Article
Evolutionary Biology
Melanie E. F. Lacava, Joanna S. Griffiths, Luke Ellison, Evan W. Carson, Tien-Chieh Hung, Amanda J. Finger
Summary: Adaptation to captivity can lead to reduced fitness in the wild due to domestication. A study on delta smelt in a conservation hatchery revealed a small but significant increase in age at maturity over a decade. The trait of maturation timing was influenced by phenotypic plasticity and the time of year fish were born. However, highly domesticated fish showed a loss of plasticity, possibly due to breeding practices in the hatchery. This loss of plasticity may affect the ability of hatchery fish to align maturation with population peaks and result in lower fitness in the wild.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Agriculture, Dairy & Animal Science
Semiu Folaniyi Bello, Raman Akinyanju Lawal, Adeniyi Charles Adeola, Qinghua Nie
Summary: Chicken is a valuable source of protein and the subject of research due to its genetic and phenotypic variations resulting from natural and artificial selection. Various approaches, including whole genome sequencing, have been used to detect selection signatures and identify candidate genes in different chicken breeds. In addition, gene enrichment analyses help determine pathways and gene ontology related to specific traits in chicken. This review summarizes different studies on selection signatures and provides suggestions for future research to strengthen the findings and understand the importance of selection in chicken conservation for the growing human population.
Article
Biochemistry & Molecular Biology
Clare J. Venney, Raphael Bouchard, Julien April, Eric Normandeau, Laurie Lecomte, Guillaume Cote, Louis Bernatchez
Summary: Captive rearing in salmon hatcheries can have significant impacts on fish phenotype and fitness, even without genetic changes. This study used whole genome methylation sequencing to investigate the epigenetic effects of hatchery rearing on Atlantic salmon. The results showed sex-specific effects and complex patterns of inheritance, indicating the need for further research on minimizing these effects in conservation efforts.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Automation & Control Systems
Sergii Voronov, Voronov Daniel Jung, Erik Frisk
Summary: The paper introduces a forest-based variable selection algorithm, named Variable Depth Distribution, to measure the importance of variables. The algorithm is developed for datasets with correlated variables and can identify important variables in different applications.
ENGINEERING APPLICATIONS OF ARTIFICIAL INTELLIGENCE
(2021)
Article
Agriculture, Dairy & Animal Science
William Mulvaney, Md Moshiur Rahman, Levi S. Lewis, Jiayi Cheng, Tien-Chieh Hung
Summary: This study reports the successful weaning of captive cultured longfin smelt onto a dry commercial pellet feed. The results highlight that juvenile longfin smelt can utilize dry feeds while maintaining a healthy body condition.
Article
Multidisciplinary Sciences
Radost Stanimirova, Katelyn Tarrio, Konrad Turlej, Kristina McAvoy, Sophia Stonebrook, Kai-Ting Hu, Paulo Arevalo, Eric L. Bullock, Yingtong Zhang, Curtis E. Woodcock, Pontus Olofsson, Zhe Zhu, Christopher P. Barber, Carlos M. Souza Jr, Shijuan Chen, Jonathan A. Wang, Foster Mensah, Marco Calderon-Loor, Michalis Hadjikakou, Brett A. Bryan, Jordan Graesser, Dereje L. Beyene, Brian Mutasha, Sylvester Siame, Abel Siampale, Mark A. Friedl
Summary: This study created a global database of nearly 2 million training units using advanced cloud computing platforms and machine learning algorithms. The database spans the period from 1984 to 2020 and is relevant for research on land cover and land cover change mapping. The database provides high-quality training data and ensures data accuracy through a cross-validation procedure.
Article
Entomology
James P. Strange, Amber D. Tripodi, Thuy-Tien T. Lindsay, James D. Herndon, Joyce Knoblett, Morgan E. Christman, N. Pinar Barkan, Jonathan B. U. Koch
Summary: This study reported the successful nest initiation and establishment rates of 15 western North American Bombus species and generated a timeline of colony development. The results showed significant variations in nest success and colony growth dynamics among different species. This study contributes to the knowledge of systematic nesting biology of western North American Bombus species and provides valuable information for conservationists and researchers.
JOURNAL OF INSECT SCIENCE
(2023)
Article
Forestry
Colin S. Shanley, Daniel R. Eacker, Conor P. Reynolds, Bonnie M. B. Bennetsen, Sophie L. Gilbert
Summary: This study utilized LiDAR technology to build a winter habitat model for Sitka black-tailed deer and analyzed the habitat selection patterns. The model showed improved accuracy and could enhance conservation and restoration planning across large managed forest landscapes.
FOREST ECOLOGY AND MANAGEMENT
(2021)
Article
Forestry
Tristan Eckerter, Veronika Braunisch, Gesine Pufal, Alexandra M. Klein
Summary: Forest management intensity in Europe has varying implications for structural and environmental conditions, as well as the conservation of ecological communities. This study found that silvicultural treatments promoting rare habitat structures can enhance trap-nesting bees, wasps, and their parasitoids. Forest management and associated vegetation characteristics influenced the abundance, richness, parasitism rates, and network structure of the bee/wasp-parasitoid communities. Clear-cut plots showed the highest abundance and richness, while unmanaged plots had the lowest. The results highlight the importance of early successional habitats and different forest management types in shaping the size and speciality of host-parasitoid networks.
FOREST ECOLOGY AND MANAGEMENT
(2022)
Article
Agriculture, Multidisciplinary
Brenda G. Diaz-Hernandez, Carlos A. Colombo, Jonathan A. Morales-Marroquin, Mariana Sanita-Rodrigues, Joaquim A. Azevedo-Filho, Maria I. Zucchi
Summary: This study analyzed the genetic diversity of artificially selected Macaúba palms and found no significant loss of genetic diversity in the species. This has important implications for protecting genetic diversity and reducing genetic vulnerability in agricultural development.
ANNALS OF APPLIED BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Leqi Tian, Wenbin Wu, Tianwei Yu
Summary: Random Forest (RF) is a popular machine learning method for classification and regression tasks, and it performs well under low sample size situations. However, there are issues with gene selection using RF as the important genes are usually scattered on the gene network, which conflicts with the biological assumption of functional consistency. To address this issue, we propose the Graph Random Forest (GRF) method, which incorporates external topological information to identify highly connected important features. The algorithm achieves equivalent classification accuracy to RF while selecting interpretable feature sub-graphs.
Article
Ecology
Daniel W. Sallee, Brock R. McMillan, Kent R. Hersey, Steven L. Petersen, Randy T. Larsen
Summary: Spatial modeling showed that habitat use by female mule deer was influenced by other ungulate species, but competition did not affect their survival and growth.
JOURNAL OF WILDLIFE MANAGEMENT
(2023)
Article
Forestry
Rasmus Mohr Mortensen, Michelle Fyrstelin Fuller, Lars Dalby, Thomas Bjorneboe Berg, Peter Sunde
Summary: The research studied habitat selection of hazel dormouse in intensively managed woodlands in Denmark. The study found that the species strongly selected sites with high abundance-weighted species richness and high vegetation density of woody plants, and had specific habitat requirements related to food and safety. The results provide relatively simple means for accommodating the habitat needs of hazel dormouse in managed forests.
FOREST ECOLOGY AND MANAGEMENT
(2022)
Article
Agriculture, Dairy & Animal Science
Agathe Gaffard, Clotilde Loiseau, Vincent Bretagnolle, Olivier Pays, Jerome Moreau
Summary: Farmland bird populations have declined over the past 50 years in Europe and North America. Partridges fed with organic grains have better post-release survival rates and overall healthier bodies.
APPLIED ANIMAL BEHAVIOUR SCIENCE
(2022)
Article
Plant Sciences
Aabid Hussain Mir, Kiranmay Sarma, Krishna Upadhaya
Summary: In the state of Meghalaya, northeast India, more than 80% of forest lands are owned and managed by local communities. However, these forests are facing severe threats due to human disturbances. A recent study conducted in the Khasi Hills of Meghalaya assessed the plant diversity and identified community forests for priority conservation. The study found a total of 1,300 plant species, with 400 species being rare, endemic, or threatened. Reserve forests had the highest species richness, followed by sacred forests and village forests. The majority of the forests showed high species richness, irreplaceability level, and vulnerability level. An area of 7,661.56 hectares of community forests fell under the high priority category, calling for immediate conservation actions. The study provides a conservation priority map to guide protection strategies for community forests.
Article
Biochemistry & Molecular Biology
Charles D. Waters, Jeffrey J. Hard, David E. Fast, Curtis M. Knudsen, William J. Bosch, Kerry A. Naish
Correction
Ecology
Devon E. Pearse, Nicola J. Barson, Torfinn Nome, Guangtu Gao, Matthew A. Campbell, Alicia Abadia-Cardoso, Eric C. Anderson, David E. Rundio, Thomas H. Williams, Kerry A. Naish, Thomas Moen, Sixin Liu, Matthew Kent, Michel Moser, David R. Minkley, Eric B. Rondeau, Marine S. O. Brieuc, Simen Rod Sandve, Michael R. Miller, Lucydalila Cedillo, Kobi Baruch, Alvaro G. Hernandez, Gil Ben-Zvi, Doron Shem-Tov, Omer Barad, Kirill Kuzishchin, John Carlos Garza, Steven T. Lindley, Ben F. Koop, Gary H. Thorgaard, Yniv Palti, Sigbjorn Lien
NATURE ECOLOGY & EVOLUTION
(2020)
Article
Ecology
Samuel A. May, Garrett J. McKinney, Ray Hilborn, Lorenz Hauser, Kerry A. Naish
ECOLOGY AND EVOLUTION
(2020)
Article
Biochemistry & Molecular Biology
Charles D. Waters, Anthony Clemento, Tutku Aykanat, John Carlos Garza, Kerry A. Naish, Shawn Narum, Craig R. Primmer
Summary: Studying the genetic basis of age at maturity in four species of Pacific salmonids revealed heterogeneous genetic architecture of this key life-history trait across the species. While significant associations were found between six6 and age at maturity in two species, particularly strong in Steelhead, no significant associations were detected between vgll3 and age at maturity in any of the species.
Correction
Genetics & Heredity
Quentin Rougemont, Jean-Sebastien Moore, Thibault Leroy, Eric Normandeau, Eric B. Rondeau, Ruth E. Withler, Donald M. Van Doornik, Penelope A. Crane, Kerry A. Naish, John Carlos Garza, Terry D. Beacham, Ben F. Koop, Louis Bernatchez
Article
Virology
Daniel G. Hernandez, William Brown, Kerry A. Naish, Gael Kurath
Summary: This study assessed IHNV susceptibility in Chinook salmon populations in the Columbia River Basin, finding little intra-species variation in susceptibility to UC or MD IHNV infection or disease, with a few exceptions in the lower CRB spring-run population. This suggests that factors other than host susceptibility may influence the ecology of IHNV in the CRB.
Article
Microbiology
David J. Paez, Rachel L. Powers, Peng Jia, Natalia Ballesteros, Gael Kurath, Kerry A. Naish, Maureen K. Purcell
Summary: The study showed that host immune responses and water temperature interact to modulate virus persistence, with higher temperatures accelerating virus replication but colder temperatures favoring longer virus persistence with host immune responses. The viral RNA mainly persisted in kidney and spleen tissues, suggesting these tissues are favored targets of the virus. The results provide insights into potential host-pathogen responses to climate change by understanding the environmental drivers of host-pathogen interactions within hosts.
Article
Biochemistry & Molecular Biology
Quentin Rougemont, Amanda Xuereb, Xavier Dallaire, Jean-Sebastien Moore, Eric Normandeau, Eric B. Rondeau, Ruth E. Withler, Donald M. Van Doornik, Penelope A. Crane, Kerry A. Naish, John Carlos Garza, Terry D. Beacham, Ben F. Koop, Louis Bernatchez
Summary: This study investigated the genomic basis of local adaptation in Coho salmon across North America and found that migration distance is the primary selective factor. Several candidate genetic variations associated with long-distance migration and altitude were also identified.
Review
Evolutionary Biology
Robin S. Waples, Michael J. Ford, Krista Nichols, Marty Kardos, Jim Myers, Tasha Q. Thompson, Eric C. Anderson, Ilana J. Koch, Garrett McKinney, Michael R. Miller, Kerry Naish, Shawn R. Narum, Kathleen G. O'Malley, Devon E. Pearse, George R. Pess, Thomas P. Quinn, Todd R. Seamons, Adrian Spidle, Kenneth Warheit, Stuart C. Willis
Summary: The strong associations between adult migration timing and specific alleles in the genomic region of Chinook salmon and steelhead have raised questions about incorporating genomics data into conservation unit configuration decisions. The study suggests that specific alleles are required for early migration and that considering early-migrating populations as reliable sources for genetic resources is important. The existence of large-effect loci can affect evolutionary potential and adaptability.
JOURNAL OF HEREDITY
(2022)
Article
Agriculture, Dairy & Animal Science
Victor Martinez, Phillip J. Dettleff, Nicolas Galarce, Cristian Bravo, Jessica Dorner, Robert N. Iwamoto, Kerry Naish
Summary: Understanding the genetic status of aquaculture strains is crucial for sustainable management. Coho salmon in Chile's aquaculture industry has faced various events that have shaped its genome. Comparisons with strains from other countries revealed differences in effective population size, highlighting the need for measures to maintain genetic diversity and long-term sustainability.
Article
Fisheries
Joseph P. Dietrich, Mary Beth Rew Hicks, Jeffrey J. Hard, Krista M. Nichols, Christopher J. Langdon, Konstantin Divilov, Blaine Schoolfield, Mary R. Arkoosh
Summary: Marine bivalves account for 14% of global aquaculture production, with oysters representing about 33% of this production. Disease outbreaks caused by Vibrio coralliiyticus pose a major problem in oyster hatchery production. This study demonstrates that selective breeding can enhance the resistance of oyster larvae to Vibrio coralliiyticus, but multiple generations of breeding are expected for significant improvement.
Article
Evolutionary Biology
Samuel A. May, Jeffrey J. Hard, Michael J. Ford, Kerry A. Naish, Eric J. Ward
Summary: Quantitative models can predict the effects of environmental or anthropogenic factors on the dynamics of wild populations by simulating the inheritance and evolution of fitness-linked traits. Non-random mating is underestimated in wild populations and plays a significant role in diversity-stability relationships. A novel individual-based quantitative genetic model is introduced, incorporating assortative mating for reproductive timing, and demonstrates its utility by simulating a salmonid lifecycle and comparing model outputs to theoretical expectations. The simulations show that assortative mating can result in more resilient and productive populations compared to random mating, and factors such as trait correlations, environmental variability, and strength of selection also impact population growth.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Genetics & Heredity
Eric B. Rondeau, Kris A. Christensen, David R. Minkley, Jong S. Leong, Michelle T. T. Chan, Cody A. Despins, Anita Mueller, Dionne Sakhrani, Carlo A. Biagi, Quentin Rougemont, Eric Normandeau, Steven J. M. Jones, Robert H. Devlin, Ruth E. Withler, Terry D. Beacham, Kerry A. Naish, Jose M. Yanez, Roberto Neira, Louis Bernatchez, William S. Davidson, Ben F. Koop
Summary: The coho salmon populations in North America have significantly declined, and analysis of genomic data suggests bottleneck events after glacial retreat as a possible cause. A chromosome-level genome assembly and genome resequencing of 83 coho salmon were performed to aid in stock management and conservation efforts.
G3-GENES GENOMES GENETICS
(2023)
Article
Virology
David J. Paez, Douglas McKenney, Maureen K. Purcell, Kerry A. Naish, Gael Kurath
Summary: The study provides evidence for the theory of the evolution of pathogen specialization and generalism, showing that specialist pathogens have higher fitness in their specialized hosts but lower fitness in nonspecialized hosts, while generalist pathogens have moderate fitness in all hosts. The findings demonstrate the trade-offs in within-host replicative fitness resulting from the natural evolution of specialist and generalist virus lineages in multi-host ecosystems.