Article
Genetics & Heredity
Cyrill John P. Godinez, Peter June D. Dadios, Dinah M. Espina, Megumi Matsunaga, Masahide Nishibori
Summary: The Philippines is a hotspot for animal genetic resources, with Philippine chickens showing high haplotypic diversity across Southeast Asia and Oceania. Maternal lineage haplogroup D predominates within the population, with evidence suggesting a Philippine origin of Pacific chickens. Philippine chickens also exhibit low genetic differentiation and high gene flow into the Pacific chicken population, with signals of expansion and population growth in Southeast Asia.
FRONTIERS IN GENETICS
(2021)
Review
Biochemistry & Molecular Biology
Jun Feng, Zhaowei Chen, Wei Liang, Zhongping Wei, Guohua Ding
Summary: The kidney, which is a mitochondria-rich organ, is affected by mitochondria-related pathologies. Damage to mitochondrial DNA (mtDNA) plays a role in kidney diseases, including acute kidney injury (AKI) and chronic kidney disease (CKD). MtDNA damage is closely associated with loss of kidney function, and the levels of mtDNA in peripheral serum and urine can reflect kidney injury. Alleviating mtDNA damage can promote mitochondrial function recovery and reduce kidney injury. Therefore, mtDNA damage may serve as a novel biomarker for assessing kidney injury and provide a new therapeutic option for kidney diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Mariceli Baia Leao Barros, Danilo do Rosario Pinheiro, Barbara do Nascimento Borges
Summary: Glioblastoma (GBM) is a highly aggressive tumor originating from neural stem cells of the central nervous system, with mutations in mitochondrial DNA (mtDNA) leading to mitochondrial dysfunction, playing a crucial role in GBM pathogenesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Pedro G. Nachtigall, Felipe G. Grazziotin, Inacio L. M. Junqueira-de-Azevedo
Summary: MITGARD is an automated pipeline that reliably recovers mitochondrial genomes from RNA-seq data of various sources. The tool can reconstruct mitogenomes across different species and sequencing schemes, demonstrating its effectiveness even in scenarios of low-sequencing depth. Additionally, MITGARD's use of phylogenetically related references allows for the recovery of entire mitogenomes or most mitochondrial genes, making it valuable for biodiversity projects and evolutionary studies.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Julia Leme Pablos, Ana Kristina Silva, Noemy Seraphim, Luiza de Moraes Magaldi, Anete Pereira de Souza, Andre Victor Lucci Freitas, Karina Lucas Silva-Brandao
Summary: The study on Atlantic Forest White Morpho butterflies shows that there is no clear species diversification and population structure among the populations, suggesting that the current distinction between the two species is unreasonable. Northern samples exhibit more intragroup structure, and clustering tests indicate the existence of three genetic clusters, with turnover between the states of Paran ' a and Sa similar to o Paulo.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Genevieve Trombly, Afaf Milad Said, Alexei P. Kudin, Viktoriya Peeva, Janine Altmueller, Kerstin Becker, Karl Koehrer, Gabor Zsurka, Wolfram S. Kunz
Summary: The study investigated the effects of hydrogen peroxide on mitochondrial DNA integrity. The results showed that hydrogen peroxide treatment resulted in DNA breaks, which were then repaired through rapid repair of single-strand breaks and degradation of double-strand breaks-generated linear fragments. Inactivation of mitochondrial DNA degradation resulted in the persistence of linear fragments in mutant cells without affecting the repair of single-strand breaks. These findings highlight the interplay between DNA repair and degradation processes, and the potential generation of somatic mitochondrial DNA deletions.
Article
Genetics & Heredity
Isabel Salado, Michaela Preick, Natividad Lupianez-Corpas, Alberto Fernandez-Gil, Carles Vila, Michael Hofreiter, Jennifer A. A. Leonard
Summary: Gray wolves in the Iberian Peninsula have declined in range and population size due to human persecution and habitat fragmentation. However, they have never gone extinct in Iberia and their numbers have increased and stabilized in recent decades. Despite population growth, genetic diversity has declined, indicating that even expanding populations can lose genetic diversity.
Review
Biochemistry & Molecular Biology
Siyang Liao, Li Chen, Zhiyin Song, He He
Summary: Mitochondrion is an organelle responsible for cellular respiration and ATP production. Its DNA, known as mtDNA, encodes essential subunits of respiratory complexes and can be damaged, leading to mitochondrial dysfunction and diseases. Cells employ multiple pathways to repair and remove damaged mtDNA in order to maintain mitochondrial quality and cellular homeostasis.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
(2022)
Article
Parasitology
Huiying Chen, Haowei Dong, Hao Yuan, Wenqi Shan, Qiuming Zhou, Xiangyu Li, Heng Peng, Yajun Ma
Summary: The accurate identification of sandfly species is crucial due to their role in transmitting medically significant diseases. However, conventional identification methods are time consuming and require experienced staff. This study investigates the use of DNA barcodes to identify common sandfly species in China and finds that mitochondrial DNA markers are effective in distinguishing these species.
Article
Genetics & Heredity
Martin Bodner, Ugo A. Perego, J. Edgar Gomez, Ricardo M. Cerda-Flores, Nicola Rambaldi Migliore, Scott R. Woodward, Walther Parson, Alessandro Achilli
Summary: Mexico is a rich source for anthropological and population genetic studies, with a high diversity of ethnic and linguistic groups. Despite most Mexicans identifying as mixed rather than Indigenous, maternal inherited mitochondrial DNA reveals an overwhelming Indigenous American legacy in the modern Mexican population. This suggests a low European contribution to the Mexican gene pool by female colonizers.
Article
Oncology
Tarek Zaidieh, James R. Smith, Karen E. Ball, Qian An
Summary: Our study revealed novel significant associations between the total number of variations in the mitochondrial respiratory chain (MRC) complex I and III genes, mtDNAcn, ROS levels, and ROS-associated drug response. Furthermore, functional variations in complexes I/III correlated significantly and positively with mtDNAcn, ROS levels and drug resistance, indicating they might mechanistically influence these parameters in cancer cells.
Article
Multidisciplinary Sciences
J. R. Connell, M. C. Benton, R. A. Lea, H. G. Sutherland, J. Chaseling, L. M. Haupt, K. M. Wright, L. R. Griffiths
Summary: This study reports a pedigree derived mutation rate for the human mitochondrial genome and compares it with published mutation rates. The pedigree derived mutation rates are found to be higher and heteroplasmy mutations are more common, providing new insights into the evolution of the human mitochondrial genome.
SCIENTIFIC REPORTS
(2022)
Article
Ecology
Nina Vasiljevic, Nadja V. Morf, Josef Senn, Silvia Perez-Espona, Federica Mattucci, Nadia Mucci, Gaia Moore-Jones, Simone Roberto Rolando Pisano, Adelgunde Kratzer, Rob Ogden
Summary: This study investigates the recolonization of roe deer in Switzerland in the early 1800s and finds evidence of natural immigration from neighboring countries. The study also reveals weak genetic differentiation among different topographic regions in Switzerland. The genetic data support the recognition of a single roe deer management unit in Switzerland and the potential for geographic origin assignment using nuclear markers for law enforcement purposes.
ECOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Yan Xiao, Xing-Juan Li, Xiao-Long Jiang, Chun Li, Xiang-Peng Li, Wei-Ping Li, Dai-Ke Tian
Summary: This study investigated the population genetic structure and distribution dynamics of Begonia grandis in China using chloroplast DNA markers and species distribution modeling. The results showed high genetic diversity, strong genetic differentiation, and significant phylogeographical structure in B. grandis. The Yunnan-Guizhou Plateau, Three Gorges region, and Daba Mountains were identified as potential refugia for this species.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Endocrinology & Metabolism
Jay Kumar, Ghulam Mohammad, Kumari Alka, Renu A. Kowluru
Summary: Mitochondrial dysfunction plays a critical role in the development of diabetic retinopathy. Hyperglycemia downregulates the mtDNA-encoded LncRNA cytochrome B (LncCytB) in retinal endothelial cells, leading to impaired mtDNA packaging and increased vulnerability to damage.
Article
Evolutionary Biology
Laura Kamp, Gilberto Pasinelli, Pietro Milanesi, Sergei V. Drovetski, Ziemowit Kosinski, Serguei Kossenko, Hugo Robles, Manuel Schweizer
Article
Biochemistry & Molecular Biology
Joseph P. Zilko, Dan Harley, Birgita Hansen, Alexandra Pavlova, Paul Sunnucks
Article
Biochemistry & Molecular Biology
Nicholas J. Clark, Sergei Drovetski, Gary Voelker
Article
Ornithology
Tiago M. Rodrigues, Edward H. Miller, Sergei V. Drovetski, Robert M. Zink, Jon Fjeldsa, David Goncalves
Summary: The study looked at phenotypic differentiation in two shorebird species, finding that while there were no significant differences in skeletal variables between the species, there were significant differences in plumage traits. These differences suggest a more rapid divergence in socially selected traits between the species than in traits related to resource use.
Article
Evolutionary Biology
Maiko L. Lutz, Zeb Tonkin, Jian D. L. Yen, Glen Johnson, Brett A. Ingram, Joanne Sharley, Jarod Lyon, David G. Chapple, Paul Sunnucks, Alexandra Pavlova
Summary: By utilizing genetic diversity from different sources, population reintroductions can create populations with low risk of harmful inbreeding and well-equipped for adaptation to future environments. The study assessed the outcomes of reintroducing Macquaria australasica into the Ovens River using genetically diverse Yarra and moderately diverse Dartmouth sources, showing that combining compatible stocks can benefit restoration of wildlife populations.
EVOLUTIONARY APPLICATIONS
(2021)
Review
Ecology
Rebecca E. Koch, Katherine L. Buchanan, Stefania Casagrande, Ondi Crino, Damian K. Dowling, Geoffrey E. Hill, Wendy R. Hood, Matthew McKenzie, Mylene M. Mariette, Daniel W. A. Noble, Alexandra Pavlova, Frank Seebacher, Paul Sunnucks, Eve Udino, Craig R. White, Karine Salin, Antoine Stier
Summary: The critical role that energy turnover plays in understanding variation in performance and fitness among individuals has long been recognized by biologists. While whole-organism metabolic studies have provided key insights into ecological and evolutionary processes, constraints at subcellular levels, such as within mitochondria, can also optimize metabolism. This exploration of mitochondrial aerobic metabolism's influence on organismal performance highlights important areas for future research in understanding ecological and evolutionary processes.
TRENDS IN ECOLOGY & EVOLUTION
(2021)
Article
Ecology
Yael S. Rodger, Alexandra Pavlova, Steve Sinclair, Melinda Pickup, Paul Sunnucks
Summary: Conservation management can be enhanced by understanding genetic diversity and evolutionary history. The Button Wrinklewort daisy has become endangered due to habitat loss and livestock grazing, with genetic analysis showing strong population differentiation between regions. Despite lower recent census sizes, the last two remaining Victorian populations have the highest genetic diversity among the populations studied.
Article
Biochemistry & Molecular Biology
Diana A. Robledo-Ruiz, Alexandra Pavlova, Rohan H. Clarke, Michael J. L. Magrath, Bruce Quin, Katherine A. Harrisson, Han Ming Gan, Gabriel W. Low, Paul Sunnucks
Summary: The article presents an analytical framework for evaluating the efficacy of breeding management strategies for wild populations, showing that the proposed strategies did not significantly improve genetic quality or reduce inbreeding in the critically endangered helmeted honeyeater population. The results demonstrate the usefulness of the analytical framework for testing different in situ breeding strategies and making evidence-based management decisions.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biodiversity Conservation
Joseph P. Zilko, Dan Harley, Alexandra Pavlova, Paul Sunnucks
Summary: Genetic rescue can reduce the extinction risk of inbred populations, with the risk of genetic swamping. Simulation results suggest that translocating highland possums into lowland populations can rapidly increase population size, alleviate inbreeding depression, but may reduce the frequency of locally unique alleles.
Article
Biochemistry & Molecular Biology
Alexandra Pavlova, Katherine A. Harrisson, Rustam Turakulov, Yin Peng Lee, Brett A. Ingram, Dean Gilligan, Paul Sunnucks, Han Ming Gan
Summary: This study identified sex-linked loci in Macquarie perch and developed a cost-effective sexing assay using genomic and resequencing data. The research revealed high instability of sex chromosomes in Percichthyidae fishes, with differences in sex-linked positions observed between species and populations.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biodiversity Conservation
Maiko L. Lutz, Paul Sunnucks, David G. Chapple, Dean Gilligan, Mark Lintermans, Alexandra Pavlova
Summary: This study assessed the genetic outcomes of interbreeding between two lineages of a threatened freshwater fish species, and found no adverse effects from genetic mixing of populations separated by over 100,000 years.
CONSERVATION GENETICS
(2022)
Article
Biodiversity Conservation
Alexandra Pavlova, Sara Petrovic, Katherine A. Harrisson, Karina Cartwright, Elizabeth Dobson, Laura L. Hurley, Meagan Lane, Michael J. L. Magrath, Kimberly A. Miller, Bruce Quin, Monique Winterhoff, Jian D. L. Yen, Paul Sunnucks
Summary: Small, isolated populations face the risk of extinction due to inbreeding depression, loss of beneficial variation, and reduced adaptability. Genetic rescue through gene flow from diverse sources is the most effective way to improve their fitness. However, the use of a different subspecies as a potential source of immigrants may result in reduced fitness of mixed offspring. Test cases are necessary to evaluate and manage such risky rescues.
BIOLOGICAL CONSERVATION
(2023)
Article
Biochemistry & Molecular Biology
Diana A. Robledo-Ruiz, Lana Austin, J. Nevil Amos, Jesus Castrejon-Figueroa, Daniel K. P. Harley, Michael J. L. Magrath, Paul Sunnucks, Alexandra Pavlova
Summary: Identifying sex-linked markers in genomic datasets is crucial for accurate genetic analysis and interpretation. However, current methods often neglect certain types of sex-linked variation. In this study, we developed new R functions that can reliably identify sex-linked loci and infer the genetic sex of individuals. We tested these functions on bird and mammal species and found that they achieved high accuracy in distinguishing sex-linked loci from autosomal loci. Furthermore, we demonstrated that failure to remove sex-linked loci can lead to incorrect biological inferences and management recommendations. Our functions provide a convenient tool for removing sex-linked loci in reduced-representation datasets and sexing individuals.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Microbiology
Gary R. Graves, Kenan O. Matterson, Christopher M. Milensky, Brian K. Schmidt, Michael J. O'Mahoney, Sergei Drovetski
Article
Ornithology
James Q. Radford, Nevil Amos, Katherine Harrisson, Paul Sunnucks, Alexandra Pavlova
Summary: This review article highlights the impact of habitat loss and fragmentation on population adaptation, as well as the finding that high genetic connectivity does not necessarily indicate healthy populations. The study conducted on woodland bird species in central Victoria, Australia provides valuable insights for conservation management strategies.
EMU-AUSTRAL ORNITHOLOGY
(2021)
