DOI: 10.5061/dryad.m905qfv88
title: Asian elephant Microsatellite raw fragment files produced from faecal samples collected in the 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: The dataset was generated from Asian elephant faecal samples
 collected in the Prey Lang Extended Landscape, Cambodia. The
 microsatellites were PCR amplified in multiplex sets and flourescently
 labelled primers were used to visualise the fragment sizes on an ABI
 Genetic Analyzer. These files are those generated by the ABI fragment
 analysis.
description: # Microsatellite raw fragment files
 [https://doi.org/10.5061/dryad.m905qfv88](https://doi.org/10.5061/dryad.m905qfv88) These files were generated from Asian elephant faecal samples collected in the Prey Lang Extended Landscape, Cambodia. The samples were collected for individual identification via genetic methods. The DNA was extracted and a panel of 9 microsatellites were amplified via two multiplex reactions. ## Description of the data and file structure Each faecal sample has a unique identifier that starts with PLE followed by 3 digits, e.g. PLE052. The second part of each file name refers to the microsatellite multiplex set, multiplex Set 1 (P1), and multiplex set 2 (P2). The microsatellites in each set are as follows: | Oligo Name  | Sequence (5' to 3')  | 5' Dye  | Reference  | | :-------------------------------- | :----------------------- | :------ | :--------------------------- | | Microsatellite multiplex 1 (P1):  |   |   |   | | Emu03\_Eleph\_F  | AGAAGCAAAACCCATGAAGC  | NED  | Kongrit et al. 2008  | | Emu03\_Eleph\_R  | TTGAAACTTGCCAGCCTCTT  |   | | | Emu04\_Eleph\_F  | TGACTCTCCCTCTTCTGCATC  | FAM  | Kongrit et al. 2008  | | Emu04\_Eleph\_R  | GGCTGAGAGGGAAAGAAATTG  |   | | | Emu07\_Eleph\_F  | GAGCAGTGCCTTTCGTGAC  | VIC  | Kongrit et al. 2008  | | Emu07\_Eleph\_R  | AGCCTGGGAGGTAAGTAGCA  |   | | | Emu12\_Eleph\_F  | CAAAGAAGACCCATGTTCC  | PET  | Kongrit et al. 2008  | | Emu12\_Eleph\_R  | CTGACTATGGGGGAGACTGC  |   | | | FH48\_Eleph\_F  | GAGTCTCCATAATCAAGAGCG  | FAM  | Comstock et al. 2000  | | FH48\_Eleph\_R  | CCTCCCTGGAATCTGTACAG  |   | | | Microsatellite multiplex 2 (P2):  |   |   |   | | Emu10\_Eleph\_F  | AATCGACTCAGCAGCAACAG  | FAM  | Kongrit et al. 2008  | | Emu10\_Eleph\_R  | CCAGTAAATCCATATCACTCGTC  |   | | | Emu15\_Eleph\_F  | TTCGGGATGTTCTCTTCTGT  | NED  | Kongrit et al. 2008  | | Emu15\_Eleph\_R  | GGGGCTTAACTAATAGGCTTCA  |   | | | Emu17\_Eleph\_F  | CACTCAGAGTTCCAAGAAGCAG  | VIC  | Kongrit et al. 2008  | | Emu17\_Eleph\_R  | TGCCAGCCATTTCCTCTC  |   | | | LafMS03\_Eleph\_F  | CATATGAACATACCGGAAC  | PET  | Nyakaana and Arctander 1998  | | LafMS03\_Eleph\_R  | GAAACTCCTCGAGTAGTAGAA  |   | | Each sample was run in triplicate so there are 6 files associated with each sample. The naming structure of each fragment analysis file is as follows, `[sample name]_[multiplex set]_[replicate number]_PLE_Msat_[Plate number]_[Well location].fsa` e.g. PLE054_P1_R1_PLE_Msat_Plate04_C01.fsa Each file can be opened in microsatellite genotyping software such as Geneious Prime, the FRAGMAN package in R, GeneMapper or OSIRIS.