Article
Agricultural Engineering
Jafar Mehdi, Danish Husain, Abhilasha Srivastava, Namita Gupta, Karuna Shanker, Mohammad Talha, Raj Kishori Lal, Birendra Kumar, Anil Kumar Gupta
Summary: This study conducted extensive morphometric and chemometric mapping of natural populations of Cannabis in India, revealing a strong correlation between their genetic diversity and regional distribution. The findings provide a foundation for identifying and selecting lines with key agronomic traits for maximizing the potential of this promising crop.
INDUSTRIAL CROPS AND PRODUCTS
(2023)
Review
Ecology
Jolle W. Jolles
Summary: The field of biology has experienced significant technological advancement due to increasing processing power, high-level computing, and global information sharing. Low-cost single-board computers are expected to further revolutionize the field. The Raspberry Pi, a widely used single-board computer, has been increasingly adopted by biologists in various disciplines for a diverse range of applications, but its uptake by the scientific community remains limited. efforts to increase awareness and usage of the Raspberry Pi among scientists could help democratize science and advance biological understanding.
METHODS IN ECOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Lucas Busta, Ismail Dweikat, Shirley J. Sato, Haolin Qu, Yong Xue, Bangjun Zhou, Lu Gan, Bin Yu, Thomas E. Clemente, Edgar B. Cahoon, Chi Zhang
Summary: This study investigates the phytochemistry and genomics of feral Cannabis populations collected from Nebraska. It found that both male and female flower tissues produced cannabinoids, with cannabidiol being the primary cannabinoid. The expression of genes related to cannabinoid biosynthesis was higher in female flowers, suggesting transcriptional control of cannabinoid abundance. DNA sequencing revealed that the feral Cannabis plants from Nebraska are more similar to hemp-type Cannabis plants than drug-type plants. This research provides foundational knowledge for future studies of feral Nebraska Cannabis.
Article
Plant Sciences
Prakash Goudappa Patil, Shivani Jamma, N. Manjunatha, Abhishek Bohra, Somnath Pokhare, Karuppannan Dhinesh Babu, Ashutosh A. A. Murkute, Rajiv A. A. Marathe
Summary: This study conducted a survey of gene-based marker systems in the Tunisia genome, resulting in the development of a saturated linkage map and the identification of polymorphic markers. The genetic diversity of pomegranate genotypes was analyzed using these markers.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agricultural Engineering
Yash Pandey, Trishna Chaturvedi, Harsh Swaroop, Anil Kumar Gupta, Karuna Shanker, Gunjan Tiwari
Summary: The present study investigated the genetic diversity among wild cannabis accessions in the North Indian Himalayas using phytochemical and molecular genotyping. Significant genetic differentiation was observed among the studied populations, and the major cannabinoids in Indian Cannabis sativa germplasm were identified. Results showed that SCoT and CBDP markers are ideal for studying the genetic relationship among geographically different populations of C.sativa, and highly diverse populations can be used in Indian cannabis breeding programs.
INDUSTRIAL CROPS AND PRODUCTS
(2023)
Article
Forestry
Clara Vega, Victoria Fernandez, Luis Gil, Maria Valbuena-Carabana
Summary: This study evaluates the clonal and fine-scale spatial genetic structure of English holly in a sub-Mediterranean mixed forest in central Spain. The results show high clonal diversity and strong fine-scale genetic structure in the dense coppiced area, while the open woody pasture area exhibits weaker structure. Current management strategies do not seem to negatively affect the genetic diversity of this species.
Article
Environmental Sciences
Bernardo Rocha, Paula Matos, Paolo Giordani, Lohmus Piret, Cristina Branquinho, Joan Casanelles-Abella, Cristiana Aleixo, Nicolas Deguines, Tiit Hallikma, Lauri Laanisto, Marco Moretti, Marta Alos Orti, Roeland Samsonj, Piotr Tryjanowski, Pedro Pinho
Summary: In order to create more resilient cities, it is important to understand the effects of global change drivers in urban areas. Previous studies have used lichens as ecological indicators to monitor these effects, but only in single-city studies. This study aimed to quantify the impact of broad-scale environmental drivers on lichen biodiversity-based metrics in an urban context, where local drivers also play a role. By sampling epiphytic lichens across a continental gradient, the researchers found that 15% of the variance in lichen metrics could be explained by broad-scale drivers, with air pollution showing more importance than climate. This suggests that further research is needed to understand the effects of climate change, and that both spatial scales should be considered when using lichens as ecological indicators in cities at continental to global scales.
ENVIRONMENTAL POLLUTION
(2022)
Article
Computer Science, Artificial Intelligence
Yuefang Gao, Zhen-Wei Huang, Zi-Yuan Huang, Ling Huang, Yingjie Kuang, Xiaojun Yang
Summary: Recently, neighborhood-based collaborative filtering has been used more and more in personalized recommender systems. However, the traditional approach of selecting a fixed number of nearest users/items as neighbors has limitations. To address this issue, a new recommender system called Multi-scale Broad Collaborative Filtering (MBCF) is proposed, which captures rich information from different numbers of nearest users/items. Instead of using deep neural networks (DNNs), the Broad Learning System (BLS) is adopted to learn the complex nonlinear relationships between users and items, achieving satisfactory recommendation performance while avoiding overfitting. Extensive experiments on eight benchmark datasets demonstrate the effectiveness of the proposed MBCF algorithm.
KNOWLEDGE-BASED SYSTEMS
(2023)
Article
Plant Sciences
Daniela Vergara, Ezra L. Huscher, Kyle G. Keepers, Rahul Pisupati, Anna L. Schwabe, Mitchell E. McGlaughlin, Nolan C. Kane
Summary: The Cannabis varieties produced by the National Institute on Drug Abuse (NIDA) lack diversity and potency compared to commercially produced Cannabis, and are genetically divergent from those in the private legal market. Research results based on NIDA's varieties are not generalizable due to their lack of diversity in various aspects of the genome, hindering scientific investigation into the effects of Cannabis after consumption.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Jackson M. J. Oultram, Joseph L. Pegler, Greg M. Symons, Timothy A. Bowser, Andrew L. Eamens, Christopher P. L. Grof, Darren J. Korbie
Summary: This study assessed the genetic diversity of 10 Cannabis varieties through reduced representation shotgun sequencing, providing fundamental knowledge for the development of the pharmaceutical and recreational markets. The analysis identified 172 SNPs associated with genetic structure, which could be used to design a targeted resequencing panel for screening genetic relationships and scientific classification of Cannabis plants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Genetics & Heredity
Olfa Saddoud Debbabi, Sameh Rahmani Mnasri, Fathi Ben Amar, M'barek Ben Naceur, Cinzia Montemurro, Monica Marilena Miazzi
Summary: Tunisia, located at the crossroad of the Mediterranean Basin, has been a strategic place for gene flow of olive species. Simple Sequence Repeats (SSRs) have been used to study the genetic diversity of olive crops, identify interesting genotypes, and prepare for challenges brought by climate changes.
Article
Agronomy
Chaymae Benkirane, Majida Charif, Christina M. Mueller, Yassine Taaifi, Farid Mansouri, Mohamed Addi, Mohammed Bellaoui, Hana Serghini-Caid, Ahmed Elamrani, Malika Abid
Summary: This study assessed the genetic diversity of cannabis in four regions of Morocco and found that the local Beldia population has high genetic diversity compared to the introduced Critical cultivar. The study also revealed gene flow between the two populations and emphasized the need for conservation strategies to protect the local genetic heritage of Morocco.
GENETIC RESOURCES AND CROP EVOLUTION
(2023)
Article
Biotechnology & Applied Microbiology
Yisong Li, Zhong-Zhi Sun, Jin-Cheng Rong, Bin-Bin Xie
Summary: The study revealed high intraspecies genomic diversity of M. luteus and highlighted that gene gain/loss events and extensive recombination events played key roles in the genome evolution. As a free-living species, some lineages have recently developed or are developing a mammal-associated lifestyle.
Article
Ecology
Evan Kopsala, Christopher Kyle, Eric Howe, Derek Potter, Kaela Beauclerc, Joseph M. Northrup
Summary: Characterizing patterns and drivers of dispersal is crucial for understanding animal ecology and informing conservation strategies. In this study, microsatellite data from 3941 black bears in 73 sampling areas were used to characterize dispersal through gene flow. Spatial models were fitted to investigate potential drivers of dispersal patterns. The results suggested positive density-dependent dispersal with a male bias, and a relationship between dispersal and food productivity gradients. These findings provide valuable insights into the drivers of dispersal in a wide-ranging mammal.
Article
Biotechnology & Applied Microbiology
Balnd M. Albarzinji, Farhad M. Abdulkarim, Shaho A. Hussein, Dlshad Rashid, Hayder Lazim
Summary: This study investigates the population relationship of the Sorani Kurdish population in Sulaymaniyah province using DNA samples. The results show that the J2 subclade predominates in this population, and they cluster with Asian populations while being furthest from European and African populations.
Article
Biodiversity Conservation
G. Yannic, V Helfer, R. Sermier, B. R. Schmidt, L. Fumagalli
Summary: Delineating population boundaries in anthropogenic landscapes is crucial for biology domains focusing on ecology, evolution, and conservation. This task is particularly challenging for amphibian species reproducing in aquatic habitats but living in terrestrial habitats, highlighting the difficulty of defining management units in open systems.
CONSERVATION GENETICS
(2021)
Article
Multidisciplinary Sciences
Judith Schneider, Eduard Mas-Carrio, Catherine Jan, Christian Miquel, Pierre Taberlet, Katarzyna Michaud, Luca Fumagalli
Summary: Stomach content analyses are a valuable tool in human forensic science to interpret perimortem events. DNA metabarcoding has the potential to increase sensitivity and taxonomic resolution in identifying food components. This pilot study applied DNA metabarcoding to assess plant and vertebrate components of human stomach content samples, showing promising perspectives for biomedical dietary surveys.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Christophe Dufresnes, Alan Brelsford, Daniel L. Jeffries, Glib Mazepa, Tomasz Suchan, Daniele Canestrelli, Alfredo Nicieza, Luca Fumagalli, Sylvain Dubey, Inigo Martinez-Solano, Spartak N. Litvinchuk, Miguel Vences, Nicolas Perrin, Pierre-Andre Crochet
Summary: Research on frog and toad hybrid zones suggests that as lineages diverge, parts of the genome resist introgression, indicating that anuran speciation involves the gradual accumulation of multiple barrier loci scattered across the genome. This highly polygenic nature of reproductive isolation, along with the lack of hemizygous sex chromosomes, may explain the slower speciation clock in amphibians compared to other vertebrates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Guangpeng Ren, Xu Zhang, Ying Li, Kate Ridout, Martha L. Serrano-Serrano, Yongzhi Yang, Ai Liu, Gudasalamani Ravikanth, Muhammad Ali Nawaz, Abdul Samad Mumtaz, Nicolas Salamin, Luca Fumagalli
Summary: The study reveals the domestication history of Cannabis sativa, indicating that it was first domesticated in early Neolithic times in East Asia, and that both hemp and drug cultivars diverged from an ancestral gene pool in China. Candidate genes associated with traits differentiating hemp and drug cultivars were identified, as well as evidence for loss of function of genes involved in cannabinoid synthesis during selection.
Article
Ecology
Qian S. Zhang, Jerome Goudet, Bruce S. Weir
Summary: Inbreeding estimators that rely on sample allele frequencies as estimates are influenced by pedigrees and the reference population, while allele-sharing estimators provide consistent rankings across all studies and individuals, particularly with a large number of SNPs.
Article
Biochemistry & Molecular Biology
Tristan Cumer, Ana Paula Machado, Guillaume Dumont, Vasileios Bontzorlos, Renato Ceccherelli, Motti Charter, Klaus Dichmann, Nicolaos Kassinis, Rui Lourenco, Francesca Manzia, Hans-Dieter Martens, Laure Prevost, Marko Rakovic, Ines Roque, Felipe Siverio, Alexandre Roulin, Jerome Goudet
Summary: The complex history of barn owl populations across the Western Palearctic region reveals the impact of climatic variations and landscape barriers on the splitting and evolution of populations. The study identifies two distinct lineages colonizing Europe and the Levant before the last glaciation, with a secondary contact zone in Anatolia. Additionally, it shows that barn owls recolonized Europe from two glacial refugia in Iberia and Italy, with communication between the glacial lineages now occurring via eastern Europe.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Ana Paula Machado, Alexandros Topaloudis, Tristan Cumer, Eleonore Lavanchy, Vasileios Bontzorlos, Renato Ceccherelli, Motti Charter, Nicolaos Kassinis, Petros Lymberakis, Francesca Manzia, Anne-Lyse Ducrest, Melanie Dupasquier, Nicolas Guex, Alexandre Roulin, Jerome Goudet
Summary: The study of insular populations is crucial for the development of evolutionary theory, as successful colonization of an island is influenced by various factors. This study on barn owls from Crete and Cyprus revealed that these populations have distinct genetic characteristics and demographic histories. The research provides empirical evidence for the impact of stochastic processes on isolated populations in island-mainland systems.
Article
Biochemistry & Molecular Biology
Ana Paula Machado, Tristan Cumer, Christian Iseli, Emmanuel Beaudoing, Anne-Lyse Ducrest, Melanie Dupasquier, Nicolas Guex, Klaus Dichmann, Rui Lourenco, John Lusby, Hans-Dieter Martens, Laure Prevost, David Ramsden, Alexandre Roulin, Jerome Goudet
Summary: Research suggests that barn owls colonized the British Isles directly from a white-colored refugium in the Iberian Peninsula after the last glaciation, rather than crossing over Doggerland as previously believed. They maintained their white color in the British Isles through low gene flow with the mainland, suggesting neutral processes rather than selection for the contrasting color. This unexpected colonization route may have implications for other species from the paleo community as well.
Article
Biology
Andre Silva Marostica, Kelly Nunes, Erick C. Castelli, Nayane S. B. Silva, Bruce S. Weir, Jerome Goudet, Diogo Meyer
Summary: In his 1972 paper 'The apportionment of human diversity', Lewontin demonstrated that genetic diversity is mainly attributed to differences within populations. However, selection can affect diversity of specific genes or genomic regions. This study focuses on genetic diversity at the human leucocyte antigen (HLA) loci, which play a critical role in adaptive immunity. The findings show balancing selection on HLA genes over large timescales, as indicated by low F-ST values. However, when analyzing HLA alleles defined by single-nucleotide polymorphisms (SNPs), significant frequency differences between geographic regions are observed. These differences have implications for bone marrow transplantation, particularly in regions with a deficit of donors matching MHC region of African ancestry, as seen in Brazil's bone marrow registry.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Ecology
Tristan Cumer, Ana Paula Machado, Felipe Siverio, Sidi Imad Cherkaoui, Ines Roque, Rui Lourenco, Motti Charter, Alexandre Roulin, Jerome Goudet
Summary: Islands and the organisms that inhabit them have long been of interest to biologists. The Canary Islands, with its endemic species, is a unique location to study the effect of neutral and adaptive mechanisms on genomic and phenotypical divergence. By analyzing the genomes of barn owls in the Canaries, researchers have identified genetic markers associated with adaptation to insular environments, such as body proportions and blood pressure in the eastern islands, and hypoxia in the western islands. These findings highlight the interplay between neutral and adaptive forces in shaping divergence and early speciation.
Article
Ecology
Loic Brun, Judith Schneider, Eduard Mas Carrio, Pooja Dongre, Pierre Taberlet, Erica van de Waal, Luca Fumagalli
Summary: Assessing the diet of wild animals is crucial for understanding their ecology and trophic relationships. This study compares two methods (environmental DNA and observations) and finds that DNA metabarcoding has higher taxonomic coverage and resolution. Seasonality has a significant effect on plant and arthropod consumption, and vervet monkeys adapt their diet according to available resources.
ECOLOGY AND EVOLUTION
(2022)
Review
Biodiversity Conservation
P. J. Stephenson, Maria Cecilia Londono-Murcia, Paulo A. Borges, Louw Claassens, Heidrun Frisch-Nwakanma, Nicholas Ling, Sapphire McMullan-Fisher, Jessica J. Meeuwig, Kerrigan Marie Machado Unter, Judith L. Walls, Ian J. Burfield, Danilo do Carmo Vieira Correa, Gary N. Geller, Irina Montenegro Paredes, Leonard K. Mubalama, Yaa Ntiamoa-Baidu, Ignacio Roesler, Francesco Rovero, Yash Pal Sharma, Nara Wisesa Wiwardhana, Jun Yang, Luca Fumagalli
Summary: This article reviews the importance of enhancing biodiversity monitoring, assesses the challenges involved, and identifies potential solutions. It highlights the urgent need to strengthen capacity for biodiversity monitoring, especially in poorer, high-biodiversity countries where data gaps are significant. The article also emphasizes the use of modern tools and technologies to fill taxonomic and geographic data gaps, and the importance of stakeholders adopting best monitoring practices, making data openly available, and companies investing in collecting necessary data for sustainability.
Article
Biodiversity Conservation
Ines Moreno, Jerome Marcel Walter Gippet, Luca Fumagalli, P. J. Stephenson
Summary: Understanding the availability and biases of species data is crucial for effective conservation decision-making. This study conducted a case study in East Africa to evaluate data biases, factors influencing data availability, and the consequences for conservation. The results showed that data on vertebrates were more available than invertebrates, and countries with higher tourism income had more priority species and more species with data. The main challenges to data accessibility were high expenses, technological challenges, and a lack of resources for data processing and analysis.
BIODIVERSITY AND CONSERVATION
(2023)
Article
Biochemistry & Molecular Biology
Eleonore Lavanchy, Jerome Goudet
Summary: Genomic measures of inbreeding based on IBD segments are widely used but often rely on assumptions that can affect the accuracy of estimation. In this study, we simulated data from different genomic representations and compared the performance of two software programs for estimating IBD segments. We found that the density of SNPs required for accurate estimation varied between the two programs and was influenced by the demographic history of the population. We recommend researchers consider the specific characteristics of their data and choose the appropriate method for inbreeding estimation.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Multidisciplinary Sciences
Christophe Dufresnes, Ludovic Dutoit, Alan Brelsford, Fardo Goldstein-Witsenburg, Laura Clement, Adria Lopez-Baucells, Jorge Palmeirim, Igor Pavlinic, Dino Scaravelli, Martin Sevcik, Philippe Christe, Jerome Goudet
Summary: Traditional genotyping methods are limited in quantifying genetic diversity and structure, while next-generation sequencing has not been properly tested in highly mobile species. This study compared microsatellite and RAD-sequencing analyses in investigating population structure in the declining bent-winged bat across Europe. The results show that microsatellites were not informative in individual-based analyses, but genomic SNPs provided resolution on regional substructures and confirmed suspicions of philopatry and spatial partitioning in the species.
SCIENTIFIC REPORTS
(2023)
