المؤلفون: Evelien de Greef, Alexander Suh, Matt J. Thorstensen, Kira E. Delmore, Kevin C. Fraser

المصدر: Scientific Reports, Vol 13, Iss 1, Pp 1-7 (2023)

مصطلحات موضوعية: Medicine, Science

الوصف: Abstract The impact of climate change on spring phenology poses risks to migratory birds, as migration timing is controlled predominantly by endogenous mechanisms. Despite recent advances in our understanding of the underlying genetic basis of migration timing, the ways that migration timing phenotypes in wild individuals may map to specific genomic regions requires further investigation. We examined the genetic architecture of migration timing in a long-distance migratory songbird (purple martin, Progne subis subis) by integrating genomic data with an extensive dataset of direct migratory tracks. A moderate to large amount of variance in spring migration arrival timing was explained by genomics (proportion of phenotypic variation explained by genomics = 0.74; polygenic score R 2 = 0.24). On chromosome 1, a region that was differentiated between migration timing phenotypes contained genes that could facilitate nocturnal flights and act as epigenetic modifiers. Overall, these results advance our understanding of the genomic underpinnings of migration timing.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2045-2322Test

الوصول الحر: https://doaj.org/article/d426aa415a0e44fcb55d826a8c666c33Test

المؤلفون: Gwangseok R. Yoon, Matt J. Thorstensen, William S. Bugg, Ian A. Bouyoucos, David Deslauriers, W. Gary Anderson

المصدر: Ecology and Evolution, Vol 13, Iss 9, Pp n/a-n/a (2023)

مصطلحات موضوعية: fish, intraspecific variation, metabolic scaling, oxygen consumption rate, population, Ecology, QH540-549.5

الوصف: Abstract Environmental temperatures differ across latitudes in the temperate zone, with relatively lower summer and fall temperatures in the north leading to a shorter growing season prior to winter. As an adaptive response, during early life stages, fish in northern latitudes may grow faster than their conspecifics in southern latitudes, which potentially manifests as different allometric relationships between body mass and metabolic rate. In the present study, we examined if population or year class had an effect on the variation of metabolic rate and metabolic scaling of age‐0 lake sturgeon (Acipenser fulvescens) by examining these traits in both a northern (Nelson River) and a southern (Winnipeg River) population. We compiled 6 years of data that used intermittent flow respirometry to measure metabolic rate within the first year of life for developing sturgeon that were raised in the same environment at 16°C. We then used a Bayesian modeling approach to examine the impacts of population and year class on metabolic rate and mass‐scaling of metabolic rate. Despite previous reports of genetic differences between populations, our results showed that there were no significant differences in standard metabolic rate, routine metabolic rate, maximum metabolic rate, and metabolic scaling between the two geographically separated populations at a temperature of 16°C. Our analysis implied that the lack of metabolic differences between populations could be due to family effects/parental contribution, or the rearing temperature used in the study. The present research provided insights for conservation and reintroduction strategies for these populations of lake sturgeon, which are endangered or threatened across most of their natural range.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2045-7758Test

الوصول الحر: https://doaj.org/article/06ea5ac6afb1429fa1135d047ad93b6aTest

المؤلفون: Jennifer D. Jeffrey, Matt J. Thorstensen, Eva C. Enders, Jason R. Treberg, Ken M. Jeffries

المصدر: FACETS, Vol 8, Iss , Pp 1-15 (2023)

مصطلحات موضوعية: RNA-seq, transcriptional plasticity, non-model fish, non-lethal sampling, environmental stress, Education, Science

الوصف: Lake Winnipeg, Manitoba, is Canada’s second largest commercial inland freshwater fishery, and concern over collapse of the walleye fishery is growing. Molecular techniques have been increasingly used to study responses of wild organisms to environmental and anthropogenic stressors. The present study used transcriptomics to examine the physiology of wild-caught walleye (Sander vitreus (Mitchell, 1818)) across Lake Winnipeg using non-lethal techniques. Gill transcriptomes of walleye sampled from the north and south basins of Lake Winnipeg, and the channel connecting them, exhibited distinct profiles implicating regionally specific biological responses. North basin walleye exhibited transcriptomic responses indicative of exposure to environmental stressors. Transcriptomic patterns suggested a shift to increased reliance on anaerobic metabolism and up-regulation of hypoxia-sensitive genes in north basin fish, possibly representing exposure to low-oxygen conditions. Exposure to environmental stressors may also have driven increases in gene transcripts associated with proteasomal catabolism, DNA repair, molecular chaperones, and ion regulation. North basin fish also exhibited transcriptomic patterns indicative of gill remodeling via regulation of the mTOR pathway, cytoskeleton reorganization, and fatty acid synthesis. Our results highlight the complexity of examining wild fish across environmental gradients but also the potential use of molecular techniques in elucidating organismal sensitivity to local environmental factors.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2371-1671Test

الوصول الحر: https://doaj.org/article/7e4af94363e54abc8f9ef7b0adf7c1b5Test

المؤلفون: Matt J. Thorstensen, Peter T. Euclide, Jennifer D. Jeffrey, Yue Shi, Jason R. Treberg, Douglas A. Watkinson, Eva C. Enders, Wesley A. Larson, Yasuhiro Kobayashi, Ken M. Jeffries

المصدر: Ecology and Evolution, Vol 12, Iss 5, Pp n/a-n/a (2022)

مصطلحات موضوعية: adaptive variation, genomic architecture, haplotype, Sander vitreus, selection, walleye, Ecology, QH540-549.5

الوصف: Abstract Differences in genomic architecture between populations, such as chromosomal inversions, may play an important role in facilitating adaptation despite opportunities for gene flow. One system where chromosomal inversions may be important for eco‐evolutionary dynamics is in freshwater fishes, which often live in heterogenous environments characterized by varying levels of connectivity and varying opportunities for gene flow. In the present study, reduced representation sequencing was used to study possible adaptation in n = 345 walleye (Sander vitreus) from three North American waterbodies: Cedar Bluff Reservoir (Kansas, USA), Lake Manitoba (Manitoba, Canada), and Lake Winnipeg (Manitoba, Canada). Haplotype and outlier‐based tests revealed a putative chromosomal inversion that contained three expressed genes and was nearly fixed in walleye assigned to Lake Winnipeg. These patterns exist despite the potential for high gene flow between these proximate Canadian lakes, suggesting that the inversion may be important for facilitating adaptive divergence between the two lakes despite gene flow. However, a specific adaptive role for the putative inversion could not be tested with the present data. Our study illuminates the importance of genomic architecture consistent with local adaptation in freshwater fishes. Furthermore, our results provide additional evidence that inversions may facilitate local adaptation in many organisms that inhabit connected but heterogenous environments.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2045-7758Test

الوصول الحر: https://doaj.org/article/23a9ce89d58747b48966552403ecef23Test

المؤلفون: Matt J. Thorstensen, Melinda R. Baerwald, Ken M. Jeffries

المصدر: BMC Genomics, Vol 22, Iss 1, Pp 1-12 (2021)

مصطلحات موضوعية: Transcriptomics, Microsatellites, Evolution, Plasticity, Population genetics, Outlier test, Biotechnology, TP248.13-248.65, Genetics, QH426-470

الوصف: Abstract Background Messenger RNA sequencing is becoming more common in studies of non-model species and is most often used for gene expression-based investigations. However, the method holds potential for numerous other applications as well—including analyses of alternative splicing, population structure, and signatures of selection. To maximize the utility of mRNA data sets, distinct analyses may be combined such as by exploring dynamics between gene expression with signatures of selection in the context of population structure. Here, we compare two published data sets describing two populations of a minnow species endemic to the San Francisco Estuary (Sacramento splittail, Pogonichthys macrolepidotus): a microsatellite data set showing population structure, and an mRNA whole transcriptome data set obtained after the two populations were exposed to a salinity challenge. We compared measures of population structure and genetic variation using single nucleotide polymorphisms (SNPs) called from mRNA from the whole transcriptome sequencing study with those patterns determined from microsatellites. For investigating plasticity and evolution, intra- and inter-population transcriptome plasticity was investigated with differential gene expression, differential exon usage, and gene expression variation. Outlier SNP analysis was also performed on the mRNA data set and signatures of selection and phenotypic plasticity were investigated on an individual-gene basis. Results We found that mRNA sequencing revealed patterns of population structure consistent with those found with microsatellites, but with lower magnitudes of genetic variation and population differentiation consistent with widespread purifying selection expected when using mRNA. In addition, within individual genes, phenotypic plasticity or signatures of selection were found in almost mutual exclusion (except heatr6, nfu1, slc22a6, sya, and mmp13). Conclusions These results show that an mRNA sequencing data set may have multiple uses, including describing population structure and for investigating the mechanistic interplay of evolution and plasticity in adaptation. MRNA sequencing thus complements traditional sequencing methods used for population genetics, in addition to its utility for describing phenotypic plasticity.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/1471-2164Test

الوصول الحر: https://doaj.org/article/fb81a1e72ac942caad76a0fddb1bac96Test

المؤلفون: Matt J. Thorstensen, Carolyn A. Vandervelde, William S. Bugg, Sonya Michaleski, Linh Vo, Theresa E. Mackey, Michael J. Lawrence, Ken M. Jeffries

المصدر: Frontiers in Genetics, Vol 13 (2022)

مصطلحات موضوعية: sublethal, aquatic, genomic, RNA-seq, transcriptomic, molecular, Genetics, QH426-470

الوصف: Freshwater ecosystems and fishes are enormous resources for human uses and biodiversity worldwide. However, anthropogenic climate change and factors such as dams and environmental contaminants threaten these freshwater systems. One way that researchers can address conservation issues in freshwater fishes is via integrative non-lethal movement research. We review different methods for studying movement, such as with acoustic telemetry. Methods for connecting movement and physiology are then reviewed, by using non-lethal tissue biopsies to assay environmental contaminants, isotope composition, protein metabolism, and gene expression. Methods for connecting movement and genetics are reviewed as well, such as by using population genetics or quantitative genetics and genome-wide association studies. We present further considerations for collecting molecular data, the ethical foundations of non-lethal sampling, integrative approaches to research, and management decisions. Ultimately, we argue that non-lethal sampling is effective for conducting integrative, movement-oriented research in freshwater fishes. This research has the potential for addressing critical issues in freshwater systems in the future.

وصف الملف: electronic resource

العلاقة: https://www.frontiersin.org/articles/10.3389/fgene.2022.795355/fullTest; https://doaj.org/toc/1664-8021Test

الوصول الحر: https://doaj.org/article/d54f0286f6f2450f99d8588a5061a756Test

المؤلفون: Matt J. Thorstensen, Jennifer D. Jeffrey, Jason R. Treberg, Douglas A. Watkinson, Eva C. Enders, Ken M. Jeffries

المصدر: Ecology and Evolution, Vol 10, Iss 14, Pp 7173-7188 (2020)

مصطلحات موضوعية: adaptive variation, gene flow, outlier loci, population genomics, transcriptomics, Ecology, QH540-549.5

الوصف: Abstract RNA sequencing is an effective approach for studying aquatic species yielding both physiological and genomic data. However, its population genetic applications are not well‐characterized. We investigate this possible role for RNA sequencing for population genomics in Lake Winnipeg, Manitoba, Canada, walleye (Sander vitreus). Lake Winnipeg walleye represent the largest component of the second‐largest freshwater fishery in Canada. In the present study, large female walleye were sampled via nonlethal gill biopsy over two years at three spawning sites representing a latitudinal gradient in the lake. Genetic variation from sequenced mRNA was analyzed for neutral and adaptive markers to investigate population structure and possible adaptive variation. We find low population divergence (FST = 0.0095), possible northward gene flow, and outlier loci that vary latitudinally in transcripts associated with cell membrane proteins and cytoskeletal function. These results indicate that Lake Winnipeg walleye may be effectively managed as a single demographically connected metapopulation with contributing subpopulations and suggest genomic differences possibly underlying observed phenotypic differences. Despite its high cost relative to other genotyping methods, RNA sequencing data can yield physiological in addition to genetic information discussed here. We therefore argue that it is useful for addressing diverse molecular questions in the conservation of freshwater species.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2045-7758Test

الوصول الحر: https://doaj.org/article/b8e4858255f14fa0951935d0f2d9496aTest

المؤلفون: Corey A. Krabbenhoft, Stuart A. Ludsin, Elizabeth A. Marschall, Richard R. Budnik, L. Zoe Almeida, Christopher L. Cahill, Holly S. Embke, Zachary S. Feiner, Patrick J. Schmalz, Matt J. Thorstensen, Michael J. Weber, Melissa R. Wuellner, Gretchen J.A. Hansen

المصدر: Fisheries. 48:141-156

مصطلحات موضوعية: Aquatic Science, Nature and Landscape Conservation

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_________::dea23dbe4ecd7cfd28ea7e4f8c607f4eTest
https://doi.org/10.1002/fsh.10884Test

المؤلفون: William S. Bugg, Matt J. Thorstensen, Katie E. Marshall, W. Gary Anderson, Ken M. Jeffries

المصدر: Molecular Ecology.

مصطلحات موضوعية: Genetics, Ecology, Evolution, Behavior and Systematics

الوصف: Rising mean and variance in temperatures elevate threats to endangered freshwater species such as lake sturgeon,Acipenser fulvescens. Previous research demonstrated that higher temperatures during development result in physiological consequences for lake sturgeon populations throughout Manitoba, Canada, with alteration of metabolic rate, thermal tolerance, transcriptional responses, growth, and mortality. We acclimated lake sturgeon (30 – 60 days post fertilization, a period of high mortality) from northern and southern populations (56° 02′ 46.5″ N, 96° 54′ 18.6″ W and 50° 17′ 52″ N, 95° 32′ 51″ W respectively, separated by approximately 650 km) within Manitoba to current (summer highs of 20-23°C) and future projected (+2-3°C) environmental temperatures of 16, 20, and 24°C for 30 days, and measured gill transcriptional responses using RNAseq. Transcripts revealed SNPs consistent with genetically distinct populations and transcriptional responses altered by acclimation temperature. There were a higher number of differentially expressed transcripts observed in the southern, compared to the northern, population as temperatures increased, indicating enhanced transcriptional plasticity. Both lake sturgeon populations responded to elevated acclimation temperatures by downregulating the transcription of genes involved in protein synthesis and energy production. Further, there were population-specific thresholds for the downregulation of processes promoting transcriptional plasticity as well as mitochondrial function as the northern population showed decreases at 20°C, while this capacity was not diminished until 24°C in the southern population. These transcriptional responses highlight the molecular impacts of increasing temperatures for divergent lake sturgeon populations during vulnerable developmental periods and the critical influence of transcriptome plasticity on acclimation capacity.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d7a0a8f16a8acdffe57f9ef991196617Test
https://doi.org/10.1111/mec.16967Test

المؤلفون: Jennifer D. Jeffrey, Lilian M. Wiens, Jason R. Treberg, Ken M. Jeffries, Geoffrey M. Klein, Matt J. Thorstensen

المصدر: Journal of Great Lakes Research. 47:603-613

مصطلحات موضوعية: 0106 biological sciences, Osmerus, Ecology, biology, 010604 marine biology & hydrobiology, Nutritional status, 010501 environmental sciences, Aquatic Science, Structural basin, Protein degradation, biology.organism_classification, Fish measurement, 01 natural sciences, Rainbow smelt, Fishery, 14. Life underwater, Smelt, Ecology, Evolution, Behavior and Systematics, Body condition, 0105 earth and related environmental sciences

الوصف: The invasive rainbow smelt (Osmerus mordax) was an abundant food source for Lake Winnipeg walleye (Sander vitreus), especially in the north basin of the lake, until the smelt’s collapse in approximately 2013. We quantified changing length-at-age (≈ growth rates) and relative mass (≈ body condition) in Lake Winnipeg walleye caught for a gillnet index data set. Here, walleye showed smaller length-at-age, particularly young fish in the north basin, over time. This approach to assessing growth suggests a constraint in the north basin fish, possibly a nutritional limitation between 2017 and 2018, that was not present in the south. We then analyzed a separate group of walleye (≥452 mm in fork length) sampled in 2017 as part of a large-scale tracking study, which had a similar slope in length-mass relationship to large walleye caught in that year for the gillnet index data. A panel of metabolites in whole blood samples associated with amino acid metabolism and protein turnover was compared. These metabolites revealed elevated essential amino acids in fish caught in the Dauphin River, and suggest that protein degradation may be elevated in north basin walleye. Therefore, based on both growth estimates and metabolites associated with protein balance, we suggest there were spatially distinct separations affecting Lake Winnipeg walleye with decreased nutritional status of walleye in the north basin of Lake Winnipeg being of particular concern.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_________::18bcdf06610f6aa9103639163587ca6fTest
https://doi.org/10.1016Test/j.jglr.2020.06.015