Article
Biochemistry & Molecular Biology
Thibaut Paul Patrick Sellinger, Diala Abu-Awad, Aurelien Tellier
Summary: Various methods based on SMC have been developed to infer population demographic history using full genome sequence data, but a comprehensive investigation into the limitations of these methods is lacking. Researchers have introduced a tool to infer the best case convergence of SMC methods and evaluated the inference accuracy when assumptions are violated. Additionally, they emphasize the importance of the transition matrix in SMC methods.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Biology
Mateusz Baca, Danijela Popovic, Alexander K. Agadzhanyan, Katarzyna Baca, Nicholas J. Conard, Helen Fewlass, Thomas Filek, Michal Golubinski, Ivan Horacek, Monika V. Knul, Magdalena Krajcarz, Maria Krokhaleva, Loic Lebreton, Anna Lemanik, Lutz C. Maul, Doris Nagel, Pierre Noiret, Jerome Primault, Leonid Rekovets, Sara E. Rhodes, Aurelien Royer, Natalia V. Serdyuk, Marie Soressi, John R. Stewart, Tatiana Strukova, Sahra Talamo, Jaroslaw Wilczynski, Adam Nadachowski
Summary: By studying the ancient mitochondrial genomes of narrow-headed voles from Europe and Asia, the researchers found that the evolution of narrow-headed voles and collared lemings was influenced by climate fluctuations. They also identified time-structured mtDNA lineages in European narrow-headed voles during the Late Pleistocene, which helped explain the drivers of dynamics in steppe- and cold-adapted species.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biodiversity Conservation
Jamieson C. Botsch, Aayush N. Zaveri, Lucas A. Nell, Amanda R. Mccormick, K. Riley Book, Joseph S. Phillips, Arni Einarsson, Anthony R. Ives
Summary: While climate warming is expected to reduce body size of ectotherms, this study finds mixed evidence. The body size of midge Tanytarsus gracilentus showed only a slight decrease, contrary to theoretical expectations, despite increasing temperatures. The study highlights the complex interactions between temperature, population size, and food quality in determining average body size trends in ectotherms.
GLOBAL CHANGE BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Rebecca S. Taylor, Micheline Manseau, Cornelya F. C. Klutsch, Jean L. Polfus, Audrey Steedman, Dave Hervieux, Allicia Kelly, Nicholas C. Larter, Mary Gamberg, Helen Schwantje, Paul J. Wilson
Summary: The study found that a major population expansion of caribou occurred at the start of the last glacial period, with effective population sizes reaching 700,000 to 1,000,000 individuals, one of the highest for any mammal species recorded. Mitochondrial analyses dated introgression events prior to the last glacial maximum, demonstrating the importance of pre-LGM events in shaping demographic history.
Article
Biochemistry & Molecular Biology
James B. Dorey, Scott V. C. Groom, Alejandro Velasco-Castrillon, Mark I. Stevens, Michael S. Y. Lee, Michael P. Schwarz
Summary: There is substantial debate on the roles of climate change and human activities on biodiversity and species demographies over the Holocene. Molecular approaches can be used to disentangle the impacts of humans and climate change on tropical pollinators.
Article
Geography, Physical
Xiaobo Jin, Wentao Ma, Chuanlian Liu
Summary: This study reveals the long-term increase in coccolith size over the Pleistocene in global oceans and its impact on the carbon cycle. The researchers analyze the data from the Ocean Drilling Program Site 1143 in the South China Sea and find that Earth eccentricity controls coccolith size diversity and calcite export production in tropical oceans. Additionally, they propose that the increased availability of oceanic alkalinity may contribute to the long-term increase in coccolith size.
QUATERNARY SCIENCE REVIEWS
(2022)
Article
Biochemistry & Molecular Biology
Nathan W. Byer, Matthew L. Holding, Miranda M. Crowell, Todd W. Pierson, Thomas E. Dilts, Eveline S. Larrucea, Kevin T. Shoemaker, Marjorie D. Matocq
Summary: The study revealed that spatially separated populations of pygmy rabbits exhibit local adaptation, potentially driven by genetic loci with functional annotations related to plant secondary compound metabolism. Additionally, populations in the Mono Basin of California likely diverged from other Great Basin populations during late Pleistocene climate oscillations, demonstrating adaptive differentiation despite limited gene flow and small effective population size.
Article
Biochemistry & Molecular Biology
Zeqi Yao, Kehui Liu, Shanjun Deng, Xionglei He
Summary: The study introduces a new coalescent method, i-coalescent analysis, which computes the instantaneous coalescent rate by using a phylogenetic tree of sampled alleles. It accurately reconstructs population size dynamics of highly structured populations, although larger sample sizes are often required for structured populations.
JOURNAL OF GENETICS AND GENOMICS
(2021)
Article
Biology
Konstantina Agiadi, Frederic Quillevere, Rafal Nawrot, Theo Sommeville, Marta Coll, Efterpi Koskeridou, Jan Fietzke, Martin Zuschin
Summary: Mesopelagic fishes play crucial roles in marine food webs, are a vast but largely untapped food resource, and contribute significantly to the biological carbon pump. However, their future under climate change scenarios remains uncertain.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Environmental Sciences
Leanne Faulks, Prashant Kaushik, Shoji Taniguchi, Masashi Sekino, Reiichiro Nakamichi, Yuki Yamamoto, Hiroka Fujimori, Chiaki Okamoto, Sakie Kodama, Ayu Daryani, Angel Faye Manwong, Ishmerai Galang, Noritaka Mochioka, Kiyo Araki, Motoo Suzuki, Yoshitsugu Kaji, Takumi Ichiki, Tetsuya Matsunaga, Hiroshi Hakoyama
Summary: This article assesses the demographic history of the endangered Japanese eel and finds evidence of two population bottlenecks. The overall level of genetic diversity is relatively low, but there is no evidence of inbreeding. These research data will help model the extinction risk of Japanese eel.
AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS
(2022)
Article
Environmental Sciences
Anne C. Pisor, Xavier Basurto, Kristina G. Douglass, Katharine J. Mach, Elspeth Ready, Jason M. Tylianakis, Ashley Hazel, Michelle A. Kline, Karen L. Kramer, J. Stephen Lansing, Mark Moritz, Paul E. Smaldino, Thomas F. Thornton, James Holland Jones
Summary: Communities should have a say in determining climate change adaptation strategies, as the fairness and effectiveness of such strategies depend on their involvement. Researchers and development actors can support communities and gain valuable insights from them.
NATURE CLIMATE CHANGE
(2022)
Review
Biochemistry & Molecular Biology
Khalid Anwar, Rohit Joshi, Om Parkash Dhankher, Sneh L. Singla-Pareek, Ashwani Pareek
Summary: Plants face increasing frequencies of multiple abiotic stresses in nature, and their responses to these combined and sequential stresses differ from those triggered by individual stress. Studies have shown that there are interacting signaling pathways between various abiotic stresses, which are crucial for enhancing crops' tolerance to multiple stress combinations.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Ecology
Gerard Martinez- De Leon, Arianne Marty, Martin Holmstrup, Madhav P. Thakur
Summary: This study used a trait-based approach to investigate the population responses of soil-dwelling Collembola species to extreme heat events. The results showed that while resistance remained consistent across species, the recovery response of the most heat-sensitive species was strongly affected. The detrimental effects of heat on fecundity were found to be responsible for changes in the body size distribution of recovering populations.
Article
Ecology
Billie Maguire, Jewel Tomasula, Tyler Rippel, Gina M. Wimp, Matthew B. Hamilton
Summary: As anthropogenic change alters and fragments habitats, the flood tolerant low elevation marsh grass (Spartina alterniflora) is displacing the flood intolerant high elevation marsh grass (Spartina patens) in coastal salt marshes of eastern North America. The genetic analysis of Tumidagena minuta, a specialist herbivore of Spartina patens, showed that although habitat loss and isolation have increased, the genetic diversity and structure of the T. minuta population have remained relatively stable.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Environmental Sciences
Yuwei Wang, Na Zhao, Xiaozhe Yin, Chaoyang Wu, Mingxing Chen, Yimeng Jiao, Tianxiang Yue
Summary: The increasing exposure to extreme heatwaves in urban areas poses various threats and challenges to human society. Current research on this topic has limitations in terms of oversimplification of human exposure to heatwaves and neglect of perceived temperature and body comfort, leading to unreliable estimates of future results. This study provides the first global fine-resolution projection of future urban population exposure to heatwaves by 2100, indicating the rising exposure in all four shared socioeconomic pathways. The results highlight the need for policy improvements and sustainable development planning in coastal and low-altitude cities.
ENVIRONMENT INTERNATIONAL
(2023)
Article
Parasitology
Peter Halvarsson, Katarina Gustafsson, Johan Hoglund
Summary: A questionnaire survey conducted in Sweden among sheep owners revealed low usage of anthelmintic drugs and high unawareness of gastrointestinal nematode infections (GIN) risks. The study also identified the potential development of anthelmintic resistance due to treating sheep without prior diagnosis.
VETERINARY PARASITOLOGY- REGIONAL STUDIES AND REPORTS
(2022)
Editorial Material
Ecology
Giulio Formenti, Kathrin Theissinger, Carlos Fernandes, Iliana Bista, Aureliano Bombarely, Christoph Bleidorn, Claudio Ciofi, Angelica Crottini, Jose A. Godoy, Jacob Hoglund, Joanna Malukiewicz, Alice Mouton, Rebekah A. Oomen, Sadye Paez, Per J. Palsboll, Christophe Pampoulie, Maria J. Ruiz-Lopez, Hannes Svardal, Constantina Theofanopoulou, Jan de Vries, Ann-Marie Waldvogel, Guojie Zhang, Camila J. Mazzoni, Erich D. Jarvis, Miklos Balint
Summary: Progress in genome sequencing has enabled the generation of large-scale reference genomes, representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, allowing comprehensive analyses in population and functional genomics, and are expected to revolutionize conservation genomics.
TRENDS IN ECOLOGY & EVOLUTION
(2022)
Article
Parasitology
T. A. Yazwinski, J. Hoglund, A. Permin, M. Gauly, C. Tucker
Summary: This article is about the revision of poultry guidelines to assess the efficacy of anthelmintic drugs against helminth parasites in chickens and turkeys. It provides updates on the procedures and considerations for these evaluations, as well as emphasizes the importance of accuracy and excellence in conducting such studies.
VETERINARY PARASITOLOGY
(2022)
Article
Parasitology
Paulius Baltrusis, Stephen R. Doyle, Peter Halvarsson, Johan Hoglund
Summary: The study reveals that in a field population from Sweden, despite an 89% reduction in parasites after ivermectin treatment, the surviving population remained highly genetically similar to the population before treatment, indicating that resistance likely evolved over time and is present on diverse haplotypes. The data provide new insights into the genome-wide effects of ivermectin selection in a field population and confirm the role of a previously identified quantitative trait locus in the development of resistance to ivermectin.
INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE
(2022)
Article
Biodiversity Conservation
Venkat Talla, Veronika Mrazek, Jacob Hoglund, Niclas Backstrom
Summary: The clouded apollo butterfly in Sweden is currently endangered and only found in three geographically separated populations. Conservation efforts include habitat restoration and captive breeding. By using whole-genome resequencing and population genomic approaches, we found that the different populations in Sweden have similar but comparatively low levels of genetic diversity, with significant genetic differentiation between the northernmost and southern populations. We also discovered population sub-structure in one of the populations. These findings provide insights into the genetic consequences of population declines and fragmentation, and important information for the conservation of clouded apollo butterflies in Sweden.
CONSERVATION GENETICS
(2023)
Article
Evolutionary Biology
Snaebjorn Palsson, Pawel Wasowicz, Starri Heiomarsson, Kristinn Petur Magnusson
Summary: Betula pubescens Ehrh. (mountain birch) is the only forest-forming tree in Iceland. The forest area in Iceland has dramatically declined due to habitat fragmentation and disturbance. Genetic studies have shown hybridization between B. pubescens and Betula nana L. occurs in Iceland. This study assessed the genetic variation within and among remaining birch forests in Iceland and found limited effects of fragmentation and hybridization on genetic variation within sites, but clear genetic divergence among forests from different regions.
JOURNAL OF HEREDITY
(2023)
Article
Biodiversity Conservation
Sara Martin-Garcia, Maria Cortazar-Chinarro, Mariano Rodriguez-Recio, Jose Jimenez, Jacob Hoglund, Emilio Virgos
Summary: Choosing the most appropriate sampling method is crucial for estimating population size. This study compared two commonly used sampling methods for the red fox and found that camera trapping provided a slightly higher minimum number of individuals compared to DNA faecal genotyping. Abundance estimates from camera trapping were positively correlated with the number of individuals detected, while there was a non-significant negative relationship between DNA faecal genotyping and abundance estimates.
BIODIVERSITY AND CONSERVATION
(2023)
Article
Parasitology
Niclas Hogberg, Anna Hessle, Lena Lidfors, Johan Hoglund
Summary: This study investigated the effects of mixed gastrointestinal nematode (GIN) infections on the growth and post-weaning activity patterns of ram lambs. The lambs and ewes were grazed in pastures naturally contaminated with GIN, and were divided into low parasite exposure (LP) and high parasite exposure (HP) groups. The results showed that delayed weaning age reduced the adverse effects of GIN infection on body weight gain, while an earlier weaning age reduced the risk of Haemonchus contortus infection. Automated behavior recordings were also demonstrated to be a potential diagnostic tool for nematode infections in sheep.
VETERINARY PARASITOLOGY
(2023)
Review
Agriculture, Dairy & Animal Science
Johan Hoglund, Katarina Gustafsson
Summary: In Sweden, sheep are often treated for gastrointestinal parasites before being let out to pasture with their lambs in the spring, which may increase resistance selection. However, the evidence for the effectiveness of this strategy is inconclusive, and further research is needed to address this issue.
Article
Agriculture, Dairy & Animal Science
B. Tarbiat, N. Enweji, D. S. Jansson, E. Wallstrom, E. Osterman-Lind, J. Hoglund
Summary: Poultry roundworms have re-emerged in European countries due to noncaged housing, impacting bird welfare and productivity. The Swedish Egg Association initiated a control program in 2009, but its data have not been fully explored, and understanding of producer perception is inadequate. This study addresses these issues through analyzing program data and conducting an online survey. The findings highlight the need for strategic sampling, appropriate diagnostic tools, and education on anthelmintics use and resistance development.
JOURNAL OF APPLIED POULTRY RESEARCH
(2023)
Article
Genetics & Heredity
Theodore E. Squires, Patrik Rodin-Morch, Giulio Formenti, Alan Tracey, Linelle Abueg, Nadolina Brajuka, Erich Jarvis, Eva C. Halapi, Pall Melsted, Jacob Hoglund, Kristinn Petur Magnusson
Summary: The Rock Ptarmigan, a cold-adapted game bird, has a high-quality reference genome and mitogenome assembled from PacBio HiFi and Hi-C sequencing. The genome size is 1.03 Gb with an average gene length of 33,605 bp and 16,078 protein-coding genes. This new reference genome will enhance our understanding of the Rock Ptarmigan's evolutionary history, vulnerability to climate change, and serve as a benchmark for related species.
G3-GENES GENOMES GENETICS
(2023)
Review
Agriculture, Dairy & Animal Science
Johannes Charlier, Tong Wang, Sien H. Verschave, Johan Hoeglund, Edwin Claerebout
Summary: Gastrointestinal nematode infections pose a significant threat to the health and well-being of calves in pasture-based rearing systems. The serum pepsinogen assay, although an established tool, is not widely implemented due to its high cost and lack of standardization. This study evaluates the O. ostertagi-Ab ELISA as a cost-effective and robust alternative diagnostic method for first-season grazing calves and suggests that it can replace the serum pepsinogen assay for monitoring purposes at the end of the grazing season.
Article
Biochemical Research Methods
Petur Helgi Einarsson, Pall Melsted
Summary: We propose a compression scheme and its implementation in BUStools software for BUS files. Our algorithm achieves smaller file sizes and faster compression and decompression speeds compared to gzip. We evaluated our algorithm on 533 BUS files from scRNA-seq experiments, resulting in a 8.3x reduction in file size and a compressed dataset size of 122GB.
Article
Biochemistry & Molecular Biology
M. Cortazar-Chinarro, A. Richter-Boix, P. Rodin-Morch, P. Halvarsson, J. B. Logue, A. Laurila, J. Hoglund
Summary: Microbiomes play a crucial role in determining the ecology and behavior of their hosts. This study investigated the effects of geography, evolutionary history, and host genetics on the skin microbiome diversity and structure in a widespread amphibian. The results showed that microbiome diversity was correlated with host genetic diversity, and the bacterial community composition varied between geographical clusters and specific host genetic variations.