Genetic ancestry of introduced populations of sand lizard (Lacerta agilis) in Wales.
The purpose of this investigation was to use a state-of-the-art whole genome sequencing approach to test the three most plausible hypotheses for the origin of the Gower population of Lacerta agilis. Assessing the origin and ancestry of Gower sand lizards is a fundamental step in assessing the need and desirability for conservation action to preserve the population, or, in the case of an introduced population of a non-native lineage, to consider the case for removal. The date is presented in a report format with tables of DNA sequencing results presented in table and graphs
- Identification
- Extent
- Distribution
- Quality
- Keywords
- Spatial Reference System
- Content
- Constraints
- Maintenance
- Metadata
Identification
- Identifier
- NRW_DS125331
- Metadata Language
- English
- Lineage
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This investigation used 16 buccal swab DNA extractions which had been collected previously as part of a PhD investigation in Bangor University. DNA extraction was carried out using a Qiagen DNeasy Blood and Tissue Kit. Buccal swabs were processed by cutting half of the spongy tip of the swab and treating it as ‘tissue’ when following the manufacturers protocol. DNA quantification was assessed using a Qubit 3 fluorometer with the dsDNA HS assay kit, following the manufacturer’s protocol. Library preparation, quality control and whole genome sequencing on an Illumina NovaSeq Instrument (2x 150 bp PE reads) to a target 8x coverage was carried out by Novagene Ltd. Initial data processing involved trimming adapter sequences (synthetic DNA sequences that can occur as part of the sequencing process) from PE reads, requiring a single base overlap between adapter and read (setting “-O 1”), and removing short reads < 30 bp in length (setting -m 30), using the program Cutadapt v. 1.18 (Martin 2011). Overlapping PE read pairs were then identified and merged using the program FLASH v. 1.2.11 (Magoč & Salzberg 2011) using default parameter settings. The merged and unmerged PE reads were then mapped to the reference genome assembly of the sand lizard in separate analyses using the “mem” algorithm of the program bwa v. 0.7.17, using default parameter settings. The program samtools v. 1.3.1 (Li et al. 2009) was then used to filter out unmapped reads (setting “-F 4”), secondary mapped reads (setting “-F 256”) and reads with low mapping quality (setting “-q 30”). Samtools was then used to sort reads by their 5’ mapping position (command “sort”) and remove potential PCR duplicates. Finally, samtools was used to combine the merged and unmerged PE read data into a single file in bam format. Finally, samtools was used to combine the merged and unmerged PE read data into a single file in bam format for further analysis. Further Genetic Analysis is described fully in report.
- Additional Information
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Owens JB, Wilkinson JW, Wüster W, Barlow A, Papadopulos A. 2022. Genetic ancestry of introduced populations of sand lizard (Lacerta agilis) in Wales. NRW Evidence Report. Report No: 596, 30pp, Natural Resources Wales, Bangor.
- Dataset Reference Date (Publication)
- 2022-09-16
Temporal Extent
- Begin date
- 2019-01-01
- End date
- 2022-03-31
- Topic category
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- Environment
Extent
Extent
- Geographic Extent
- Wales (WLS)
))
Distribution
- Format Type and Description
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Database
Database
()
- Specification
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Documents [A] Digital versions of the contract report: Microsoft Word document(s); and an equivalent Adobe Portable Document Format version. Database [A] A series of data files in Fastq Format
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Database
Database
()
Quality
Data quality
- Quality Scope
- Dataset
- Lineage
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This investigation used 16 buccal swab DNA extractions which had been collected previously as part of a PhD investigation in Bangor University. DNA extraction was carried out using a Qiagen DNeasy Blood and Tissue Kit. Buccal swabs were processed by cutting half of the spongy tip of the swab and treating it as ‘tissue’ when following the manufacturers protocol. DNA quantification was assessed using a Qubit 3 fluorometer with the dsDNA HS assay kit, following the manufacturer’s protocol. Library preparation, quality control and whole genome sequencing on an Illumina NovaSeq Instrument (2x 150 bp PE reads) to a target 8x coverage was carried out by Novagene Ltd. Initial data processing involved trimming adapter sequences (synthetic DNA sequences that can occur as part of the sequencing process) from PE reads, requiring a single base overlap between adapter and read (setting “-O 1”), and removing short reads < 30 bp in length (setting -m 30), using the program Cutadapt v. 1.18 (Martin 2011). Overlapping PE read pairs were then identified and merged using the program FLASH v. 1.2.11 (Magoč & Salzberg 2011) using default parameter settings. The merged and unmerged PE reads were then mapped to the reference genome assembly of the sand lizard in separate analyses using the “mem” algorithm of the program bwa v. 0.7.17, using default parameter settings. The program samtools v. 1.3.1 (Li et al. 2009) was then used to filter out unmapped reads (setting “-F 4”), secondary mapped reads (setting “-F 256”) and reads with low mapping quality (setting “-q 30”). Samtools was then used to sort reads by their 5’ mapping position (command “sort”) and remove potential PCR duplicates. Finally, samtools was used to combine the merged and unmerged PE read data into a single file in bam format. Finally, samtools was used to combine the merged and unmerged PE read data into a single file in bam format for further analysis. Further Genetic Analysis is described fully in report.
Keywords
Keywords
- Type
- Theme
Citation
- Date (Publication)
- 2008-06-01
Keywords
- NRW Thesaurus
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- sand lizards
- Lacerta agilis
- lizards
- lacerta
- genetic conservation
- Gower
- Type
- Theme
Citation
- Date (Publication)
- 2023-12-31
Keywords
Spatial Reference System
- Code
- NONE
Content
Content Information
NRW Profile
Custom Elements
- NRW Related Title
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Genetic ancestry of introduced populations of sand lizard (Lacerta agilis) in Wales
Constraints
Constraints
Limitations on Public Access and Use
- Restriction type
- Other restrictions
Access Constraints Directive
- Limitations
- INSPIRE_Directive_Article13_1h
Access Constraints Text
- Other constraints
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Access restrictions on this data have not been determined. It may contain sensitive information and therefore may be restricted under legislation. NRW may provide access to this dataset on request, however NRW may not release, publish or disseminate the data or derived products freely without further assessment.
Use Constraints
- Use constraints type
- Other restrictions
- Other constraints
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Data may only be re-used externally under provision and in line with the terms of a NRW licence following an assessment of the data.
Attribution Statement
- Other constraints
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Not Licenced for Re-use
Metadata
Metadata
- File Identifier
- 4f4c4942-4343-5764-6473-313235333331 XML
- Metadata Language
- English
- Resource type
- Dataset
- Metadata Date
- 2024-05-31T09:29:10.072Z
- Metadata Standard Name
- NRW
- Metadata Standard Version
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1.0