Article
Biochemistry & Molecular Biology
Alexander J. F. Verry, Eduard Mas-Carrio, Gillian C. Gibb, Ludovic Dutoit, Bruce C. Robertson, Jonathan M. Waters, Nicolas J. Rawlence
Summary: This study used mitochondrial genome sequencing to examine the phylogeny and evolutionary history of the South Island takahe and the moho in Aotearoa New Zealand. The study found that the takahe populations lacked deep phylogeographic structure, while the moho exhibited significant spatial genetic structure. The takahe experienced a sudden demographic decline after human arrival, leading to a loss of mitochondrial genetic diversity. The study also supported a sister species relationship between the takahe and the moho, with a divergence time of approximately 1.5 million years ago.
Article
Entomology
Wenqiang Zhang, Long Lin, Yuhui Ding, Feng Zhang, Junxia Zhang
Summary: This study sequenced and assembled the mitochondrial genomes of two species of jumping spiders, Corythalia opima and Parabathippus shelfordi. By comparing well-characterized mitogenomes of multiple salticid species, the researchers explored the common features and differences in the mitochondrial genomes of jumping spiders and investigated their implications for evolution and taxonomy.
Article
Biotechnology & Applied Microbiology
Xue-Ying Ge, Tong Liu, Ya Kang, Hao-Yu Liu, Yu-Xia Yang
Summary: This study focuses on an important and unusual subfamily of fireflies, Ototretinae. The authors sequenced and annotated three mitogenomes from this subfamily and discovered a novel gene rearrangement in the Stenocladius species. The phylogenetic analyses also revealed some discrepancies in the evolutionary relationship within the Ototretinae subfamily, requiring further investigation.
Article
Agriculture, Dairy & Animal Science
Shiliang Liu, Shuqiao Wang, Qian Chen, Chuang Zhou, Yucheng Lin
Summary: In this study, the first four complete mitochondrial genomes of mysmenid spiders were reported, and it was found that T. yunnanense showed high variability compared to Yamaneta. Phylogenetic analysis revealed that Mysmenidae is closely related to the family Tetragnathidae. These findings contribute to a better understanding of the population genetics, molecular biology, and phylogenetics of these spiders.
Article
Biotechnology & Applied Microbiology
Yingfeng Niu, Chengwen Gao, Jin Liu
Summary: Among the Mangifera species, mango (Mangifera indica) is an important commercial fruit crop. This study sequenced and compared the mitochondrial genomes of three Mangifera species, and found that the gene content and the codon usage pattern of Mangifera mitochondrial genomes is similar across various species. Gene transfer from the chloroplast genome to the mitochondrial genome was also identified.
Article
Genetics & Heredity
Ran Li, Zhenxing Ma, Changfa Zhou
Summary: The study determined the complete mitogenomes of two species of the family Neoephemeridae, revealing the phylogenetic relationships and evolution of this group. The results supported the monophyly of seven studied families and provided insights into the importance of genes like COI and ND2 in the evolutionary history of mayflies. The analysis of selection pressures and reconstruction of phylogenetic trees helped determine the relationships between families within the group.
Editorial Material
Biochemical Research Methods
Lin Tang
Summary: The development of methods helps to push the limits of completeness in genome sequences.
Article
Genetics & Heredity
Chen Wang, Peiyuan Ye, Min Liu, Yue Zhang, Haiqing Feng, Jingyu Liu, Haolang Zhou, Junjie Wang, Xiao Chen
Summary: This study sequenced the complete mitogenomes of four grouper species and analyzed their phylogenetic relationship. The results showed that the genera Cephalopholis and Epinephelus are not monophyletic, and species within the same clade share similar mitogenomic features.
Article
Agriculture, Dairy & Animal Science
Lian Wu, Yao Tong, Sam Pedro Galilee Ayivi, Kenneth B. Storey, Jia-Yong Zhang, Dan-Na Yu
Summary: This study investigates the selective pressures and phylogenetic relationships of skinks using mitochondrial genomes. The results show differences in mitochondrial genomes between limbless and limbed skinks, with one positively selected site found in the mitochondrial genes of limbless skinks. Structural and functional analysis reveals that this site is located in mitochondrial protein complex I.
Article
Environmental Sciences
Eggy Triana Putri, Damin Lee, Haena Kwak, Yukyung Kim, Tomoyuki Nakano, Joong-Ki Park
Summary: The subclass Patellogastropoda, consisting of approximately 350 species worldwide, is one of the most primitive groups of Gastropoda. The internal phylogeny within this subclass, especially the relationships of Acmaeidae with other patellogastropod families, is not fully understood. In this study, we determined the complete mitochondrial genome sequences of two Acmaeidae species (Acmaea mitra and Niveotectura pallida) and one Lottiidae species (Discurria insessa), and combined them with sequences from 20 other limpet species for phylogenetic analysis. The resulting phylogenetic trees revealed two clades within Patellogastropoda, with Acmaeidae and Pectinodontidae being the most closely related.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Entomology
Tinghao Yu, Yalin Zhang
Summary: Mileewinae, a small subfamily of Cicadellidae, has been found to form a monophyletic group within the family with a closer phylogenetic relationship to Typhlocybinae. The analysis of mitochondrial genomes provides valuable insights into the taxonomic status and phylogenetic relationships of Mileewinae.
Article
Entomology
Jing Liu, Yuyu Wang, Ruyue Zhang, Chengmin Shi, Weicheng Lu, Jing Li, Ming Bai
Summary: This study sequenced and analyzed three complete mt genomes of Erotylinae for the first time and conducted a comparative mt genomic analysis with Languriinae. The results revealed similarities in mt genome characteristics between Erotylinae and Languriinae, providing valuable information for future research. Mitochondrial genomes of Erotylinae showed consistent arrangements with other Coleoptera species, while differences in start and stop codons were observed between Languriinae and Erotylinae species. Phylogenetic analyses supported the monophyly of Erotylidae and showed the close relationship between Erotylinae and Xenocelinae, with Languriinae nested within Erotylidae.
Article
Plant Sciences
Inom Juramurodov, Dilmurod Makhmudjanov, Ziyoviddin Yusupov, Komiljon Tojibaev
Summary: This study conducted comprehensive analysis on the complete chloroplast genomes of six Hedysarum species, and discovered high similarity in terms of genome size, gene sequences, and lacking IR region. Additionally, repetitive sequence regions and SSRs were reported for each species. Phylogenetic analyses showed that Hedysarum species form a monophyletic clade closely related to other legume genera. The study provides valuable genetic information for further research on the genus, including evolutionary studies, phylogenetic relationships, population genetics, and species identification.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Yingfeng Niu, Chengwen Gao, Jin Liu
Summary: The study reported and compared four newly sequenced plastid genomes of the genus Mangifera, finding high similarities among them. Certain DNA sequences were identified as potential DNA barcodes for Mangifera, and interspecies relationships were well resolved based on whole plastid genome data. Additionally, the study revealed large fragments transferred from the plastid genome to the mitochondrial genome.
Article
Genetics & Heredity
Wenli Zhu, Lin Yang, Jiankun Long, Zhimin Chang, Nian Gong, Yinlin Mu, Shasha Lv, Xiangsheng Chen
Summary: In this study, the mitochondrial genomic characteristics of three insect pests collected from bamboo plants in Guizhou Province, China were reported. Detailed descriptions and digital photographs of the damaged conditions and life histories of two of the pests were provided. The mitochondrial genome sequences of the three pests were sequenced and analyzed, and phylogenetic trees were constructed. The study contributes to the improvement of the bamboo pest database and provides information for the development of pest control methods.
Article
Biochemistry & Molecular Biology
Michelle Magliolo, Stefan Prost, Pablo Orozco-terWengel, Pamela Burger, Anna S. Kropff, Antoinette Kotze, J. Paul Grobler, Desire Lee Dalton
Summary: Cheetahs are listed as vulnerable due to threats such as habitat loss, human-wildlife conflict, and illegal wildlife trade. A validated SNP array was developed to monitor legal and illegal trade in South Africa, providing an important tool for accurate parentage assignment and forensic investigations. The array demonstrated high resolving power for individual identification and genetic discrimination of cheetah subspecies.
MOLECULAR BIOLOGY REPORTS
(2021)
Article
Ecology
Kristoffer Sahlin, Marisa C. W. Lim, Stefan Prost
Summary: NGSpeciesID is a program that generates highly accurate consensus sequences from long-read amplicon sequencing technologies by clustering reads and employing polishing strategies, improving quality while reducing preprocessing and software installation, enabling rapid processing of a large number of samples with similar consensus accuracy to current pipelines.
ECOLOGY AND EVOLUTION
(2021)
Article
Biology
Monica M. Sheffer, Anica Hoppe, Henrik Krehenwinkel, Gabriele Uhl, Andreas W. Kuss, Lars Jensen, Corinna Jensen, Rosemary G. Gillespie, Katharina J. Hoff, Stefan Prost
Summary: This study successfully assembled a chromosome-level reference genome of the European wasp spider, providing a valuable tool for more in-depth future research.
Article
Genetics & Heredity
Nina Vasiljevic, Marisa Lim, Emily Humble, Adeline Seah, Adelgunde Kratzer, Nadja Morf, Stefan Prost, Rob Ogden
Summary: This study validates the use of ONT MinION sequence data in conjunction with the NGSpeciesID pipeline for species identification. It establishes that the consensus DNA sequences generated by MinION sequencing are accurate enough for forensic genetic species identification purposes.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Ellie E. Armstrong, Anubhab Khan, Ryan W. Taylor, Alexandre Gouy, Gili Greenbaum, Alexandre Thiery, Jonathan T. Kang, Sergio A. Redondo, Stefan Prost, Gregory Barsh, Christopher Kaelin, Sameer Phalke, Anup Chugani, Martin Gilbert, Dale Miquelle, Arun Zachariah, Udayan Borthakur, Anuradha Reddy, Edward Louis, Oliver A. Ryder, Yadvendradev Jhala, Dmitri Petrov, Laurent Excoffier, Elizabeth Hadly, Uma Ramakrishnan
Summary: Species conservation can benefit from understanding evolutionary and genetic history. Tigers, especially Indian tigers with high genomic diversity, may experience recent inbreeding events due to connectivity loss in fragmented habitats. Demographic models suggest subspecies divergence within the last 20,000 years, with Amur and Sumatran tigers showing different patterns of selection for metabolic and body size regulation genes. Further investigation on local adaptation is recommended prior to genetic rescue efforts.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biology
J. Robert Macey, Stephan Pabinger, Charles G. Barbieri, Ella S. Buring, Vanessa L. Gonzalez, Daniel G. Mulcahy, Dustin P. DeMeo, Lara Urban, Paul M. Hime, Stefan Prost, Aaron N. Elliott, Neil J. Gemmell
Summary: Two deeply divergent, co-existing, fully functional mitochondrial genomes have been identified in a single Tuatara, revealing potential adaptive advantages for the unusually cold-tolerant reptile and posing significant implications for mitochondrial evolution and function studies.
COMMUNICATIONS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Johanna von Seth, Nicolas Dussex, David Diez-del-Molino, Tom van der Valk, Verena E. Kutschera, Marcin Kierczak, Cynthia C. Steiner, Shanlin Liu, M. Thomas P. Gilbert, Mikkel-Holger S. Sinding, Stefan Prost, Katerina Guschanski, Senthilvel K. S. S. Nathan, Selina Brace, Yvonne L. Chan, Christopher W. Wheat, Pontus Skoglund, Oliver A. Ryder, Benoit Goossens, Anders Gotherstrom, Love Dalen
Summary: Highly endangered species like the Sumatran rhinoceros are facing threats from inbreeding which could lead to higher risk of extinction for small, isolated populations. The presence of genetic burden and inbreeding in rhinoceros populations suggest that assisted gene flow among different populations may be needed in the future to reduce the risk of inbreeding depression.
NATURE COMMUNICATIONS
(2021)
Article
Biodiversity Conservation
Sarah Ashley Mueller, Stefan Prost, Ole Anders, Christine Breitenmoser-Wursten, Oddmund Kleven, Peter Klinga, Marjeta Konec, Alexander Kopatz, Jarmila Krojerova-Prokesova, Tomma Lilli Middelhoff, Gabriela Obexer-Ruff, Tobias Erik Reiners, Krzysztof Schmidt, Magda Sindicic, Tomaz Skrbinsek, Branislav Tam, Alexander P. Saveljev, Galsandorj Naranbaatar, Carsten Nowak
Summary: Reintroductions of large carnivores may result in decreased genetic diversity and increased inbreeding. This study examines the genetic outcomes of reintroducing the Eurasian lynx and finds that reintroduced populations have lower genetic diversity and higher levels of inbreeding compared to natural populations. The study highlights the importance of considering genetic factors in reintroduction programs and advocates for regular genomic assessments to safeguard genetic diversity.
BIOLOGICAL CONSERVATION
(2022)
Article
Ecology
Karen Greig, Nicolas J. Rawlence
Summary: The pre-human Aotearoa New Zealand fauna was dominated by avian and reptilian species. The introduction of novel mammalian predators, including the kiore and kuri, by East Polynesian colonists had significant impacts on the ecosystem. The ecological impacts of the kuri, in particular, require further assessment.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Article
Biochemical Research Methods
Aaron Pomerantz, Kristoffer Sahlin, Nina Vasiljevic, Adeline Seah, Marisa Lim, Emily Humble, Susan Kennedy, Henrik Krehenwinkel, Sven Winter, Rob Ogden, Stefan Prost
Summary: This protocol outlines steps for DNA amplicon sequencing using miniaturized laboratory equipment, allowing for rapid identification of biological specimens. Utilizing sequence-based applications such as DNA barcoding technique for classification can support conservation and biosurveillance efforts.
Article
Biology
K. Ann Horsburgh, Devri B. Beckett, Anna L. Gosling
Summary: This study investigates the genetic diversity of southern African sheep and reveals limited genetic diversity among them. Modern southern African sheep show close relationships with archaeological sheep, implying an ancestor-descendant relationship. Even the sheep that do not show a close relationship with archaeological sheep cluster closely together, indicating their descent from indigenous sheep rather than historic introductions of exotic breeds.
Article
Biochemistry & Molecular Biology
Stefan Prost, Ana Paula Machado, Julia Zumbroich, Lisa Preier, Sarita Mahtani-Williams, Rene Meissner, Katerina Guschanski, Jaelle C. Brealey, Carlos Rodriguez Fernandes, Paul Vercammen, Luke T. B. Hunter, Alexei V. Abramov, Martin Plasil, Petr Horin, Lena Godsall-Bottriell, Paul Bottriell, Desire Lee Dalton, Antoinette Kotze, Pamela Anna Burger
Summary: Cheetahs, as apex predators, play important roles in ecosystems, but they are facing a precarious conservation status due to habitat loss, human-wildlife conflict, and illegal trafficking. A comprehensive genome-wide analysis of cheetah phylogeography revealed that their genetic differentiation is more complex than previously thought, with distinct genetic characteristics in East African cheetahs compared to Southern African cheetahs. Inbreeding was observed in critically endangered Iranian and Northwestern subspecies, and cheetahs were found to have the lowest genome-wide heterozygosity among big cats. These findings provide valuable information for evidence-based conservation policy decisions and protecting this species in light of ongoing translocations and the threat of illegal trafficking.
Article
Biodiversity Conservation
M. Magliolo, V. N. Naude, V. C. van der Merwe, S. Prost, P. Orozco-terWengel, P. A. Burger, A. Kotze, J. P. Grobler, D. L. Dalton
Summary: In South Africa, the cheetah population is divided into free-roamers, managed metapopulation, and captive facilities. To preserve overall genetic variation, interventions such as genetic exchanges and supplementation with unrelated individuals are proposed. Simulation results showed that without intervention or with only genetic exchanges, there were significant losses of heterozygosity and an increase in the frequencies of close relatives. However, introducing individuals from captive facilities maintained genetic diversity and relatedness.
ANIMAL CONSERVATION
(2023)
Article
Agriculture, Dairy & Animal Science
K. Ann Horsburgh, Anna L. Gosling, Ethan E. Cochrane, Patrick Kirch, Jillian A. Swift, Mark D. McCoy
Summary: This study examines the genetic origins and migration routes of domestic pigs in Polynesia using ancient DNA analysis. The results suggest that the founding populations of pigs in Polynesia can be traced back to northern peninsular Southeast Asia, and were brought to the islands through long-distance voyages by Austronesian-speaking people. The findings highlight the significance of domestic pigs in understanding the settlement history of Polynesia.
Article
Archaeology
Anna L. Gosling, Edana Lord, James Boocock, Sophia Cameron-Christie, K. Ann Horsburgh, Olga Kardailsky, Stefan Prost, Stephen Wilcox, David Addison, Adam Thompson, John Kalolo, Andrew C. Clarke, Elizabeth A. Matisoo-Smith
Summary: This study compares the genomic data of the current population and ancient individuals from Tokelau, finding less genetic diversity compared to other Polynesian populations. Rare mitochondrial lineages suggest prehistoric settlement by people from the northwest. Ancient DNA data supports the previous population abandonment and resettlement on Atafu, the northernmost atoll of Tokelau, from a population of Samoan or Samoan-origin. The study also reveals links between Tokelau and other atoll populations in the western Pacific.
JOURNAL OF ISLAND & COASTAL ARCHAEOLOGY
(2023)