Article
Biochemical Research Methods
Maryam Rabiee, Siavash Mirarab
Summary: The paper introduces a scalable likelihood-based approach called quartet co-estimation for co-estimation under the multi-species coalescent model. By independently inferring gene tree distributions and computing species tree topology and branch length, the method updates gene tree posterior probabilities based on the resulting species tree. Experimental results on simulations and a biological dataset demonstrate better accuracy compared to traditional methods.
Article
Multidisciplinary Sciences
Thibault Latrille, Nicolas Rodrigue, Nicolas Lartillot
Summary: Adaptation in protein-coding sequences can be detected using either multiple sequence alignments across species or polymorphism data within a population. Traditional phylogenetic codon models have limitations due to purifying selection, but recent developments in mutation-selection codon models provide a more detailed assessment of mutation, purifying, and positive selection. This exome-wide analysis shows that proteins and sites detected to be under adaptation at the phylogenetic scale are also under adaptation at the population-genetic scale, reconciling the two approaches and enabling integrative models and analyses across individuals and populations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Agriculture, Dairy & Animal Science
Mohd Hairul Salleh, Yuzine Esa, Rozihan Mohamed
Summary: Technological advancements in molecular approaches, such as DNA barcoding, have allowed for a better understanding of the genetic divergence and characteristics of the Southern River Terrapin population in Malaysia. Through the analysis of COI DNA barcodes, 16 haplotypes were identified, suggesting potential cryptic species between the Northern and Southern River Terrapins.
Article
Multidisciplinary Sciences
Menachem Goren, Nir Stern
Summary: A new species of shrimp-goby, Cryptocentrus steinhardti n. sp., was discovered off the southern Israeli Mediterranean coast, distinct from previously bar-coded gobies. Despite phylogenetic clustering with the shrimp-gobies group, a morphological study supported the assignment of the fish to Cryptocentrus and highlighted the need for revision within the genus based on integrated characteristics. This finding marks the third record of an invasive shrimp goby in the Mediterranean Sea, raising ecological questions about potential fish-shrimp symbiosis in a newly invaded territory.
Article
Forestry
Robin Wilgan, Tomasz Leski
Summary: Invasive tree species can have significant effects on biodiversity and ecosystem functioning, and the role of ectomycorrhizal fungi in the acclimatization and invasion of these species is crucial. This study examined ectomycorrhizal fungi associated with two alien tree species, Quercus rubra and Carya, in Europe. The results showed that although the richness of ectomycorrhizal fungi was similar on both species, there were differences in their composition. The invasive Q. rubra had a higher abundance of long-distance exploration type fungi, while the non-invasive Carya had a higher abundance of short-distance exploration type fungi.
Article
Environmental Sciences
Jhonny Capichoni Massante, Melanie Kobel, Pedro Pinho, Pille Gerhold, Cristina Branquinho, Alice Nunes
Summary: The study finds a decoupling in the response of the phylogenetic structure of annual and perennial components of plant communities to aridity in Mediterranean drylands, with a greater impact of environmental factors. The annuals and perennials show contrasting responses in species richness and phylogenetic structure, with a negative correlation between the two.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Plant Sciences
Rong Huang, Xuena Xie, Fang Li, Enwei Tian, Zhi Chao
Summary: The chloroplast genomes of Mediterranean Bupleurum species were reported for the first time, supporting them as a basal clade of Bupleurum with important insights into their evolutionary history and species classification. Chloroplast genome information is essential in advancing our understanding on phylogenetic study.
Article
Plant Sciences
Achyut Kumar Banerjee, Fengxiao Tan, Hui Feng, Xinru Liang, Jiakai Wang, Minghui Yin, Hao Peng, Yuting Lin, Nannan Zhang, Yelin Huang
Summary: This study aimed to understand the phylogenetic relationship between alien plant species at different stages of invasion and the influence of environmental filtering process on this relationship. The results showed that phylogenetically related species tend to cluster together at smaller spatial scales, indicating the importance of environmental filtering process. The presence of close relatives in the community may facilitate the successful naturalization and invasion of introduced alien species. Temperature has a stronger effect on phylogenetic patterns than precipitation, especially at smaller spatial scales. Different plant families showed different phylogenetic patterns, but all tend to form more clustered assemblages.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Ecology
Konstantinos Voulgaris, Anastasios Varkoulis, Stefanos Zaoutsos, Antonios Stratakis, Dimitris Vafidis
Summary: This study examined the mechanical properties of the test and spines of three sea urchin species in the Mediterranean, highlighting the robustness of S. granularis test and the flexibility of D. setosum spines. Porosity was found to play a key role in fracture prevention in the skeleton, with implications for defensive adaptations and invasive species strategies.
ECOLOGY AND EVOLUTION
(2021)
Article
Biodiversity Conservation
Hong Qian, Marcel Rejmanek, Shenhua Qian
Summary: The study found that invasive species are phylogenetically clustered subsets of naturalized species, and more harmful invasive species show stronger phylogenetic clustering in their naturalized species pools. These findings have significant implications for predicting and controlling invasive species based on phylogenetic relatedness.
DIVERSITY AND DISTRIBUTIONS
(2022)
Article
Genetics & Heredity
Ruitao Yu, Leining Feng, Xiangqun Yuan
Summary: The study reports the mitochondrial genome sequence analysis of the invasive alien species Stictocephala bisonia found in Taibai County, Shaanxi Province, China, supporting the monophyletic hypothesis of treehoppers and suggesting that Smiliinae could be proposed as a separate family.
MITOCHONDRIAL DNA PART B-RESOURCES
(2021)
Article
Genetics & Heredity
Guangyu Yu, Shengchang Lai, Song Liao, Yufeng Cao, Weijun Li, Chengpeng Long, Hagus Tarno, Jianguo Wang
Summary: The complete mitochondrial genomes of four species of beetles in the tribe Scolytoplatypodini were sequenced and annotated. The gene contents and arrangements were similar to other beetles. Phylogenetic analysis confirmed the relationship between Scolytoplatypodini and other tribes of Scolytinae. This study contributes to the understanding of the evolution of Scolytoplatypodini and other related species.
Article
Biology
Katja Birker, Shuchao Ge, Natalie J. Kirkland, Jeanne L. Theis, James Marchant, Zachary C. Fogarty, Maria A. Missinato, Sreehari Kalvakuri, Paul Grossfeld, Adam J. Engler, Karen Ocorr, Timothy J. Nelson, Alexandre R. Colas, Timothy M. Olson, Georg Vogler, Rolf Bodmer
Summary: Researchers conducted whole genome sequencing on HLHS patients and their parents, identifying candidate genes related to the disease. Functional testing in a fruit fly heart model revealed the involvement of genes related to mitochondrial morphology and energy production. Additionally, the study suggests an oligogenic basis for HLHS, with the potential involvement of multiple genes and pathways. Further research on these candidate genes and their interactions can contribute to a better understanding of HLHS and other congenital heart diseases.
Article
Biodiversity Conservation
Celine Bellard, Camille Bernery, Camille Leclerc
Summary: Biological invasions play a significant role in global biodiversity decline, with potential extinction debt and shifts in ecological strategies and evolutionary history of mammals and birds. The impact of invasive species on phylogenetic and trait dimensions of diversity is evident, particularly in the Oceanian realm, suggesting the need for a comprehensive approach in future studies to prioritize spatial strategies for combatting IAS threats worldwide.
GLOBAL CHANGE BIOLOGY
(2021)
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
Multidisciplinary Sciences
Ahmed Hossam Mahmoud, Mohammad Abul Farah, Ahmed Rady, Khalid Mashai Alanazi, Osama Mohammed, Nabil Amor, Khaloud Mohammed Alarjani
JOURNAL OF KING SAUD UNIVERSITY SCIENCE
(2020)
Article
Zoology
D. W. Hart, Y. S. Alharbi, N. C. Bennett, K. S. Schoeman, N. M. Amor, O. B. Mohammed, A. N. Alagaili
JOURNAL OF ZOOLOGY
(2020)
Article
Multidisciplinary Sciences
Ahmed M. Tolah, Saad B. Al Masaudi, Sherif A. El-Kafrawy, Ahmed A. Mirza, Steve M. Harakeh, Ahmed M. Hassan, Mohammed A. Alsaadi, Abdulrahman A. Alzahrani, Ghaleb A. Alsaaidi, Nabil M. S. Amor, Abdulaziz N. Alagaili, Anwar M. Hashem, Esam I. Azhar
Article
Ecology
Rory P. Wilson, Hannah J. Williams, Mark D. Holton, Agustina di Virgilio, Luca Borger, Jonathan R. Potts, Richard Gunner, Alex Arkwright, Andreas Fahlman, Nigel C. Bennett, Abdulaziz Alagaili, Nik C. Cole, Carlos M. Duarte, David M. Scantlebury
ECOLOGY AND EVOLUTION
(2020)
Article
Oceanography
Javier Urra, Desiree Palomino, Pablo Lozano, Emilio Gonzalez-Garcia, Carlos Farias, Angel Mateo-Ramirez, Luis Miguel Fernandez-Salas, Nieves Lopez-Gonzalez, Yolanda Vila, Covadonga Orejas, Patricia Puerta, Jesus Rivera, Lea-Anne Henry, Jose L. Rueda
Summary: Gazul MV in the northeastern Gulf of Cádiz is identified as a shallow mud volcano within the Shallow Field of Fluid Expulsion, which is considered an important area for biodiversity and geology. The study reveals diverse habitats and associated biodiversity in Gazul MV, while also highlighting anthropogenic impacts on the area.
DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS
(2021)
Article
Biotechnology & Applied Microbiology
O. B. Mohammed, N. M. S. Amor, S. A. Omer, A. N. Alagaili
Summary: This study conducted molecular detection and characterization of piroplasms in Ethiopian or desert hedgehogs in Saudi Arabia, finding Theileria DNA in 45.5% of blood samples with no significant difference in prevalence between males and females or between juveniles and adults. Four haplotypes of Theileria sp. were detected, with H1 being the predominant haplotype. The partial 18S rRNA sequences of Theileria sp. from hedgehogs grouped with benign Theileria spp.
LETTERS IN APPLIED MICROBIOLOGY
(2021)
Article
Public, Environmental & Occupational Health
Rihab Lagha, Fethi Ben Abdallah, Asmaa A. H. ALKhammash, Nabil Amor, Mohamed M. Hassan, Imed Mabrouk, Majid Alhomrani, Ahmed Gaber
Summary: 30 clinical isolates of Klebsiella pneumoniae exhibited heterogeneity in antibiotic resistance profiles and high genetic diversity, with most being multidrug-resistant. Genetic variability, as shown by PCR genotyping of porins and efflux pumps, is an important factor to consider in controlling outbreaks of K. pneumoniae. (GTG)5-genotyping showed a significant correlation with antibiotic resistance patterns, suggesting its potential use in predicting antibiotic resistance profiles of K. pneumoniae.
JOURNAL OF INFECTION AND PUBLIC HEALTH
(2021)
Article
Multidisciplinary Sciences
Osama B. Mohammed, Nabil M. S. Amor, Sawsan A. Omer, Abdulaziz N. Alagaili
Summary: The study aimed to establish hematological and biochemical reference intervals for the Ethiopian hedgehog. Significant differences were observed between males and females in hematological values, as well as significant changes in biochemical profiles before and after hibernation. These findings provide a basis for further research in hematology and biochemistry of the desert hedgehog.
JOURNAL OF KING SAUD UNIVERSITY SCIENCE
(2021)
Article
Ecology
D. W. Hart, Y. S. Alharbi, N. C. Bennett, N. M. Amor, O. B. Mohammed, A. N. Alagaili
Summary: Research on female Lesser Egyptian jerboas in central Saudi Arabia showed that their reproduction is severely constrained by unpredictable rainfall and extreme temperature variation, but they exhibit plasticity in their breeding strategy. As global warming continues, understanding how desert-adapted species reproduce may help identify temperate species at risk due to climate change.
JOURNAL OF ARID ENVIRONMENTS
(2021)
Article
Veterinary Sciences
Nabil Amor, Bandar H. Alotaibi, Paolo Merella, Osama B. Mohammed, Abdulaziz N. Alagaili
Summary: This study provides the first molecular characterization of six rodent taxa in Saudi Arabia and confirms the spread of rodent-associated Coxiella burnetii strains. The results facilitate the assessment of health risks associated with rodents and the development of strategies to control the increasing impacts of Q fever.
VETERINARY RESEARCH COMMUNICATIONS
(2022)
Correction
Veterinary Sciences
Bandar H. Alotaibi, Nabil Amor, Paolo Merella, Osama B. Mohammed, Abdulaziz N. Alagaili
VETERINARY RESEARCH COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Ruoa Almahallawi, Sawsan A. Omer, Hind Hazazi, Nabil Amor, Hussni O. Mohammed, Osama B. Mohammed
Summary: This study investigated the prevalence of anaplasmosis among sheep and goats in two cities in western Saudi Arabia. The results showed a significant difference in the prevalence of the disease between goats and sheep, with a higher prevalence in Tabuk. Furthermore, age and season were found to have an impact on the infection rate.
JOURNAL OF KING SAUD UNIVERSITY SCIENCE
(2022)
Article
Parasitology
Sarra Farjallah, Nabil Amor, Giovanni Garippa, Francisco E. Montero, Maria Villora-Montero, Osama Badri Mohamed, Paolo Merella
Summary: This study provides the first contribution to the population genetic variation of Sparicotyle chrysophrii. The analysis based on molecular markers revealed that only one species of the parasite is found on the gills of Sparus aurata in the Mediterranean Sea. Additionally, a new undescribed sister species of S. chrysophrii may exist based on samples isolated from a different host species in the Adriatic Sea.
PARASITOLOGY RESEARCH
(2023)
Article
Entomology
Samia Q. Alghamdi, Hadil A. Alkathiry, Alexandr A. Stekolnikov, Abdulaziz N. Alagaili, Benjamin L. Makepeace
Summary: Collections of chigger mites were conducted on murid rodents in Al Bahah and 'Asir, southwestern Saudi Arabia. A total of 561 chiggers belonging to 19 species were collected from 54 rodents of Acomys dimidiatus and Mus musculus. One new species, Odontacarus thesigeri n. sp., was described, and five species were recorded in Saudi Arabia for the first time, including Microtrombicula abyssinica, Microtrombicula felis, Microtrombicula saperoi, Schoengastiella hypoderma, and Schoutedenichia originalis.
