SNP genotyping raw flourescent values from Asian Elephant in Prey Lang Extended Landscape, Cambodia
Data files
Jan 24, 2025 version files 1.73 MB
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20210521_AEL_SNP002_KS01c_data.xls
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20210521_AEL_SNP004_KS02c_data.xls
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20210524_AEL_SNP005_KS01c_data.xls
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20210524_AEL_SNP010_KS02c_data.xls
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20210525_AEL_SNP011_KS01c_data.xls
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20210526_AEL_SNP013_KS01c_data.xls
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20210526_AEL_SNP016_KS02c_data.xls
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20210527_AEL_SNP021_KS01B_data.xls
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20210527_AEL_SNP023_KS02c_data.xls
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20210531_AEL_SNP025_KS01c_data.xls
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20210601_AEL_SNP026_KS01c_data.xls
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20210602_AEL_SNP027_KS01c_data.xls
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20210602_AEL_SNP029_KS02c_data.xls
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20210603_AEL_SNP031_KS01c_data.xls
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20210603_AEL_SNP033_KS02c_data.xls
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20210604_AEL_SNP035_KS01a_data.xls
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20210608_AEL_SNP036_KS01c_data.xls
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20210609_AEL_SNP037_KS01c_data.xls
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20210609_AEL_SNP039_KS02b_data.xls
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20210610_AEL_SNP002_KS02c_data.xls
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20210610_AEL_SNP40_KS01c_data.xls
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20210611_AEL_SNP004_KS01c_data.xls
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20210617_AEL_SNP025_KS03c.xls
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20210618_AEL_SNP026_KS01c_data.xls
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20210621_AEL_SNP021_KS01c_data.xls
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20210621_AEL_SNP027_KS01c_data.xls
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20210621_AEL_SNP029_KS02c_data.xls
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20210621_AEL_SNP031_KS03c_data.xls
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20210622_AEL_SNP033_KS01c_data.xls
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20210622_AEL_SNP035_KS02c_data.xls
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20210622_AEL_SNP036_KS03c_data.xls
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20210624_AEL_SNP037_KS01c_data.xls
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20210625_AEL_SNP039_KS01c_data.xls
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20210625_AEL_SNP040_KS02c_data.xls
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20210629_AEL_SNP002_KS01c_data.xls
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20210630_AEL_SNP004_KS01c_data.xls
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20210630_AEL_SNP005_KS02c_data.xls
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20210701_AEL_SNP010_KS01c_data.xls
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20210701_AEL_SNP011_KS02c_data.xls
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20210701_AEL_SNP013_KS03c_data.xls
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20210702_AEL_SNP016_KS01c_data.xls
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20210702_AEL_SNP021_KS02c_data.xls
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20210703_AEL_SNP023_KS01c_data.xls
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20210705_AEL_SNP025_KS01c_data.xls
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20210705_AEL_SNP026_KS02C_data.xls
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20210706_AEL_SNP027_KS01c_data.xls
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20210706_AEL_SNP029_KS02c_data.xls
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20210707_AEL_SNP031_KS01c_data.xls
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20210708_AEL_SNP033_KS01c_data.xls
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20210713_AEL_SNP005_010_KS02c_data.xls
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20210713_AEL_SNP011_013_KS03c_data.xls
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20210714_AEL_SNP002_004_KS03b_data.xls
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20210714_AEL_SNP016_021_KS01c_data.xls
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20210714_AEL_SNP023_025_KS02c_data.xls
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20210715_AEL_SNP026_027_KS01c_data.xls
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20210715_AEL_SNP033_035_KS02c_data.xls
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20210716_AEL_SNP029_031_KS02c_data.xls
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20210716_AEL_SNP036_037_KS01c_data.xls
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20210719_AEL_SNP039_040_KS01c_data.xls
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20210721_AEL_SNP035_KS01c_data.xls
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README.md
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Abstract
Asian elephant (Elephas maximus) populations are declining and becoming increasingly fragmented. In central-northern Cambodia, the Prey Lang Extended Landscape (PLEL) encompasses a vast area composed largely of lowland evergreen and semi-evergreen forest, with the potential to support Asian elephant population recovery in the country.
To inform effective landscape-level conservation planning, this study provides the first reliable population size estimate for Asian elephants in PLEL, based on non-invasive genetic sampling during the 2020-2021 dry season in three protected areas: Prey Lang, Preah Roka and Chhaeb Wildlife Sanctuaries. Further, it provides an assessment of the species’ range, habitat suitability and connectivity within the landscape.
Thirty-five unique genotypes (individuals) were identified, of which 6 were detected in both Chhaeb and Preah Roka Wildlife Sanctuaries, providing evidence that elephants move readily between these neighbouring protected areas. However, no unique genotypes were shared between Chhaeb/Preah Roka and the less functionally connected southerly Prey Lang Wildlife Sanctuary. The southern population is estimated to number 31 (95% CI: 24-41) individuals. The Preah Roka / Chhaeb Wildlife Sanctuaries or northern population is estimated to number 20 (95% CI: 13-22) individuals.
Habitat loss is prevalent both outside and inside the three protected areas however large swathes of suitable elephant habitat remain within the landscape. Fragmentation has occurred and connectivity outside of these protected areas is very limited. While restoring the ability of elephants to move between Preah Rokar/Chhaeb and Prey Lang Wildlife Sanctuaries would represent an ideal scenario, the practicality of implementing such a restoration project is challenging. We recommend protection of remaining suitable habitat and reduction of threats and disturbance to elephants within these areas should be top priorities as the landscape holds the potential to be restored to a national stronghold for this flagship species, in turn resulting in the protection of a vast array of biodiversity.
README: SNP genotyping raw flourescent values from Asian Elephant in Prey Lang Extended Landscape, Cambodia
https://doi.org/10.5061/dryad.ttdz08m5g
The uploaded files contain the raw fluorescent measurements obtained from the ABI StepOne machine. Two flourescent measures were obtained per sample, one corresponding to allele 1 and the other corresponding to Allele 2. The degree of flourescent measured at each allows a genotype to be identified for each sample.
Description of the data and file structure
Each dung sample has a unique identifier that begins with PLE followed by three digits, e.g. PLE052. Each SNP has a uniquely identifiable SNP assay that begins with AEL_SNP and followed by three digits, e.g. AELSNP002. DNA was extracted from each of the dung samples and genotyping was attempted using each of the 20 SNP assays. The sample set was split into 4 subsets, each of which was run twenty times on the STEPOne machine, each time with a different SNP assay. The excel files here contain the raw florescent readings obtained at the end of the PCR run using the protocol outlined in the manuscript. Each file is labelled in the following way [DATE-RUN][AEL][SNP-ASSAY-ID][INITIALS-OF-TECHNICIAN].xls, e.g. 20210521_AEL_SNP002_KS01c_data. Each excel file contains the samples ID in column B and the SNP_ASSAY ID in column C. The fourth sample set was smaller and so the files associated with these contains the results of two SNP assays.
Each has 6 file descriptors in cells A1-A6 (titles) & B1-B6 (values), as follows:
Block Type - size of the multi-well plate being run on the machine - always 48well
Chemistry - Reference to the Assay type which is KASP for all runs (termed OTHER because it is non-Taqman).
Experiment File Name - The folder filename where the file was automatically saved on completion of the machine reading.
Experiment Run End Time - The date and time that the run finished on the machine.
Instrument Type - Always STEPONE as this is the laboratory machine used.
Passive Reference - Always ROX as this was the flourescent standard loaded in all runs.
Each file then has the flourescent reading data recorded from row A8. Cells A8-U8 contain the headings and below these are recorded the values associated with each sample:
Well - This is the well on the 48-well plate that the sample was loaded into (values from A1 - F8)
Sample Name - The name of the sample in each well, as described above each Asian elephant sample has a unique identifier.
SNP Assay - The name of the Single Nucleotide Polymorphism (SNP) being genotyped, each of the 20 SNPs has a unique identifier.
Task -N/A
Allele1 DeltaRn - The magnitude of the flourescent signal generated by the Allele 1 binding. The ΔRn value is determined by the following formula: (Rn+) – (Rn-). A sample Standard of known concentration has been used to construct a standard curve when the machine is calibrated. By running standards of varying concentrations, a standard curve from which you can extrapolate the quantity of an unknown sample.
Allele2 DeltaRn - The magnitude of the flourescent signal generated by the Allele 2 binding. The ΔRn value is determined by the following formula: (Rn+) – (Rn-) Standard of known concentration that has been used to construct a standard curve when the machine is calibrated. By running standards of varying concentrations, a standard curve from which you can extrapolate the quantity of an unknown sample.
Pass.Ref - The Passive reference*:* The flourescent value of the ROX dye that provides an internal reference to which the reporter dye signal can be normalized during data analysis. Normalization is necessary to correct for forestallment fluctuations caused by changes in concentration or volume.
Quality(%) - N/A
Call - the genotype assigned to the sample either automatically or manually after visualisation.
Method - whether the genotype has been assigned automatically by the machine or manually by visualisation of graphic results.
Allele1 Ct Threshold - The PCR cycle number at which the fluorescence meets the threshold in the amplification plot.
Allele1 Automatic Baseline - N/A
Allele1 Baseline Start - start of range used to define background flourescence
Allele1 Baseline End - end of range used to define background flourescence
Allele2 Ct Threshold - The PCR cycle number at which the fluorescence meets the threshold in the amplification plot.
Allele2 Automatic Baseline - N/A
Allele2 Baseline Start - start of range used to define background flourescence
Allele2 Baseline End - end of range used to define background flourescence
Comments - N/A
Methods
Dung samples from Asian elephants were collected from the Prey Lang Exended Landscape, Cambodia. DNA was extracted and individual identification via genetic markers was attempted on each sample. A panel of 20 Single Nucleotide Polymorphisms, known in Asian elephants, were genotyped via KASP assays on an ABI STEPONE machine. The uploaded files contain the raw flouresent measurements obtained from the ABI StepOne machine.