Frullania nisquallensis Species Confirmation, Attu Island, Alaska, 2018

Identification_Information:

Citation:

Citation_Information:

Originator: Talbot, S.L. (ORCID: 0000-0002-3312-7214)
Originator: Pierson, B.J. (ORCID: 0000-0001-8233-874X)
Originator: Gravley, M.C. (ORCID: 0000-0002-4947-0236)
Originator: Sage, G.K. (ORCID: 0000-0003-1431-2286)
Publication_Date: 20180525
Title:

Geospatial_Data_Presentation_Form: spreadsheet
Publication_Information:

Publication_Place: Anchorage, AK
Publisher: U.S. Geological Survey, Alaska Science Center

Other_Citation_Details:

Suggested citation: Talbot, S.L., Pierson, B.J., Gravley, M.C., and Sage, G.K., 2018, Frullania nisquallensis Species Confirmation, Attu Island, Alaska, 2018: U.S. Geological Survey data release, https://doi.org/10.5066/P92H3W9D.

Online_Linkage: https://doi.org/10.5066/P92H3W9D
Larger_Work_Citation:

Citation_Information:

Originator: Talbot, S.L. (ORCID: 0000-0002-3312-7214)
Publication_Date: 2000
Title:

Developing and Applying Molecular Tools to Natural Resource Problems in Alaska

Geospatial_Data_Presentation_Form: web site
Online_Linkage: https://alaska.usgs.gov/portal/project.php?project_id=378

Description:

Abstract:

This dataset contains sampling, molecular methods, and partial tRNA-Leu DNA sequence information for three individual Frullania nisquallensis.

Purpose:

A genetic species determination to either Frullania nisquallensis or Frullania subarctica was required in a review of an associated manuscript (see cross-reference below). The samples in question were archived along with others in the original collection at UBC, and the three in question were accessed for the current analyses.

Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2018

Currentness_Reference: observed

Status:

Progress: Complete
Maintenance_and_Update_Frequency: None planned

Spatial_Domain:

Description_of_Geographic_Extent: Attu Island, Aleutian Islands, Alaska, USA.
Bounding_Coordinates:

West_Bounding_Coordinate: 172.15
East_Bounding_Coordinate: 172.23
North_Bounding_Coordinate: 52.85
South_Bounding_Coordinate: 52.82

Keywords:

Theme:

Theme_Keyword_Thesaurus: USGS Metadata Identifier
Theme_Keyword: USGS:ASC181

Theme:

Theme_Keyword_Thesaurus: ISO 19115 Topic Category
Theme_Keyword: biota

Theme:

Theme_Keyword_Thesaurus: MeSH-National Library of Medicine
Theme_Keyword: Frullania
Theme_Keyword: Hepatophyta
Theme_Keyword: Sequence Analysis, DNA

Theme:

Theme_Keyword_Thesaurus: USGS Thesaurus
Theme_Keyword: sciences
Theme_Keyword: life sciences
Theme_Keyword: genetics
Theme_Keyword: polymerase chain reaction
Theme_Keyword: vegetation
Theme_Keyword: DNA sequencing
Theme_Keyword: botany
Theme_Keyword: morphology (biological)
Theme_Keyword: systematics and taxonomy

Theme:

Theme_Keyword_Thesaurus: USGS CSA Biocomplexity Thesaurus
Theme_Keyword: Plants
Theme_Keyword: Bryophyta
Theme_Keyword: Bryophytes
Theme_Keyword: Liverworts

Theme:

Theme_Keyword_Thesaurus: NASA GCMD Earth Science Keywords Thesaurus
Theme_Keyword: earth science
Theme_Keyword: biological classification
Theme_Keyword: plants
Theme_Keyword: mosses/hornworts/liverworts

Place:

Place_Keyword_Thesaurus: USGS Geographic Names Information System
Place_Keyword: State of Alaska
Place_Keyword: Attu Island
Place_Keyword: West Mountains
Place_Keyword: Kingfisher Creek
Place_Keyword: Casco Bay
Place_Keyword: Massacre Bay

Place:

Place_Keyword_Thesaurus: none
Place_Keyword: 37 Hill

Taxonomy:

Keywords/Taxon:

Taxonomic_Keyword_Thesaurus: None
Taxonomic_Keywords: Frullania nisquallensis
Taxonomic_Keywords: collection
Taxonomic_Keywords: single species
Taxonomic_Keywords: plants
Taxonomic_Keywords: vegetation

Taxonomic_System:

Classification_System/Authority:

Classification_System_Citation:

Citation_Information:

Originator: Söderström, L.
Originator: A. Hagborg
Originator: M. von Konrat
Originator: S. Bartholomew-Began
Originator: David Bell
Originator: L. Briscoe
Originator: E. Brown
Originator: D. Christine Cargill
Originator: D. P. Costa
Originator: B. J. Crandall-Stotler
Originator: E. D. Cooper
Originator: G. Dauphin
Originator: J. J. Engel
Originator: K. Feldberg
Originator: D. Glenny
Originator: S. Robbert Gradstein
Originator: X. He
Originator: J. Heinrichs
Originator: J. Hentschel
Originator: A. Luiza Ilkiu-Borges
Originator: T. Katagiri
Originator: N. A. Konstantinova
Originator: J. Larraín
Originator: D. G. Long
Originator: M. Nebel
Originator: T. Pócs
Originator: F. Puche
Originator: E. Reiner-Drehwald
Originator: M. A. M. Renner
Originator: A. Sass-Gyarmati
Originator: A. Schäfer-Verwimp
Originator: J. Gabriel Segarra Moragues
Originator: R. E. Stotler
Originator: P. Sukkharak
Originator: B. M. Thiers
Originator: J. Uribe
Originator: J. Váňa
Originator: J. Carlos Villarreal
Originator: M. Wigginton
Originator: L. Zhang
Originator: R.-L. Zhu
Publication_Date: 2016
Title: World checklist of hornworts and liverworts
Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: PhytoKeys
Issue_Identification: 59

Publication_Information:

Publication_Place: Online
Publisher: Pensoft Publishers

Online_Linkage: https://phytokeys.pensoft.net/articles.php?id=6261

Taxonomic_Procedures:

Species were identified by skilled observers in the field based on morphology and habitat.

Vouchers:

Specimen: herbarium specimens
Repository:

Contact_Information:

Contact_Person_Primary:

Contact_Person: Olivia Lee
Contact_Organization: UBC Herbarium-Beaty Biodiversity Museum

Contact_Position: Bryophyte Collection Manager
Contact_Address:

Address_Type: mailing and physical
Address: University of British Columbia
Address: 3529-6270 University Blvd.
City: Vancouver
State_or_Province: British Columbia
Postal_Code: V6T 1Z4
Country: Canada

Contact_Voice_Telephone: 604.822.3344
Contact_Facsimile_Telephone: 604.822.6089
Contact_Electronic_Mail_Address: ubc.herbarium@ubc.ca

Taxonomic_Classification:

Taxon_Rank_Name: Kingdom
Taxon_Rank_Value: Plantae
Taxonomic_Classification:

Taxon_Rank_Name: Division
Taxon_Rank_Value: Marchantiophyta
Taxonomic_Classification:

Taxon_Rank_Name: Class
Taxon_Rank_Value: Jungermanniopsida
Taxonomic_Classification:

Taxon_Rank_Name: Subclass
Taxon_Rank_Value: Jungermanniidae
Taxonomic_Classification:

Taxon_Rank_Name: Order
Taxon_Rank_Value: Porellales
Taxonomic_Classification:

Taxon_Rank_Name: Suborder
Taxon_Rank_Value: Jubulineae
Taxonomic_Classification:

Taxon_Rank_Name: Family
Taxon_Rank_Value: Frullaniaceae
Taxonomic_Classification:

Taxon_Rank_Name: Genus
Taxon_Rank_Value: Frullania
Taxonomic_Classification:

Taxon_Rank_Name: Species
Taxon_Rank_Value: Frullania nisquallensis

Access_Constraints: None.
Use_Constraints:

If you use these data in a publication, presentation, or other product, it is requested that you credit USGS and the authors of this data for their contribution to your work.

Point_of_Contact:

Contact_Information:

Contact_Organization_Primary:

Contact_Organization: U.S. Geological Survey, Alaska Science Center

Contact_Address:

Address_Type: Mailing and Physical
Address: 4210 University Drive
City: Anchorage
State_or_Province: AK
Postal_Code: 99508
Country: USA

Contact_Voice_Telephone: 907-786-7000
Contact_Electronic_Mail_Address: ascweb@usgs.gov

Data_Set_Credit:

Tissue samples for DNA extraction and analyses were obtained from the University of British Columbia Beaty Biodiversity Museum, 2212 Main Mall, Vancouver, B.C. Canada V5T 1Z4; info@beatymuseum.ubc.ca; tel. 604-827-4955; fax 604-822-0686 (Accession No. B183630, B183733, B186122[collection number 116193]).

Cross_Reference:

Citation_Information:

Originator: Talbot, S.S.
Originator: Schofield, W.B.
Originator: Vana, J.
Originator: Talbot, S.L. (ORCID: 0000-0002-3312-7214)
Publication_Date: 2018
Title:

Liverworts from Attu Island, Near Islands, Aleutian Islands, Alaska with comparison to the Commander Islands, Russian Federation

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Botanica Pacifica
Issue_Identification: TBD

Publication_Information:

Publication_Place: online
Publisher:

Botanical Garden-Institute Far Eastern Branch Russian Academy of Sciences

Online_Linkage: http://dx.doi.org/10.17581/bp

Data_Quality_Information:

Attribute_Accuracy:

Attribute_Accuracy_Report:

University of British Columbia Beaty Biodiversity Museum Accession and Collection numbers/sampling information were cross-checked and verified to match the accompanying metadata and worksheet. One sample was found to share an accession number (B186122) with an unrelated specimen, so both UBC Accession and Collection numbers should be used to reference the correct specimen (Collection number 116193). Latitude/longitude inconsistencies (UBC coordinates did not map to Attu Island) were confirmed with collectors and presented location data in conjunction with verbal location descriptions are believed to be accurate. Collectors have requested UBC database correction. Sampling locations were formally labelled and cross-referenced to the Geographic Names Information Service (GNIS). For quality control purposes, DNA was extracted and sequenced bidirectionally and ambiguities resolved by comparing forward and reverse sequence. Any unresolvable ambiguities were edited manually with IUPAC nucleotide codes.

Logical_Consistency_Report:

Sequences obtained were entered into the National Center for Biotechnology Information (NCBI) nucleotide Basic Local Alignment Search Tool (BLAST) and searched against all Frullania (taxid:95763) to identify most concordant species identification.

Completeness_Report:

All samples reported include complete sequence and sampling data.

Positional_Accuracy:

Horizontal_Positional_Accuracy:

Horizontal_Positional_Accuracy_Report:

Geospatial data were acquired from the contributing data sources. These methods were not documented in the source data.

Lineage:

Methodology:

Methodology_Type: Lab
Methodology_Description:

Extraction and DNA quantification procedures followed Gravley et al. (2018).

Methodology_Citation:

Citation_Information:

Originator: Gravley, M.C. (ORCID: 0000-0002-4947-0236)
Originator: Sage, G.K. (ORCID: 0000-0003-1431-2286)
Originator: Talbot, S.L. (ORCID: 0000-0002-3312-7214)
Originator: Carlson, M.L.
Publication_Date: 20180423
Title:

Development and characterization of 12 polymorphic microsatellite loci in the sea sandwort, Honckenya peploides (L.) Ehrh.

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: J. Plant Res.
Issue_Identification: not assigned by publisher

Publication_Information:

Publication_Place: Online
Publisher: Springer Japan

Other_Citation_Details: https://link.springer.com/journal/10265
Online_Linkage: https://doi.org/10.1007/s10265-018-1036-7

Methodology:

Methodology_Type: Lab
Methodology_Description:

Primer sequences (F) 5'-AATAGGTGCAGAGACTCG-3' (R) 5-'CCCTCATGGTCTATAAAGCC-3' were designed spanning conserved Frullania subarctica and F. nisquallensis sequences of portions of trna-L publicly available in Genbank (NCBI Sequences for Frullania, 2018).

Methodology:

Methodology_Type: Lab
Methodology_Description:

Polymerase chain reaction (PCR) amplifications were carried out in a 20-μL volume with 2–100 ng genomic DNA, 0.5 μM each primer, 1.0 μM dNTPs, 10× PCR Perkin Elmer Cetus #1 buffer, and 0.2 units Taq polymerase. PCR reactions began with 94 ºC for 10 min followed by 40 cycles of 94°C for 30 sec, 50 °C for 30 sec, and 72 °C for 90 sec with a 30 min final extension at 72 °C. ExoSAP-IT® (USB Corporation, Cleveland, OH) was used to remove excess primers and dNTPs in PCR products. Purified products were cycle-sequenced via simultaneous bidirectional sequencing (SBS; LI-COR 1999) using a commercial kit (Sequitherm LCII 2.0: Epicentre Technologies, Madison, WI).

Source_Information:

Source_Citation:

Citation_Information:

Originator: UBC
Publication_Date: 2018
Title: UBC, 2018
Geospatial_Data_Presentation_Form: samples
Series_Information:

Series_Name:

Index Herbariorum: A Global Directory of Public Herbaria and Associated Staff

Issue_Identification: New York Botanical Garden’s Virtual Herbarium

Publication_Information:

Publication_Place: online
Publisher: New York Botanical Garden

Other_Citation_Details:

UBC is the discipline-recognized (http://sweetgum.nybg.org/science/ih/) designation for the University of British Columbia, Beaty Museum of Biodiversity, Herbarium.

Online_Linkage: http://bridge.botany.ubc.ca/herbarium/database.php

Type_of_Source_Media: Tissue samples
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2018

Source_Currentness_Reference: observed

Source_Citation_Abbreviation: UBC, 2018
Source_Contribution:

Tissue samples for DNA extraction and analyses were obtained from the University of British Columbia Beaty Biodiversity Museum, 2212 Main Mall, Vancouver, B.C. Canada V5T 1Z4; info@beatymuseum.ubc.ca; tel. 604-827-4955; fax 604-822-0686 (Accession/Collection No. B183630/115271, B183733/115424, B186122/116193).

Source_Information:

Source_Citation:

Citation_Information:

Originator: Unknown
Publication_Date: 20180510
Title:

tRNA-Leu (trnL) gene, partial sequences of Frullania subarctica and F. nisquallensis, GenBank

Geospatial_Data_Presentation_Form: application/service
Online_Linkage: https://www.ncbi.nlm.nih.gov/genbank/

Type_of_Source_Media: Digital and/or Hardcopy
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 201805

Source_Currentness_Reference: observed

Source_Citation_Abbreviation: NCBI Sequences for Frullania, 2018
Source_Contribution:

Five sequences of Frullania subarctica (Genbank Accessions: KC918787, KC918788, KC918789, KC918790, KC918791) and 12 sequences of Frullania nisquallensis (Genbank Accessions: HM167701, HM167702, HM167703, HM167704, HM167705, HM167706, HM167707, HM167708, HM167709, HM167710, HM167711, HM167712) were used to identify areas conserved across species for primer design which encompassed variable sites that differentiate the two species and for alignment of sequences obtained in the current study.

Source_Information:

Source_Citation:

Citation_Information:

Originator: Unknown
Publication_Date: 20180510
Title: Reference database of known Frullania DNA sequences, NCBI
Geospatial_Data_Presentation_Form: application/service
Online_Linkage:

https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

Type_of_Source_Media: Digital and/or Hardcopy
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 20180510

Source_Currentness_Reference: observed

Source_Citation_Abbreviation: NCBI Frullania Blast Search, 2018
Source_Contribution:

DNA sequences obtained in the current study were queried against all known Frullania sequences in GenBank using the Basic Local Alignment Search Tool (BLAST) and confirmed to be more concordant with F. nisquallensis, than F. subarctica.

Source_Information:

Source_Citation:

Citation_Information:

Development and characterization of 12 polymorphic microsatellite loci in the sea sandwort, Honckenya peploides (L.) Ehrh.

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: J. Plant Res.
Issue_Identification: not assigned by publisher

Publication_Information:

Publication_Place: Online
Publisher: Springer Japan

Other_Citation_Details: https://link.springer.com/journal/10265
Online_Linkage: https://doi.org/10.1007/s10265-018-1036-7

Type_of_Source_Media: Publication
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 20180423

Source_Currentness_Reference: observed

Source_Citation_Abbreviation: Gravley et al., 2018
Source_Contribution: DNA extraction methods

Process_Step:

Process_Description:

tRNA-Leu(trnL) gene partial sequences from opposite strands were reconciled using LI-COR eSeq imaging software with visual proofing and aligned using AlignIR 2.0 (LI-COR, Inc., Lincoln, NE).

Process_Date: 20180506

Process_Step:

Process_Description:

The resulting 224 base pair sequence (partial tRNA-Leu[trnL] gene) of the three samples in the current study were aligned using AlignIR 2.0 (LI-COR, Inc., Lincoln, NE) to the five Frullania subarctica and 12 sequences of Frullania nisquallensis used for primer design (NCBI Sequences for Frullania, 2018). Three variable sites were identified: one insertion at position 34 was found in one of the reference F. nisquallensis (HM167712) and one of the samples in the current study and positions 62 and 138 were substitutions shared with F. nisquallensis references and not F. subarctica.

Process_Date: 20180506

Process_Step:

Process_Description:

Resulting partial tRNA-L sequences from samples in this study were queried against all publicly available Frullania (taxid:95763) sequences in GenBank and noted to align most concordantly with Frullania nisquallensis (NCBI Frullania Blast Search, 2018).

Source_Used_Citation_Abbreviation: NCBI Frullania Blast Search, 2018
Process_Date: 20180531

Entity_and_Attribute_Information:

Detailed_Description:

Entity_Type:

Entity_Type_Label: frullania_trnlSequence_Attu_Talbot_2000.csv
Entity_Type_Definition: Data set
Entity_Type_Definition_Source: Author defined

Attribute:

Attribute_Label: UBC_Accession
Attribute_Definition:

The UBC_Accession is the University of British Columbia's Herbarium Bryophyte database accession number and, in conjunction with the UBC_Collection attribute, identifies the individual specimen from which DNA was extracted for this data release.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

The collection number is a 6 digit unique identifier, in this case preceded with the letter "B" indicating the specimen is from their Bryophyte collection.

Attribute:

Attribute_Label: UBC_Collection
Attribute_Definition:

The UBC_Collection is the University of British Columbia's Herbarium Bryophyte database collection number and, in conjunction with the UBC_Accession attribute, identifies the individual specimen from which DNA was extracted for this data release.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain: The collection number is a 6 digit unique identifier.

Attribute:

Attribute_Label: Species
Attribute_Definition: Species determination assigned to the specimen.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Frullania nisquallensis
Enumerated_Domain_Value_Definition:

This indicates the specimen was collected and identified in the field as Frullania nisquallensis [Sull.]

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: Latitude
Attribute_Definition:

This indicates the latitude at which the specimen was sampled from the field.

Attribute_Definition_Source: Confirmed by field botanist, S.S. Talbot
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 52.84299389
Range_Domain_Maximum: 52.85269972
Attribute_Units_of_Measure: decimal degrees

Attribute:

Attribute_Label: Longitude
Attribute_Definition:

This indicates the longitude at which the specimen was sampled from the field.

Attribute_Definition_Source: Confirmed by field botanist, S.S. Talbot
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 173.15
Range_Domain_Maximum: 173.2425
Attribute_Units_of_Measure: decimal degrees

Attribute:

Attribute_Label: Elevation
Attribute_Definition:

This indicates the elevation in meters at which the specimen was sampled from the field.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 76.2
Range_Domain_Maximum: 213.36
Attribute_Units_of_Measure: meters

Attribute:

Attribute_Label: Site_Description
Attribute_Definition:

The Site_Description indicates the sampling location using general terms based on known land marks.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Place names used in the Site_Description were cross-referenced to the Geographic Names Information Service (GNIS) when possible. "37 Hill" could not be located in a formal record and is presumed to be a local placename.

Attribute:

Attribute_Label: Date_Collected
Attribute_Definition:

The Date_Collected indicates the date a specimen was obtained from the field.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 2000 Aug 03
Range_Domain_Maximum: 2000 Aug 26
Attribute_Units_of_Measure: YYYY MMM DD

Attribute:

Attribute_Label: Collector
Attribute_Definition:

The Collector indicates names of the botanists credited with collecting the specimen.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: W.B. Schofield
Enumerated_Domain_Value_Definition: This specimen is credited to Wilfred Borden Schofield.
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: W.B. Schofield, S.S. Talbot
Enumerated_Domain_Value_Definition:

This specimen is credited to Wilfred Borden Schofield and Stephen S. Talbot.

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: Lab_ID
Attribute_Definition: Lab_ID indicates the Alaska Science Center sample label.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: FRNI 116193
Enumerated_Domain_Value_Definition:

The "FRNI" is an abbreviation of the genus (Frullania) and species (nisquallensis) followed by the UBC Herbarium bryophyte database collection number.

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: FRNI 115271
Enumerated_Domain_Value_Definition:

The "FRNI" is an abbreviation of the genus (Frullania) and species (nisquallensis) followed by the UBC Herbarium bryophyte database collection number.

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: FRNI 115424
Enumerated_Domain_Value_Definition:

The "FRNI" is an abbreviation of the genus (Frullania) and species (nisquallensis) followed by the UBC Herbarium bryophyte database collection number.

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: GenBank_Accession
Attribute_Definition:

This is the NCBI GenBank Accession Number. This number may be used to retrieve detailed sample and sequence information from https://www.ncbi.nlm.nih.gov/.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

This is an alphanumeric accession number searchable from https://www.ncbi.nlm.nih.gov/.

Frullania nisquallensis Species Confirmation, Attu Island, Alaska, 2018

Metadata: