Evaluation of in-field DNA degradation of mitochondrial- and genomic DNA in snowsampled faecal pellets from rock ptarmigan (Lagopus muta)
The use of non invasive genetic sampling (NGS) have become increasingly relevant in genetic studies applied to ecology. Reliable methods should be tailored to species and environments. Rock ptarmigan (Lagopus muta) spend their entire lifecycle in the alpine region and roost in snow holes to save ene...
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Høgskolen i Telemark
2012
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Online Access: | http://hdl.handle.net/11250/2438890 |
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fthsbuskerudcom:oai:brage.bibsys.no:11250/2438890 2023-05-15T17:06:22+02:00 Evaluation of in-field DNA degradation of mitochondrial- and genomic DNA in snowsampled faecal pellets from rock ptarmigan (Lagopus muta) Bergan, Frode 2012-11-05T10:28:48Z http://hdl.handle.net/11250/2438890 eng eng Høgskolen i Telemark © Copyright The Author. All rights reserved Fjellryper 480 Master thesis 2012 fthsbuskerudcom 2017-04-28T14:02:17Z The use of non invasive genetic sampling (NGS) have become increasingly relevant in genetic studies applied to ecology. Reliable methods should be tailored to species and environments. Rock ptarmigan (Lagopus muta) spend their entire lifecycle in the alpine region and roost in snow holes to save energy and avoid predation. Faecal pellets (FP) were collected from 20 individual rock ptarmigan snow roosts in the Lifjell mountain area in Telemark, Norway repeatedly between 17 january and 7 july, 2010. DNA was extracted from 146 samples, and degradation evaluated in PCR products of mitochondrial DNA (mtDNA), and 3 genomic DNA (nDNA) microsatellites. For mtDNA, the mean duration in 20 roosts was 73.8 and 59.4 days respectively in a best and worst case scenario. For the 3 nDNA microsatellites, mean duration times varied between 38.8 - 58.1 and 20.9 - 45.8 days respectively in a best and worst case scenario. MtDNA had a significantly longer duration than nDNA, and duration times between individual nDNA microsatellites varied significantly. Overall PCR error rates in the study period were 0.48 for mtDNA and 0.53 - 0.68 for 3 nDNA microsatellites. DNA degradation appeared to accelerate considerably when frozen, snow covered FPs eventually became exposed to higher temperatures and precipitation during the spring snow-melt. FPs from rock ptarmigan snow roosts serves as a promising DNA source in genetic studies, and method may be applied to other snowroosting grouse. Published version Master Thesis Lagopus muta rock ptarmigan University of South-Eastern Norway: USN Open Archive (Brage) Norway Lifjell ENVELOPE(15.314,15.314,66.862,66.862) |
institution |
Open Polar |
collection |
University of South-Eastern Norway: USN Open Archive (Brage) |
op_collection_id |
fthsbuskerudcom |
language |
English |
topic |
Fjellryper 480 |
spellingShingle |
Fjellryper 480 Bergan, Frode Evaluation of in-field DNA degradation of mitochondrial- and genomic DNA in snowsampled faecal pellets from rock ptarmigan (Lagopus muta) |
topic_facet |
Fjellryper 480 |
description |
The use of non invasive genetic sampling (NGS) have become increasingly relevant in genetic studies applied to ecology. Reliable methods should be tailored to species and environments. Rock ptarmigan (Lagopus muta) spend their entire lifecycle in the alpine region and roost in snow holes to save energy and avoid predation. Faecal pellets (FP) were collected from 20 individual rock ptarmigan snow roosts in the Lifjell mountain area in Telemark, Norway repeatedly between 17 january and 7 july, 2010. DNA was extracted from 146 samples, and degradation evaluated in PCR products of mitochondrial DNA (mtDNA), and 3 genomic DNA (nDNA) microsatellites. For mtDNA, the mean duration in 20 roosts was 73.8 and 59.4 days respectively in a best and worst case scenario. For the 3 nDNA microsatellites, mean duration times varied between 38.8 - 58.1 and 20.9 - 45.8 days respectively in a best and worst case scenario. MtDNA had a significantly longer duration than nDNA, and duration times between individual nDNA microsatellites varied significantly. Overall PCR error rates in the study period were 0.48 for mtDNA and 0.53 - 0.68 for 3 nDNA microsatellites. DNA degradation appeared to accelerate considerably when frozen, snow covered FPs eventually became exposed to higher temperatures and precipitation during the spring snow-melt. FPs from rock ptarmigan snow roosts serves as a promising DNA source in genetic studies, and method may be applied to other snowroosting grouse. Published version |
format |
Master Thesis |
author |
Bergan, Frode |
author_facet |
Bergan, Frode |
author_sort |
Bergan, Frode |
title |
Evaluation of in-field DNA degradation of mitochondrial- and genomic DNA in snowsampled faecal pellets from rock ptarmigan (Lagopus muta) |
title_short |
Evaluation of in-field DNA degradation of mitochondrial- and genomic DNA in snowsampled faecal pellets from rock ptarmigan (Lagopus muta) |
title_full |
Evaluation of in-field DNA degradation of mitochondrial- and genomic DNA in snowsampled faecal pellets from rock ptarmigan (Lagopus muta) |
title_fullStr |
Evaluation of in-field DNA degradation of mitochondrial- and genomic DNA in snowsampled faecal pellets from rock ptarmigan (Lagopus muta) |
title_full_unstemmed |
Evaluation of in-field DNA degradation of mitochondrial- and genomic DNA in snowsampled faecal pellets from rock ptarmigan (Lagopus muta) |
title_sort |
evaluation of in-field dna degradation of mitochondrial- and genomic dna in snowsampled faecal pellets from rock ptarmigan (lagopus muta) |
publisher |
Høgskolen i Telemark |
publishDate |
2012 |
url |
http://hdl.handle.net/11250/2438890 |
long_lat |
ENVELOPE(15.314,15.314,66.862,66.862) |
geographic |
Norway Lifjell |
geographic_facet |
Norway Lifjell |
genre |
Lagopus muta rock ptarmigan |
genre_facet |
Lagopus muta rock ptarmigan |
op_rights |
© Copyright The Author. All rights reserved |
_version_ |
1766061499723284480 |