Data_Sheet_1_Historical DNA Metabarcoding of the Prey and Microbiome of Trematomid Fishes Using Museum Samples.docx
Antarctic specimens collected during various research expeditions are preserved in natural history collections around the world potentially offering a cornucopia of morphological and molecular data. Historical samples of marine species are, however, often preserved in formaldehyde which may render t...
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ftfrontimediafig:oai:figshare.com:article/7145684 2023-05-15T13:56:49+02:00 Data_Sheet_1_Historical DNA Metabarcoding of the Prey and Microbiome of Trematomid Fishes Using Museum Samples.docx Franz M. Heindler Henrik Christiansen Bruno Frédérich Agnes Dettaï Gilles Lepoint Gregory E. Maes Anton P. Van de Putte Filip A. M. Volckaert 2018-09-28T06:24:17Z https://doi.org/10.3389/fevo.2018.00151.s001 https://figshare.com/articles/Data_Sheet_1_Historical_DNA_Metabarcoding_of_the_Prey_and_Microbiome_of_Trematomid_Fishes_Using_Museum_Samples_docx/7145684 unknown doi:10.3389/fevo.2018.00151.s001 https://figshare.com/articles/Data_Sheet_1_Historical_DNA_Metabarcoding_of_the_Prey_and_Microbiome_of_Trematomid_Fishes_Using_Museum_Samples_docx/7145684 CC BY 4.0 CC-BY Evolutionary Biology Ecology Invasive Species Ecology Landscape Ecology Conservation and Biodiversity Behavioural Ecology Community Ecology (excl. Invasive Species Ecology) Ecological Physiology Freshwater Ecology Marine and Estuarine Ecology (incl. Marine Ichthyology) Population Ecology Terrestrial Ecology natural history museum notothenioidei 16S rRNA COI Southern Ocean Antarctica Dataset 2018 ftfrontimediafig https://doi.org/10.3389/fevo.2018.00151.s001 2018-10-03T22:57:28Z Antarctic specimens collected during various research expeditions are preserved in natural history collections around the world potentially offering a cornucopia of morphological and molecular data. Historical samples of marine species are, however, often preserved in formaldehyde which may render them useless for genetic analysis. We sampled stomachs and hindguts from 225 Trematomus specimens from the Natural History Museum London. These samples were initially collected between 20 and 100 years ago and fixed in either formaldehyde or ethanol. A 313 bp fragment of the cytochrome c oxidase subunit I (COI) was amplified and sequenced for prey item identification in the stomach and a 450 bp region of the 16S rRNA gene to investigate microbiome composition in the gut system. Both data sets were characterized by large dropout rates during extensive quality controls. Eventually, no unambiguous results regarding stomach content (COI) were retained, possibly due to degraded DNA, inefficient primers and contamination. In contrast, reliable microbiome composition data (16S rRNA) was obtained from 26 samples. These data showed a correlation in change of microbiome composition with fish size as well as year of the catch, indicating a microbiome shift throughout ontogeny and between samples from different decades. A comparison with contemporary samples indicated that the intestinal microbiome of Trematomus may have drastically changed within the last century. Further extensive studies are needed to confirm these patterns with higher sample numbers. Molecular analyses of museum stored fish can provide novel micro evolutionary insights that may benefit current efforts to prioritize conservation units in the Southern Ocean. Dataset Antarc* Antarctic Antarctica Southern Ocean Frontiers: Figshare Antarctic Southern Ocean |
institution |
Open Polar |
collection |
Frontiers: Figshare |
op_collection_id |
ftfrontimediafig |
language |
unknown |
topic |
Evolutionary Biology Ecology Invasive Species Ecology Landscape Ecology Conservation and Biodiversity Behavioural Ecology Community Ecology (excl. Invasive Species Ecology) Ecological Physiology Freshwater Ecology Marine and Estuarine Ecology (incl. Marine Ichthyology) Population Ecology Terrestrial Ecology natural history museum notothenioidei 16S rRNA COI Southern Ocean Antarctica |
spellingShingle |
Evolutionary Biology Ecology Invasive Species Ecology Landscape Ecology Conservation and Biodiversity Behavioural Ecology Community Ecology (excl. Invasive Species Ecology) Ecological Physiology Freshwater Ecology Marine and Estuarine Ecology (incl. Marine Ichthyology) Population Ecology Terrestrial Ecology natural history museum notothenioidei 16S rRNA COI Southern Ocean Antarctica Franz M. Heindler Henrik Christiansen Bruno Frédérich Agnes Dettaï Gilles Lepoint Gregory E. Maes Anton P. Van de Putte Filip A. M. Volckaert Data_Sheet_1_Historical DNA Metabarcoding of the Prey and Microbiome of Trematomid Fishes Using Museum Samples.docx |
topic_facet |
Evolutionary Biology Ecology Invasive Species Ecology Landscape Ecology Conservation and Biodiversity Behavioural Ecology Community Ecology (excl. Invasive Species Ecology) Ecological Physiology Freshwater Ecology Marine and Estuarine Ecology (incl. Marine Ichthyology) Population Ecology Terrestrial Ecology natural history museum notothenioidei 16S rRNA COI Southern Ocean Antarctica |
description |
Antarctic specimens collected during various research expeditions are preserved in natural history collections around the world potentially offering a cornucopia of morphological and molecular data. Historical samples of marine species are, however, often preserved in formaldehyde which may render them useless for genetic analysis. We sampled stomachs and hindguts from 225 Trematomus specimens from the Natural History Museum London. These samples were initially collected between 20 and 100 years ago and fixed in either formaldehyde or ethanol. A 313 bp fragment of the cytochrome c oxidase subunit I (COI) was amplified and sequenced for prey item identification in the stomach and a 450 bp region of the 16S rRNA gene to investigate microbiome composition in the gut system. Both data sets were characterized by large dropout rates during extensive quality controls. Eventually, no unambiguous results regarding stomach content (COI) were retained, possibly due to degraded DNA, inefficient primers and contamination. In contrast, reliable microbiome composition data (16S rRNA) was obtained from 26 samples. These data showed a correlation in change of microbiome composition with fish size as well as year of the catch, indicating a microbiome shift throughout ontogeny and between samples from different decades. A comparison with contemporary samples indicated that the intestinal microbiome of Trematomus may have drastically changed within the last century. Further extensive studies are needed to confirm these patterns with higher sample numbers. Molecular analyses of museum stored fish can provide novel micro evolutionary insights that may benefit current efforts to prioritize conservation units in the Southern Ocean. |
format |
Dataset |
author |
Franz M. Heindler Henrik Christiansen Bruno Frédérich Agnes Dettaï Gilles Lepoint Gregory E. Maes Anton P. Van de Putte Filip A. M. Volckaert |
author_facet |
Franz M. Heindler Henrik Christiansen Bruno Frédérich Agnes Dettaï Gilles Lepoint Gregory E. Maes Anton P. Van de Putte Filip A. M. Volckaert |
author_sort |
Franz M. Heindler |
title |
Data_Sheet_1_Historical DNA Metabarcoding of the Prey and Microbiome of Trematomid Fishes Using Museum Samples.docx |
title_short |
Data_Sheet_1_Historical DNA Metabarcoding of the Prey and Microbiome of Trematomid Fishes Using Museum Samples.docx |
title_full |
Data_Sheet_1_Historical DNA Metabarcoding of the Prey and Microbiome of Trematomid Fishes Using Museum Samples.docx |
title_fullStr |
Data_Sheet_1_Historical DNA Metabarcoding of the Prey and Microbiome of Trematomid Fishes Using Museum Samples.docx |
title_full_unstemmed |
Data_Sheet_1_Historical DNA Metabarcoding of the Prey and Microbiome of Trematomid Fishes Using Museum Samples.docx |
title_sort |
data_sheet_1_historical dna metabarcoding of the prey and microbiome of trematomid fishes using museum samples.docx |
publishDate |
2018 |
url |
https://doi.org/10.3389/fevo.2018.00151.s001 https://figshare.com/articles/Data_Sheet_1_Historical_DNA_Metabarcoding_of_the_Prey_and_Microbiome_of_Trematomid_Fishes_Using_Museum_Samples_docx/7145684 |
geographic |
Antarctic Southern Ocean |
geographic_facet |
Antarctic Southern Ocean |
genre |
Antarc* Antarctic Antarctica Southern Ocean |
genre_facet |
Antarc* Antarctic Antarctica Southern Ocean |
op_relation |
doi:10.3389/fevo.2018.00151.s001 https://figshare.com/articles/Data_Sheet_1_Historical_DNA_Metabarcoding_of_the_Prey_and_Microbiome_of_Trematomid_Fishes_Using_Museum_Samples_docx/7145684 |
op_rights |
CC BY 4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fevo.2018.00151.s001 |
_version_ |
1766264396427821056 |