Mitochondrial COXI sequences and associated metazoan abundances in soils collected from the McMurdo Dry Valleys, Antarctica from 1995 to 2022

Summary

Abstract: 

As part of an ongoing long-term sampling effort conducted by the McMurdo Dry Valleys Long Term Ecological Research (LTER) project, the top 10 cm of soil was collected from sampling sites across the McMurdo Dry Valleys region of Antarctica. A subset of these samples representing each valley and a differing disturbance legacy from the last glacial maximum were analyzed for this data package. Samples were collected between 1995 and 2022. In each sample, the abundances of three genera of nematodes (Scottnema, Eudorylaimus, and Plectus), tardigrades, and rotifers were calculated. Following metazoan extractions, individual Scottnema lindsayae were selected for mitochondrial Cytochrome c oxidase I (COX1) Sanger dideoxy sequencing. Sequencing resulted in 249 assembled sequences of 285 base pairs after alignment and trimming.

Date Range: 

December 1, 1995 to February 28, 2022
Data Citation
Jackson, A.C., Wall, D.H., Adams, B.J. 2023. Mitochondrial COXI sequences and associated metazoan abundances in soils collected from the McMurdo Dry Valleys, Antarctica from 1995 to 2022. Environmental Data Initiative. DOI: 10.6073/pasta/45337fb617c40312ea55ea97133a4c5e. Dataset accessed 15 July 2024.
Dataset(s)

Description: 

List of each individual Scottnema lindsayae sanger sequenced for a portion of the mitochondrial DNA COX1 gene and the corresponding aligned and trimmed sequences.

Variables (click to expand): 

dataset_code
  • Label: Dataset Code
  • Definition: Internal dataset code.
  • Type: Nominal
  • Missing values: None specified
sequence_id
  • Label: Sequence ID
  • Definition: Individual Scottnema lindsayae sequence identifier.
  • Type: Nominal
  • Missing values: None specified
site
  • Label: Site Name
  • Definition: Name of the location where soils were sampled.
  • Type: Nominal
  • Missing values: None specified
species
  • Label: Species
  • Definition: Species identity.
  • Type: Nominal
  • Missing values: None specified
seq_coi
  • Label: Sequence
  • Definition: Assembled sequences from a portion of the mitochondrial COX1 gene.
  • Type: Nominal
  • Missing values: None specified
ncbi_accn
  • Label: NCBI Accession Number
  • Definition: NCBI nucleotide accession number corresponding with each sequence. https://www.ncbi.nlm.nih.gov/nuccore/?term=OP456699:OP456947[accn]
  • Type: Nominal
  • Missing values: None specified

Description: 

List of each individual Scottnema sanger sequenced for 28S large subunit ribosomal ribonucleic acid (LSU) and the corresponding aligned and trimmed LSU sequence.

Variables (click to expand): 

dataset_code
  • Label: Dataset Code
  • Definition: Internal dataset code.
  • Type: Nominal
  • Missing values: None specified
sequence_id
  • Label: Sequence ID
  • Definition: Individual Scottnema lindsayae sequence identifier.
  • Type: Nominal
  • Missing values: None specified
site
  • Label: Site Name
  • Definition: Name of the location where soils were sampled.
  • Type: Nominal
  • Missing values: None specified
species
  • Label: Species
  • Definition: Species identity.
  • Type: Nominal
  • Missing values: None specified
seq_lsu
  • Label: Sequence
  • Definition: Assembled sequences of a portion of the 28S large subunit ribosomal ribonucleic acid (LSU) gene.
  • Type: Nominal
  • Missing values: None specified
ncbi_accn
  • Label: NCBI Accession Number
  • Definition: NCBI nucleotide accession number corresponding with each sequence. https://www.ncbi.nlm.nih.gov/nuccore/?term=OP692666:OP692695[accn]
  • Type: Nominal
  • Missing values: None specified

Description: 

Sample locations and corresponding molecular diversity metrics from each sampling population. This table also contains the nematode counts from each sampling location and sample site metadata.

Variables (click to expand): 

dataset_code
  • Label: Dataset Code
  • Definition: Internal dataset code.
  • Type: Nominal
  • Missing values: None specified
site
  • Label: Site Name
  • Definition: Name of the location where soils were sampled.
  • Type: Nominal
  • Missing values: None specified
valley
  • Label: Valley Name
  • Definition: The name of the dry valley each site is located in.
  • Type: Nominal
  • Missing values: None specified
year_collected
  • Label: Collection Year
  • Definition: Year that soils were collected in, corresponding with the associated austral summer field season. E.g., 2019 means samples were collected over the 2018-2019 field season (i.e., between December 2018 and February 2019).
  • Type: Date/time
  • Date format: YYYY
  • Missing values: None specified
latitude
  • Label: Latitude
  • Definition: Latitude of sampling sites taken by GPS.
  • Type: Physical quantity
  • Unit: decimalDegrees
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
longitude
  • Label: Longitude
  • Definition: Longitude of sampling sites taken by GPS.
  • Type: Physical quantity
  • Unit: decimalDegrees
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
distance_to_coast_km
  • Label: Distance to Coast
  • Definition: A linear distance from the sample site to the coast.
  • Type: Physical quantity
  • Unit: kilometer
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
lgm_glacial_history
  • Label: Last Glacial Maximum Glacial History
  • Definition: Status of the site as a site that has either remained undisturbed or disturbed by glacial incursion or paleolake inundation during the last glacial maximum (LGM).
  • Type: Code list
  • Codes:
    • disturbed = Disturbed during the Last Glacial Maximum.
    • undisturbed = Undisturbed during the Last Glacial Maximum.
  • Missing values: None specified
elevation_m
  • Label: Elevation
  • Definition: Elevation of the sampling sites.
  • Type: Physical quantity
  • Unit: meter
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
number_of_sequences
  • Label: Number of Sequences
  • Definition: Number of individuals sanger sequenced from each sampling site.
  • Type: Nominal
  • Missing values: None specified
number_of_haplotypes
  • Label: Number of Haplotypes
  • Definition: Number of haplotypes recovered from sequenced individual nematodes from each sampling site.
  • Type: Nominal
  • Missing values: None specified
number_of_polymorphic_sites
  • Label: Number of Polymorphic Sites
  • Definition: Number of polymorphic sites among the haplotypes from sequenced individual nematodes from each sampling site.
  • Type: Nominal
  • Missing values: None specified
tajimas_d
  • Label: Tajima's D
  • Definition: Tajima’s D is a neutrality test statistic, calculated as the difference between mean number of pairwise nucleotide differences and polymorphic sites within each sampling site.
  • Type: Nominal
  • Missing values: None specified
tajimas_d_p
  • Label: Tajima's D p-value
  • Definition: The p-value calculated from 1,000 permutations of Tajima’s D test.
  • Type: Nominal
  • Missing values: None specified
fus_fs
  • Label: Fu’s FS
  • Definition: Fu’s FS neutrality test statistic.
  • Type: Nominal
  • Missing values: None specified
fus_fs_p
  • Label: Fu's FS p-value
  • Definition: The p-value calculated from 1,000 permutations of Fu’s FS test.
  • Type: Nominal
  • Missing values: None specified
haplotype_diversity_mean
  • Label: Haplotype Diversity Mean
  • Definition: The mean probability that two randomly sampled nucleotides will differ calculated over 1,000 permutations.
  • Type: Nominal
  • Missing values: None specified
haplotype_diversity_sd
  • Label: Haplotype Diversity Standard Deviation
  • Definition: The standard deviation of haplotype diversity.
  • Type: Nominal
  • Missing values: None specified
nucleotide_diversity_mean
  • Label: Nucleotide Diversity Mean
  • Definition: The nucleotide diversity averaged over all loci calculated as the average number of nucleotide differences per site among sequences from the same sampling site over 1,000 permutations.
  • Type: Nominal
  • Missing values: None specified
nucleotide_diversity_sd
  • Label: Nucleotide Diversity Standard Deviation
  • Definition: The standard deviation of nucleotide diversity.
  • Type: Nominal
  • Missing values: None specified
within_pop_fst_mean
  • Label: Within Population Fst Mean
  • Definition: Mean genetic divergence within each sampling site.
  • Type: Nominal
  • Missing values: None specified
within_pop_fst_sd
  • Label: Within Population Fst Standard Deviation
  • Definition: The standard deviation of within population genetic differentiation (FST).
  • Type: Nominal
  • Missing values: None specified
expected_heterozygosity_mean
  • Label: Expected Heterozygosity Mean
  • Definition: The expected heterozygosity over all loci.
  • Type: Nominal
  • Missing values: None specified
expected_heterozygosity_sd
  • Label: Expected Heterozygosity Standard Deviation
  • Definition: The standard deviation of the expected heterozygosity over all loci.
  • Type: Nominal
  • Missing values: None specified
soil_moisture
  • Label: Soil Moisture
  • Definition: Gravimetric water content of the sample as percent grams of water per gram of soil.
  • Type: Physical quantity
  • Unit: gramsPerGram
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
SML
  • Label: Scottnema Male Live
  • Definition: The total number of living male Scottnema lindsayae adult nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent.
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
SMD
  • Label: Scottnema Male Dead
  • Definition: The total number of dead male Scottnema adult nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent.
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
SFL
  • Label: Scottnema Female Live
  • Definition: The total number of living female Scottnema lindsayae adult nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
SFD
  • Label: Scottnema Female Dead
  • Definition: The total number of dead female Scottnema lindsayae adult nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
SJL
  • Label: Scottnema Juvenile Live
  • Definition: The total number of living juvenile Scottnema nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent.
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
SJD
  • Label: Scottnema Juvenile Dead
  • Definition: The total number of dead juvenile Scottnema nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent.
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
sa
  • Label: Scottnema Adult
  • Definition: The total number of living and dead Scottnema lindsayae adult nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent.
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
sj
  • Label: Scottnema Juvenile
  • Definition: The total number of living and dead Scottnema lindsayae juvenile nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent.
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
STL
  • Label: Scottnema Total Live
  • Definition: Total number of living Scottnema lindsayae (juvenile and adults) nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent.
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
STD
  • Label: Scottnema Total Dead
  • Definition: The total number of dead Scottnema lindsayae (juvenile and adults) nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent.
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
STLD
  • Label: Total Scottnema Live and Dead
  • Definition: The total number of live + dead Scottnema lindsayae (juvenile and adults) nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent.
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
EML
  • Label: Eudorylaimus Male Live
  • Definition: The total number of living male Eudorylaimus spp. adult nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
EMD
  • Label: Eudorylaimus Male Dead
  • Definition: The total number of dead male Eudorylaimus spp. adult nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
EFL
  • Label: Eudorylaimus Female Live
  • Definition: The total number of living female Eudorylaimus spp. adult nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
EFD
  • Label: Eudorylaimus Female Dead
  • Definition: The total number of dead female Eudorylaimus spp. adult nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
EJL
  • Label: Eudorylaimus Juvenile Live
  • Definition: The total number of living juvenile Eudorylaimus spp. adult nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
EJD
  • Label: Eudorylaimus Juvenile Dead
  • Definition: The total number of dead juvenile Eudorylaimus spp. adult nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
EA
  • Label: Eudorylaimus Adult
  • Definition: The total number of living and dead Eudorylaimus spp. adult nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent.
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
EJ
  • Label: Eudorylaimus Juvenile
  • Definition: The total number of living and dead Eudorylaimus spp. juvenile nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
ETL
  • Label: Total Eudorylaimus Live
  • Definition: total number of living Eudorylaimus spp. (juvenile and adults) nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
ETD
  • Label: Total Eudorylaimus Dead
  • Definition: The total number of dead Eudorylaimus spp. (juvenile and adults) nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
ETLD
  • Label: Total Eudorylaimus Live and Dead
  • Definition: The total number of live + dead Eudorylaimus spp. (juvenile and adults) nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
PFL
  • Label: Plectus Female Live
  • Definition: The total number of living female Plectus spp. adult nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
PFD
  • Label: Plectus Female Dead
  • Definition: The total number of dead female Plectus spp. adult nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
PJL
  • Label: Plectus Juvenile Live
  • Definition: The total number of living juvenile Plectus spp. adult nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
PJD
  • Label: Plectus Juvenile Dead
  • Definition: The total number of dead juvenile Plectus spp. adult nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
PA
  • Label: Plectus Adult
  • Definition: The total number of living and dead Plectus spp. adult nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
PJ
  • Label: Plectus Juvenile
  • Definition: The total number of living and dead Plectus spp. juvenile nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
PTL
  • Label: Total Plectus Live
  • Definition: total number of living Plectus spp. (juvenile and adults) nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
PTD
  • Label: Total Plectus Dead
  • Definition: The total number of dead Plectus spp. (juvenile and adults) nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
PTLD
  • Label: Total Plectus Live and Dead
  • Definition: The total number of live + dead Plectus spp. (juvenile and adults) nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
TOTAL_ROTIFERS
  • Label: total rotifers
  • Definition: total number of rotifers per kg soil oven dry weight equivalent present in a sample
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
TOTAL_TARDIGRADES
  • Label: Total Tardigrades
  • Definition: Total number of tardigrades per kg soil oven dry weight equivalent present in a sample.
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: 0
  • Precision: Not specified
  • Missing values:
    • Null = None given
total_mites
  • Label: Total Mites
  • Definition: Total number of mites per kg soil oven dry weight equivalent present in a sample.
  • Type: Physical quantity
  • Unit: # kg/soil
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
total_nematodes_live
  • Label: Total Live Nematodes
  • Definition: The total number of living nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent.
  • Type: Nominal
  • Missing values: None specified
total_nematodes_dead
  • Label: Total Dead Nematodes
  • Definition: The total number of dead nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent.
  • Type: Nominal
  • Missing values: None specified
total_nematodes_livedead
  • Label: Total Live and Dead Nematodes
  • Definition: The total number of living and dead nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent.
  • Type: Nominal
  • Missing values: None specified

Description: 

Haplotypes specific to each sampling site.

Variables (click to expand): 

dataset_code
  • Label: Dataset Code
  • Definition: Internal dataset code.
  • Type: Nominal
  • Missing values: None specified
site
  • Label: Site Name
  • Definition: Name of the location were soils were sampled.
  • Type: Nominal
  • Missing values: None specified
haplotype_id
  • Label: Haplotype ID
  • Definition: Haplotype identifiers specific to each sampling site.
  • Type: Nominal
  • Missing values: None specified

Short name: 

SOILS_SCOTT

Dataset ID: 

269
People

Principal Investigator(s): 

Contact: 

Associated Personnel: 

Data Manager