aviv, Israel.
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Meng X, Wang D, Pang Q, Wang H, Zhou H. Multiple independent origins of duplicated mitochondrial control regions indicate an apomorphy in the Thysanoptera (Insecta). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22087. [PMID: 38288498 DOI: 10.1002/arch.22087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/20/2023] [Accepted: 01/11/2024] [Indexed: 02/01/2024]
Abstract
The mitochondrial genome (mitogenome) of thrips is characterized by the presence of control region (CR) duplication. However, the evolution pattern of duplicated CRs in thrips is still unclear. In this study, the multiple independent origins of duplicated CR indicated that the CR duplication was not an ancestral state for Thysanoptera. The macroevolutionary pattern suggested that the earliest CR duplication event occurred in the middle Cretaceous (94.85 Ma) coincided with rearrangement events forming the ancestors of Aeolothripidae, but much later than that forming the ancestors of the suborder Terebrantia. The mitogenome with duplicated CRs showed a higher rate of gene rearrangement. The sequence similarity of the CR copies and divergence time were negatively correlated, indicating age-related deterioration of mitochondrial function. No significant differences were found in the mitochondrial DNA, the P123 and P4FD between the single and multiple-CR charactered mitogenomes, which suggested that the duplicated CRs may not affect the replication process in thrip mitogenome. The mitogenomes with duplicated CRs (mean: 0.0088 subs/s/my) show a significantly increased evolutionary rate than that with a single one (mean: 0.0058 subs/s/my). However, it seems that this higher evolutionary rate did not have adaptive mechanisms in Terebrantia. We speculated that the duplicated CRs may cause a more intense production of energy by mitochondria, and an accelerated mutation and substitution rate is expected in such mitogenomes. Our study provided new insights into the presence of CR duplications and their evolution in the mitogenomes of thrips.
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Affiliation(s)
| | - Dong Wang
- Qingdao Technical College, Qingdao, China
| | - Qiang Pang
- Qingdao Technical College, Qingdao, China
| | - Heng Wang
- Rizhao Agricultural Technology Service Center, Rizhao, China
| | - Hongxu Zhou
- Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
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Maharjan S, Gamper H, Yamaki Y, Henley RY, Li NS, Suzuki T, Suzuki T, Piccirilli JA, Wanunu M, Seifert E, Wallace DC, Hou YM. Post-Transcriptional Methylation of Mitochondrial-tRNA Differentially Contributes to Mitochondrial Pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.09.569632. [PMID: 38106193 PMCID: PMC10723379 DOI: 10.1101/2023.12.09.569632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Human mitochondrial tRNAs (mt-tRNAs), critical for mitochondrial biogenesis, are frequently associated with pathogenic mutations. These mt-tRNAs have unusual sequence motifs and require post-transcriptional modifications to stabilize their fragile structures. However, whether a modification that stabilizes a wild-type (WT) mt-tRNA structure would also stabilize its pathogenic variants is unknown. Here we show that the N 1 -methylation of guanosine at position 9 (m 1 G9) of mt-Leu(UAA), while stabilizing the WT tRNA, has an opposite and destabilizing effect on variants associated with MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes). This differential effect is further demonstrated by the observation that demethylation of m 1 G9, while damaging to the WT tRNA, is beneficial to the major pathogenic variant, improving its structure and activity. These results have new therapeutic implications, suggesting that the N 1 -methylation of mt-tRNAs at position 9 is a determinant of pathogenicity and that controlling the methylation level is an important modulator of mt-tRNA-associated diseases.
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Guerin MN, Ellis T, Ware MJ, Manning A, Coley A, Amini A, Chung G, Gunsalus KC, Bracht JR. Evolution of a biological thermocouple by adaptation of cytochrome c oxidase in a subterrestrial metazoan. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.05.570156. [PMID: 38106155 PMCID: PMC10723328 DOI: 10.1101/2023.12.05.570156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
In this study we report a naturally evolved temperature-sensing electrical regulator in the cytochrome c oxidase of the Devil Worm, Halicephalobus mephisto. This extremophile metazoan was isolated 1.3 km underground in a South African goldmine, where it adapted to heat and potentially to hypoxia, making its mitochondrial sequence a likely target of adaptational change. We obtained the full mitochondrial genome sequence of this organism, and show through dN/dS analysis statistically robust evidence of positive selection in H. mephisto cytochrome c oxidase subunits. Seventeen of these positively-selected amino acid substitutions were localized in proximity to the H- and K-pathway proton channels of the complex. Surprisingly, the H. mephisto cytochrome c oxidase proton pump completely shuts down at low temperatures (20°C) leading to approximately a 4.8-fold reduction in the transmembrane proton gradient voltage (ΔΨm) compared to optimal temperature (37°C). Direct measurement of oxygen consumption found a corresponding 4.7-fold drop at 20°C compared to 37°C. Correspondingly, the lifecycle of H. mephisto takes four-fold longer at the low temperature compared to higher. This elegant evolutionary adaptation creates a finely-tuned mitochondrial temperature sensor, allowing this ectothermic organism to maximize its reproductive success in varying environmental temperatures. Our study shows that evolutionary innovation may remodel core metabolism to make it more accurately map onto environmental variation.
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Affiliation(s)
- Megan N Guerin
- American University Biology Department, 4400 Massachusetts Avenue, NW, Washington, DC, United States, 20016
| | - TreVaughn Ellis
- American University Biology Department, 4400 Massachusetts Avenue, NW, Washington, DC, United States, 20016
| | - Mark J Ware
- American University Biology Department, 4400 Massachusetts Avenue, NW, Washington, DC, United States, 20016
| | - Alexandra Manning
- American University Biology Department, 4400 Massachusetts Avenue, NW, Washington, DC, United States, 20016
| | - Ariana Coley
- American University Biology Department, 4400 Massachusetts Avenue, NW, Washington, DC, United States, 20016
| | - Ali Amini
- American University Mathematics and Statistics Department, 4400 Massachusetts Avenue, NW, Washington, DC, United States, 20016
| | - George Chung
- New York University, Center for Genomics and Systems Biology, New York, NY 10003
| | - Kristin C Gunsalus
- New York University, Center for Genomics and Systems Biology, New York, NY 10003
| | - John R Bracht
- American University Biology Department, 4400 Massachusetts Avenue, NW, Washington, DC, United States, 20016
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The mitochondrial genomes of big-eared bats, Macrotus waterhousii and Macrotus californicus (Chiroptera: Phyllostomidae: Macrotinae). Gene 2023; 863:147295. [PMID: 36804001 DOI: 10.1016/j.gene.2023.147295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/25/2023] [Accepted: 02/15/2023] [Indexed: 02/21/2023]
Abstract
In the species-rich family Phyllostomidae, the genus Macrotus ('big eared' bats) contains only two species; Macrotus waterhousii, distributed in western, central, and southern Mexico, Guatemala and some Caribbean Islands, and Macrotus californicus, distributed in the southwestern USA, and in the Baja California peninsula and the state of Sonora in Mexico. In this study, we sequenced and assembled the mitochondrial genome of Macrotus waterhousii and characterized in detail this genome and that of the congeneric M. californicus. Then, we examined the phylogenetic position of Macrotus in the family Phyllostomidae based on protein coding genes (PCGs). The AT-rich mitochondrial genomes of M. waterhousii and M. californicus are 16,792 and 16,691 bp long, respectively, and each encode 13 PCGs, 22 tRNA genes, 2 rRNA genes, and a putative non-coding control region 1,336 and 1,232 bp long, respectively. Mitochondrial synteny in Macrotus is identical to that reported before for all other cofamilial species. In the two studied species, all tRNAs exhibit a 'typical' cloverleaf secondary structure with the exception of trnS1, which lacks the D arm. A selective pressure analysis demonstrated that all PCGs are under purifying selection. The CR of the two species feature three domains previously reported in other mammals, including bats: extended terminal associated sequences (ETAS), central (CD), and conserved sequence block (CSB). A phylogenetic analysis based on the 13 mitochondrial PCGs demonstrated that Macrotus is monophyletic and the subfamily Macrotinae is a sister group of all remaining phyllostomids in our analysis, except Micronycterinae. The assembly and detailed analysis of these mitochondrial genomes represents a step further to continue improving the understanding of phylogenetic relationships within the species-rich family Phyllostomidae.
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An evolutionary medicine perspective on the cetacean pulmonary immune system - The first identification of SP-D and LBP in the bottlenose dolphin (Tursiops truncatus). Respir Physiol Neurobiol 2023; 312:104038. [PMID: 36871862 DOI: 10.1016/j.resp.2023.104038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/12/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023]
Abstract
Evolutionary medicine expresses the present status of biomolecules affected by past evolutionary events. To clarify the whole picture of cetacean pneumonia, which is a major threat to cetaceans, their pulmonary immune system should be studied from the perspective of evolutionary medicine. In this in silico study, we focused on cetacean surfactant protein D (SP-D) and lipopolysaccharide-binding protein (LBP) as two representative molecules of the cetacean pulmonary immune system. Sequencing and analyzing SP-D and LBP in the bottlenose dolphin (Tursiops truncatus) lung and liver tissue collected post-mortem elucidated not only basic physicochemical properties but also their evolutionary background. This is the first study to report the sequences and expression of SP-D and LBP in the bottlenose dolphin. Besides, our findings also suggest the direction of an evolutionary arms race in the cetacean pulmonary immune system. These results have important positive implications for cetacean clinical medicine.
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Caña-Bozada V, Morales-Serna FN. PANAS: Pipeline and a Case Study to Obtain Synonymous and Nonsynonymous Substitution Rates in Genes of Platyhelminthes. COMP PARASITOL 2023. [DOI: 10.1654/copa-d-22-00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- Víctor Caña-Bozada
- Centro de Investigación en Alimentación y Desarrollo, A. C., Mazatlán 82112, Sinaloa, Mexico
| | - Francisco N. Morales-Serna
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mazatlán 82040, Sinaloa, Mexico
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van Staden M, Ebert DA, da Silva C, Bester-van der Merwe AE. Comparative analyses of the complete mitochondrial genomes of two southern African endemic guitarfish, Acroteriobatus annulatus and A. blochii. Int J Biol Macromol 2022; 223:1094-1106. [PMID: 36372109 DOI: 10.1016/j.ijbiomac.2022.10.285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/18/2022] [Accepted: 10/30/2022] [Indexed: 11/13/2022]
Abstract
Shark-like rays (order Rhinopristiformes) are among the most threatened cartilaginous fish globally. Despite this, unresolved taxonomic issues still exist within the group. To date, no studies have used complete mitochondrial genomes to assess the phylogenetic placement of Acroteriobatus within the non-monophyletic family Rhinobatidae. The current study reports the first complete mitochondrial genomes for Acroteriobatus annulatus and A. blochii. Similar to other rhinopristiforms, the complete sequences of A. annulatus (16,773 bp) and A. blochii (16,771 bp) were circular molecules with gene organisations identical to that of the typical vertebrate mitogenome. The A + T content was higher than the G + C content, with a bias towards A and C nucleotides observed in all complete mitogenomes. The stem-and-loop secondary structures of the putative origin of light-strand replication were found to have highly conserved synthesis and stem regions, with all substitutions and indels restricted to the loop structure. The ratios of non-synonymous to synonymous substitution rates indicated that purifying selection has been the dominant driver of evolution in rhinopristiform mitogenomes. Phylogenetic reconstructions placed Acroteriobatus as a sister-group to Rhinobatos, confirming its affiliation with the family Rhinobatidae. However, based on its apparent polyphyly with the aforementioned genera, the familial assignment of Pseudobatos is not fully resolved and requires further investigation.
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Affiliation(s)
- Michaela van Staden
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - David A Ebert
- Pacific Shark Research Center, Moss Landing Marine Laboratories, Moss Landing, CA 95039, USA; South African Institute for Aquatic Biodiversity, Private Bag 1015, Grahamstown 6140, South Africa; Department of Ichthyology, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Charlene da Silva
- Department of Forestry, Fisheries and the Environment, Private Bag X2, Rogge Bay 8012, South Africa
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Al-Otaibi WM, Alghamdi KM, Mahyoub JA. Molecular characterization and phylogenetic relationships among Rhynchophorus sp. haplotypes in Makkah Al-Mukarramah Region-KSA. Saudi J Biol Sci 2022; 29:103388. [PMID: 35923599 PMCID: PMC9340515 DOI: 10.1016/j.sjbs.2022.103388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/14/2022] [Accepted: 07/17/2022] [Indexed: 11/29/2022] Open
Abstract
The study aims at detecting and characterizing haplotypes of red palm weevil (RPW) Rhynchophorus sp. in the Western region of Saudi Arabia based on the cytochrome oxidase subunit I (COI) gene sequence. The results indicated the occurrence of 17 nucleotide substitutions, of which three were nonsynonymous (NS). These three NS substitutions resulted in the variation in amino acid sequence in three positions, out of 133. These amino acids are isoleucine/valine, glycine/serine, and arginine/histidine. Based on the chemical properties of the cytochrome C oxidase (COX) enzyme, it is likely that the change at the first position has no effect, while changes at the other two positions can affect the chemical properties of the enzyme. At the three-dimensional (3D) level, the first two positions exist at the border or inside loop 3–4 of the enzyme, while the third position exists inside loop 4–5. These two loops influence the folding pattern of the enzyme, thus, likely affecting the function of the enzyme. However, it is unlikely that variations in the three positions will affect the binding ability of the heme group, which promotes the action of the COX enzyme in the electron transport chain. Variations in chemical properties and 3D structure of COX enzyme might be an evolutionary process (positive selection) that promotes in-time and in-site adaptation to the insect. In conclusion, this study can be helpful in pest management programs and in tracing RPW geographic spread and migration in Saudi Arabia.
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Affiliation(s)
- Wafa Mohammed Al-Otaibi
- Department of Biology, Faculty of Science, Taif University, Taif, Saudi Arabia
- Corresponding author.
| | - Khalid Mohammed Alghamdi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jazem A. Mahyoub
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- IBB University, Ibb, Republic of Yemen
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13
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Mitogenome selection in the evolution of key ecological strategies in the ancient hexapod class Collembola. Sci Rep 2022; 12:14810. [PMID: 36045215 PMCID: PMC9433435 DOI: 10.1038/s41598-022-18407-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 08/10/2022] [Indexed: 11/09/2022] Open
Abstract
A longstanding question in evolutionary biology is how natural selection and environmental pressures shape the mitochondrial genomic architectures of organisms. Mitochondria play a pivotal role in cellular respiration and aerobic metabolism, making their genomes functionally highly constrained. Evaluating selective pressures on mitochondrial genes can provide functional and ecological insights into the evolution of organisms. Collembola (springtails) are an ancient hexapod group that includes the oldest terrestrial arthropods in the fossil record, and that are closely associated with soil environments. Of interest is the diversity of habitat stratification preferences (life forms) exhibited by different species within the group. To understand whether signals of positive selection are linked to the evolution of life forms, we analysed 32 published Collembola mitogenomes in a phylomitogenomic framework. We found no evidence that signatures of selection are correlated with the evolution of novel life forms, but rather that mutations have accumulated as a function of time. Our results highlight the importance of nuclear-mitochondrial interactions in the evolution of collembolan life forms and that mitochondrial genomic data should be interpreted with caution, as complex selection signals may complicate evolutionary inferences.
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14
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Ennis CC, Ortega J, Baeza JA. First genomic resource for an endangered neotropical mega-herbivore: the complete mitochondrial genome of the forest-dweller (Baird's) tapir ( Tapirus bairdii). PeerJ 2022; 10:e13440. [PMID: 35669959 PMCID: PMC9166683 DOI: 10.7717/peerj.13440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/25/2022] [Indexed: 01/14/2023] Open
Abstract
Baird's tapir, or the Central American Tapir Tapirus bairdii (family Tapiridae), is one of the largest mammals native to the forests and wetlands of southern North America and Central America, and is categorized as 'endangered' on the 2014 IUCN Red List of Threatened Species. This study reports, for the first time, the complete mitochondrial genome of T. bairdii and examines the phylogenetic position of T. bairdii amongst closely related species in the same family and order to which it belongs using mitochondrial protein-coding genes (PCG's). The circular, double-stranded, A-T rich mitochondrial genome of T. bairdii is 16,697 bp in length consisting of 13 protein-coding genes (PCG's), two ribosomal RNA genes (rrnS (12s ribosomal RNA and rrnL (16s ribosomal RNA)), and 22 transfer RNA (tRNA) genes. A 33 bp long region was identified to be the origin of replication for the light strand (OL), and a 1,247 bp long control region (CR) contains the origin of replication for the heavy strand (OH). A majority of the PCG's and tRNA genes are encoded on the positive, or heavy, strand. The gene order in T. baiirdi is identical to that of T. indicus and T. terrestris, the only two other species of extant tapirs with assembled mitochondrial genomes. An analysis of Ka/Ks ratios for all the PCG's show values <1, suggesting that all these PCGs experience strong purifying selection. A maximum-likelihood phylogenetic analysis supports the monophyly of the genus Tapirus and the order Perissodactyla. The complete annotation and analysis of the mitochondrial genome of T. bairdii will contribute to a better understanding of the population genomic diversity and structure of this species, and it will assist in the conservation and protection of its dwindling populations.
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Affiliation(s)
- Caroline C. Ennis
- Biological Sciences, Clemson University, Clemson, SC, United States of America
| | - Jorge Ortega
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de Mexico, Mexico DF, Mexico
| | - J. Antonio Baeza
- Biological Sciences, Clemson University, Clemson, SC, United States of America,Departamento de Biologia Marina, Universidad Catolica del Norte, Coquimbo, IV Region, Chile,Smithsonian Marine Station at Fort Pierce, Smithsonian Institute, Fort Pierce, FL, United States of America
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15
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Kim TW, Park SS, Park HS. Effects of Exercise Training during Advanced Maternal Age on the Cognitive Function of Offspring. Int J Mol Sci 2022; 23:ijms23105517. [PMID: 35628329 PMCID: PMC9142119 DOI: 10.3390/ijms23105517] [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: 04/06/2022] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 11/23/2022] Open
Abstract
Advanced maternal age (AMA) denotes an age of ≥35 years during the time of delivery. Maternal metabolism affects the offspring’s physical and neurological development as well as their cognitive function. This study aimed to elucidate the effects of exercise training among old female animals on the cognitive function, hippocampal neuroplasticity, mitochondrial function, and apoptosis in the offspring. We found that the offspring of mothers with AMA without exercise training had decreased spatial learning and memory, brain-derived neurotrophic factor (BDNF) and postsynaptic density protein 95 (PSD-95) protein levels, neurogenesis, and mitochondrial function, as well as hippocampal cell death. Contrastingly, offspring of mothers with AMA with exercise training showed improved spatial learning, memory, hippocampal neuroplasticity, and mitochondrial function. These findings indicate that despite the AMA, increasing fitness through exercise significantly contributes to a positive prenatal environment for fetuses. The maternal exercises augmented the hippocampal levels of BDNF, which prevents decreased cognitive function in the offspring of mothers with AMA.
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Affiliation(s)
- Tae-Woon Kim
- Department of Human Health Care, Gyeongsang National University, Jinju 52725, Korea;
| | - Sang-Seo Park
- School of Health and Kinesiology, University of Nebraska at Omaha, Omaha, NE 68182, USA;
| | - Hye-Sang Park
- Department of Physiology, College of Medicine, KyungHee University, Seoul 02453, Korea
- Correspondence:
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Demirtaş S. Phylogeographic structure of the Persian Squirrel, Sciurus anomalus Güldenstädt, 1785 (Mammalia: Rodentia) in the Anatolian Peninsula, based on mitochondrial DNA sequences: implications for metapopulation. ZOOLOGY IN THE MIDDLE EAST 2022. [DOI: 10.1080/09397140.2022.2058193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Sadık Demirtaş
- Department of Biology, Faculty of Arts and Sciences, Ondokuz Mayıs University, Samsun, Turkey
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17
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Insights on the historical biogeography of Philippine domestic pigs and its relationship with continental domestic pigs and wild boars. PLoS One 2022; 17:e0254299. [PMID: 35344556 PMCID: PMC8959178 DOI: 10.1371/journal.pone.0254299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 03/14/2022] [Indexed: 11/19/2022] Open
Abstract
The Philippine archipelago was believed to have never been connected to the Asian continent even during the severe Quaternary sea-level drops. As a result, the history of domestic pig (Sus scrofa) dispersal in the Philippines remains controversial and must have some anthropogenic origin associated with human migration events. In this study, the context of origin, dispersal, and the level of genetic introgression in Philippine domestic pigs were deduced using mitochondrial DNA D-loop analysis altogether with domestic pigs and wild boar corresponding to their geographic origin. The results revealed considerable genetic diversity (0.900±0.016) and widespread Asian pig-ancestry (94.60%) in the phylogenetic analysis, with admixed European pig-origin (5.10%) harboring various fractions of ancestry from Berkshire and Landrace. The close genetic connection between the continental wild boars and domestic pigs present in the Philippine domestic pigs corroborates our hypothesis of a genetic signal that may be associated with the recently reported multiple waves of human migrations to the Philippines. The Haplogroup D7, reported to occur only in Indo-Burma Biodiversity Hotspots, included a high frequency of Philippine domestic pig haplotypes (54.08%), which poses an interesting challenge because its distribution is not consistent with the hypothesized migration route of Neolithic Austronesian-speaking populations. We detected the first Pacific Clade signature and ubiquitously distributed D2 haplotypes (Asian major) on several Philippine islands. The analyses of mismatch distribution and neutrality test were consistent with the Bayesian skyline plot which showed a long stationary period of effective population size. The population decline was consistent with the pronounced population bottleneck in Asian and European pigs during the interglacial periods of the Pleistocene. The results of this study will support the conservation strategies and improvements of economically important genetic resources in the Philippines.
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Erić P, Patenković A, Erić K, Tanasković M, Davidović S, Rakić M, Savić Veselinović M, Stamenković-Radak M, Jelić M. Temperature-Specific and Sex-Specific Fitness Effects of Sympatric Mitochondrial and Mito-Nuclear Variation in Drosophila obscura. INSECTS 2022; 13:insects13020139. [PMID: 35206713 PMCID: PMC8880146 DOI: 10.3390/insects13020139] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/20/2022] [Accepted: 01/22/2022] [Indexed: 12/28/2022]
Abstract
Simple Summary Does variation in the mitochondrial DNA sequence influence the survival and reproduction of an individual? What is the purpose of genetic variation of the mitochondrial DNA between individuals from the same population? As a simple laboratory model, Drosophila species can give us the answer to this question. Creating experimental lines with different combinations of mitochondrial and nuclear genomic DNA and testing how successful these lines were in surviving in different experimental set-ups enables us to deduce the effect that both genomes have on fitness. This study on D. obscura experimentally validates theoretical models that explain the persistence of mitochondrial DNA variation within populations. Our results shed light on the various mechanisms that maintain this type of variation. Finally, by conducting the experiments on two experimental temperatures, we have shown that environmental variations can support mitochondrial DNA variation within populations. Abstract The adaptive significance of sympatric mitochondrial (mtDNA) variation and the role of selective mechanisms that maintain it are debated to this day. Isofemale lines of Drosophila obscura collected from four populations were backcrossed within populations to construct experimental lines, with all combinations of mtDNA Cyt b haplotypes and nuclear genetic backgrounds (nuDNA). Individuals of both sexes from these lines were then subjected to four fitness assays (desiccation resistance, developmental time, egg-to-adult viability and sex ratio) on two experimental temperatures to examine the role of temperature fluctuations and sex-specific selection, as well as the part that interactions between the two genomes play in shaping mtDNA variation. The results varied across populations and fitness components. In the majority of comparisons, they show that sympatric mitochondrial variants affect fitness. However, their effect should be examined in light of interactions with nuDNA, as mito-nuclear genotype was even more influential on fitness across all components. We found both sex-specific and temperature-specific differences in mitochondrial and mito-nuclear genotype ranks in all fitness components. The effect of temperature-specific selection was found to be more prominent, especially in desiccation resistance. From the results of different components tested, we can also infer that temperature-specific mito-nuclear interactions rather than sex-specific selection on mito-nuclear genotypes have a more substantial role in preserving mtDNA variation in this model species.
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Affiliation(s)
- Pavle Erić
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”–National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (A.P.); (K.E.); (M.T.); (S.D.); (M.R.)
- Correspondence: ; Tel.: +381-112-078-334
| | - Aleksandra Patenković
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”–National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (A.P.); (K.E.); (M.T.); (S.D.); (M.R.)
| | - Katarina Erić
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”–National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (A.P.); (K.E.); (M.T.); (S.D.); (M.R.)
| | - Marija Tanasković
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”–National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (A.P.); (K.E.); (M.T.); (S.D.); (M.R.)
| | - Slobodan Davidović
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”–National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (A.P.); (K.E.); (M.T.); (S.D.); (M.R.)
| | - Mina Rakić
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”–National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (A.P.); (K.E.); (M.T.); (S.D.); (M.R.)
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (M.S.V.); (M.S.-R.); (M.J.)
| | - Marija Savić Veselinović
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (M.S.V.); (M.S.-R.); (M.J.)
| | - Marina Stamenković-Radak
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (M.S.V.); (M.S.-R.); (M.J.)
| | - Mihailo Jelić
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (M.S.V.); (M.S.-R.); (M.J.)
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19
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Layos JKN, Godinez CJP, Liao LM, Yamamoto Y, Masangkay JS, Mannen H, Nishibori M. Origin and Demographic History of Philippine Pigs Inferred from Mitochondrial DNA. Front Genet 2022; 12:823364. [PMID: 35145546 PMCID: PMC8822243 DOI: 10.3389/fgene.2021.823364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 12/28/2021] [Indexed: 01/27/2023] Open
Abstract
The Philippines is a mega-diverse country that lies at the crossroads of past human migrations in the Asia-Pacific region and is believed to have never been connected to the Asian continent, even during the major sea-level subsidence of the Quaternary. As a result, the history of pig dispersal in the Philippines remains controversial, due to limited molecular studies and absence of archaeological evidence of pig domestication. This study provides the first comprehensive analysis of 184 complete mitochondrial DNA D-loop region from Philippine pigs to elucidate their early dispersal history by performing a phylogenetic comparison with wild boars and domestic pigs worldwide. The results showed a demographic signal of the ancestry of Philippine pigs that had a close genetic relationship with those from the mainland Southeast Asia and Northeast Asia, suggesting gene flow that may have resulted from human migration and trade. Here we have suggested two possible dispersal routes. One parallels the Neolithic expansion in Island Southeast Asia and Oceania via Northeast Asia, the other from the mainland Southeast Asia, into Palawan and Sulu Archipelago as early as prehistoric times via the Sundaic Region. Despite geographic barriers to migration, numerous genetic lineages have persisted across the Philippine islands, even justifying the recognition of a Philippine Lanyu subclade. The prehistoric population history suggests a demographic expansion that coincided with the interglacial periods of the Pleistocene and may have spread from the southern regions into the eastern and central regions of the Philippines. The intriguing signal of discrepancy discovered between the ancestral pattern and distribution range of the numerous endemic Philippine wild pigs opens a challenging new approach to illuminate complexity among these animals. Our study has contributed significantly towards completing the sparse molecular studies on Philippine pigs, an essential for creating win-win conservation measures.
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Affiliation(s)
- John King N. Layos
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- College of Agriculture and Forestry, Capiz State University, Mambusao, Philippines
| | - Cyrill John P. Godinez
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- Department of Animal Science, Visayas State University, Baybay City, Philippines
| | - Lawrence M. Liao
- Laboratory of Aquatic Botany, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yoshio Yamamoto
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Joseph S. Masangkay
- College of Veterinary Medicine, University of the Philippines, Los Baños, Philippines
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Masahide Nishibori
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- Department of Animal Science, Visayas State University, Baybay City, Philippines
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20
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Sun CH, Huang Q, Zeng XS, Li S, Zhang XL, Zhang YN, Liao J, Lu CH, Han BP, Zhang Q. Comparative analysis of the mitogenomes of two Corydoras (Siluriformes, Loricarioidei) with nine known Corydoras, and a phylogenetic analysis of Loricarioidei. Zookeys 2022; 1083:89-107. [PMID: 35115873 PMCID: PMC8803743 DOI: 10.3897/zookeys.1083.76887] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/06/2022] [Indexed: 01/04/2023] Open
Abstract
Corydoras is a speciose catfish genus from South America with widely investigated phylogenetic and evolutionary relationships. The complete mitogenomes of C. aeneus and C. paleatus were sequenced, assembled, and annotated using next-generation sequencing. The genome arrangements, gene contents, genome structures, base compositions, evolutionary features, codon usage, and tRNA structures of the two mitogenomes were compared and analyzed with nine published mitogenomes of Corydoras. Phylogenetic analysis was performed using concatenated nucleotide sequences with 13 protein-coding genes and two rRNAs with 44 mitogenomes of Siluriformes. These results provide information on the mitogenomes of eleven Corydoras species and evolutionary relationships within the suborder Loricarioidei, which may be applicable for further phylogenetic and taxonomic studies on Siluriformes and Loricarioidei.
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21
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Saada J, McAuley RJ, Marcatti M, Tang TZ, Motamedi M, Szczesny B. Oxidative stress induces Z-DNA-binding protein 1-dependent activation of microglia via mtDNA released from retinal pigment epithelial cells. J Biol Chem 2022; 298:101523. [PMID: 34953858 PMCID: PMC8753185 DOI: 10.1016/j.jbc.2021.101523] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 12/17/2021] [Accepted: 12/19/2021] [Indexed: 11/28/2022] Open
Abstract
Oxidative stress, inflammation, and aberrant activation of microglia in the retina are commonly observed in ocular pathologies. In glaucoma or age-related macular degeneration, the chronic activation of microglia affects retinal ganglion cells and photoreceptors, respectively, contributing to gradual vision loss. However, the molecular mechanisms that cause activation of microglia in the retina are not fully understood. Here we show that exposure of retinal pigment epithelial (RPE) cells to chronic low-level oxidative stress induces mitochondrial DNA (mtDNA)-specific damage, and the subsequent translocation of damaged mtDNA to the cytoplasm results in the binding and activation of intracellular DNA receptor Z-DNA-binding protein 1 (ZBP1). Activation of the mtDNA/ZBP1 pathway triggers the expression of proinflammatory markers in RPE cells. In addition, we show that the enhanced release of extracellular vesicles (EVs) containing fragments of mtDNA derived from the apical site of RPE cells induces a proinflammatory phenotype of microglia via activation of ZBP1 signaling. Collectively, our report establishes oxidatively damaged mtDNA as an important signaling molecule with ZBP1 as its intracellular receptor in the development of an inflammatory response in the retina. We propose that this novel mtDNA-mediated autocrine and paracrine mechanism for triggering and maintaining inflammation in the retina may play an important role in ocular pathologies. Therefore, the molecular mechanisms identified in this report are potentially suitable therapeutic targets to ameliorate development of ocular pathologies.
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Affiliation(s)
- Jamal Saada
- Department of Ophthalmology and Visual Sciences, University of Texas Medical Branch, Galveston, Texas, USA; Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Ryan J McAuley
- Department of Neuroscience, Cell Biology and Anatomy, University of Texas Medical Branch, Galveston, Texas, USA
| | - Michela Marcatti
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, USA; Department of Neurology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Tony Zifeng Tang
- Department of Neuroscience, Cell Biology and Anatomy, University of Texas Medical Branch, Galveston, Texas, USA
| | - Massoud Motamedi
- Department of Ophthalmology and Visual Sciences, University of Texas Medical Branch, Galveston, Texas, USA
| | - Bartosz Szczesny
- Department of Ophthalmology and Visual Sciences, University of Texas Medical Branch, Galveston, Texas, USA; Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, USA.
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22
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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.
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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.
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Vivas-Toro I, Ortega J, Baeza JA. The complete mitochondrial genome of the Honduran white bat Ectophylla alba (Allen 1982) (Chiroptera: Phyllostomidae). Gene 2021; 802:145868. [PMID: 34364911 DOI: 10.1016/j.gene.2021.145868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/01/2021] [Accepted: 07/30/2021] [Indexed: 11/18/2022]
Abstract
The Honduran white bat, Ectophylla alba (Allen 1982), is one of eight species belonging to the family Phyllostomidae that exclusively roosts in tents. Due to its restricted distribution, habitat specificity, and diet requirements, E. alba has been strongly affected by habitat loss and fragmentation during the last decade. In this study, we developed the first genomic resource for this species; we assembled and analyzed in detail the complete mitochondrial genome of E. alba. The mitogenome of E. alba is 16,664 bp in length and is comprised of 13 protein coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes (tRNAs), and a putative Control Region (CR) 1,232 bp in length. Gene arrangement in the mitochondrial chromosome of E. alba is identical to that reported before in other species of co-familiar bats. All PCGs are under purifying selection, with atp8 experiencing the least selective pressure. In all PCGs, codons ending with adenine are preferred over others ending in thymine and cytosine. Except tRNA-Serine 1, all tRNAs exhibit a cloverleaf secondary structure. The CR of E. alba exhibits three domains commonly described in other mammals, including bats; extended terminal associated sequences (ETAS), central, and conserved sequence block (CSB). A ML phylogenetic reconstruction of the family Phyllostomidae based on all 13 mitochondrial PCGs confirms the monophyletic status of the subfamily Sternodermatinae and indicates the close relationship between E. alba and the genus Artibeus. This is the first genomic resource developed for E. alba and represents the first step to improving our understanding of the genomic underpinnings involved in the evolution of specialization as well as acclimatization and adaptation to local and global change of specialist bats.
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Affiliation(s)
- Isabela Vivas-Toro
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Quimicobiológicas, Departamento de Zoologia, Escuela Nacional de Ciencias Biologicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Sto. Tomas, 11340 CDMX, Mexico
| | - Jorge Ortega
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Quimicobiológicas, Departamento de Zoologia, Escuela Nacional de Ciencias Biologicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Sto. Tomas, 11340 CDMX, Mexico
| | - J Antonio Baeza
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA; Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, FL 34949, USA; Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.
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Ogoh K, Futahashi R, Ohmiya Y. Intraspecific nucleotide polymorphisms in seven complete sequences of mitochondrial DNA of the luminous ostracod, Vargula hilgendorfii (Crustacea, Ostracoda). GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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25
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Provenance and genetic diversity of the non-native geckos Phelsuma grandis Gray 1870 and Gekko gecko (Linnaeus 1758) in southern Florida, USA. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02463-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Zapelloni F, Jurado-Rivera JA, Jaume D, Juan C, Pons J. Comparative Mitogenomics in Hyalella (Amphipoda: Crustacea). Genes (Basel) 2021; 12:genes12020292. [PMID: 33669879 PMCID: PMC7923271 DOI: 10.3390/genes12020292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 02/02/2023] Open
Abstract
We present the sequencing and comparative analysis of 17 mitochondrial genomes of Nearctic and Neotropical amphipods of the genus Hyalella, most from the Andean Altiplano. The mitogenomes obtained comprised the usual 37 gene-set of the metazoan mitochondrial genome showing a gene rearrangement (a reverse transposition and a reversal) between the North and South American Hyalella mitogenomes. Hyalella mitochondrial genomes show the typical AT-richness and strong nucleotide bias among codon sites and strands of pancrustaceans. Protein-coding sequences are biased towards AT-rich codons, with a preference for leucine and serine amino acids. Numerous base changes (539) were found in tRNA stems, with 103 classified as fully compensatory, 253 hemi-compensatory and the remaining base mismatches and indels. Most compensatory Watson–Crick switches were AU -> GC linked in the same haplotype, whereas most hemi-compensatory changes resulted in wobble GU and a few AC pairs. These results suggest a pairing fitness increase in tRNAs after crossing low fitness valleys. Branch-site level models detected positive selection for several amino acid positions in up to eight mitochondrial genes, with atp6 and nad5 as the genes displaying more sites under selection.
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Affiliation(s)
- Francesco Zapelloni
- Department of Biology, University of the Balearic Islands, Ctra. Valldemossa km 7,5, 07122 Palma, Spain; (F.Z.); (J.A.J.-R.); (C.J.)
| | - José A. Jurado-Rivera
- Department of Biology, University of the Balearic Islands, Ctra. Valldemossa km 7,5, 07122 Palma, Spain; (F.Z.); (J.A.J.-R.); (C.J.)
| | - Damià Jaume
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/Miquel Marquès 21, 07190 Esporles, Spain;
| | - Carlos Juan
- Department of Biology, University of the Balearic Islands, Ctra. Valldemossa km 7,5, 07122 Palma, Spain; (F.Z.); (J.A.J.-R.); (C.J.)
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/Miquel Marquès 21, 07190 Esporles, Spain;
| | - Joan Pons
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/Miquel Marquès 21, 07190 Esporles, Spain;
- Correspondence: ; Tel.: +34-971-173-332
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Spatial Genetic Structure and Demographic History of the Wild Boar in the Qinling Mountains, China. Animals (Basel) 2021; 11:ani11020346. [PMID: 33572967 PMCID: PMC7912324 DOI: 10.3390/ani11020346] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/23/2021] [Accepted: 01/27/2021] [Indexed: 12/04/2022] Open
Abstract
Simple Summary The wild boar is native to the temperate region of Eurasia, which is now one of the most widely distributed mammals worldwide. The recent expansion in the wild boar population has attracted a lot of attention, which may cause great damage to ecosystems. Elucidating the patterns of the population structure, genetic diversity, population origin, and colonization route of wild boar is very helpful in the conservation and management of wild populations. Phylogeographic analysis has proven to be a powerful tool. Here, 82 samples of wild boars in 16 sampling locations were collected in Qinling Mountains (QM). Genetic analysis was conducted based on the mitochondrial control region and nuclear genes. The level of genetic diversity of wild boars in QM was lower than the total population in East Asia, but higher than European population. No obvious phylogeographic pattern were found. The effective population size was under demographic equilibrium in the past. Abstract Species dispersal patterns and population genetic structure can be influenced by geographical features. Qinling Mountains (QM) provide an excellent area for phylogeographic study. The phylogeography of Asian-wide wild boars revealed the colonization route. However, the impact of the QM on genetic diversity, genetic structure and population origin is still poorly understood. In this study, genetic analysis of wild boar in the QM was conducted based on the mitochondrial control region (943 bp) and twelve microsatellite loci of 82 individuals in 16 sampling locations. Overall genetic haplotype diversity was 0.86, and the nucleotide diversity was 0.0079. A total of 17 new haplotypes were detected. The level of genetic diversity of wild boars in QM was lower than in East Asia, but higher than in Europe. Phylogenetic analysis showed the weak genetic divergence in QM. Mismatch analysis, neutrality tests, and Bayesian Skyline Plot (BSP) results revealed that the estimates of effective population size were under demographic equilibrium in the past. Spatial analysis of molecular variance indicated no obvious phylogeographic structure.
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Phillips MJ, Shazwani Zakaria S. Enhancing mitogenomic phylogeny and resolving the relationships of extinct megafaunal placental mammals. Mol Phylogenet Evol 2021; 158:107082. [PMID: 33482383 DOI: 10.1016/j.ympev.2021.107082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/21/2020] [Accepted: 01/11/2021] [Indexed: 10/22/2022]
Abstract
Mitochondrial genomes provided the first widely used sequences that were sufficiently informative to resolve relationships among animals across a wide taxonomic domain, from within species to between phyla. However, mitogenome studies supported several anomalous relationships and fell partly out of favour as sequencing multiple, independent nuclear loci proved to be highly effective. A tendency to blame mitochondrial DNA (mtDNA) has overshadowed efforts to understand and ameliorate underlying model misspecification. Here we find that influential assessments of the infidelity of mitogenome phylogenies have often been overstated, but nevertheless, substitution saturation and compositional non-stationarity substantially mislead reconstruction. We show that RY coding the mtDNA, excluding protein-coding 3rd codon sites, partitioning models based on amino acid hydrophobicity and enhanced taxon sampling improve the accuracy of mitogenomic phylogeny reconstruction for placental mammals, almost to the level of multi-gene nuclear datasets. Indeed, combined analysis of mtDNA with 3-fold longer nuclear sequence data either maintained or improved upon the nuclear support for all generally accepted clades, even those that mtDNA alone did not favour, thus indicating "hidden support". Confident mtDNA phylogeny reconstruction is especially important for understanding the evolutionary dynamics of mitochondria themselves, and for merging extinct taxa into the tree of life, with ancient DNA often only accessible as mtDNA. Our ancient mtDNA analyses lend confidence to the relationships of three extinct megafaunal taxa: glyptodonts are nested within armadillos, the South American ungulate, Macrauchenia is sister to horses and rhinoceroses, and sabre-toothed and scimitar cats are the monophyletic sister-group of modern cats.
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Affiliation(s)
- Matthew J Phillips
- School of Biology and Environmental Science, Queensland University of Technology, 2 George Street, Brisbane 4000, QLD, Australia.
| | - Sarah Shazwani Zakaria
- School of Biology and Environmental Science, Queensland University of Technology, 2 George Street, Brisbane 4000, QLD, Australia; School of Biology, Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM) Caw. Negeri Sembilan, Kuala Pilah 72000, Malaysia
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29
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Sayenko EM, Soroka M, Akiyama YB, Uechi T, Ito K, Kondo M. Taxonomic status of genera Nodularia, Middendorffinaia and Inversiunio (Bivalvia: Unionidae) from South-East Asia: morphometric, genetic and GenBank data. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1844817] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Elena M. Sayenko
- Federal Scientific Centre of East Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences, pr. 100-letiya Vladivostoka, 159, Vladivostok, 690022, Russia
| | - Marianna Soroka
- Institute of Biology, University of Szczecin, Felczaka 3c, Szczecin, 71-412, Poland
| | - Yoshihiro B. Akiyama
- Coastal, Marine and Disaster Prevention Department, National Institute for Land and Infrastructure Management, Ministry of Land, Infrastructure, Transport and Tourism, 3-1-1 Nagase, Yokosuka, Kanagawa, 239-0829, Japan
| | - Takeru Uechi
- Department of Environmental Management, Faculty of Agriculture, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan
| | - Kengo Ito
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Mio Kondo
- The Biodiversity Centre of Research Institute of Environment, Agriculture and Fisheries, Osaka Prefecture, 10-4 Koyamotomachi, Neyagawa, Osaka, 572-0088, Japan
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30
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Levy MA, Kerkhof J, Belmonte FR, Kaufman BA, Bhai P, Brady L, Bursztyn LLCD, Tarnopolsky M, Rupar T, Sadikovic B. Validation and clinical performance of a combined nuclear-mitochondrial next-generation sequencing and copy number variant analysis panel in a Canadian population. Am J Med Genet A 2020; 185:486-499. [PMID: 33300680 DOI: 10.1002/ajmg.a.61998] [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: 08/31/2020] [Revised: 11/12/2020] [Accepted: 11/14/2020] [Indexed: 12/17/2022]
Abstract
Diagnosing mitochondrial disorders is a challenge due to the heterogeneous clinical presentation and large number of associated genes. A custom next generation sequencing (NGS) panel was developed incorporating the full mitochondrial genome (mtDNA) plus 19 nuclear genes involved in structural mitochondrial defects and mtDNA maintenance. This assay is capable of simultaneously detecting small gene sequence variations and larger copy number variants (CNVs) in both the nuclear and mitochondrial components along with heteroplasmy detection down to 5%. We describe technical validations of this panel and its implementation for clinical testing in a Canadian reference laboratory, and report its clinical performance in the initial 950 patients tested. Using this assay, we demonstrate a diagnostic yield of 18.1% of patients with known pathogenic variants. In addition to the common 5 kb mtDNA deletion, we describe significant contribution of pathogenic CNVs in both the mitochondrial genome and nuclear genes in this patient population.
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Affiliation(s)
- Michael A Levy
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Frances R Belmonte
- Division of Cardiology, Center for Metabolism and Mitochondrial Medicine and Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Brett A Kaufman
- Division of Cardiology, Center for Metabolism and Mitochondrial Medicine and Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Pratibha Bhai
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Lauren Brady
- Division of Neuromuscular and Neurometabolic Disease, Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | | | - Mark Tarnopolsky
- Division of Neuromuscular and Neurometabolic Disease, Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Tony Rupar
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.,Departments of Biochemistry and Paediatrics, Schulich School of Medicine & Dentistry, Western University, and Biochemical Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
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31
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Lee Y, Ni G, Shin J, Kim T, Kern EMA, Kim Y, Kim SC, Chan B, Goto R, Nakano T, Park JK. Phylogeography of Mytilisepta virgata (Mytilidae: Bivalvia) in the northwestern Pacific: Cryptic mitochondrial lineages and mito-nuclear discordance. Mol Phylogenet Evol 2020; 157:107037. [PMID: 33278586 DOI: 10.1016/j.ympev.2020.107037] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 11/18/2020] [Accepted: 11/30/2020] [Indexed: 10/22/2022]
Abstract
The purplish bifurcate mussel Mytilisepta virgata is widely distributed and represents one of the major components of the intertidal community in the northwestern Pacific (NWP). Here, we characterized population genetic structure of NWP populations throughout nearly their whole distribution range using both mitochondrial (mtDNA cox1) and nuclear (ITS1) markers. Population genetic analyses for mtDNA cox 1 sequences revealed two monophyletic lineages (i.e., southern and northern lineages) geographically distributed according to the two different surface water temperature zones in the NWP. The timing of the lineage split is estimated at the Pliocene- mid-Pleistocene (5.49-1.61 Mya), which is consistent with the timing of the historical isolation of the East Sea/Sea of Japan from the South and East China Seas due to sea level decline during glacial cycles. Historical sea level fluctuation during the Pliocene-Pleistocene and subsequent adaptation of mussels to different surface water temperature zones may have contributed to shaping the contemporary genetic diversity and deep divergence of the two mitochondrial lineages. In contrast to mtDNA sequences, a clear lineage split between the two mitochondrial lineages was not found in ITS1 sequences, which showed a star-like structure composed of a mixture of southern and northern mitochondrial lineages. Possible reasons for this type of mito-nuclear discordance include stochastic divergence in the coalescent processes of the two molecular markers, or balancing selection under different marine environments. Cryptic speciation cannot be ruled out from these results, and future work using genomic analyses is required to address whether the thermal physiology of these mussels corresponds to the deep divergence of their mitochondrial genes and to test for the existence of morphologically indistinguishable but genetically separate cryptic species.
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Affiliation(s)
- Yucheol Lee
- Division of EcoScience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, South Korea
| | - Gang Ni
- Ministry of Education Key Laboratory of Mariculture, Ocean University of China, Qingdao 266003, Shandong, China
| | - Jinkyung Shin
- Division of EcoScience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, South Korea
| | - Taeho Kim
- Division of EcoScience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, South Korea
| | - Elizabeth M A Kern
- Division of EcoScience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, South Korea
| | - Yuseob Kim
- Division of EcoScience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, South Korea
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon, Gyeonggi-do 16419, South Korea
| | - Benny Chan
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ryutaro Goto
- Seto Marine Biological Laboratory, Kyoto University, 459 Shirahama, Nishimuro, Wakayama 649-2211, Japan
| | - Tomoyuki Nakano
- Seto Marine Biological Laboratory, Kyoto University, 459 Shirahama, Nishimuro, Wakayama 649-2211, Japan
| | - Joong-Ki Park
- Division of EcoScience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, South Korea.
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32
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Tasdogan A, McFadden DG, Mishra P. Mitochondrial DNA Haplotypes as Genetic Modifiers of Cancer. Trends Cancer 2020; 6:1044-1058. [PMID: 32980320 DOI: 10.1016/j.trecan.2020.08.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/05/2020] [Accepted: 08/18/2020] [Indexed: 02/06/2023]
Abstract
Mitochondria play an essential role in cellular metabolism, generation of reactive oxygen species (ROS), and the initiation of apoptosis. These properties enable mitochondria to be crucial integrators in the pathways of tumorigenesis. An open question is to what extent variation in the mitochondrial genome (mtDNA) contributes to the biological heterogeneity observed in human tumors. In this review, we summarize our current understanding of the role of mtDNA genetics in relation to human cancers.
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Affiliation(s)
- Alpaslan Tasdogan
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - David G McFadden
- Department of Internal Medicine, Department of Biochemistry, Simmons Comprehensive Cancer Center, Division of Endocrinology, Program in Molecular Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Prashant Mishra
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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33
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Choi SK, Kim KS, Ranyuk M, Babaev E, Voloshina I, Bayarlkhagva D, Chong JR, Ishiguro N, Yu L, Min MS, Lee H, Markov N. Asia-wide phylogeography of wild boar (Sus scrofa) based on mitochondrial DNA and Y-chromosome: Revising the migration routes of wild boar in Asia. PLoS One 2020; 15:e0238049. [PMID: 32834019 PMCID: PMC7444817 DOI: 10.1371/journal.pone.0238049] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/07/2020] [Indexed: 01/04/2023] Open
Abstract
Genetics of pigs has been well studied in Europe and Asia, but most of previous studies of molecular phylogeny of Sus scrofa have been based on sequences of both wild and domestic forms. In this study we analysed genetic traits of Sus scrofa from 13 regions in Asia (including previously undisclosed Eastern Caucasus and Trans-Baikal regions) using purely wild boar samples. Mitochondrial control region and Y-chromosome genes (AMELY & USP9Y) were employed to resolve phylogeographic relationships. We discussed spatio-temporal dynamics of wild boar distribution and compared molecular data to morphological and cytogenetic data on wild boar variability and taxonomy. A total of 51 haplotypes were detected in mtDNA control region and five haplotypes were found in combined sequences of Y-chromosome genes. The phylogeography of Asia-wide wild boars supported a hypothesis of migration from South-East Asia to South Asia, followed by migration to East and West Asia. We present a hypothesis about independent dispersal of wild boars into West Asia from South and North-East Asia. Mitochondrial DNA phylogeny generally fits the morphologically based intraspecies taxonomy. Distribution of chromosomal variants of wild boar presently does not show clear correlation with mtDNA clades.
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Affiliation(s)
- Sung Kyoung Choi
- Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
- National Forensic Service Seoul Institute, Seoul, Republic of Korea
| | - Kyung Seok Kim
- Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, Iowa, United States of America
| | - Maryana Ranyuk
- Institute of Plant and Animal Ecology Ural Branch of Russian Academy of Sciences, Yekaterinburg, Russian Federation
| | - Elmar Babaev
- Caspian Institute of biological Resources of Dagestan Scientific Center of Russian Academy of Sciences, Makhachkala, Russian Federation
| | - Inna Voloshina
- Lazovsky State Nature Reserve, Lazo, Primorsky Krai, Russian Federation
| | | | | | - Naotaka Ishiguro
- Laboratory of Food and Environmental Hygiene, Veterinary Medicine, Gifu University, Gifu, Japan
| | - Li Yu
- Laboratory for Conservation and Utilization of Bio-resource and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Mi-Sook Min
- Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Hang Lee
- Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
- * E-mail: (HL); (NM)
| | - Nickolay Markov
- Institute of Plant and Animal Ecology Ural Branch of Russian Academy of Sciences, Yekaterinburg, Russian Federation
- * E-mail: (HL); (NM)
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34
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Mays HL, Oehler DA, Morrison KW, Morales AE, Lycans A, Perdue J, Battley PF, Cherel Y, Chilvers BL, Crofts S, Demongin L, Fry WR, Hiscock J, Kusch A, Marin M, Poisbleau M, Quillfeldt P, Raya Rey A, Steinfurth A, Thompson DR, Weakley LA. Phylogeography, Population Structure, and Species Delimitation in Rockhopper Penguins (Eudyptes chrysocome and Eudyptes moseleyi). J Hered 2020; 110:801-817. [PMID: 31737899 DOI: 10.1093/jhered/esz051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 08/10/2019] [Indexed: 01/05/2023] Open
Abstract
Rockhopper penguins are delimited as 2 species, the northern rockhopper (Eudyptes moseleyi) and the southern rockhopper (Eudyptes chrysocome), with the latter comprising 2 subspecies, the western rockhopper (Eudyptes chrysocome chrysocome) and the eastern rockhopper (Eudyptes chrysocome filholi). We conducted a phylogeographic study using multilocus data from 114 individuals sampled across 12 colonies from the entire range of the northern/southern rockhopper complex to assess potential population structure, gene flow, and species limits. Bayesian and likelihood methods with nuclear and mitochondrial DNA, including model testing and heuristic approaches, support E. moseleyi and E. chrysocome as distinct species lineages with a divergence time of 0.97 Ma. However, these analyses also indicated the presence of gene flow between these species. Among southern rockhopper subspecies, we found evidence of significant gene flow and heuristic approaches to species delimitation based on the genealogical diversity index failed to delimit them as species. The best-supported population models for the southern rockhoppers were those where E. c. chrysocome and E. c. filholi were combined into a single lineage or 2 lineages with bidirectional gene flow. Additionally, we found that E. c. filholi has the highest effective population size while E. c. chrysocome showed similar effective population size to that of the endangered E. moseleyi. We suggest that the current taxonomic definitions within rockhopper penguins be upheld and that E. chrysocome populations, all found south of the subtropical front, should be treated as a single taxon with distinct management units for E. c. chrysocome and E. c. filholi.
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Affiliation(s)
- Herman L Mays
- Department of Biological Sciences, Marshall University, Huntington, WV
| | - David A Oehler
- Wildlife Conservation Society, Bronx, NY.,Feather Link, Inc., Cincinnati, OH
| | | | - Ariadna E Morales
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY
| | - Alyssa Lycans
- Department of Biological Sciences, Marshall University, Huntington, WV
| | - Justin Perdue
- Department of Biological Sciences, Marshall University, Huntington, WV
| | - Phil F Battley
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Yves Cherel
- Centre d'Etudes Biologiques de Chizé, UMR 7372 du CNRS-La Rochelle Université, Villiers-en-Bois, France
| | - B Louise Chilvers
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Sarah Crofts
- Falklands Conservation, Stanley, Falkland Islands
| | | | | | - Jo Hiscock
- Department of Conservation, Invercargill, New Zealand
| | - Alejandro Kusch
- Wildlife Conservation Society, Bronx, NY.,Feather Link, Inc., Cincinnati, OH
| | - Manuel Marin
- Feather Link, Inc., Cincinnati, OH.,Section of Ornithology, Natural History Museum of Los Angeles County, Los Angeles, CA
| | - Maud Poisbleau
- Department of Biology, Behavioural Ecology and Ecophysiology Group, University of Antwerp, Antwerp (Wilrijk), Belgium
| | - Petra Quillfeldt
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Andrea Raya Rey
- National Scientific and Technical Research Council, Austral Center for Scientific Investigation, Ushuaia, Argentina.,Institute of Polar Science, National University of Tierra del Fuego, Ushuaia, Argentina.,Wildlife Conservation Society, Buenos Aires, Argentina
| | - Antje Steinfurth
- FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch, South Africa.,RSPB Centre for Conservation Science, Royal Society for the Protection of Birds, Cambridge, UK
| | - David R Thompson
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
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35
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Asadi Aghbolaghi M, Ahmadzadeh F, H. Kiabi B, Keyghobadi N. Evolutionary history of the Persian squirrel (Sciurus anomalus): It emerged on the Eurasian continent in the Miocene. ZOOL ANZ 2020. [DOI: 10.1016/j.jcz.2020.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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36
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Mitochondria, spermatogenesis, and male infertility - An update. Mitochondrion 2020; 54:26-40. [PMID: 32534048 DOI: 10.1016/j.mito.2020.06.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 06/02/2020] [Accepted: 06/08/2020] [Indexed: 12/14/2022]
Abstract
The incorporation of mitochondria in the eukaryotic cell is one of the most enigmatic events in the course of evolution. This important organelle was thought to be only the powerhouse of the cell, but was later learnt to perform many other indispensable functions in the cell. Two major contributions of mitochondria in spermatogenesis concern energy production and apoptosis. Apart from this, mitochondria also participate in a number of other processes affecting spermatogenesis and fertility. Mitochondria in sperm are arranged in the periphery of the tail microtubules to serve to energy demand for motility. Apart from this, the role of mitochondria in germ cell proliferation, mitotic regulation, and the elimination of germ cells by apoptosis are now well recognized. Eventually, mutations in the mitochondrial genome have been reported in male infertility, particularly in sluggish sperm (asthenozoospermia); however, heteroplasmy in the mtDNA and a complex interplay between the nucleus and mitochondria affect their penetrance. In this article, we have provided an update on the role of mitochondria in various events of spermatogenesis and male fertility and on the correlation of mitochondrial DNA mutations with male infertility.
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37
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Hu C, Pan T, Wu Y, Zhang C, Chen W, Chang Q. Spatial genetic structure and historical demography of East Asian wild boar. Anim Genet 2020; 51:557-567. [PMID: 32510675 DOI: 10.1111/age.12955] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/21/2020] [Accepted: 05/01/2020] [Indexed: 11/30/2022]
Abstract
Pleistocene climatic fluctuations may have had a profound impact on the evolutionary history of many species. The geographical pattern of European wild boar (Sus scrofa) is clearly studied, and it was greatly influenced by ancient climatic events, especially the Last Glacial Maximum. Previous research on genetic variation has mainly focused on the origin and distribution histories of domestic pigs. However, some questions have not been answered, including those concerning the genetic diversity, geographical pattern and possible historic influence of climate on East Asian wild boar (EAWB). Employing the control region of mtDNA (511 bp), we investigated the contributions of historic climate, which possibly shaped the genetic pattern of wild boar. Given that the level of genetic diversity of wild boars is higher in East Asia than in Europe, 172 haplotypes were detected from 680 individuals. Phylogenetic analysis demonstrated the complex phylogeographic structure of EAWB. Mismatch analysis, neutrality tests and the Bayesian Skyline Plot results all retrieved signals of a rapid population expansion, which might have played an important role in driving the formation of complex spatial genetic structure. Genetic data and species distribution modelling showed that the Last Glacial Maximum had weak effect on the distribution of the EAWB. We suggest that, in shaping spatial genetic structure in East Asian, long-term gene flow and population history played more important roles than Pleistocene climate fluctuations.
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Affiliation(s)
- C Hu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210046, China
| | - T Pan
- School of Life Sciences, Anhui Normal University, Wuhu, Anhui, 230039, China
| | - Y Wu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210046, China
| | - C Zhang
- Faculty of Life Science and Chemical Engineering, Jiangsu Second Normal University, Nanjing, Jiangsu, 210013, China
| | - W Chen
- College of Environment and Ecology, Jiangsu Open University (The City Vocational College of Jiangsu), Nanjing, Jiangsu, 210036, China
| | - Q Chang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210046, China
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Diroma MA, Varvara AS, Attimonelli M, Pesole G, Picardi E. Investigating Human Mitochondrial Genomes in Single Cells. Genes (Basel) 2020; 11:genes11050534. [PMID: 32403285 PMCID: PMC7290567 DOI: 10.3390/genes11050534] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 12/18/2022] Open
Abstract
Mitochondria host multiple copies of their own small circular genome that has been extensively studied to trace the evolution of the modern eukaryotic cell and discover important mutations linked to inherited diseases. Whole genome and exome sequencing have enabled the study of mtDNA in a large number of samples and experimental conditions at single nucleotide resolution, allowing the deciphering of the relationship between inherited mutations and phenotypes and the identification of acquired mtDNA mutations in classical mitochondrial diseases as well as in chronic disorders, ageing and cancer. By applying an ad hoc computational pipeline based on our MToolBox software, we reconstructed mtDNA genomes in single cells using whole genome and exome sequencing data obtained by different amplification methodologies (eWGA, DOP-PCR, MALBAC, MDA) as well as data from single cell Assay for Transposase Accessible Chromatin with high-throughput sequencing (scATAC-seq) in which mtDNA sequences are expected as a byproduct of the technology. We show that assembled mtDNAs, with the exception of those reconstructed by MALBAC and DOP-PCR methods, are quite uniform and suitable for genomic investigations, enabling the study of various biological processes related to cellular heterogeneity such as tumor evolution, neural somatic mosaicism and embryonic development.
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Affiliation(s)
- Maria Angela Diroma
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Via Giovanni Amendola 118, 70126 Bari, Italy; (M.A.D.); (G.P.)
| | - Angelo Sante Varvara
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, Via Orabona 4, 70125 Bari, Italy; (A.S.V.); (M.A.)
| | - Marcella Attimonelli
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, Via Orabona 4, 70125 Bari, Italy; (A.S.V.); (M.A.)
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Via Giovanni Amendola 118, 70126 Bari, Italy; (M.A.D.); (G.P.)
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, Via Orabona 4, 70125 Bari, Italy; (A.S.V.); (M.A.)
| | - Ernesto Picardi
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Via Giovanni Amendola 118, 70126 Bari, Italy; (M.A.D.); (G.P.)
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, Via Orabona 4, 70125 Bari, Italy; (A.S.V.); (M.A.)
- Correspondence: ; Tel.: +39-0805442179
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Derouiche L, Irzagh A, Rahmouni R, Tahri R, Hadjeloum M, Bouhadad R, Fernandes C. Deep mitochondrial DNA phylogeographic divergence in the threatened aoudad Ammotragus lervia (Bovidae, Caprini). Gene 2020; 739:144510. [PMID: 32109559 DOI: 10.1016/j.gene.2020.144510] [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: 11/22/2019] [Revised: 02/20/2020] [Accepted: 02/24/2020] [Indexed: 12/13/2022]
Abstract
The aoudad or Barbary sheep (Ammotragus lervia) is a threatened ungulate emblematic of North Africa, whose population structure and subspecific taxonomy have not been examined genetically. This knowledge is essential and urgently needed to inform ongoing conservation and management efforts. We analysed the mitochondrial cytochrome b gene and four nuclear genes (casein kappa, spectrin beta nonerythrocytic 1, thyroglobulin, thyrotropin subunit beta) for the first phylogeographic survey of the aoudad, and uncovered a deep Mediterranean-Saharan mitochondrial split separating two highly distinct evolutionary lineages. Their level of divergence is greater than or comparable to those observed between several pairs of congeneric species of different caprine genera. The split was estimated to have occurred in the Early Pleistocene, about 1.3 million years ago. None of the four nuclear genes surveyed, chosen because they have been used in phylogeographic and species-level phylogenetic studies of bovids, allowed us to detect, likely due to their slow evolutionary rate, the substantial and geographically coherent subdivision revealed by mitochondrial DNA. This study is evidence and testament to the ability of mitochondrial DNA, probably unrivalled by any other single-locus marker, as an exploratory tool for investigating population genealogy and history and identifying potential evolutionarily significant units for conservation in animals.
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Affiliation(s)
- Louiza Derouiche
- LBEIG, Population Genetics & Conservation Unit, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, BP 32 El-Alia, Bab Ezzouar, 16111, Algiers, Algeria.
| | - Ahmed Irzagh
- Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Saad Dahlab de Blida, route de Soumâa, BP 270, 09000 Blida, Algeria
| | - Rafiq Rahmouni
- Réserve de Chasse de Tlemcen, Direction Générale des Forêts (DGF), Boulevard de Lala Sitti, Tlemcen, Algeria
| | | | - Mohamed Hadjeloum
- Bureau de la Gestion et Protection de la Faune, Direction Générale des Forêts (DGF), Algiers, Algeria
| | - Rachid Bouhadad
- LBEIG, Population Genetics & Conservation Unit, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, BP 32 El-Alia, Bab Ezzouar, 16111, Algiers, Algeria
| | - Carlos Fernandes
- CE3C - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal.
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Kuhle B, Chihade J, Schimmel P. Relaxed sequence constraints favor mutational freedom in idiosyncratic metazoan mitochondrial tRNAs. Nat Commun 2020; 11:969. [PMID: 32080176 PMCID: PMC7033119 DOI: 10.1038/s41467-020-14725-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 01/30/2020] [Indexed: 01/05/2023] Open
Abstract
Metazoan complexity and life-style depend on the bioenergetic potential of mitochondria. However, higher aerobic activity and genetic drift impose strong mutation pressure and risk of irreversible fitness decline in mitochondrial (mt)DNA-encoded genes. Bilaterian mitochondria-encoded tRNA genes, key players in mitochondrial activity, have accumulated mutations at significantly higher rates than their cytoplasmic counterparts, resulting in foreshortened and fragile structures. Here we show that fragility of mt tRNAs coincided with the evolution of bilaterian animals. We demonstrate that bilaterians compensated for this reduced structural complexity in mt tRNAs by sequence-independent induced-fit adaption to the cognate mitochondrial aminoacyl-tRNA synthetase (aaRS). Structural readout by nuclear-encoded aaRS partners relaxed the sequence constraints on mt tRNAs and facilitated accommodation of functionally disruptive mutational insults by cis-acting epistatic compensations. Our results thus suggest that mutational freedom in mt tRNA genes is an adaptation to increased mutation pressure that was associated with the evolution of animal complexity. Bilaterian mitochondria-encoded tRNA genes accumulate mutations at higher rates than their cytoplasmic tRNA counterparts, resulting in idiosyncratic structures. Here the authors suggest an evolutionary basis for the observed mutational freedom of mitochondrial (mt) tRNAs and reveal the associated co-adaptive structural and functional changes in mt aminoacyl-tRNA synthetases.
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Affiliation(s)
- Bernhard Kuhle
- The Skaggs Institute for Chemical Biology, Scripps Research, La Jolla, CA, 92037, USA. .,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA. .,Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA.
| | - Joseph Chihade
- Department of Chemistry, Carleton College, 1 North College St., Northfield, MN, 55057, USA
| | - Paul Schimmel
- The Skaggs Institute for Chemical Biology, Scripps Research, La Jolla, CA, 92037, USA. .,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA. .,Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA. .,Department of Molecular Medicine, The Scripps Florida Research Institute, Jupiter, FL, 33458, USA.
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Chang H, Qiu Z, Yuan H, Wang X, Li X, Sun H, Guo X, Lu Y, Feng X, Majid M, Huang Y. Evolutionary rates of and selective constraints on the mitochondrial genomes of Orthoptera insects with different wing types. Mol Phylogenet Evol 2020; 145:106734. [PMID: 31972240 DOI: 10.1016/j.ympev.2020.106734] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 12/30/2022]
Abstract
Orthoptera is the most diverse order of polyneopterans, and the forewing and hindwing of its members exhibit extremely variability from full length to complete loss in many groups; thus, this order provides a good model for studying the effects of insect flight ability on the evolutionary constraints on and evolutionary rate of the mitochondrial genome. Based on a data set of mitochondrial genomes from 171 species, including 43 newly determined, we reconstructed Orthoptera phylogenetic relationships and estimated the divergence times of this group. The results supported Caelifera and Ensifera as two monophyletic groups, and revealed that Orthoptera originated in the Carboniferous (298.997 Mya). The date of divergence between the suborders Caelifera and Ensifera was 255.705 Mya, in the late Permian. The major lineages of Acrididae seemed to have radiated in the Cenozoic, and the six patterns of rearrangement of 171 Orthoptera mitogenomes mostly occurred in the Cretaceous and Cenozoic. Based on phylogenetic relationships and ancestral state reconstruction, we analysed the evolutionary selection pressure on and evolutionary rate of mitochondrial protein-coding genes (mPCGs). The results indicated that during approximately 300 Mya of evolution, these genes experienced purifying selection to maintain their function. Flightless orthopteran insects accumulated more non-synonymous mutations than flying species and experienced more relaxed evolutionary constraints. The different wing types had different evolutionary rates, and the mean evolutionary rate of Orthoptera mitochondrial mPCGs was 13.554 × 10-9 subs/s/y. The differences in selection pressures and evolutionary rates observed between the mitochondrial genomes suggested that functional constraints due to locomotion play an important role in the evolution of mitochondrial DNA in orthopteran insects with different wing types.
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Affiliation(s)
- Huihui Chang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
| | - Zhongying Qiu
- School of Basic Medical Sciences & Shaanxi Key Laboratory of Brain Disorders, Xi'an Medical University, Xi'an 710021, China
| | - Hao Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
| | - Xiaoyang Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
| | - Xuejuan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
| | - Huimin Sun
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
| | - Xiaoqiang Guo
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Yingchun Lu
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Xiaolei Feng
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
| | - Muhammad Majid
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
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Tikochinski Y, Carreras C, Tikochinski G, Vilaça ST. Population-specific signatures of intra-individual mitochondrial DNA heteroplasmy and their potential evolutionary advantages. Sci Rep 2020; 10:211. [PMID: 31937820 PMCID: PMC6959243 DOI: 10.1038/s41598-019-56918-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 12/03/2019] [Indexed: 01/16/2023] Open
Abstract
Heteroplasmy is the existence of more than one mitochondrial DNA (mtDNA) variant within a cell. The evolutionary mechanisms of heteroplasmy are not fully understood, despite being a very common phenomenon. Here we combined heteroplasmy measurements using high throughput sequencing on green turtles (Chelonia mydas) with simulations to understand how heteroplasmy modulates population diversity across generations and under different demographic scenarios. We found heteroplasmy to be widespread in all individuals analysed, with consistent signal in individuals across time and tissue. Significant shifts in haplotype composition were found from mother to offspring, signalling the effect of the cellular bottleneck during oogenesis as included in the model. Our model of mtDNA inheritance indicated that heteroplasmy favoured the increase of population diversity through time and buffered against population bottlenecks, thus indicating the importance of this phenomenon in species with reduced population sizes and frequent population bottlenecks like marine turtles. Individuals with recent haplotypes showed higher levels of heteroplasmy than the individuals with ancient haplotypes, suggesting a potential advantage of maintaining established copies when new mutations arise. We recommend using heteroplasmy through high throughput sequencing in marine turtles, as well as other wildlife populations, for diversity assessment, population genetics, and mixed stock analysis.
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Affiliation(s)
- Yaron Tikochinski
- Faculty of Marine Sciences, Ruppin Academic Center, Michmoret, Israel
| | - Carlos Carreras
- Department of Genetics, Microbiology and Statistics and IRBio, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain
| | | | - Sibelle T Vilaça
- Leibniz Institute for Zoo and Wildlife Research, Department of Evolutionary Genetics, Berlin, Germany. .,Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany. .,Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
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43
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Sabir JSM, Rabah S, Yacoub H, Hajrah NH, Atef A, Al-Matary M, Edris S, Alharbi MG, Ganash M, Mahyoub J, Al-Hindi RR, Al-Ghamdi KM, Hall N, Bahieldin A, Kamli MR, Rather IA. Molecular evolution of cytochrome C oxidase-I protein of insects living in Saudi Arabia. PLoS One 2019; 14:e0224336. [PMID: 31682609 PMCID: PMC6827904 DOI: 10.1371/journal.pone.0224336] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 10/10/2019] [Indexed: 11/19/2022] Open
Abstract
The study underpins barcode characterization of insect species collected from Saudi Arabia and explored functional constraints during evolution at the DNA and protein levels to expect the possible mechanisms of protein evolution in insects. Codon structure designated AT-biased insect barcode of the cytochrome C oxidase I (COI). In addition, the predicted 3D structure of COI protein indicated tyrosine in close proximity with the heme ligand, depicted substitution to phenylalanine in two Hymenopteran species. This change resulted in the loss of chemical bonding with the heme ligand. The estimated nucleotide substitution matrices in insect COI barcode generally showed a higher probability of transversion compared with the transition. Computations of codon-by-codon nonsynonymous substitutions in Hymenopteran and Hemipteran species indicated that almost half of the codons are under positive evolution. Nevertheless, codons of COI barcode of Coleoptera, Lepidoptera and Diptera are mostly under purifying selection. The results reinforce that codons in helices 2, 5 and 6 and those in loops 2–3 and 5–6 are mostly conserved and approach strong purifying selection. The overall results argue the possible evolutionary position of Hymenopteran species among those of other insects.
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Affiliation(s)
- Jamal S. M. Sabir
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Samar Rabah
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Haitham Yacoub
- Department of Biological Sciences, Faculty of Science, University of Jeddah, Dahaban, Saudi Arabia
| | - Nahid H. Hajrah
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Ahmed Atef
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Mohammed Al-Matary
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Sherif Edris
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Mona G. Alharbi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Magdah Ganash
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Jazem Mahyoub
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Rashad R. Al-Hindi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Khalid M. Al-Ghamdi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Neil Hall
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
- The Genome Analysis Center, Norwich Research Park, Norwich, United Kingdom
| | - Ahmed Bahieldin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Majid R. Kamli
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Irfan A. Rather
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
- * E-mail: ,
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Wang ZH, Liu Y, Chaitankar V, Pirooznia M, Xu H. Electron transport chain biogenesis activated by a JNK-insulin-Myc relay primes mitochondrial inheritance in Drosophila. eLife 2019; 8:49309. [PMID: 31612862 PMCID: PMC6809605 DOI: 10.7554/elife.49309] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/13/2019] [Indexed: 12/25/2022] Open
Abstract
Oogenesis features an enormous increase in mitochondrial mass and mtDNA copy number, which are required to furnish mature eggs with an adequate supply of mitochondria and to curb the transmission of deleterious mtDNA variants. Quiescent in dividing germ cells, mtDNA replication initiates upon oocyte determination in the Drosophila ovary, which necessitates active mitochondrial respiration. However, the underlying mechanism for this dynamic regulation remains unclear. Here, we show that an feedforward insulin-Myc loop promotes mitochondrial respiration and biogenesis by boosting the expression of electron transport chain subunits and of factors essential for mtDNA replication and expression, and for the import of mitochondrial proteins. We further reveal that transient activation of JNK enhances the expression of the insulin receptor and initiates the insulin-Myc signaling loop. This signaling relay promotes mitochondrial biogenesis in the ovary, and thereby plays a role in limiting the transmission of deleterious mtDNA mutations. Our study demonstrates cellular mechanisms that couple mitochondrial biogenesis and inheritance with oocyte development.
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Affiliation(s)
- Zong-Heng Wang
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Yi Liu
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Vijender Chaitankar
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Mehdi Pirooznia
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Hong Xu
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
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Rakotoarivelo AR, O’Donoghue P, Bruford MW, Moodley Y. An ancient hybridization event reconciles mito-nuclear discordance among spiral-horned antelopes. J Mammal 2019. [DOI: 10.1093/jmammal/gyz089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Abstract
The spiral-horned antelopes (genus Tragelaphus) are among the most phenotypically diverse of all large mammals, and evolved in Africa during an adaptive radiation that began in the late Miocene, around 6 million years ago. Tragelaphus was able to exploit the habitat heterogeneity created by Plio-Pleistocene paleoclimatic fluctuations and tectonic processes to eventually occupy almost every habitat type in present day sub-Saharan Africa. The smallest of the spiral-horned antelopes, the bushbuck (T. scriptus), is also widely distributed across Africa, but is genetically divided into polyphyletic Scriptus and Sylvaticus mitochondrial (mt)DNA superlineages that inhabit opposite halves of the continent, suggesting the convergent evolution of independent bushbuck species. In this study, we provide a species tree reconstruction for the genus Tragelaphus and show that Scriptus and Sylvaticus are reciprocally monophyletic at nuclear DNA loci, comprising a single species across its African range. Given that mtDNA will sort into species-specific lineages more quickly than nuclear DNA, only an ancient interspecific hybridization event between a female from a now-extinct Tragelaphus species and a proto-Scriptus bushbuck male can reconcile the mito-nuclear incongruence. This extinct species diverged from the nyala (T. angasii) in the Pliocene about 4.1 million years ago. This study adds to an increasing body of evidence that suggests interspecific hybridization may be more common than previously thought.
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Affiliation(s)
- Andrinajoro R Rakotoarivelo
- Department of Zoology, University of Venda, Thohoyandou, Republic of South Africa
- Natiora Ahy, Lot Bis, Ampahibe, Antananarivo, Madagascar
| | | | - Michael W Bruford
- Cardiff School of Biosciences, Sir Martin Evans Building, Cardiff University, Museum Avenue, Cardiff, United Kingdom
| | - Yoshan Moodley
- Department of Zoology, University of Venda, Thohoyandou, Republic of South Africa
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Aghbolaghi MA, Ahmadzadeh F, Kiabi B, Keyghobadi N. The permanent inhabitant of the oak trees: phylogeography and genetic structure of the Persian squirrel (Sciurus anomalus). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz032] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Marzieh Asadi Aghbolaghi
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, Tehran, Iran
| | - Faraham Ahmadzadeh
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, Tehran, Iran
| | - Bahram Kiabi
- Department of Aquatic Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Nusha Keyghobadi
- Department of Biology, the University of Western Ontario, London, ON, Canada
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47
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Voss RS, Jansa SA. Minimal genetic divergence among South American samples of the water opossum Chironectes minimus: evidence for transcontinental gene flow? MAMMALIA 2019. [DOI: 10.1515/mammalia-2018-0073] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Cytochrome b sequences from South American specimens of the water opossum Chironectes minimus exhibit uncorrected pairwise differences of 0.6% or less among samples collected thousands of kilometers apart (in Guyana, Bolivia and southeastern Brazil). Despite published evidence of population divergence from recent analyses of craniodental morphology, our results suggest extensive gene flow or recent range expansion across the South American landscapes currently occupied by this seldom-collected species.
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48
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Zhang Y, Wang ZH, Liu Y, Chen Y, Sun N, Gucek M, Zhang F, Xu H. PINK1 Inhibits Local Protein Synthesis to Limit Transmission of Deleterious Mitochondrial DNA Mutations. Mol Cell 2019; 73:1127-1137.e5. [PMID: 30772175 DOI: 10.1016/j.molcel.2019.01.013] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 11/05/2018] [Accepted: 01/09/2019] [Indexed: 12/22/2022]
Abstract
We have previously proposed that selective inheritance, the limited transmission of damaging mtDNA mutations from mother to offspring, is based on replication competition in Drosophila melanogaster. This model, which stems from our observation that wild-type mitochondria propagate much more vigorously in the fly ovary than mitochondria carrying fitness-impairing mutations, implies that germ cells recognize the fitness of individual mitochondria and selectively boost the propagation of healthy ones. Here, we demonstrate that the protein kinase PINK1 preferentially accumulates on mitochondria enriched for a deleterious mtDNA mutation. PINK1 phosphorylates Larp to inhibit protein synthesis on the mitochondrial outer membrane. Impaired local translation on defective mitochondria in turn limits the replication of their mtDNA and hence the transmission of deleterious mutations to the offspring. Our work confirms that selective inheritance occurs at the organelle level during Drosophila oogenesis and provides molecular entry points to test this model in other systems.
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Affiliation(s)
- Yi Zhang
- National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Zong-Heng Wang
- National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Yi Liu
- National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Yong Chen
- National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Nuo Sun
- National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Marjan Gucek
- National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Fan Zhang
- National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Hong Xu
- National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA.
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49
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Uddin A, Mazumder TH, Chakraborty S. Understanding molecular biology of codon usage in mitochondrial complex IV genes of electron transport system: Relevance to mitochondrial diseases. J Cell Physiol 2018; 234:6397-6413. [DOI: 10.1002/jcp.27375] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/17/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Arif Uddin
- Department of Zoology Moinul Hoque Choudhury Memorial Science College Hailakandi Assam India
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Siegenthaler A, Wangensteen OS, Soto AZ, Benvenuto C, Corrigan L, Mariani S. Metabarcoding of shrimp stomach content: Harnessing a natural sampler for fish biodiversity monitoring. Mol Ecol Resour 2018; 19:206-220. [PMID: 30358106 PMCID: PMC7379652 DOI: 10.1111/1755-0998.12956] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 10/08/2018] [Accepted: 10/10/2018] [Indexed: 11/30/2022]
Abstract
Given their positioning and biological productivity, estuaries have long represented key providers of ecosystem services and consequently remain under remarkable pressure from numerous forms of anthropogenic impact. The monitoring of fish communities in space and time is one of the most widespread and established approaches to assess the ecological status of estuaries and other coastal habitats, but traditional fish surveys are invasive, costly, labour intensive and highly selective. Recently, the application of metabarcoding techniques, on either sediment or aqueous environmental DNA, has rapidly gained popularity. Here, we evaluate the application of a novel, high‐throughput DNA‐based monitoring tool to assess fish diversity, based on the analysis of the gut contents of a generalist predator/scavenger, the European brown shrimp, Crangon crangon. Sediment and shrimp samples were collected from eight European estuaries, and DNA metabarcoding (using both 12S and COI markers) was carried out to infer fish assemblage composition. We detected 32 teleost species (16 and 20, for 12S and COI, respectively). Twice as many species were recovered using metabarcoding than by traditional net surveys. By comparing and interweaving trophic, environmental DNA and traditional survey‐based techniques, we show that the DNA‐assisted gut content analysis of a ubiquitous, easily accessible, generalist species may serve as a powerful, rapid and cost‐effective tool for large‐scale, routine estuarine biodiversity monitoring.
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Affiliation(s)
- Andjin Siegenthaler
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Owen S Wangensteen
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Ana Z Soto
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Chiara Benvenuto
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Laura Corrigan
- Environment Agency, Tyneside House, Newcastle upon Tyne, UK
| | - Stefano Mariani
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, UK
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