Article
Environmental Sciences
Miguel Baltazar-Soares, Andre R. A. Lima, Goncalo Silva, Elie Gaget
Summary: The introduction of genomic resources in fisheries management has enhanced our understanding of stock dynamics by adding a temporal point of view. By integrating genomic information with temporal projections from Species Distribution Models (SDMs), we can inform about potential future range expansions, contractions, and suitable habitats for fish stocks based on their evolutionary potential. This framework combines the advantages of SDMs and genomic data to improve forecasting ability in fisheries management.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Multidisciplinary Sciences
William R. Shoemaker, Stuart E. Jones, Mario E. Muscarella, Megan G. Behringer, Brent K. Lehmkuhl, Jay T. Lennon
Summary: Research shows that under limited resources, most bacterial taxa can survive, with a wide range of extinction times. Despite the lack of exogenous resources, bacterial populations continue to evolve and acquire numerous mutations. While adapting to environmental pressures, bacterial lifespan is extended through scavenging dead cells.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Ecology
Alberto Jimenez-Valverde, Pedro Aragon, Jorge M. Lobo
Summary: Estimating local suitability with species distribution models (SDMs) can indicate the maximum abundance attainable by species, but the abundance-suitability relationship is typically wedge-shaped. The shape of this relationship is directly related to maximum abundance and is influenced by SDM quality and species prevalence.
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2021)
Article
Biochemistry & Molecular Biology
Song Cao, Chen Shi, Bing Wang, Peng Xiu, Yong Wang, Yang Liu, Guirong Wang
Summary: Male moths use pheromone communication systems to distinguish potential mates from other species, contributing to reproductive isolation and speciation. This study identified key amino acids controlling substrate selectivity of pheromone receptors and elucidated the molecular mechanism of diversification in pheromone recognition systems through molecular dynamics simulations and functional analysis.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Article
Ecology
Francis K. C. Hui, David I. Warton, Scott D. Foster, Christopher R. Haak
Summary: We introduce community-level basis function models (CBFMs) as an approach for spatiotemporal joint distribution modelling. CBFMs can be viewed as related to spatiotemporal latent variable models, where the latent variables are replaced by a set of pre-specified spatiotemporal basis functions which are common across species. CBFMs can be used for a variety of reasons, such as inferring patterns of habitat use in space and time, understanding how residual covariation between species varies spatially and/or temporally, and spatiotemporal predictions of species-and community-level quantities.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Biodiversity Conservation
David J. Baker, Ilya M. D. Maclean, Martin Goodall, Kevin J. Gaston
Summary: Legislation often requires mitigation of biodiversity impacts in planning and development processes, but lack of knowledge about priority species distributions undermines protections. Integrating species distribution modelling frameworks into ecological impact assessments can enhance biodiversity protection in planning and development processes.
JOURNAL OF APPLIED ECOLOGY
(2021)
Article
Ecology
Savvas Zotos, Marilena Stamatiou, Ioannis N. Vogiatzakis
Summary: Improving knowledge on species distribution is crucial for species conservation and management. This study uses species distribution models to predict the distribution of the Cyprus grass snake, an elusive species. The results significantly improve previous estimations and provide new perspectives on the species ecology and conservation.
ECOLOGICAL INFORMATICS
(2022)
Article
Ecology
Martin Jung
Summary: Most knowledge about species and habitats is not evenly distributed and biased in space, time, and taxonomic and functional knowledge. However, there is a large amount of biodiversity data available. The challenge is to effectively integrate the various sources of data, especially for species distribution models, in order to accurately address global challenges. This paper presents a modeling framework that integrates different data sources and introduces innovative concepts for creating more realistic and constrained spatial predictions. The ibis.iSDM R-package provides convenience functions and supports parameter transformations, data preparation, spatial-temporal projections, and ecological constraints.
ECOLOGICAL INFORMATICS
(2023)
Article
Ecology
Lan Jiang, Yu Chen, De Bi, Yunpeng Cao, Jiucui Tong
Summary: WRKY I genes are identified in seven Rosaceae species, with selective expansion in Chinese pear and apple. Analysis of gene microsynteny reveals more WRKY I-containing segments in P. bretschneideri and M. domestica genomes. Strong purifying selection on WRKY domains contributes to stability of structure and function. Functional redundancy of duplicated PbWRKY genes suggests evolution from common ancestry and neo-functionalization or sub-functionalization. The study provides insight into WRKY I gene evolution in Rosaceae genomes and suggests gene loss and gain rates are not in equilibrium.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Lu Gong, Xiaoxia Ding, Wan Guan, Danchun Zhang, Jing Zhang, Junqi Bai, Wen Xu, Juan Huang, Xiaohui Qiu, Xiasheng Zheng, Danyan Zhang, Shijie Li, Zhihai Huang, He Su
Summary: This study sequenced and analyzed the complete chloroplast genomes of three species in genus Amomum, identifying genetic markers for species identification and evolutionary analysis. The findings revealed a natural hybridization event in A. villosum and provided insights into the evolutionary relationships within the genus.
Article
Biodiversity Conservation
Owen G. Osborne, Henry G. Fell, Hannah Atkins, Jan van Tol, Daniel Phillips, Leonel Herrera-Alsina, Poppy Mynard, Greta Bocedi, Cecile Gubry-Rangin, Lesley T. Lancaster, Simon Creer, Meis Nangoy, Fahri Fahri, Pungki Lupiyaningdyah, I. Made Sudiana, Berry Juliandi, Justin M. J. Travis, Alexander S. T. Papadopulos, Adam C. Algar
Summary: This study introduces an algorithm for generating simulated species occurrence points that mimic the spatial structure of real datasets, applicable to any geographic domain and any number of species. Testing reveals that many species distribution models may fit well with the data but are not significantly better than null expectations, with few cases of high niche divergence.
Article
Biochemistry & Molecular Biology
Sally C. Y. Lau, Jan M. Strugnell, Chester J. Sands, Catarina N. S. Silva, Nerida G. Wilson
Summary: Understanding the drivers of evolutionary innovation is crucial for understanding how evolutionary processes unfold. This study examined the Southern Ocean brittle stars and found that the species Ophionotus victoriae and O. hexactis are closely related with interspecific gene flow. Different refugia were identified for each species during the late Pleistocene, and gene flow was observed between different oceanic currents and local oceanographic regimes. A strong association was detected between outlier loci and salinity in O. hexactis, suggesting adaptation related to evolutionary innovations. These findings provide valuable insights into the drivers of innovation in the Southern Ocean fauna.
Article
Ecology
Shaykhah Aldossari, Dirk Husmeier, Jason Matthiopoulos
Summary: Predictive species distribution models (SDMs) are increasingly important in ecology, especially in the context of rapid environmental change. This study focuses on the Generalised Functional Response (GFR) framework, which formulates SDM coefficients as functions of habitat availability. The study proposes several refinements to the GFR approach, including the use of local radial basis functions (RBF) and ensemble approaches such as random forests (RFs) and extreme gradient boosting (XGBoost). The results indicate that these refined methods consistently outperform traditional SDMs and the original GFR model in terms of predictive performance.
ECOLOGICAL INFORMATICS
(2022)
Article
Plant Sciences
Jibin Miao, Perla Farhat, Wentao Wang, Markus Ruhsam, Richard Milne, Heng Yang, Sonam Tso, Jialiang Li, Jingjing Xu, Lars Opgenoorth, Georg Miehe, Kangshan Mao
Summary: This study explores the genetic variation, speciation, and demographic history of two narrow-endemic juniper species from the Qinghai-Tibet Plateau. The results show that the two species diverged in the late Pliocene and continued interspecific gene flow until the Last Glacial Maximum. Additionally, it highlights differences in habitat adaptation, genetic diversity, and genetic load between the two species.
Review
Biodiversity Conservation
Stefano Mammola, Julien Petillon, Axel Hacala, Jeremy Monsimet, Sapho-Lou Marti, Pedro Cardoso, Denis Lafage
Summary: Species distribution models are essential tools for ecologists to explore species distributions and answer questions related to biogeography, climate change, and conservation biology. Most studies focused on well-known organisms or charismatic and economically important arthropod species, with limited research on terrestrial arthropod predators. The use of SDMs in mapping the geography of arthropod predators is still in a nascent stage, with potential for future research using modern data sources and new modeling approaches.
DIVERSITY AND DISTRIBUTIONS
(2021)
Article
Zoology
H. Christoph Liedtke, John Lyakurwa, Lucinda P. Lawson, Michele Menegon, Marina Garrido-Priego, Jean Mariaux, Wilirk Ngalason, Alan Channing, Nisha R. Owen, Gabriela B. Bittencourt-Silva, Mark Wilkinson, Joanna G. Larson, Vaclav Gvozdik, Simon P. Loader
Summary: Records of biodiversity are crucial for assessing conservation priorities. However, there is a lack of baseline data for regions of key biodiversity importance. This study focuses on compiling and quantifying amphibian survey efforts in the Ukaguru Mountains in Tanzania over the past 30 years. The results show that although the total species numbers remain low compared to other Eastern Arc Mountains, the surveys frequently recorded new and endemic species. However, there are concerns about the declining population of some endemic species and the increasing deforestation rate in the region.
AFRICAN JOURNAL OF HERPETOLOGY
(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
Engineering, Environmental
Marco Salvatori, Valentina Oberosler, Margherita Rinaldi, Alessandro Franceschini, Stefania Truschi, Paolo Pedrini, Francesco Rovero
Summary: Outdoor recreation in natural areas is becoming more popular globally, but its long-term effects on wildlife are poorly understood. This study investigated whether tourism in the Dolomites, Italy, affected wild mammals in the long term and if it resulted in spatial or temporal avoidance. Camera trapping was used to detect mammal occurrences over seven summers at 60 consistently sampled sites. Overall, human presence increased over the 7-year period, but both community and species-level occurrences of mammals also increased. However, human activities caused temporal avoidance in the whole community and spatial avoidance in bigger-sized species.
Article
Multidisciplinary Sciences
Lucinda P. Lawson, Simon P. Loader, John V. Lyakurwa, H. Christoph Liedtke
Summary: The spiny-throated reed frog species group is a small radiation of Hyperolius frogs from East Africa. A genetic exploration was conducted to understand the distinctness and relationships of a new lineage found within this group. Through a reduced-representation genome-wide Single Nucleotide Polymorphism (SNP) dataset, the phylogenetic relationships were fully resolved, placing the new lineage as an early diverging lineage within the group.
Article
Multidisciplinary Sciences
Andrea F. Vallejo-Vargas, Douglas Sheil, Asuncion Semper-Pascual, Lydia Beaudrot, Jorge A. Ahumada, Emmanuel Akampurira, Robert Bitariho, Santiago Espinosa, Vittoria Estienne, Patrick A. Jansen, Charles Kayijamahe, Emanuel H. Martin, Marcela Guimaraes Moreira Lima, Badru Mugerwa, Francesco Rovero, Julia Salvador, Fernanda Santos, Wilson Roberto Spironello, Eustrate Uzabaho, Richard Bischof
Summary: This study examines the diel activity patterns of tropical mammals in protected forests across different biogeographic regions. The findings suggest that the activity of herbivores and insectivores is constrained by thermoregulation, while the activity of carnivores is influenced by bottom-up processes and the activity of small omnivores and insectivores is regulated by top-down processes. Overall, diel activity in tropical mammal communities is shaped by similar processes and constraints, reflecting body mass and trophic guilds.
NATURE COMMUNICATIONS
(2022)
Article
Ecology
Claudia Barelli, Valentina Oberosler, Nathalie Cavada, Arafat S. Mtui, Steven Shinyambala, Francesco Rovero
Summary: Anthropogenic activities have led to the loss of tropical forests, which poses a threat to global biodiversity and ecosystem services. Non-human primates, especially those targeted by hunting, have experienced a significant decline in population abundance and have struggled to recover even after receiving increased protection. However, other primate species have shown a slight increase in abundance with improved habitat protection. These findings highlight the species-specific vulnerability to anthropogenic disturbances and recovery patterns in primate populations.
Article
Plant Sciences
Iris Hordijk, Daniel S. Maynard, Simon P. Hart, Lidong Mo, Hans ter Steege, Jingjing Liang, Sergio de-Miguel, Gert-Jan Nabuurs, Peter B. Reich, Meinrad Abegg, C. Yves Adou Yao, Giorgio Alberti, Angelica M. Almeyda Zambrano, Braulio V. Alvarado, Alvarez-Davila Esteban, Patricia Alvarez-Loayza, Luciana F. Alves, Christian Ammer, Clara Anton-Fernandez, Alejandro Araujo-Murakami, Luzmila Arroyo, Valerio Avitabile, Gerardo A. Aymard C, Timothy Baker, Radomir Balazy, Olaf Banki, Jorcely Barroso, Meredith L. Bastian, Jean-Francois Bastin, Luca Birigazzi, Philippe Birnbaum, Robert Bitariho, Pascal Boeckx, Frans Bongers, Olivier Bouriaud, Pedro H. S. Brancalion, Susanne Brandl, Roel Brienen, Eben N. Broadbent, Helge Bruelheide, Filippo Bussotti, Roberto Cazzolla Gatti, Ricardo G. Cesar, Goran Cesljar, Robin Chazdon, Han Y. H. Chen, Chelsea Chisholm, Emil Cienciala, Connie J. Clark, David B. Clark, Gabriel Colletta, David Coomes, Fernando Cornejo Valverde, Jose J. Corral-Rivas, Philip Crim, Jonathan Cumming, Selvadurai Dayanandan, Andre L. de Gasper, Mathieu Decuyper, Geraldine Derroire, Ben DeVries, Ilija Djordjevic, Amaral Ieda, Aurelie Dourdain, Engone Obiang Nestor Laurier, Brian Enquist, Teresa Eyre, Adande Belarmain Fandohan, Tom M. Fayle, Leandro V. Ferreira, Ted R. Feldpausch, Leena Finer, Markus Fischer, Christine Fletcher, Lorenzo Frizzera, Javier G. P. Gamarra, Damiano Gianelle, Henry B. Glick, David Harris, Andrew Hector, Andrea Hemp, Geerten Hengeveld, Bruno Herault, John Herbohn, Annika Hillers, Euridice N. Honorio Coronado, Cang Hui, Hyunkook Cho, Thomas Ibanez, Il Bin Jung, Nobuo Imai, Andrzej M. Jagodzinski, Bogdan Jaroszewicz, Vivian Johanssen, Carlos A. Joly, Tommaso Jucker, Viktor Karminov, Kuswata Kartawinata, Elizabeth Kearsley, David Kenfack, Deborah Kennard, Sebastian Kepfer-Rojas, Gunnar Keppel, Mohammed Latif Khan, Timothy Killeen, Hyun Seok Kim, Kanehiro Kitayama, Michael Koehl, Henn Korjus, Florian Kraxner, Diana Laarmann, Mait Lang, Simon Lewis, Huicu Lu, Natalia Lukina, Brian Maitner, Yadvinder Malhi, Eric Marcon, Beatriz Schwantes Marimon, Ben Hur Marimon-Junior, Andrew Robert Marshall, Emanuel Martin, Olga Martynenko, Jorge A. Meave, Omar Melo-Cruz, Casimiro Mendoza, Cory Merow, Miscicki Stanislaw, Abel Monteagudo Mendoza, Vanessa Moreno, Sharif A. Mukul, Philip Mundhenk, Maria G. Nava-Miranda, David Neill, Victor Neldner, Radovan Nevenic, Michael Ngugi, Pascal A. Niklaus, Jacek Oleksyn, Petr Ontikov, Edgar Ortiz-Malavasi, Yude Pan, Alain Paquette, Alexander Parada-Gutierrez, Elena Parfenova, Minjee Park, Mar Parren, Narayanaswamy Parthasarathy, Pablo L. Peri, Sebastian Pfautsch, Oliver L. Phillips, Nicolas Picard, Maria Teresa Piedade, Daniel Piotto, Nigel C. A. Pitman, Irina Polo, Lourens Poorter, Axel Dalberg Poulsen, John R. Poulsen, Hans Pretzsch, Freddy Ramirez Arevalo, Zorayda Restrepo-Correa, Mirco Rodeghiero, Samir Rolim, Anand Roopsind, Francesco Rovero, Ervan Rutishauser, Purabi Saikia, Christian Salas-Eljatib, Peter Schall, Dmitry Schepaschenko, Michael Scherer-Lorenzen, Bernhard Schmid, Jochen Schongart, Eric B. Searle, Vladimir Seben, Josep M. Serra-Diaz, Douglas Sheil, Anatoly Shvidenko, Javier Silva-Espejo, Marcos Silveira, James Singh, Plini Sist, Ferry Slik, Bonaventure Sonke, Alexandre F. Souza, Krzysztof Sterenczak, Jens-Christian Svenning, Miroslav Svoboda, Ben Swanepoel, Natalia Targhetta, Nadja Tchebakova, Raquel Thomas, Elen Tikhonova, Peter Umunay, Vladimir Usoltsev, Renato Valencia, Fernando Valladares, Fons van Der Plas, Do Van Tran, Michael E. Van Nuland, Rodolfo Vasquez Martinez, Hans Verbeeck, Helder Viana, Alexander C. Vibrans, Simone Vieira, Klaus von Gadow, Hua-Feng Wang, James Watson, Gijsbert D. A. Werner, Susan K. Wiser, Florian Wittmann, Verginia Wortel, Roderick Zagt, Tomasz Zawila-Niedzwiecki, Chunyu Zhang, Xiuhai Zhao, Mo Zhou, Zhi-Xin Zhu, Irie Casimir Zo-Bi, Thomas W. Crowther
Summary: Biodiversity is important for ecosystems, with higher species richness often leading to increased productivity. However, the relationship between biodiversity and productivity varies across environments and is less pronounced at high levels of species richness. Community evenness can mediate this relationship, and our study shows that it is negatively correlated with species richness and plays a crucial role in the biodiversity-productivity relationship.
JOURNAL OF ECOLOGY
(2023)
News Item
Biodiversity Conservation
Kofi Amponsah-Mensah, Yaa Ntiamoa-Baidu, Francesco Rovero, P. J. Stephenson
Article
Biodiversity Conservation
Nathalie van Vliet, Simon Quintero, Jonas Muhindo, Jonas Nyumu, Paolo Omar Cerutti, Robert Nasi, Francesco Rovero
Summary: In this study, the camera-trap assessment of terrestrial mammals in the Yangambi landscape was conducted for the first time, revealing lower occupancy and species richness compared to other conservation areas in the Congo Basin. The dominant species in the community are known for their high resilience, while large ungulates and medium-sized carnivores were found to have low abundances. The study also identified the presence of four threatened species, emphasizing the need for landscape-level conservation and collaborative management involving local communities.
Article
Ecology
Ilaria Greco, Christina Lynette Paddock, Grainne Michelle McCabe, Claudia Barelli, Steven Shinyambala, Arafat S. Mtui, Francesco Rovero
Summary: The decline of mammals worldwide necessitates quantitative population assessments, especially for range-restricted and threatened species. However, estimating robust abundances for elusive or difficult to detect species presents challenges. In this study, we calibrated density estimates from acoustic surveys with occupancy estimates from camera-trapping detections to determine the abundance of the endangered Sanje mangabey (Cercocebus sanjei) in the Udzungwa Mountains of Tanzania. Our results indicate higher density and abundance in the nature reserve compared to previous studies, providing optimism for the species' status despite potential vulnerability to human disturbance.
Article
Behavioral Sciences
Maximilian L. Allen, Francesco Rovero, Valentina Oberosler, Claudio Augugliaro, Miha Krofel
Summary: Olfactory communication is crucial for Pallas's cats to communicate and delineate territories, and they may reduce advertising their presence in response to the occurrence of snow leopards to minimize predation risk.
Article
Ecology
Lucinda P. Lawson, Simon P. Loader, John V. Lyakurwa, Michele Menegon, H. Christoph Liedtke
Summary: Human impact on ecosystems has significantly altered the environment globally. While deforestation has been extensively studied, the introduction of non-native plantations also has major consequences. This study examines the effects of land use change on amphibian communities in the Udzungwa Plateau in Tanzania by comparing surveys conducted before and after the introduction of non-native plantations. The results indicate that local extinctions may have occurred, with remaining amphibians confined to wetlands. This study highlights the urgent need for further research on the impact of non-native plantations on natural communities.
Article
Ecology
Daniel Gorczynski, Francesco Rovero, Arafat Mtui, Steven Shinyambala, Joseph Martine, Chia Hsieh, Luke Frishkoff, Lydia Beaudrot
Summary: The habitat surface area of tropical forest floors plays an important role in promoting animal occupancy and functional diversity. Greater habitat surface area provides more resources and habitat space, leading to higher animal diversity.
Article
Multidisciplinary Sciences
Alexis Marchesini, Andrea Silverj, Sara Torre, Omar Rota-Stabelli, Matteo Girardi, Iacopo Passeri, Ilaria Fracasso, Federico Sebastiani, Cristiano Vernesi
Summary: In this study, the European beech was subjected to whole-genome resequencing, revealing clear genetic differentiation at the chloroplast, mitochondrial, and nuclear genome levels. The divergence between the Alpine and Apennine populations was dated back to approximately 660 thousand years ago, indicating a long history of separation. This information has important conservation implications for the adaptation of this tree species to ongoing climate changes.
Article
Ecology
Asuncion Semper-Pascual, Douglas Sheil, Lydia Beaudrot, Pierre Dupont, Soumen Dey, Jorge Ahumada, Emmanuel Akampurira, Robert Bitariho, Santiago Espinosa, Patrick A. A. Jansen, Marcela Guimaraes Moreira Lima, Emanuel H. H. Martin, Badru Mugerwa, Francesco Rovero, Fernanda Santos, Eustrate Uzabaho, Richard Bischof
Summary: The occurrence dynamics of wildlife populations in protected areas are influenced by anthropogenic stressors, particularly affecting habitat specialists and generalist species differently. The study found that colonization probability of habitat specialists is influenced by local-scale forest cover when the landscape-scale fragmentation is low, while survival probability of generalist species is more affected by the forest edge when the landscape-scale human population density is low.
NATURE ECOLOGY & EVOLUTION
(2023)