DOI: 10.5061/dryad.ttdz08m5g
title: SNP genotyping raw flourescent values from Asian Elephant in Prey Lang Extended Landscape, Cambodia

description: 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.
description: 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.
description: # SNP genotyping raw flourescent values from Asian Elephant in Prey Lang
 Extended Landscape, Cambodia
 [https://doi.org/10.5061/dryad.ttdz08m5g](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