Emily C Palmquist
Gerard J Allan
20210422
Plant genetic structure data from riparian areas within the Grand Canyon region in northern Arizona
comma-separated tabular data
Flagstaff, AZ
U.S. Geological Survey
https://doi.org/10.5066/P9JLNJGJ
Emily C. Palmquist
Gerard J. Allan
Kiona Ogle
Thomas Whitham
Bradley J. Butterfield
Patrick B. Shafroth
2021
Riverine complexity and life history inform restoration in riparian environments in the southwestern U.S.
journal manuscript
Wiley Online Library
Restoration Ecology
https://doi.org/10.1111/rec.13418
These data represent nuclear microsatellite data collected from four riparian plant species that occur in and around Grand Canyon National Park: Populus fremontii (POFR), Salix gooddingii (SAGO), Salix exigua (SAEX), and Prosopis glandulosa (PRGL). These data were collected for population genetic analysis to help inform native plant material development in Grand Canyon National Park. Leaf samples were collected at sites spanning 470 km of the Colorado River between Glen Canyon Dam and Lake Mead and in tributaries. Known revegetation areas were not sampled. We aimed to collect leaf tissue from at least 15 individuals at each sample site. If there were fewer than 15 individuals per species at a site, leaf tissue was collected from every individual. Leaves were immediately dried and stored in silica gel. For P. fremontii, S. gooddingii, and P. glandulosa, total genomic DNA was extracted from dried leaf tissue using a high-molecular weight protocol with modifications. For S. exigua, DNeasy Plant Minikits were used. We amplified 9, 9, 11, and 13 loci for P. fremontii, S. gooddingii, S. exigua, and P. glandulosa, respectively. All loci were amplified using polymerase chain reaction (PCR) and fragment analysis processed on an ABI 3730xl Genetic Analyzer with GeneScan LIZ500 internal size standard. Allele fragment sizes were scored using GeneMarker v2.2.0. Loci that were missing more than 5% of values, were not polymorphic, or could not be reliably scored were omitted. Nine loci were included for P. fremontii, six for S. gooddingii, eight for P. glandulosa, and nine for S. exigua. All species are diploid, so each microsatellite locus has two values. Associated with the microsatellite data are labels delineating what collection site each individual came from, which genetic group each individual was assigned to during statistical analyses, and information about those sites. Specifically, sites are noted as being on the Colorado River or on a tributary to it, and inside or outside of the canyon rims.
The purpose of these data are to characterize population genetic structure and variability in four riparian plant species that occur in and around Grand Canyon National Park: Populus fremontii (POFR), Salix gooddingii (SAGO), Salix exigua (SAEX), and Prosopis glandulosa (PRGL). These data provide information on how genetically similar individual plants of the same species are within a complex, generally dry landscape. Analyses using these data can help guide riparian restoration decisions.
These data were developed for population genetic analyses of 4 plant species; Populus fremontii (POFR), Salix gooddingii (SAGO), Salix exigua (SAEX), and Prosopis glandulosa (PRGL). They can be used to estimate genetic diversity, genetic structure, genetic relatedness, etc. Caution should be used when comparing these data to other genetic marker types (e.g., SNPs, AFLPs). If combining these data with microsatellite data of these species from other locations, caution should be used if different loci are included in the other datasets. Data users should read the entire metadata record and acquire the manuscript identified as the ‘Larger Work Citation’ to have a complete understanding of how these data were created and used. The data are specific to the uses identified above, as described in the ‘Larger Work Citation’, and any other use of these data would be inappropriate. See 'Distribution liability' statements for more information.
2017
2019
ground condition
None planned
-114.02379
-111.2000
36.965854
35.4250
USGS Thesaurus
conservation genetics
genetics
wetland ecosystems
plants (organisms)
biogeography
population and community ecology
USGS Biocomplexity Thesaurus
Genetic diversity
Population characteristics
ISO 19115 Topic Categories
biota
USGS Metadata Identifier
USGS:5f43d6c182ce4c3d1222d319
None
cottonwood
mesquite
willow
Nuclear microsatellite
population genetics
riparian plants
Geographic Names Information System (GNIS)
Arizona
Colorado River
Glen Canyon
Glen Canyon Dam
Grand Canyon
Grand Canyon National Park
Lake Mead
None
northern Arizona
southwestern U.S.
southwestern United States
none
none
Emily C Palmquist
U.S. Geological Survey
Student Trainee (Biology)
mailing and physical
2255 North Gemini Drive
Flagstaff
AZ
86001
US
928-556-7397
epalmquist@usgs.gov
This research was funded by the U.S. Bureau of Reclamation through the Glen Canyon Dam Adaptive Management Program.
No formal attribute accuracy tests were conducted
No formal logical accuracy tests were conducted
Data set is considered complete for the information presented, as described in the abstract. Users are advised to read the rest of the metadata record carefully for additional details.
No formal positional accuracy tests were conducted
No formal positional accuracy tests were conducted
Development of POFR data table: We aimed to collect leaf tissue from at least 15 individuals at each sample site. If there were fewer than 15 individuals per species at a site, leaf tissue was collected from every individual. Leaves were immediately dried and stored in silica gel. Total genomic DNA was extracted from dried leaf tissue using a high-molecular weight protocol with modifications. After screening a selection of microsatellite loci for amplification, variability, and repeatable scoring across the range, we amplified 9 loci for P. fremontii. All loci were amplified using polymerase chain reaction (PCR) and fragment analysis processed on an ABI 3730xl Genetic Analyzer with GeneScan LIZ500 internal size standard. Allele fragment sizes were scored using GeneMarker v2.2.0. Loci that were missing more than 5% of values, were not polymorphic, or could not be reliably scored were omitted. Frequency of null alleles was estimated using a Bayesian Individual Inbreeding Model (IIM) implemented in INEST v. 2.2. None of the loci had high estimated null allele frequencies. Statistical analyses were compared with and without loci that had >0.1 estimated frequencies. No loci changed the interpretation of the analyses, so were all included. All nine amplified loci were included for P. fremontii.
2018
Development of PRGL data table: We aimed to collect leaf tissue from at least 15 individuals at each sample site. If there were fewer than 15 individuals per species at a site, leaf tissue was collected from every individual. Leaves were immediately dried and stored in silica gel. Total genomic DNA was extracted from dried leaf tissue using a high-molecular weight protocol with modifications. After screening a selection of microsatellite loci for amplification, variability, and repeatable scoring across the range, we amplified 13 loci for Prosopis glandulosa. All loci were amplified using polymerase chain reaction (PCR) and fragment analysis processed on an ABI 3730xl Genetic Analyzer with GeneScan LIZ500 internal size standard. Allele fragment sizes were scored using GeneMarker v2.2.0. Loci that were missing more than 5% of values, were not polymorphic, or could not be reliably scored were omitted. Frequency of null alleles was estimated using a Bayesian Individual Inbreeding Model (IIM) implemented in INEST v. 2.2. None of the loci had high estimated null allele frequencies. Statistical analyses were compared with and without loci that had >0.1 estimated frequencies. No loci changed the interpretation of the analyses, so were all included. Eight loci remained for Prosopis glandulosa.
2019
Development of SAEX data table: We aimed to collect leaf tissue from at least 15 individuals at each sample site. If there were fewer than 15 individuals per species at a site, leaf tissue was collected from every individual. Leaves were immediately dried and stored in silica gel. Total genomic DNA was extracted from dried leaf tissue using DNeasy Plant Minikits. After screening a selection of microsatellite loci for amplification, variability, and repeatable scoring across the range, we amplified 11 loci for Salix exigua. All loci were amplified using polymerase chain reaction (PCR) and fragment analysis processed on an ABI 3730xl Genetic Analyzer with GeneScan LIZ500 internal size standard. Allele fragment sizes were scored using GeneMarker v2.2.0. Loci that were missing more than 5% of values, were not polymorphic, or could not be reliably scored were omitted. Frequency of null alleles was estimated using a Bayesian Individual Inbreeding Model (IIM) implemented in INEST v. 2.2. None of the loci had high estimated null allele frequencies. Statistical analyses were compared with and without loci that had >0.1 estimated frequencies. No loci changed the interpretation of the analyses, so were all included. Nine loci remained for S. exigua.
2019
Development of SAGO data table: We aimed to collect leaf tissue from at least 15 individuals at each sample site. If there were fewer than 15 individuals per species at a site, leaf tissue was collected from every individual. Leaves were immediately dried and stored in silica gel. Total genomic DNA was extracted from dried leaf tissue using a high-molecular weight protocol with modifications. After screening a selection of microsatellite loci for amplification, variability, and repeatable scoring across the range, we amplified 9 loci for Salix gooddingii. All loci were amplified using polymerase chain reaction (PCR) and fragment analysis processed on an ABI 3730xl Genetic Analyzer with GeneScan LIZ500 internal size standard. Allele fragment sizes were scored using GeneMarker v2.2.0. Loci that were missing more than 5% of values, were not polymorphic, or could not be reliably scored were omitted. Frequency of null alleles was estimated using a Bayesian Individual Inbreeding Model (IIM) implemented in INEST v. 2.2. None of the loci had high estimated null allele frequencies. Statistical analyses were compared with and without loci that had >0.1 estimated frequencies. No loci changed the interpretation of the analyses, so were all included. Six loci remained for S. gooddingii.
2018
Data Quality Assessment and Quality Control (QAQC): Standard processes for DNA extract and PCR quality control were followed throughout. DNA extract quality and quantity was checked using a NanoDrop spectrophotometer and gel electrophoresis. Each locus for each species was tested independently for consistent amplification and repeatable assignment of genotypes. PCR amplification was optimized for each locus, then for multiplexes of loci. In both gel and capillary electrophoresis, amplified fragments were compared to a known size standard to ensure that the PCR product consisted of alleles of the expected size range. Multiplexes of loci were developed using loci with similar amplification processes, but different fragment sizes. For capillary electrophoresis, optimal dilutions of PCR product were determined for each locus, then each multiplex set of loci, to keep the fluorescence signal within a similar range as the size standard (~200 - 4,000 relative florescence units). No template controls and template replicates were included in PCR reactions to check for cross-contamination and repeatability. Automated allele calls were made in GeneMarker using panels developed for each locus. Allele calls were verified by hand. The few samples that failed (no alleles) or had more than two peaks were redone.
2019
Finalize Data for Dissemination: Data sent to the Southwest Biological Science Center Data Steward for dissemination and preservation per USGS Data Management Policies SM 502.6, SM 502.7, SM 502.8 and SM 502.9 (1 October 2016).
2021
POFR data table
These are microsatellite data for 191 Populus fremontii individuals. Rows represent individuals of P. fremontii. The attributes PMGC333, GCPM2315, GCPM3457, GCPM1685, GCPM2900, GCPM3681, ORPM60, GCPM961, GCPM3907 represent loci. The remaining attributes are grouping variables. DNA voucher information is included in Appendix S1:Table S1 (see Larger Work Citation). Information regarding the locus repeat motif, primer sequences, fragment sizes, allelic richness, and source are provided in Appendix S1: Table S2 (see Larger Work Citation). Diversity estimates for each locus are provided in Appendix S1: Table S4 (see Larger Work Citation).
Producer defined
ind_code
This is an arbitrary number assigned to each individual for tracking purposes.
Producer defined
4
198
integer number
PMGC333
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
GCPM2315
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
GCPM3457
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
GCPM1685
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
GCPM2900
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
GCPM3681
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
ORPM60
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
GCPM961
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
GCPM3907
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
site_code
This grouping variable indicates the collection sites of the individual. This is a short-hand code that matches figures and tables in the manuscript (see Appendix S1: Table S1 and Table S3, Larger Work Citation).
Producer defined
a textual description at the data collection point, to assist in identifying its location (see Appendix S1: Table S1, Larger Work Citation)
site_name
This grouping variable indicates the collection sites of the individual. This is a nickname for each site based on the locality.
Producer defined
a textual description at the data collection point, to assist in identifying its location
river
This is a grouping variable indicating if the individual was collected on the Colorado River or in a tributary to the Colorado River. All P. fremontii were collected in tributaries.
Producer defined
trib
Tributary to the Colorado River
Producer defined
rim
This is a grouping variable indicating if the individual was collected outside of the canyons that characterize the Grand Canyon region, inside the canyons, or in the Glen Canyon region.
Producer defined
above = outside of the canyons that characterize the Grand Canyon region, below = inside the canyons, glca = in the Glen Canyon region
NJ_grp
This is a grouping variable indicating which genetic group the individual was assigned to when using a neighbor-joining tree.
Producer defined
Each group was assigned a name based on the primary geographic locality of that genetic group.
structure
This is a grouping variable indicating which genetic group the individual was assigned to when using STRUCTURE analysis.
Producer defined
Each group was assigned a name based on the primary geographic locality of that genetic group.
PRGL data table
These are microsatellite data for 225 Prosopis glandulosa individuals. Rows represent individuals of P. glandulosa. The attributes MO05, GL12, GL9, GL8, GL16 , GL18 , MO08, GL26 represent loci. The remaining attributes are grouping variables. DNA voucher information is included in Appendix S1:Table S1 (see Larger Work Citation). Information regarding the locus repeat motif, primer sequences, fragment sizes, allelic richness, and source are provided in Appendix S1: Table S2 (see Larger Work Citation). Diversity estimates for each locus are provided in Appendix S1: Table S4 (see Larger Work Citation).
Producer defined
ind_code
This is an arbitrary number assigned to each individual for tracking purposes.
Producer defined
1
241
integer number
MO05
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
GL12
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
GL9
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
GL8
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
GL16
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
GL18
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
MO08
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
GL26
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
site_code
This grouping variable indicates the collection sites of the individual. This is a short-hand code that matches figures and tables in the manuscript (see Appendix S1: Table S1 and Table S3, Larger Work Citation).
Producer defined
a textual description at the data collection point, to assist in identifying its location (see Appendix S1: Table S1, Larger Work Citation)
site_name
This grouping variable indicates the collection sites of the individual. This is a nickname for each site based on the locality.
Producer defined
a textual description at the data collection point, to assist in identifying its location
river
This is a grouping variable indicating if the individual was collected on the Colorado River (Mainstem) or in a tributary to the Colorado River (Trib).
Producer defined
Mainstem
Mainstem of the Colorado River
Producer defined
trib
Tributary to the Colorado River
Producer defined
rim
This is a grouping variable indicating if the individual was collected outside of the canyons that characterize the Grand Canyon region (rim) or inside the canyons (canyon).
Producer defined
canyon = inside the canyons, below = inside the canyons, rim = outside of the canyons that characterize the Grand Canyon region
NJ_grps
This is a grouping variable indicating which genetic group the individual was assigned to when using a neighbor-joining tree.
Producer defined
Each group was assigned a name based on the primary geographic locality of that genetic group.
structure
This is a grouping variable indicating which genetic group the individual was assigned to when using STRUCTURE analysis.
Producer defined
Each group was assigned a name based on the primary geographic locality of that genetic group.
SAEX data table
These are microsatellite data for 308 Salix exigua individuals. Rows represent individuals of S. exigua. The attributes SB80, SB243, SB210, SB85, SB88, SB233, SB207, Shum_060, PMGC223 represent loci. The remaining attributes are grouping variables. DNA voucher information is included in Appendix S1:Table S1 (see Larger Work Citation). Information regarding the locus repeat motif, primer sequences, fragment sizes, allelic richness, and source are provided in Appendix S1: Table S2 (see Larger Work Citation). Diversity estimates for each locus are provided in Appendix S1: Table S4 (see Larger Work Citation).
Producer defined
ind_code
This is an arbitrary number assigned to each individual for tracking purposes.
Producer defined
1
324
integer number
sb80
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
sb243
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
sb210
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
sb85
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
sb88
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
sb233
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
sb207
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
shum60
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
pgmc223
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
site_code
This grouping variable indicates the collection sites of the individual. This is a short-hand code that matches figures and tables in the manuscript (see Appendix S1: Table S1 and Table S3, Larger Work Citation).
Producer defined
a textual description at the data collection point, to assist in identifying its location (see Appendix S1: Table S1, Larger Work Citation)
site_name
This grouping variable indicates the collection sites of the individual. This is a nickname for each site based on the locality.
Producer defined
a textual description at the data collection point, to assist in identifying its location
river
This is a grouping variable indicating if the individual was collected on the Colorado River (Mainstem) or in a tributary to the Colorado River (Trib).
Producer defined
Mainstem
Mainstem of the Colorado River
Producer defined
trib
Tributary to the Colorado River
Producer defined
rim
This is a grouping variable indicating if the individual was collected outside of the canyons that characterize the Grand Canyon region (above) or inside the canyons (below).
Producer defined
above = outside of the canyons that characterize the Grand Canyon region, below = inside the canyons
NJ_grps
This is a grouping variable indicating which genetic group the individual was assigned to when using a neighbor-joining tree.
Producer defined
Each group was assigned a name based on the primary geographic locality of that genetic group.
structure
This is a grouping variable indicating which genetic group the individual was assigned to when using STRUCTURE analysis.
Producer defined
Each group was assigned a name based on the primary geographic locality of that genetic group.
SAGO data table
These are microsatellite data for 139 Salix gooddingii individuals. Rows represent individuals of S. goodingii. The attributes SB207, SB243, SB88, SB196, Shum76, Shum66 represent loci. The remaining attributes are grouping variables. DNA voucher information is included in Appendix S1:Table S1 (see Larger Work Citation). Information regarding the locus repeat motif, primer sequences, fragment sizes, allelic richness, and source are provided in Appendix S1: Table S2 (see Larger Work Citation). Diversity estimates for each locus are provided in Appendix S1: Table S4 (see Larger Work Citation).
Producer defined
ind_code
This is an arbitrary number assigned to each individual for tracking purposes.
Producer defined
4
184
integer number
sb207
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
sb243
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
sb88
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
sb196
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
Shum76
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
Shum66
These values represent the fragment size for each chromome at this locus.
Producer defined
a combination of integer numbers that represent the fragment size for each chromome at this locus
site_code
This grouping variable indicates the collection sites of the individual. This is a short-hand code that matches figures and tables in the manuscript (see Appendix S1: Table S1 and Table S3, Larger Work Citation).
Producer defined
a textual description at the data collection point, to assist in identifying its location (see Appendix S1: Table S1, Larger Work Citation)
site_name
This grouping variable indicates the collection sites of the individual. This is a nickname for each site based on the locality.
Producer defined
a textual description at the data collection point, to assist in identifying its location
river
This is a grouping variable indicating if the individual was collected on the Colorado River (Mainstem) or in a tributary to the Colorado River (Trib).
Producer defined
main
Mainstem of the Colorado River
Producer defined
trib
Tributary to the Colorado River
Producer defined
rim
This is a grouping variable indicating if the individual was collected outside of the canyons that characterize the Grand Canyon region (above) or inside the canyons (below).
Producer defined
above = outside of the canyons that characterize the Grand Canyon region, below = inside the canyons
NJ_grp
This is a grouping variable indicating which genetic group the individual was assigned to when using a neighbor-joining tree.
Producer defined
Each group was assigned a name based on the primary geographic locality of that genetic group.
structure
This is a grouping variable indicating which genetic group the individual was assigned to when using STRUCTURE analysis.
Producer defined
Each group was assigned a name based on the primary geographic locality of that genetic group.
U.S. Geological Survey - ScienceBase
U.S. Geological Survey
mailing and physical
Denver Federal Center, Building 810, Mail Stop 302
Denver
CO
80225
United States
1-888-275-8747
sciencebase@usgs.gov
The author(s) of these data request that data users contact them regarding intended use and to assist with understanding limitations and interpretation. Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display or utility of the data for other purposes, nor on all computer systems, nor shall the act of distribution constitute any such warranty.
The data in this zip file contains data in comma-separated (.csv) file format. The user must have software capable of uncompressing the zip file and software capable of reading or displaying machine-readable tabular data.
20210422
Emily C Palmquist
U.S. Geological Survey
Student Trainee (Biology)
mailing and physical
2255 North Gemini Drive
Flagstaff
AZ
86001
US
928-556-7397
epalmquist@usgs.gov
Content Standard for Digital Geospatial Metadata
FGDC-STD-001-1998