Article
Fisheries
Hu Chen, Junfeng Pan, Yongzhen Wang, Yanbing Qiao, Fenglu Han, Chang Xu, Ardavan Farhadi, Erchao Li
Summary: This study investigated the effects of different salinity levels on the growth, antioxidant capacity, and gut microbiota composition of the scalloped spiny lobster. The results showed that reduced salinity significantly affected the survival, weight gain, antioxidant capacity, and gut microbiota of the lobsters, with larger reductions in salinity having more detrimental effects.
Article
Medicine, Legal
Suhair M. Jabbar, Nihad A. M. Al-Rashedi
Summary: Although Iraq has a rich cultural history and unique geographic location, there is a lack of forensic reference data on mitochondrial DNA (mtDNA) control region in Iraqi populations, especially in the southern part of the country. This study conducted forensic analysis on 203 unrelated individuals in Samawah City, revealing 111 haplotypes with 143 polymorphic positions in the mtDNA control region. The data generated will be available for further research and forensic investigations.
INTERNATIONAL JOURNAL OF LEGAL MEDICINE
(2021)
Article
Biotechnology & Applied Microbiology
Ahmad Farhadi, Andrew G. Jeffs, Shane D. Lavery
Summary: This study investigates the genetic divergence and potential secondary contact patterns among geographically distant populations of the spiny lobster species complex. The analysis reveals strong regional structure and a complex evolutionary history of these populations, including a hybrid origin of one population. The findings suggest that alternating periods of divergence and gene flow have shaped the current genetic patterns in this lobster species.
Article
Medicine, Legal
Fu-Chi Yang, Bill Tseng, Chun-Yen Lin, Yu-Jen Yu, Adrian Linacre, James Chun- Lee
Summary: This study demonstrated the accuracy of population and subpopulation assignment using mitochondrial genome DNA sequences and the K-nearest neighbors algorithm. Results showed high accuracy in assigning individuals to continental populations and subpopulations, providing valuable insights for research and applications involving subpopulations.
INTERNATIONAL JOURNAL OF LEGAL MEDICINE
(2021)
Article
Anthropology
Wen-qing Yue, Mao-ling Sun, Feng Han, Jiu-jun Li, Tsewang Rigzin, Tashi Dhondup, Hai-bo Liu, Dong-yue Li, Xuan Li, Yan-ming Xu, Xiao-na Li
Summary: The study analyzed the mtDNA control region sequences of Tibetan individuals from the Naqu region of Tibet, and found a unique population structure in the Naqu Tibetan population through population comparison with other groups.
ANNALS OF HUMAN BIOLOGY
(2021)
Article
Anthropology
Yuhang Feng, Hongling Zhang, Qiyan Wang, Meiqing Yang, Yubo Liu, Jie Wang, Jiang Huang, Zheng Ren
Summary: The study analyzed the mitochondrial DNA control region in a typical Sui population, identifying 161 haplotypes and assigning samples to 80 different haplogroups. The Sui population was found to be most closely related to the Miao population in Guizhou and the Han population in Henan, as well as the Punjab and Pukhtunkhwa populations in Pakistan, and significantly differed from 43 other populations, indicating relative isolation. These findings can help establish a forensic DNA reference database in East Asia and provide insight for future anthropological research.
ANNALS OF HUMAN BIOLOGY
(2021)
Article
Agriculture, Dairy & Animal Science
Chia-Huan Ma, Po-Yu Huang, Yung-Cheng Chang, Yen-Ju Pan, Mohamad Nor Azra, Li-Li Chen, Te-Hua Hsu
Summary: Reducing fighting behavior is crucial in lobster and crab aquaculture to enhance survival rates. Providing shelter and co-culturing with live prey can significantly improve the survival of juvenile lobsters and crabs, with live prey also serving as an additional income source during harvest season.
Article
Anthropology
Zheng Ren, Yuhang Feng, Hongling Zhang, Qiyan Wang, Meiqing Yang, Yubo Liu, Cuiyun Le, Jie Wang, Jiang Huang
Summary: This study analyzed the sequences and haplogroups of the mitochondrial DNA control region in a typical Dong population in Guizhou, China. The findings revealed 180 haplotypes assigned to 97 different haplogroups. The Guizhou Dong showed the closest genetic relationship with the Han and Miao populations in China, as well as with the Punjab and Kashmiri populations in Pakistan and other world populations.
ANNALS OF HUMAN BIOLOGY
(2022)
Article
Genetics & Heredity
Lirong Jiang, Jing Liu, Suyu Li, Yufeng Wen, Xinyue Zheng, Liu Qin, Yiping Hou, Zheng Wang
Summary: This study evaluated the performance of four commonly used variant callers in the heterogeneity authentication of human mtDNA and developed a python-based nanopore analytics pipeline, CmVCall. The results showed that CmVCall can accurately identify heterogeneity and reveal significant levels of individual differences. This analysis pipeline lays a solid foundation for comprehensive research on the characteristics of the mitochondrial genome.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2023)
Article
Agronomy
Ayca Ozkan Koca, Salih B. Berkcan, Burcu Lacin Alas, Irfan Kandemir
Summary: The study revealed that the Colorado potato beetle populations in Turkey originated from Europe and have low genetic variation, possibly due to a recent spread from America. Region-specific alleles were found in areas with intensive commercial potato cultivation and insecticide use.
PEST MANAGEMENT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Martin Bodner, Christina Amory, Anna Olivieri, Francesca Gandini, Irene Cardinali, Hovirag Lancioni, Gabriela Huber, Catarina Xavier, Maria Pala, Alessandro Fichera, Lisa Schnaller, Mario Gysi, Stefania Sarno, Davide Pettener, Donata Luiselli, Martin B. Richards, Ornella Semino, Alessandro Achilli, Antonio Torroni, Walther Parson
Summary: This study investigates the potential to solve the limitations in forensic applications caused by the high number of matching haplotypes of the most common mitochondrial (mt)DNA lineages. By massively parallel sequencing a large number of mitogenomes, the study found that complete mitogenome sequencing significantly improved discrimination power and did not reveal any phylogeographic trends within Italy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Nuket Bilgen, Mervenur Guvendi, Efe Sezgin, Huseyin Can, Ahmet Efe Koseoglu, Sedef Erkunt Alak, Mert Doskaya, Cemal Un
Summary: This study investigated the mitochondrial DNA diversity in random bred cats from various regions across Turkey and compared it with the mitochondrial DNA profiles of Turkish Angora and Turkish Van breeds. The analysis identified nine 'universal' mitochondrial DNA profiles and one 'outlier' profile in random bred cats. The haplotype structure in random bred cats showed remarkable diversity compared to Turkish Angora and Van breeds. Overall, this study expands our understanding of the feline genetic landscape in Turkey and lays the foundation for future research on the evolutionary trajectories and genetic legacies of these feline populations.
Article
Biotechnology & Applied Microbiology
Vanessa de Araujo Barbosa, S. Elizabeth Graham, Brian J. Smith, Ian D. Hogg, Angela McGaughran
Summary: This study compared the resolution of mitochondrial COI and nuclear SNP markers for detecting population structure among stream insects at small spatial scales. The results showed that both types of markers can provide suitable initial estimates of fine-scale population genetic differentiation in stream insects.
Article
Zoology
Dongqi Liu, Feng Lan, Sicai Xie, Yi Diao, Yi Zheng, Junhui Gong
Summary: Genetic diversity and population structure of Coreius guichenoti populations in the upper reaches of the Yangtze River were analyzed to investigate the impact of dam constructions. While genetic diversity did not significantly differ between 2009 and 2019, population structure became stronger and some populations showed significant differentiation in 2019. Populations at higher elevations were found to be more vulnerable than those at lower elevations, calling for conservation and restoration efforts such as fish passage and artificial breeding.
Article
Cell Biology
Xiaohong Deng, Dongmei Ji, Xinyuan Li, Yuping Xu, Yu Cao, Weiwei Zou, Chunmei Liang, Jordan Lee Marley, Zhiguo Zhang, Zhaolian Wei, Ping Zhou, Yajing Liu, Yunxia Cao
Summary: Certain mtDNA D-loop variants were found to be associated with decreased risk of PCOS in a Chinese population, but no significant correlation was found between D-loop polymorphisms and clinical characteristics within the PCOS group. Haplotype analysis suggested that a specific haplotype was significantly associated with decreased risk of PCOS.
Article
Ecology
Sarah J. Withers, Stuart Parsons, Mark E. Hauber, Alistair Kendrick, Shane D. Lavery
Summary: This research examined the genetic population divergence in the North Island Rifleman, revealing several significantly divergent lineages across New Zealand's North Island and indicating isolated populations for extended periods. Modeling suggested a dynamic history of population connectivity with constraints on gene flow between regions but recent re-establishment of connectivity.
ECOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Anastasija Zaiko, Paul Greenfield, Cathryn Abbott, Ulla von Ammon, Jaret Bilewitch, Michael Bunce, Melania E. Cristescu, Anthony Chariton, Eddy Dowle, Jonathan Geller, Alba Ardura Gutierrez, Mehrdad Hajibabaei, Emmet Haggard, Graeme J. Inglis, Shane D. Lavery, Aurelija Samuiloviene, Tiffany Simpson, Michael Stat, Sarah Stephenson, Judy Sutherland, Vibha Thakur, Kristen Westfall, Susanna A. Wood, Michael Wright, Guang Zhang, Xavier Pochon
Summary: Advances in high-throughput sequencing technology are changing marine monitoring by enabling rapid and accurate detection of species in complex samples. An international experiment showed that while there was variation in results from different laboratories, the primary signal in the data was consistent, with samples grouping by geographical origin. Post hoc data clean-up, such as removing low-quality samples, improved sample classification accuracy significantly.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biodiversity Conservation
Vanessa Arranz, Rachel M. Fewster, Shane D. Lavery
Summary: This study proposes a new method for comparative multi-species meta-analysis of published population genetic data. It uses a genogeographic clustering technique to capture common spatial patterns of genetic diversity among species and enables statistical comparison of these patterns. The method provides a novel approach to discern multiple common spatial patterns and allows for more rigorous comparative studies from diverse published data.
DIVERSITY AND DISTRIBUTIONS
(2022)
Article
Ecology
Priscila M. Salloum, Anna W. Santure, Shane D. Lavery, Pierre de Villemereuil
Summary: Genome scans are powerful tools to understand genetic adaptation to future environmental conditions. However, low gene flow and population structure can lead to errors in these scans. This study compared different methods and identified candidate loci associated with environmental factors in a marine mollusc. The results highlight the importance of careful statistical controls in genome scans and suggest that further research is needed to determine the potential of non-model species to adapt to future environments.
JOURNAL OF ANIMAL ECOLOGY
(2022)
Article
Biology
James Robertson, Andrew Jeffs, Christopher Hedges, Anthony J. R. Hickey
Summary: Isoeugenol, an anaesthetic used in the transportation of live lobsters, acts as a metabolic suppressant, reducing energy expenditure and improving survival rates. This study investigates the impact of isoeugenol on mitochondrial function, with a particular focus on respiration supported by complex I and cytochrome c oxidase. The results demonstrate that isoeugenol inhibits respiration through complex I and indicates it may act as a possible target for isoeugenol's effects.
JOURNAL OF EXPERIMENTAL BIOLOGY
(2022)
Article
Fisheries
Ahmad Farhadi, Florian Pichlmueller, Bhargavi Yellapu, Shane Lavery, Andrew Jeffs
Summary: Genome-wide SNP typing can improve the management of marine species. In this study, the spiny lobster in the Indo-Pacific region was investigated. The results reveal a genetic break between populations in northern Australia and South East Asia, with significant implications for future fisheries management and aquaculture development.
ICES JOURNAL OF MARINE SCIENCE
(2022)
Article
Ecology
Angela McGaughran, Libby Liggins, Katharine A. Marske, Michael N. Dawson, Lauren M. Schiebelhut, Shane D. Lavery, L. Lacey Knowles, Craig Moritz, Cynthia Riginos
Summary: This article discusses the opportunities and challenges of comparative phylogeography in the genomic age, highlighting the importance of collecting co-distributed species and accruing species-specific ecological knowledge, as well as the availability of bioinformatic skills and user-friendly analytical tools for genomic data analysis.
JOURNAL OF BIOGEOGRAPHY
(2022)
Article
Fisheries
William J. G. McKay, Andrew G. Jeffs
Summary: This study examines the ability of larval giant kokopu to consume formulated larval diets at different ages and feeding events. The results suggest that as the larvae age, their consumption of formulated feed increases, indicating a potential to reduce the reliance on live feed. However, further research is needed to determine the impact on growth and survival.
JOURNAL OF THE WORLD AQUACULTURE SOCIETY
(2023)
Article
Green & Sustainable Science & Technology
Emilee D. Benjamin, Jenny R. Hillman, Sean J. Handley, Trevyn A. Toone, Andrew Jeffs
Summary: Providing substrate is effective for oyster and mussel restoration. This study tested the effectiveness of adding shell substrate for adult green-lipped mussel restoration and found that it provided little advantage in high-density deployments.
Article
Fisheries
Supono Supono, Maria Mugica, Stefan Spreitzenbarth, Andrew Jeffs
Summary: This study investigated the potential use of two concentrated microalgal diets as a replacement for live microalgae in bivalve nursery culture. The results showed that these diets can be used up to 50% substitution without compromising the survival and nutritional profile of juvenile green-lipped mussels.
AQUACULTURE RESEARCH
(2023)
Article
Ecology
Trevyn A. Toone, Emilee D. Benjamin, Jenny R. Hillman, Sean Handley, Andrew Jeffs
Summary: The onset of the Anthropocene has resulted in significant global declines in natural ecosystems and the valuable goods and services they provide, necessitating ecosystem restoration. However, restoring ecosystems effectively requires accurate identification of causes of decline and clear metrics of success, which can only be achieved with baseline data of pre-degradation and pre-restoration ecosystems. This study demonstrates the use of multidisciplinary baselines in the restoration of mussel reefs in New Zealand, showing how combining various sources and methods allows for comprehensive and reliable assessment of ecosystem changes and confirmation of causes of degradation. This approach provides valuable insights for restoration efforts in quantifying the scales of decline, identifying intervention areas, and establishing metrics of success.
Article
Fisheries
William McKay, Andrew Jeffs
Summary: Optimizing the live feed is crucial for successful fish larviculture, as it impacts both larval health and productivity. This study compared the growth and survival of giant kokopu larvae fed different proportions of first-molt and second-molt Artemia nauplii. The results showed that using enriched second-molt Artemia as the sole feed achieved the best total productivity.
Article
Fisheries
Alaric Mccarthy, Andrew Jeffs, Shaun Ogilvie, Dave Taylor, John Radford, Ian Tuck
Summary: This study assessed the effectiveness of using video cameras mounted on commercial trawls for a deep-sea lobster, and confirmed that video sampling can provide information on habitat associations and fishing efficiency.
Article
Fisheries
William McKay, Andrew Jeffs
Summary: The selection of artificial feed is crucial for the success of larviculture of fin fish. This study compares three commercial artificial dry feeds and finds that Otohime yields the best growth performance for giant kokopu larvae. Understanding the nutritional needs of larval giant kokopu is important for improving their commercial aquaculture production.
Article
Fisheries
Jayagopal Pozhoth, Andrew Jeffs
Summary: The study suggests that the use of isobutanol can reduce ammonia levels and mortalities during the live transport of tropical lobsters. Treatment with 50 ppm isobutanol in ambient seawater temperature is more effective than cold stunning treatment.