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Hubbard Brook Experimental Forest: Salamander genomic sequences, 2012-2019

General Information
Data Package:
Local Identifier:knb-lter-hbr.398.1
Title:Hubbard Brook Experimental Forest: Salamander genomic sequences, 2012-2019
Alternate Identifier:DOI PLACE HOLDER
Abstract:

This dataset contains genomic sequence reads for salamanders at the Hubbard Brook Experimental Forest. Data were collected from 2012 - 2019.

These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.

Publication Date:2024-03-21
For more information:
Visit: DOI PLACE HOLDER

Time Period
Begin:
2012-06-22
End:
2019-08-16

People and Organizations
Contact:Hubbard Brook Ecosystem Study [  email ]
Creator:Lowe, Winsor H (University of Montana, Division of Biological Sciences)
Creator:Addis, Brett R 
Creator:Cochrane, Madaline M 
Creator:Swartz, Lea K 

Data Entities
Data Table Name:
Manifest_BearBrook_sequences
Description:
Bear Brook genomic sequence manifest
Data Table Name:
Manifest_ParadiseBrook_sequences
Description:
Manifest of Paradise Brook salamander genomic samples
Data Table Name:
Manifest_CanyonCascadeZigzag_sequences
Description:
Manifest of salamander genomic samples from Canyon, Cascade, and Zigzag Brooks
Other Name:
NCBI_Submission1_Bear_placeholder
Description:
Salamander genomic sequences formatted for NCBI submission (Bear Brook)
Other Name:
NCBI_Submission1_CanyonCascadeZigzag_placeholder
Description:
Salamander genomic sequences formatted for NCBI submission (Canyon, Cascade, and Zigzag Brooks)
Other Name:
NCBI_Submission1_Paradise_placeholder
Description:
Salamander genomic sequences formatted for NCBI submission (Paradise Brook)
Detailed Metadata

Data Entities

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-hbr/398/1/6e1385209cfcd0411bff6773a855ca97
Name:Manifest_BearBrook_sequences
Description:Bear Brook genomic sequence manifest
Number of Records:708
Number of Columns:15

Table Structure
Object Name:Manifest_BearBrook_sequences.csv
Size:184994 byte
Authentication:1f3997e78df85859a95e54b8b5c7f8db Calculated By MD5
Text Format:
Number of Header Lines:1
Record Delimiter:\n
Orientation:column
Simple Delimited:
Field Delimiter:,
Quote Character:"

Table Column Descriptions
 sample_namesample_titlebioproject_accessionorganismstrainisolatecultivarecotypecollection_dateenv_broad_scaleenv_local_scaleenv_mediumgeo_loc_nameisol_growth_condtlat_lon
Column Name:sample_name  
sample_title  
bioproject_accession  
organism  
strain  
isolate  
cultivar  
ecotype  
collection_date  
env_broad_scale  
env_local_scale  
env_medium  
geo_loc_name  
isol_growth_condt  
lat_lon  
Definition:Sample nameSample titleBioproject accesion numberDescriptive name of organismOrganism groupDescription of specific individual from which sample was collectedCultivar name, if applicablePopulation within a speciesCollection dataEnvironment where sample was collectedSpecific sampling locationMaterial displaced by organism at time of samplingGeographic location of sampleIsolation and growth condition specificationGeographic location of sample
Storage Type:string  
string  
string  
string  
string  
string  
string  
string  
dateTime  
string  
string  
string  
string  
string  
string  
Measurement Type:nominalnominalnominalnominalnominalnominalnominalnominaldateTimenominalnominalnominalnominalnominalnominal
Measurement Values Domain:
Definitiontext
Definitiontext
Definitiontext
Allowed Values and Definitions
Enumerated Domain 
Code Definition
CodeGyrinophilus porphyriticus
DefinitionGyrinophilus porphyriticus
Source
Definitiontext
Definitiontext
Definitiontext
Definitiontext
FormatYYYY-MM-DD
Precision
Allowed Values and Definitions
Enumerated Domain 
Code Definition
CodeBear Brook
DefinitionBear Brook
Source
Definitiontext
Definitiontext
Allowed Values and Definitions
Enumerated Domain 
Code Definition
CodeUnited States: New Hampshire
DefinitionUnited States: New Hampshire
Source
Definitiontext
Definitiontext
Missing Value Code:                              
Accuracy Report:                              
Accuracy Assessment:                              
Coverage:                              
Methods:                              

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-hbr/398/1/4f81ba9e8e1314ad3fb93ea79e6789b9
Name:Manifest_ParadiseBrook_sequences
Description:Manifest of Paradise Brook salamander genomic samples
Number of Records:762
Number of Columns:15

Table Structure
Object Name:Manifest_ParadiseBrook_sequences.csv
Size:206241 byte
Authentication:083692229100b2580180333249ff245c Calculated By MD5
Text Format:
Number of Header Lines:1
Record Delimiter:\n
Orientation:column
Simple Delimited:
Field Delimiter:,
Quote Character:"

Table Column Descriptions
 sample_namesample_titlebioproject_accessionorganismstrainisolatecultivarecotypecollection_dateenv_broad_scaleenv_local_scaleenv_mediumgeo_loc_nameisol_growth_condtlat_lon
Column Name:sample_name  
sample_title  
bioproject_accession  
organism  
strain  
isolate  
cultivar  
ecotype  
collection_date  
env_broad_scale  
env_local_scale  
env_medium  
geo_loc_name  
isol_growth_condt  
lat_lon  
Definition:Sample nameSample titleBioproject accesion numberDescriptive name of organismOrganism groupDescription of specific individual from which sample was collectedCultivar name, if applicablePopulation within a speciesCollection dataEnvironment where sample was collectedSpecific sampling locationMaterial displaced by organism at time of samplingGeographic location of sampleIsolation and growth condition specificationGeographic location of sample
Storage Type:string  
string  
string  
string  
string  
string  
string  
string  
dateTime  
string  
string  
string  
string  
string  
string  
Measurement Type:nominalnominalnominalnominalnominalnominalnominalnominaldateTimenominalnominalnominalnominalnominalnominal
Measurement Values Domain:
Definitiontext
Definitiontext
Definitiontext
Allowed Values and Definitions
Enumerated Domain 
Code Definition
CodeGyrinophilus porphyriticus
DefinitionGyrinophilus porphyriticus
Source
Definitiontext
Definitiontext
Definitiontext
Definitiontext
FormatYYYY-MM-DD
Precision
Allowed Values and Definitions
Enumerated Domain 
Code Definition
CodeParadise Brook
DefinitionParadise Brook
Source
Definitiontext
Definitiontext
Allowed Values and Definitions
Enumerated Domain 
Code Definition
CodeUnited States: New Hampshire
DefinitionUnited States: New Hampshire
Source
Definitiontext
Definitiontext
Missing Value Code:                              
Accuracy Report:                              
Accuracy Assessment:                              
Coverage:                              
Methods:                              

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-hbr/398/1/05481e1a1831d18e1a1724d74c45e77a
Name:Manifest_CanyonCascadeZigzag_sequences
Description:Manifest of salamander genomic samples from Canyon, Cascade, and Zigzag Brooks
Number of Records:543
Number of Columns:15

Table Structure
Object Name:Manifest_CanyonCascadeZigzag_sequences.csv
Size:145150 byte
Authentication:240069912886aa8c2c4f3561451f7435 Calculated By MD5
Text Format:
Number of Header Lines:1
Record Delimiter:\n
Orientation:column
Simple Delimited:
Field Delimiter:,
Quote Character:"

Table Column Descriptions
 sample_namesample_titlebioproject_accessionorganismstrainisolatecultivarecotypecollection_dateenv_broad_scaleenv_local_scaleenv_mediumgeo_loc_nameisol_growth_condtlat_lon
Column Name:sample_name  
sample_title  
bioproject_accession  
organism  
strain  
isolate  
cultivar  
ecotype  
collection_date  
env_broad_scale  
env_local_scale  
env_medium  
geo_loc_name  
isol_growth_condt  
lat_lon  
Definition:Sample nameSample titleBioproject accesion numberDescriptive name of organismOrganism groupDescription of specific individual from which sample was collectedCultivar name, if applicablePopulation within a speciesCollection dataEnvironment where sample was collectedSpecific sampling locationMaterial displaced by organism at time of samplingGeographic location of sampleIsolation and growth condition specificationGeographic location of sample
Storage Type:string  
string  
string  
string  
string  
string  
string  
string  
dateTime  
string  
string  
string  
string  
string  
string  
Measurement Type:nominalnominalnominalnominalnominalnominalnominalnominaldateTimenominalnominalnominalnominalnominalnominal
Measurement Values Domain:
Definitiontext
Definitiontext
Definitiontext
Allowed Values and Definitions
Enumerated Domain 
Code Definition
CodeGyrinophilus porphyriticus
DefinitionGyrinophilus porphyriticus
Source
Definitiontext
Definitiontext
Definitiontext
Definitiontext
FormatYYYY-MM-DD
Precision
Allowed Values and Definitions
Enumerated Domain 
Code Definition
CodeCanyon Brook
DefinitionCanyon Brook
Source
Code Definition
CodeCascade Brook
DefinitionCascade Brook
Source
Code Definition
CodeZigzag Brook
DefinitionZigzag Brook
Source
Definitiontext
Definitiontext
Allowed Values and Definitions
Enumerated Domain 
Code Definition
CodeUnited States: New Hampshire
DefinitionUnited States: New Hampshire
Source
Definitiontext
Definitiontext
Missing Value Code:                              
Accuracy Report:                              
Accuracy Assessment:                              
Coverage:                              
Methods:                              

Non-Categorized Data Resource

Name:NCBI_Submission1_Bear_placeholder
Entity Type:application/zip
Description:Salamander genomic sequences formatted for NCBI submission (Bear Brook)
Physical Structure Description:
Object Name:NCBI_Submission1_Bear_placeholder.zip
Size:4435705 byte
Authentication:2af1f3c92fde03a5330e63469ea65c1d Calculated By MD5
Externally Defined Format:
Format Name:application/zip
Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-hbr/398/1/75fd040c5d148b33d5465c4756614d6b

Non-Categorized Data Resource

Name:NCBI_Submission1_CanyonCascadeZigzag_placeholder
Entity Type:application/zip
Description:Salamander genomic sequences formatted for NCBI submission (Canyon, Cascade, and Zigzag Brooks)
Physical Structure Description:
Object Name:NCBI_Submission1_CanyonCascadeZigzag_placeholder.zip
Size:4435705 byte
Authentication:2184e1dda487926dfe8fc570b7bcb432 Calculated By MD5
Externally Defined Format:
Format Name:application/zip
Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-hbr/398/1/ef36519928f0c4419af32d263804b0f3

Non-Categorized Data Resource

Name:NCBI_Submission1_Paradise_placeholder
Entity Type:application/zip
Description:Salamander genomic sequences formatted for NCBI submission (Paradise Brook)
Physical Structure Description:
Object Name:NCBI_Submission1_Paradise_placeholder.zip
Size:4435705 byte
Authentication:2184e1dda487926dfe8fc570b7bcb432 Calculated By MD5
Externally Defined Format:
Format Name:application/zip
Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-hbr/398/1/c2b07e75086b2f8fd789b057e743631a

Data Package Usage Rights

This information is released under the Creative Commons license - Attribution - CC BY (https://creativecommons.org/licenses/by/4.0/). The consumer of these data ("Data User" herein) is required to cite it appropriately in any publication that results from its use. The Data User should realize that these data may be actively used by others for ongoing research and that coordination may be necessary to prevent duplicate publication. The Data User is urged to contact the authors of these data if any questions about methodology or results occur. Where appropriate, the Data User is encouraged to consider collaboration or co-authorship with the authors. The Data User should realize that misinterpretation of data may occur if used out of context of the original study. While substantial efforts are made to ensure the accuracy of data and associated documentation, complete accuracy of data sets cannot be guaranteed. All data are made available "as is." The Data User should be aware, however, that data are updated periodically and it is the responsibility of the Data User to check for new versions of the data. The data authors and the repository where these data were obtained shall not be liable for damages resulting from any use or misinterpretation of the data. Thank you.

Keywords

By Thesaurus:
HBES VocabularyHBR, Hubbard Brook Ecosystem Study, Hubbard Brook Experimental Forest, Hubbard Brook LTER, White Mountain National Forest
LTER Controlled Vocabularyecosystems, forests, streams
LTER Core Research Areapopulations
National Research & Development TaxonomyEcology, Ecosystems, & Environment

Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

Methods and protocols used in the collection of this data package
Description:

Methods text goes here

People and Organizations

Publishers:
Organization:Environmental Data Initiative
Email Address:
info@edirepository.org
Web Address:
https://edirepository.org
Id:https://ror.org/0330j0z60
Creators:
Individual: Winsor H Lowe
Organization:University of Montana, Division of Biological Sciences
Address:
32 Campus Drive #4824,
Missoula, MT 59812-4824
Email Address:
winsor.lowe@mso.umt.edu
Id:https://orcid.org/0000-0001-5782-0200
Id:https://ror.org/0078xmk34
Individual: Brett R Addis
Email Address:
addisbrett@gmail.com
Id:https://orcid.org/0000-0002-3794-3200
Individual: Madaline M Cochrane
Email Address:
madaline.cochrane@montana.edu
Id:https://orcid.org/0000-0003-1080-8495
Individual: Lea K Swartz
Contacts:
Organization:Hubbard Brook Ecosystem Study
Email Address:
hbr-im@lternet.edu

Temporal, Geographic and Taxonomic Coverage

Temporal, Geographic and/or Taxonomic information that applies to all data in this dataset:

Time Period
Begin:
2012-06-22
End:
2019-08-16
Geographic Region:
Description:Hubbard Brook Experimental Forest
Bounding Coordinates:
Northern:  43.959Southern:  43.914
Western:  -71.8062Eastern:  -71.7022
Taxonomic Range:
Classification:
Rank Name:Kingdom
Rank Value:Animalia
Common Name:animals
Identifer:https://www.itis.gov
ID: 202423
Classification:
Rank Name:Subkingdom
Rank Value:Bilateria
Common Name:triploblasts
Identifer:https://www.itis.gov
ID: 914154
Classification:
Rank Name:Infrakingdom
Rank Value:Deuterostomia
Identifer:https://www.itis.gov
ID: 914156
Classification:
Rank Name:Phylum
Rank Value:Chordata
Common Name:chordates
Identifer:https://www.itis.gov
ID: 158852
Classification:
Rank Name:Subphylum
Rank Value:Vertebrata
Common Name:vertebrates
Identifer:https://www.itis.gov
ID: 331030
Classification:
Rank Name:Infraphylum
Rank Value:Gnathostomata
Identifer:https://www.itis.gov
ID: 914179
Classification:
Rank Name:Superclass
Rank Value:Tetrapoda
Identifer:https://www.itis.gov
ID: 914181
Classification:
Rank Name:Class
Rank Value:Amphibia
Common Name:Amphibians
Identifer:https://www.itis.gov
ID: 173420
Classification:
Rank Name:Order
Rank Value:Caudata
Common Name:Salamanders
Identifer:https://www.itis.gov
ID: 173584
Classification:
Rank Name:Family
Rank Value:Plethodontidae
Common Name:Lungless Salamanders
Identifer:https://www.itis.gov
ID: 173631
Classification:
Rank Name:Subfamily
Rank Value:Hemidactyliinae
Identifer:https://www.itis.gov
ID: 773221
Classification:
Rank Name:Genus
Rank Value:Gyrinophilus
Common Name:Cave Salamanders
Identifer:https://www.itis.gov
ID: 173713
Classification:
Rank Name:Species
Rank Value:Gyrinophilus porphyriticus
Common Name:Spring Salamander
Identifer:https://www.itis.gov
ID: 173715

Project

Parent Project Information:

Title:Salamander studies at the Hubbard Brook Experimental Forest
Personnel:
Individual: Winsor H Lowe
Organization:University of Montana, Division of Biological Sciences
Address:
32 Campus Drive #4824,
Missoula, MT 59812-4824
Email Address:
winsor.lowe@mso.umt.edu
Id:https://orcid.org/0000-0001-5782-0200
Id:https://ror.org/0078xmk34
Additional Award Information:
Funder:National Science Foundation
Funder ID:https://ror.org/021nxhr62
Number:2224545
Title:LTER: Long Term Ecological Research at the Hubbard Brook Experimental Forest (2022)
URL:https://www.nsf.gov/awardsearch/showAward?AWD_ID=2224545
Additional Award Information:
Funder:National Science Foundation
Funder ID:https://ror.org/021nxhr62
Number:1637685
Title:LTER: Long Term Ecological Research at the Hubbard Brook Experimental Forest (2016)
URL:https://www.nsf.gov/awardsearch/showAward?AWD_ID=1637685
Additional Award Information:
Funder:National Science Foundation
Funder ID:https://ror.org/021nxhr62
Number:1633026
Title:LTER: Long-Term Ecological Research at the Hubbard Brook Experimental Forest (2016b)
URL:https://www.nsf.gov/awardsearch/showAward?AWD_ID=1633026
Additional Award Information:
Funder:National Science Foundation
Funder ID:https://ror.org/021nxhr62
Number:1114804
Title:LTER: Long-Term Ecological Research at Hubbard Brook Experimental Forest (2010)
URL:https://www.nsf.gov/awardsearch/showAward?AWD_ID=1114804
Additional Award Information:
Funder:National Science Foundation
Funder ID:https://ror.org/021nxhr62
Number:DEB-1655653
Title:The causes and consequences of variation in dispersal distance (Lowe)
URL:https://www.nsf.gov/awardsearch/showAward?AWD_ID=1655653
Additional Award Information:
Funder:National Science Foundation
Funder ID:https://ror.org/021nxhr62
Number:1050459
Title:Coexistence in Stream Metacommunities (Lowe)
URL:https://www.nsf.gov/awardsearch/showAward?AWD_ID=1050459

Maintenance

Maintenance:
Description:

knb-lter-hbr.398.1: initial dataset submission

Frequency:asNeeded
Other Metadata

Additional Metadata

additionalMetadata
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        |___element 'metadata'
        |     |___text '\n         '
        |     |___element 'emlEditor'
        |     |        \___attribute 'app' = 'ezEML'
        |     |        \___attribute 'release' = '2024.02.21'
        |     |___text '\n      '
        |___text '\n   '

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