SOILS_SCOTT English utf8 dataset McMurdo Dry Valleys LTER Information Manager im@mcmlter.org pointOfContact 2023-04-11 ISO 19115-2 Geographic Information - North American Profile Metadata - Data with Biological Extensions ISO 19115-2:2009(E) Mitochondrial COXI sequences and associated metazoan abundances in soils collected from the McMurdo Dry Valleys, Antarctica from 1995 to 2022 2023-04-11 publication Abigail Jackson Brigham Young University ajackson260@gmail.com pointOfContact Diana Wall Colorado State University http://www.colostate.edu Johnson Hall 107 Fort Collins CO 80523 US Diana.Wall@colostate.edu http://wp.natsci.colostate.edu/walllab/ pointOfContact Byron Adams Brigham Young University byron_adams@byu.edu https://biology.byu.edu/adams-lab pointOfContact documentDigital 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. Name: Renée F. Brown Role: data manager completed McMurdo Dry Valleys LTER Information Manager im@mcmlter.org pointOfContact population dynamics theme LTER Core Areas English This is the Taylor Valley, a subjectively approximated contour by San Gil. We use this to denote the geographical extent of studies that encompass the whole Taylor Valley. According to Wiki contributors, the Taylor Valley is the southernmost of the three large Dry Valleys in the Transantarctic Mountains, Victoria Land, located west of McMurdo Sound. The valley extends from Taylor Glacier in the west to McMurdo Sound at Explorers Cove at the northwest head of New Harbour in the east and is about 29 kilometres (18 mi) long. It was once occupied by the receding Taylor Glacier, from which it derives its name. Taylor Valley contains Lake Bonney in the west (inward), and Lake Fryxell in the east (coastward), and Lake Hoare, Lake Chad, Mummy Pond and Parera Pond close together between the two. Further east of Lake Bonney is Pearse Valley. Taylor Valley is separated from Wright Valley in the north by Asgard Range, and from Ferrar Glacier in the south by Kukri Hills. 163.624877929690 161.707763671880 -77.808487073526 -77.519802097166 ground condition 1995-12-01 2022-02-28 Funding: Provided by several grants from the National Science Foundation for Long Term Ecological Research, most recently #OPP-1637708. Provenance: Metazoan abundance data were derived from the MCM LTER Biotic Effects (10.6073/pasta/41825ac3c486a2858c51462e968e3a42) and Elevational Transect (10.6073/pasta/6c9dea12fe86439c0d390726348b0d5f) experiments. https://mcm.lternet.edu/sites/default/files/data/mcmlter-soils-jackson-soils_scott_coiseq-20230411.csv Scottnema lindsayae mitochondrial Cytochrome c oxidase I (COI) sequences eng; US McMurdo Dry Valleys LTER Scottnema lindsayae mitochondrial Cytochrome c oxidase I (COI) sequences Data Source Definition : List of each individual Scottnema lindsayae sanger sequenced for a portion of the mitochondrial DNA COX1 gene and the corresponding aligned and trimmed sequences. Record Delimiter : \n Number of Header Lines : 1 Orientation : Column Quote Character : "Field Delimiter : , false dataset_code Internal dataset code. sequence_id Individual Scottnema lindsayae sequence identifier. site Name of the location where soils were sampled. species Species identity. seq_coi Assembled sequences from a portion of the mitochondrial COX1 gene. ncbi_accn NCBI nucleotide accession number corresponding with each sequence. https://www.ncbi.nlm.nih.gov/nuccore/?term=OP456699:OP456947[accn] DBF https://mcm.lternet.edu/sites/default/files/data/mcmlter-soils-jackson-soils_scott_coiseq-20230411.csv https://mcm.lternet.edu/sites/default/files/data/mcmlter-soils-jackson-soils_scott_lsuseq-20230411.csv Scottnema lindsayae LSU sequences eng; US McMurdo Dry Valleys LTER Scottnema lindsayae LSU sequences Data Source Definition : List of each individual Scottnema sanger sequenced for 28S large subunit ribosomal ribonucleic acid (LSU) and the corresponding aligned and trimmed LSU sequence. Record Delimiter : \n Number of Header Lines : 1 Orientation : Column Quote Character : "Field Delimiter : , false dataset_code Internal dataset code. sequence_id Individual Scottnema lindsayae sequence identifier. site Name of the location where soils were sampled. species Species identity. seq_lsu Assembled sequences of a portion of the 28S large subunit ribosomal ribonucleic acid (LSU) gene. ncbi_accn NCBI nucleotide accession number corresponding with each sequence. https://www.ncbi.nlm.nih.gov/nuccore/?term=OP692666:OP692695[accn] DBF https://mcm.lternet.edu/sites/default/files/data/mcmlter-soils-jackson-soils_scott_lsuseq-20230411.csv https://mcm.lternet.edu/sites/default/files/data/mcmlter-soils-jackson-soils_scott_popdiv-20230411.csv Scottnema lindsayae glacial history populations and genetic diversity eng; US McMurdo Dry Valleys LTER Scottnema lindsayae glacial history populations and genetic diversity Data Source Definition : 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. Record Delimiter : \n Number of Header Lines : 1 Orientation : Column Quote Character : "Field Delimiter : , false dataset_code Internal dataset code. site Name of the location where soils were sampled. valley The name of the dry valley each site is located in. year_collected 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). Date Time Format: YYYY latitude Latitude of sampling sites taken by GPS. longitude Longitude of sampling sites taken by GPS. distance_to_coast_km A linear distance from the sample site to the coast. lgm_glacial_history 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). disturbed Disturbed during the Last Glacial Maximum. undisturbed Undisturbed during the Last Glacial Maximum. elevation_m Elevation of the sampling sites. number_of_sequences Number of individuals sanger sequenced from each sampling site. number_of_haplotypes Number of haplotypes recovered from sequenced individual nematodes from each sampling site. number_of_polymorphic_sites Number of polymorphic sites among the haplotypes from sequenced individual nematodes from each sampling site. tajimas_d 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. tajimas_d_p The p-value calculated from 1,000 permutations of Tajima’s D test. fus_fs Fu’s FS neutrality test statistic. fus_fs_p The p-value calculated from 1,000 permutations of Fu’s FS test. haplotype_diversity_mean The mean probability that two randomly sampled nucleotides will differ calculated over 1,000 permutations. haplotype_diversity_sd The standard deviation of haplotype diversity. nucleotide_diversity_mean 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. nucleotide_diversity_sd The standard deviation of nucleotide diversity. within_pop_fst_mean Mean genetic divergence within each sampling site. within_pop_fst_sd The standard deviation of within population genetic differentiation (FST). expected_heterozygosity_mean The expected heterozygosity over all loci. expected_heterozygosity_sd The standard deviation of the expected heterozygosity over all loci. soil_moisture Gravimetric water content of the sample as percent grams of water per gram of soil. SML 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. SMD 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. SFL 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 SFD 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 SJL The total number of living juvenile Scottnema nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent. SJD The total number of dead juvenile Scottnema nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent. sa 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. sj 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. STL 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. STD 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. STLD 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. EML 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 EMD 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 EFL 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 EFD 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 EJL 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 EJD 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 EA 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. EJ 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 ETL 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 ETD 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 ETLD 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 PFL 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 PFD 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 PJL 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 PJD 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 PA 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 PJ 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 PTL 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 PTD 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 PTLD 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 TOTAL_ROTIFERS total number of rotifers per kg soil oven dry weight equivalent present in a sample TOTAL_TARDIGRADES Total number of tardigrades per kg soil oven dry weight equivalent present in a sample. total_mites Total number of mites per kg soil oven dry weight equivalent present in a sample. total_nematodes_live The total number of living nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent. total_nematodes_dead The total number of dead nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent. total_nematodes_livedead The total number of living and dead nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent. DBF https://mcm.lternet.edu/sites/default/files/data/mcmlter-soils-jackson-soils_scott_popdiv-20230411.csv https://mcm.lternet.edu/sites/default/files/data/mcmlter-soils-jackson-soils_scott_haplotype-20230411.csv Haplotypes eng; US McMurdo Dry Valleys LTER Haplotypes Data Source Definition : Haplotypes specific to each sampling site. Record Delimiter : \n Number of Header Lines : 1 Orientation : Column Quote Character : "Field Delimiter : , false dataset_code Internal dataset code. site Name of the location were soils were sampled. haplotype_id Haplotype identifiers specific to each sampling site. DBF https://mcm.lternet.edu/sites/default/files/data/mcmlter-soils-jackson-soils_scott_haplotype-20230411.csv dataset About 500 g of the top 10 cm of soil were collected with clean plastic scoops and sterile Whirlpak bags from sites in the MDVs during the Austral summer between 1996 to 2022. Soils were transported to the Crary Laboratory in McMurdo Station where they were stored at 4 °C until soil invertebrates and geochemistry could be performed within 48 hours. A sugar centrifugation extraction (Freckman and Virginia, 1993) was performed with a subsample of 100 g to calculate metazoan abundance. Soil invertebrates were counted and identified to species, as living or dead, life stage (juvenile or adults), and sex. Soil moisture, pH, and electrical conductivity were measured following standard protocols of the MCM LTER project (e.g., http://mcm.lternet.edu/content/soil-elevational-transect-experiment). Subsequent subsamples of 100 g were extracted in the same way at Brigham Young University to collect individual Scottnema lindsayae. Following Powers and Harris (1993) nematode extraction methods, individual S. lindsayae (Timm, 1971) were hand-picked with an eyelash tool onto 10 μl of elution buffer on a cover slip. Using a clear, sterilized 10 μl micropipette tip, the nematode was ruptured by gentle pressure and lysate confirmed in the sterile water. Lysate was moved to a 0.2 ml microcentrifuge tube. The cover slip was further cleaned with 5.2 μl of sterile water, which was added to the microcentrifuge tube. Nematode lysate was combined with 2.4 μl each of 20 μM diluted forward primer (COI-Scott-F1: 5'-GTTACAACTTTTTTGCTTATTCTCTCAC-3’) and reverse primer (COI-Scott-R2: 5’-CTGTAAAATAAGCTCGACTRTCWG-3’).  Additional extractions were performed with an alternative reverse primer with higher fidelity, but shorter sequence reads (COI-Scott-R4 5’-GCRTCRATACCTGTTACRTATATRTG-3’). Additionally, 15 μl of JumpStart™ REDTaq® ReadyMix™ Reaction Mix (Sigma-Aldrich, DE) was added to the mixture and vortexed for 30 seconds to mix. The mixture was placed in a DNA thermal cycler (Mastercycler X50s, Eppendorf, Germany) on the following settings: initial denaturation at 94°C for 5 minute, 40 cycles of denaturation at 94°C for 30 seconds, annealing at 52°C for 30 seconds, extension of 0.5°C/second ramp to 72 for 90 seconds. Followed by a final extension at 72°C for 5 minutes and hold at 4°C. Following PCR amplification, the products were screened on a 1% TAE agarose gel stained with ethidium bromide and visualized with a UV image capture (GelDoc Go, Bio-Rad Labratories, USA). Successful DNA amplifications were cleaned with a magnetic bead cleaning protocol. Mag-Bind® TotalPure NGS (Omega Bio-tek, GA) was added in a 1.2x concentration to the remaining PCR product, vortexed for 10 minutes at 2,000 rpm, centrifuged for 5 seconds, placed on a magnetic rack until bead solution was cleared. The supernatant was removed and thrown away, while the beads were washed with 200 μl 80% ethanol for 30 seconds twice. After removing all ethanol, residual ethanol was allowed to evaporate for 10 minutes.  Tubes were removed from the magnetic rack as 30 ml of elution buffer (Omega Bio-tek, GA) was added and vortexed to mix. Tubes were returned to the magnetic rack to separate the supernatant. The supernatant was removed and added to a clean 0.2 ml tube and beads discarded. DNA concentration was quantified by Quibit 4 Flurorometer (Invitrogen, USA). DNA was diluted or concentrated to 10 ng for Sanger dideoxy sequencing at the Brigham Young University Sequencing Center (Provo, UT). Analysis was conducted with a combination of ARLEQUIN v3.5.2.2 (Excoffier and Lischer., 2010), R Studio (R Core Team, 2002) utilizing pegas (Paradis, 2010), haplotypes (Aktas, 2020), poppr 2.9.3 (Kamvar, Tabima and Grunwald, 2014; Kamvar, Brooks, Grunwald, 2015), and adegenet (Jombart, 2008; Jombar and Ahmed 2011) packages. Phylogeographic reconstructions were recreated in IQ-tree with the built-in model finder and ultrafast bootstrap values (Kalyaanamoorthy et al., 2017; Hoang et al., 2018; Minh et al., 2020) and FigTree v1.4.4 (available at http://tree.bio.ed.ac.uk/software/figtree/). Bayesian Skyline plots were computed with BEAST v2.6.7 (Bouckaert et al., 2019) and tracer. References Cited: Aktas, C. (2020) “haplotypes: Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony.” Bouckaert, R. et al. (2019) “BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.” PLoS computational biology. doi: e1006650. Excoffier, L. and Lischer, H. E. L. (2010) “Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows.” Molecular Ecology Resources, pp. 10:564-567. Freckman, D. W. and Virginia, R. A. (1993) “Extraction of nematodes from Dry Valley Antarctic soils,” Polar Biology, 13(483–487). doi: https://doi.org/10.1007/BF00233139. Hoang, D. T. et al. (2018) “UFBoot2: Improving the ultrafast bootstrap approximation.” Molecular Biology and Evolution, pp. 35:518-522. Jombart, T. (2008) “adegenet: a R package for the multivariate analysis of genetic markers.” Bioinformatics, pp. 24:1403-1405. doi: 10.1093/bioinformatics/btn129. Jombart, T. and Ahmed, I. (2011) “adegenet 1.3-1: new tools for the analysis of genome-wide SNP data.” Bioinformatics. doi: 10.1093/bioinformatics/btr521. Kalyaanamoorthy, S. et al. (2017) “ModelFinder: Fast model selection for accurate phylogenetic estimates.” Nat. Methods, pp. 14:587-589. Available at: https://doi.org/10.1038/nmeth.4285. Kamvar, Z. N., Brooks, J. C. and Grunwald, N. J. (2015) “Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality.” Frontiers in Genetics, p. 6:208. doi: 10.3389/fgene.2015.00208. Kamvar, Z. N., Tabima, J. . and Grunwald, N. J. (2014) “Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction.” PeerJ. doi: 10.7717/peerj.281. Minh, B. Q. et al. (2020) “IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era.” Molecular Biology and Evolution, pp. 37: 1530-1534. Paradis, E. (2010) “pegas: an R package for population genetics with an integrated-modular approach.” Bioinformatics, pp. 26: 419-420. Powers, T. O. and Harris, T. S. (1993) “A polymerase chain reaction method for identification of five major meloidogyne species.,” Journal of nematology, 25(1), pp. 1–6. Available at: http://www.ncbi.nlm.nih.gov/pubmed/19279734%0Ahttp://www.pubmedcentral.n.... R Core Team (2002) “R: A language and environment for statistical computing. R Foundation for Statistical Computing.” Vienna, Austria. Available at: https://www.r-project.org/. Timm, R. W. (1971) “Antarctic soil and freshwater nematodes from the McMurdo Sound Region,” Proceedings Helminth Soc Washington, 38(1), pp. 42–52. Metadata Access Constraints: none Metadata Use Constraints: none annually McMurdo Dry Valleys LTER http://mcmlter.org/ pointOfContact