Article
Agronomy
Tesfakiros Semere, Siri Fjellheim, Yemane Tsehaye, Ola T. Westengen
Summary: This study aimed to inventory and assess the richness of sorghum landraces, estimate phenotypic diversity, identify race types, and predict suitable production areas based on future climate scenarios in Tigray, Northern Ethiopia. A total of 358 landraces were surveyed from 125 independent farmers' fields in 20 districts. Landraces richness, frequency of character states, and diversity levels were estimated using different indices for each zone and altitude class. Potential sites for germplasm conservation and utilization were identified in the lowlands of northwest, central, and southern zones. The study also found that all currently surveyed areas and many others in Tigray are predicted to be suitable for future sorghum production under changing climate scenarios.
GENETIC RESOURCES AND CROP EVOLUTION
(2023)
Article
Agronomy
Savannah N. Phipps, Adrienne B. Burke, Kerry Balow, Jared Smith, Timothy Murray, Arron H. Carter
Summary: This study investigated snow mold tolerance in winter wheat by analyzing a doubled haploid population derived from a cross between the Japanese variety PI 173438 and the susceptible variety WA 8137. Six quantitative trait loci (QTL) associated with snow mold tolerance were identified, with one QTL on chromosome 1D being previously unreported. Marker-assisted selection (MAS) testing showed no significant difference among the tested QTL and linked markers in separate populations. These findings highlight the complexity of breeding for snow mold tolerance using molecular markers.
Article
Biochemistry & Molecular Biology
Johanna Sunde, Yeserin Yildirim, Petter Tibblin, Dorte Bekkevold, Christian Skov, Oscar Nordahl, Per Larsson, Anders Forsman
Summary: Understanding the relative effects of isolation by distance, environment, and resistance on neutral and adaptive genetic diversity is crucial for biodiversity protection. Studies show that different modes of isolation interactively shape genetic variation patterns, with neutral variation influenced by all three modes and adaptive variation mainly influenced by environmental conditions.
Review
Biodiversity Conservation
Cassandre C. Venumiere-Lefebvre, Stewart W. Breck, Kevin R. Crooks
Summary: This study provides a global perspective on human-carnivore coexistence by analyzing literature published between 1987 and 2020. It found that the term coexistence is often used without a clear definition, with a focus on carnivore ecology and a lack of attention to social conflict. The study also revealed the dominance of European and North American authors and a bias towards larger carnivores. The authors propose a simplified definition of coexistence and encourage researchers to explore the social dimensions and broaden their study scope.
BIOLOGICAL CONSERVATION
(2022)
Article
Computer Science, Artificial Intelligence
Pei Huang, Zhaoming Kong, Mengying Xie, Xiaowei Yang
Summary: This paper proposes a robust unsupervised feature selection method that can effectively deal with the influence of many outliers on model performance. By learning a robust subspace that preserves local structure and addressing the shortcomings of traditional methods through outlier removal and Euclidean distance threshold setting, the superiority of the proposed method is demonstrated through experiments.
PATTERN RECOGNITION
(2023)
Article
Plant Sciences
Yosr Ferchichi, Anis Sakhraoui, Hela Belhaj Ltaeif, Yosr Ben Mhara, Mohamed Elimem, M'barek Ben Naceur, Zeineb Ghrabi-Gammar, Slim Rouz
Summary: This study conducted extensive prospecting missions to characterize and conserve the endemic pastoral species Medicago tunetana in Tunisia. By studying eco-geographical and morphological traits, as well as conducting molecular analysis using SSR markers, the research identified high levels of polymorphism and genetic diversity in the M. tunetana populations. Furthermore, differences and similarities among populations were discovered, providing valuable information for effective conservation programs for this perennial endemic plant species.
Article
Biochemistry & Molecular Biology
Gaston I. Jofre, Gil G. Rosenthal
Summary: The study evaluates the robustness of geographic cline analysis under different evolutionary scenarios using simulations. It found that drift can distort cline shapes and increase false positive rates for signatures of selection, particularly in older hybrid zones with low migration rates. The results suggest that geographic clines are most useful for outlier analysis in young hybrid zones with large populations of hybrid individuals.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Biochemistry & Molecular Biology
Deborah M. Leigh, Heidi E. L. Lischer, Frederic Guillaume, Christine Grossen, Torsten Gunther
Summary: Identifying local adaptation in bottlenecked species is crucial, and methods for detecting selection play an important role in species management and response to climate change. However, distinguishing selection signals from genetic drift in bottlenecked populations is challenging. This study used simulations to evaluate the accuracy of selection detection methods in Alpine ibex populations, finding high false positive rates but improved accuracy when combining multiple methods.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Mathematics
Jorge R. Sosa Donoso, Miguel Flores, Salvador Naya, Javier Tarrio-Saavedra
Summary: This work presents a methodology for detecting outliers in functional data that considers both their shape and magnitude. The Local Correlation Integral (LOCI) method, a multivariate anomaly detection technique, has been extended and adapted for functional data using distance calculations in Hilbert spaces. The methodology has been validated through simulation studies and application to real data, showing good performance in scenarios with inter-curve dependence, particularly when outliers are due to curve magnitudes. Results are further supported by the successful application of the methodology to a meteorological database, outperforming other competitive methods.
Article
Biodiversity Conservation
Helina Jolly, Terre Satterfield, Milind Kandlikar, T. R. Suma
Summary: As human-wildlife conflicts intensify, the importance of tolerance and acceptance of wildlife is increasingly emphasized. However, current conservation studies lack a comprehensive understanding of positive interactions between humans and animals, resulting in potentially inaccurate portrayals of human-animal encounters. This study explores Indigenous perspectives on human-wildlife coexistence in India by examining the viewpoints of the Kattunayakans, a forest-dwelling Adivasi community. The findings reveal that the Kattunayakans demonstrate tolerance and acceptance of wild animals, highlighting three central ideas: seeing wild animals as rational beings capable of communication, perceiving them as gods, teachers, and equals, and recognizing them as relatives with shared origins practicing dharmam. It is argued that incorporating these perspectives can enhance forest management in India and contribute to resolving human-wildlife conflicts more effectively.
CONSERVATION BIOLOGY
(2022)
Article
Biodiversity Conservation
Lorenzo Raggi, Luca C. Pacicco, Leonardo Caproni, Clara Alvarez-Muniz, Kulli Annamaa, Ana M. Barata, Diana Batir-Rusu, Maria J. Diez, Maarit Heinonen, Vojtech Holubec, Shelagh Kell, Hrvoje Kutnjak, Helene Maierhofer, Gert Poulsen, Jaime Prohens, Parthenopi Ralli, Filomena Rocha, Maria L. Rubio Teso, Dan Sandru, Pietro Santamaria, Sarah Sensen, Olivia Shoemark, Salvador Soler, Silvia Strajeru, Imke Thormann, Jens Weibull, Nigel Maxted, Valeria Negri
Summary: Over the past century, the switch from landraces to modern high yielding varieties in Europe has led to a significant reduction in crop diversity. However, a recent study has collected information on over 19,000 geo-referenced landrace cultivation sites from 14 European countries, highlighting the cultivation of 141 herbaceous and 48 tree species across the continent. Italy, Greece, Portugal, and Spain have the highest number of landrace species cultivated.
BIOLOGICAL CONSERVATION
(2022)
Article
Multidisciplinary Sciences
Jesse S. Turiel, Robert K. Kaufmann
Summary: This study compares PM2.5 measurements from government-controlled and U.S. embassy-controlled monitoring stations in Chinese cities and finds that local government systematically under-reports pollution levels when air quality is poor. The results contradict previous studies and suggest that Chinese air quality data may not be entirely reliable.
Article
Biochemical Research Methods
Rayol Mendonca-Neto, Zhi Li, David Fenyo, Claudio T. Silva, Fabiola G. Nakamura, Eduardo F. Nakamura
Summary: Breast cancer, the second most common cancer type, is the leading cause of cancer-related deaths worldwide. Gene selection is an effective approach to classify breast cancer subtypes and improve the performance of classifiers.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Computer Science, Artificial Intelligence
Aleksei Liuliakov, Luca Hermes, Barbara Hammer
Summary: Automated machine learning technologies aim to automate the selection of meta-parameters and components of machine learning training pipelines. Most current approaches focus on a single objective, neglecting the trade-off between accuracy and sparsity. This paper proposes an iterative pipeline that combines AutoML with feature selection to explore the full Pareto-front of sparse and accurate models.
APPLIED SOFT COMPUTING
(2023)
Article
Genetics & Heredity
Miriam Ruocco, Marlene Jahnke, Joao Silva, Gabriele Procaccini, Emanuela Dattolo
Summary: Plant populations of seagrass Cymodocea nodosa along a latitudinal gradient show patterns of clinal variation in genotype and phenotype, influenced by differences in photoperiod and temperature cues. The study identified potential outlier loci related to adaptive differentiation across latitudes, with some SNPs associated to specific protein-coding genes and biological processes enriched in regulation of transcription and signalling. The results suggest the importance of gene-regulatory networks and epigenetic regulation for enabling adaptation of seagrass populations along environmental gradients.
FRONTIERS IN GENETICS
(2022)
Article
Plant Sciences
Nicole Moreira Veto, Dragos Postolache, Frank L. Guzman Escudero, Elia Vajana, Ricardo Burgo Braga, Fabiano Salgueiro, Rogerio Margis, Giovanni G. Vendramin, Andreia C. Turchetto-Zolet
Summary: This study investigates population genetic structure and adaptive genetic diversity in Eugenia uniflora, a tropical tree species. The study finds spatial population structuring and higher genetic diversity in southern populations. It also identifies candidate loci potentially involved in local adaptation.
BOTANICAL JOURNAL OF THE LINNEAN SOCIETY
(2023)
Article
Evolutionary Biology
Azalea Guerra-Garcia, Idalia C. Rojas-Barrera, Jeffrey Ross-Ibarra, Roberto Papa, Daniel Pinero
Summary: This study investigates the domestication history and genetic diversity of scarlet runner beans, finding that introgression from wild relatives plays a key role in increasing the genetic diversity of cultivated populations. Domesticated varieties experienced a severe genetic bottleneck, but later recovered and showed evidence of introgression from wild populations.
Article
Biochemistry & Molecular Biology
Ivan Scotti, Hadrien Lalague, Sylvie Oddou-Muratorio, Caroline Scotti-Saintagne, Rose Ruiz Daniels, Delphine Grivet, Francois Lefevre, Philippe Cubry, Bruno Fady, Santiago C. Gonzalez-Martinez, Anne Roig, Isabelle Lesur-Kupin, Francesca Bagnoli, Vanina Guerin, Christophe Plomion, Philippe Rozenberg, Giovanni G. Vendramin
Summary: Microgeographical adaptation occurs when directional selection persists despite gene flow. This study investigates the patterns of genomic divergence in four European and Mediterranean conifers with different life-history traits and ecological requirements. The results show that selection is strong in all species but affects different loci in each. Within-population diversity at microgeographical scales is likely to be a reservoir of adaptive potential.
Article
Ecology
Felix Gugerli, Sabine Brodbeck, Bertalan Lendvay, Benjamin Dauphin, Francesca Bagnoli, Willem O. van Der Knaap, Willy Tinner, Maria Hohn, Giovanni G. Vendramin, Cesar Morales-Molino, Christoph Schworer
Summary: The study aimed to understand the historical climate shifts and their impact on Pinus cembra. The research combined genetic structure and palaeoecological findings to identify putative refugia and re-colonisation routes. The results suggest that P. cembra survived the Last Glacial Maximum in southern regions and expanded into its current range during the Late Glacial.
JOURNAL OF BIOGEOGRAPHY
(2023)
Article
Plant Sciences
Mustafa Bulut, Regina Wendenburg, Elena Bitocchi, Elisa Bellucci, Magdalena Kroc, Tania Gioia, Karolina Susek, Roberto Papa, Alisdair R. Fernie, Saleh Alseekh
Summary: This article assesses the metabolic diversity in five common legume species grown in Europe using gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS). Over 3400 metabolites were detected and quantified, including major nutritional and anti-nutritional compounds. The data generated will be valuable for metabolomics-assisted crop breeding and metabolite-based genome-wide association studies in legume species.
Article
Plant Sciences
Leonardo Perez de Souza, Elena Bitocchi, Roberto Papa, Takayuki Tohge, Alisdair R. Fernie
Summary: The process of crop domestication leads to a reduction in gene expression associated with metabolic diversity, particularly in genes involved in specialized metabolism. The reduction in diversity at the metabolite level has been assumed but never adequately assessed and quantified. This study used high coverage metabolomics to investigate metabolic diversity in common bean and found a shift towards lower diversity and specialization in domesticated bean accessions. Molecular networking analysis enabled a broader annotation of metabolites and revealed a metabolic shift from specialized metabolism to central metabolism upon domestication of this crop.
Article
Multidisciplinary Sciences
Elisa Bellucci, Andrea Benazzo, Chunming Xu, Elena Bitocchi, Monica Rodriguez, Saleh Alseekh, Valerio Di Vittori, Tania Gioia, Kerstin Neumann, Gaia Cortinovis, Giulia Frascarelli, Ester Murube, Emiliano Trucchi, Laura Nanni, Andrea Ariani, Giuseppina Logozzo, Jin Hee Shin, Chaochih Liu, Liang Jiang, Juan Jose Ferreira, Ana Campa, Giovanna Attene, Peter L. Morrell, Giorgio Bertorelle, Andreas Graner, Paul Gepts, Alisdair R. Fernie, Scott A. Jackson, Roberto Papa
Summary: A study reveals that the first common bean cultigens introduced in Europe after 1492 were of Andean origin and that hybridization, selection, and recombination played a role in shaping the genomic diversity of the European common bean. The study also highlights the adaptive introgression and selection of genes related to flowering and environmental adaptation in the process of disseminating this tropical crop to temperate Europe.
NATURE COMMUNICATIONS
(2023)
Article
Horticulture
Valeria Menga, Clara Fares, Ana Campa, Juan Jose Ferreira, Elena Bitocchi, Roberto Papa, Romina Beleggia
Summary: A study characterized 54 snap bean lines grown under organic farming for various traits and grouped them based on pod cross-section shape and color. Significant differences were observed among lines and groups for all the investigated traits. The phenolic composition and antioxidant activity of selected lines with contrasting firmness and belonging to different color groups were investigated, revealing a general decrease in some compounds after cooking. The study provides useful information for designing specific varieties for different markets and purposes.
Review
Plant Sciences
Simone Papalini, Valerio Di Vittori, Alice Pieri, Marina Allegrezza, Giulia Frascarelli, Laura Nanni, Elena Bitocchi, Elisa Bellucci, Tania Gioia, Luis Guasch Pereira, Karolina Susek, Maud Tenaillon, Kerstin Neumann, Roberto Papa
Summary: Paleogenomics focuses on the recovery, manipulation, and analysis of ancient DNA to reconstruct and analyze genomes. Herbarium collections provide valuable information for studying the taxonomy, phenotypic traits, and evolution of plants. However, the utilization of herbarium specimens for ancient DNA analysis still requires improvements due to challenges such as degradation and contamination.
Article
Plant Sciences
Madita Lauterberg, Henning Tschiersch, Roberto Papa, Elena Bitocchi, Kerstin Neumann
Summary: Precise and high-throughput phenotyping allows for improved screening of chickpea plant genetic resources with low biomass loss and reliable physiological performance. This can provide insights into drought tolerance and recovery mechanisms.
Article
Forestry
Sanna Olsson, Guia Giovannelli, Anne Roig, Ilaria Spanu, Giovanni Giuseppe Vendramin, Bruno Fady
Summary: Using the subsection Pinus as an example, this study explains the issue of weak support in phylogenetic studies of closely related pine species and suggests that popular genetic markers are not recommended for species identification purposes in European pines.
IFOREST-BIOGEOSCIENCES AND FORESTRY
(2022)