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Artikel ; Online: Genomic architecture of migration timing in a long-distance migratory songbird.

de Greef, Evelien / Suh, Alexander / Thorstensen, Matt J / Delmore, Kira E / Fraser, Kevin C

2023 Band 13, Heft 1, Seite(n) 2437

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, ... ...

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
Mesh-Begriff(e)	Animals ; Songbirds/genetics ; Animal Migration ; Seasons ; Genomics ; Swallows
Sprache	Englisch
Erscheinungsdatum	2023-02-10
Erscheinungsland	England
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-29470-7
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Tissue-specific transcriptomes reveal potential mechanisms of microbiome heterogeneity in an ancient fish.

Thorstensen, Matt J / Weinrauch, Alyssa M / Bugg, William S / Jeffries, Ken M / Anderson, W Gary

Database : the journal of biological databases and curation

2023 Band 2023

Abstract: The lake sturgeon (Acipenser fulvescens) is an ancient, octoploid fish faced with conservation challenges across its range in North America, but a lack of genomic resources has hindered molecular research in the species. To support such research, we ... ...

Abstract	The lake sturgeon (Acipenser fulvescens) is an ancient, octoploid fish faced with conservation challenges across its range in North America, but a lack of genomic resources has hindered molecular research in the species. To support such research, we created a transcriptomic database from 13 tissues: brain, esophagus, gill, head kidney, heart, white muscle, liver, glandular stomach, muscular stomach, anterior intestine, pyloric cecum, spiral valve and rectum. The transcriptomes for each tissue were sequenced and assembled individually from a mean of 98.3 million (±38.9 million SD) reads each. In addition, an overall transcriptome was assembled and annotated with all data used for each tissue-specific transcriptome. All assembled transcriptomes and their annotations were made publicly available as a scientific resource. The non-gut transcriptomes provide important resources for many research avenues. However, we focused our analysis on messenger ribonucleic acid (mRNA) observations in the gut because the gut represents a compartmentalized organ system with compartmentalized functions, and seven of the sequenced tissues were from each of these portions. These gut-specific analyses were used to probe evidence of microbiome regulation by studying heterogeneity in microbial genes and genera identified from mRNA annotations. Gene set enrichment analyses were used to reveal the presence of photoperiod and circadian-related transcripts in the pyloric cecum, which may support periodicity in lake sturgeon digestion. Similar analyses were used to identify different types of innate immune regulation across the gut, while analyses of unique transcripts annotated to microbes revealed heterogeneous genera and genes among different gut tissues. The present results provide a scientific resource and information about the mechanisms of compartmentalized function across gut tissues in a phylogenetically ancient vertebrate. Database URL: https://figshare.com/projects/Lake_Sturgeon_Transcriptomes/133143.
Mesh-Begriff(e)	Animals ; Transcriptome/genetics ; Fishes/genetics ; Gene Expression Profiling ; Databases, Factual ; Genomics
Sprache	Englisch
Erscheinungsdatum	2023-08-16
Erscheinungsland	England
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2496706-3
ISSN	1758-0463 ; 1758-0463
ISSN (online)	1758-0463
ISSN	1758-0463
DOI	10.1093/database/baad055
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: RNA sequencing describes both population structure and plasticity-selection dynamics in a non-model fish.

Thorstensen, Matt J / Baerwald, Melinda R / Jeffries, Ken M

BMC genomics

2021 Band 22, Heft 1, Seite(n) 273

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 ... ...

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.
Mesh-Begriff(e)	Animals ; Cyprinidae ; Genetics, Population ; Microsatellite Repeats/genetics ; Polymorphism, Single Nucleotide ; Selection, Genetic ; Sequence Analysis, RNA ; Whole Exome Sequencing
Sprache	Englisch
Erscheinungsdatum	2021-04-15
Erscheinungsland	England
Dokumenttyp	Journal Article
ISSN	1471-2164
ISSN (online)	1471-2164
DOI	10.1186/s12864-021-07592-4
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Elevated temperatures reduce population-specific transcriptional plasticity in developing lake sturgeon (Acipenser fulvescens).

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

Molecular ecology

2023 Band 32, Heft 14, Seite(n) 4044–4062

Abstract: Rising mean and variance in temperatures elevates threats to endangered freshwater species such as lake sturgeon, Acipenser fulvescens. Previous research demonstrated that higher temperatures during development result in physiological consequences for ... ...

Abstract	Rising mean and variance in temperatures elevates 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 we 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. Furthermore, 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.
Mesh-Begriff(e)	Animals ; Temperature ; Fishes/physiology ; Canada ; Fresh Water ; Manitoba ; Endangered Species
Sprache	Englisch
Erscheinungsdatum	2023-05-07
Erscheinungsland	England
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.16967
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Elevated temperatures reduce population‐specific transcriptional plasticity in developing lake sturgeon (Acipenser fulvescens)

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

Molecular Ecology. 2023 July, v. 32, no. 14 p.4044-4062

2023

Abstract	Rising mean and variance in temperatures elevates 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 we 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. Furthermore, 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.
Schlagwörter	Acipenser fulvescens ; acclimation ; energy ; freshwater ; gene expression regulation ; heat tolerance ; mitochondria ; mortality ; protein synthesis ; summer ; temperature ; transcription (genetics) ; transcriptome ; variance ; Manitoba
Sprache	Englisch
Erscheinungsverlauf	2023-07
Umfang	p. 4044-4062.
Erscheinungsort	John Wiley & Sons, Ltd
Dokumenttyp	Artikel ; Online
Anmerkung	JOURNAL ARTICLE
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.16967
Datenquelle	NAL Katalog (AGRICOLA)

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Artikel ; Online: Acute thermal stress elicits interactions between gene expression and alternative splicing in a fish of conservation concern.

Thorstensen, Matt J / Turko, Andy J / Heath, Daniel D / Jeffries, Ken M / Pitcher, Trevor E

The Journal of experimental biology

2022 Band 225, Heft 12

Abstract: Transcriptomic research provides a mechanistic understanding of an organism's response to environmental challenges such as increasing temperatures, which can provide key insights into the threats posed by thermal challenges associated with urbanization ... ...

Abstract	Transcriptomic research provides a mechanistic understanding of an organism's response to environmental challenges such as increasing temperatures, which can provide key insights into the threats posed by thermal challenges associated with urbanization and climate change. Differential gene expression and alternative splicing are two elements of the transcriptomic stress response that may work in tandem, but relatively few studies have investigated these interactions in fishes of conservation concern. We studied the imperilled redside dace (Clinostomus elongatus) as thermal stress is hypothesized to be an important cause of population declines. We tested the hypothesis that gene expression-splicing interactions contribute to the thermal stress response. Wild fish exposed to acute thermal stress were compared with both handling controls and fish sampled directly from a river. Liver tissue was sampled to study the transcriptomic stress response. With a gene set enrichment analysis, we found that thermally stressed fish showed a transcriptional response related to transcription regulation and responses to unfolded proteins, and alternatively spliced genes related to gene expression regulation and metabolism. One splicing factor, prpf38b, was upregulated in the thermally stressed group compared with the other treatments. This splicing factor may have a role in the Jun/AP-1 cellular stress response, a pathway with wide-ranging and context-dependent effects. Given large gene interaction networks and the context-dependent nature of transcriptional responses, our results highlight the importance of understanding interactions between gene expression and splicing for understanding transcriptomic responses to thermal stress. Our results also reveal transcriptional pathways that can inform conservation breeding, translocation and reintroduction programs for redside dace and other imperilled species by identifying appropriate source populations.
Mesh-Begriff(e)	Alternative Splicing ; Animals ; Cyprinidae/physiology ; RNA Splicing Factors ; Temperature ; Transcriptome
Chemische Substanzen	RNA Splicing Factors
Sprache	Englisch
Erscheinungsdatum	2022-06-27
Erscheinungsland	England
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218085-6
ISSN	1477-9145 ; 0022-0949
ISSN (online)	1477-9145
ISSN	0022-0949
DOI	10.1242/jeb.244162
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: Comparison of metabolic rate between two genetically distinct populations of lake sturgeon.

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

Ecology and evolution

2023 Band 13, Heft 9, Seite(n) e10470

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 ... ...

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 (
Sprache	Englisch
Erscheinungsdatum	2023-08-30
Erscheinungsland	England
Dokumenttyp	Journal Article
ZDB-ID	2635675-2
ISSN	2045-7758
ISSN	2045-7758
DOI	10.1002/ece3.10470
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: Morphology and blood metabolites reflect recent spatial and temporal differences among Lake Winnipeg walleye, Sander vitreus

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

International Association for Great Lakes Research Journal of Great Lakes research. 2021 June, v. 47, no. 3

2021

Abstract: 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 (≈ ... ...

Abstract	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.
Schlagwörter	Osmerus mordax ; Sander vitreus ; amino acid metabolism ; basins ; blood ; body condition ; data collection ; fish ; gillnets ; lakes ; metabolites ; nutritional status ; protein degradation ; research ; rivers
Sprache	Englisch
Erscheinungsverlauf	2021-06
Umfang	p. 603-613.
Erscheinungsort	Elsevier B.V.
Dokumenttyp	Artikel
Anmerkung	NAL-AP-2-clean
ZDB-ID	2163239-X
ISSN	0380-1330 ; 0380-1330
ISSN (online)	0380-1330
ISSN	0380-1330
DOI	10.1016/j.jglr.2020.06.015
Datenquelle	NAL Katalog (AGRICOLA)

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Artikel: Non-Lethal Sampling Supports Integrative Movement Research in Freshwater Fish.

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

Frontiers in genetics

2022 Band 13, Seite(n) 795355

Abstract: 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 ... ...

Abstract	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
Sprache	Englisch
Erscheinungsdatum	2022-04-25
Erscheinungsland	Switzerland
Dokumenttyp	Journal Article ; Review
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2022.795355
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: A chromosomal inversion may facilitate adaptation despite periodic gene flow in a freshwater fish.

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

Ecology and evolution

2022 Band 12, Heft 5, Seite(n) e8898

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- ... ...

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
Sprache	Englisch
Erscheinungsdatum	2022-05-07
Erscheinungsland	England
Dokumenttyp	Journal Article
ZDB-ID	2635675-2
ISSN	2045-7758
ISSN	2045-7758
DOI	10.1002/ece3.8898
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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