Delineating genetic management units of sambar deer (Rusa unicolor) in south-eastern Australia, using opportunistic tissue sampling and targeted scat collection
- Davies, Christopher, Wright, Wendy, Wedrowicz, Faye, Pacioni, Carlo, Hogan, Fiona
- Authors: Davies, Christopher , Wright, Wendy , Wedrowicz, Faye , Pacioni, Carlo , Hogan, Fiona
- Date: 2022
- Type: Text , Journal article
- Relation: Wildlife Research Vol. 49, no. 2 (2022), p. 147-157
- Full Text:
- Reviewed:
- Description: Context: Invasive species are major drivers of biodiversity loss, requiring management to reduce their ecological impacts. Population genetics can be applied to delineate management units, providing information that can help plan and improve control strategies. Aim: The present study aims to use a genetic approach to test the existence of three previously proposed sambar deer populations in south-eastern Australia. In doing so, the study aims to delineate management units of sambar deer in south-eastern Australia. Methods: Sambar deer DNA was sourced opportunistically from tissue samples and targeted scat collection. Samples were collected from three areas in Victoria, south-eastern Australia: Mt Cole (MC), French Island (FI) and eastern Victoria (EV). Contemporary population structure was assessed using a suite of 11 polymorphic microsatellite markers. The number of maternal sambar deer lineages in south-eastern Australia was investigated through sequencing of the mitochondrial (mt)DNA control region. Key results: Three distinct genetic clusters were identified. Differentiation among inferred clusters was found to be high, with FST ranging from 0.24 between EV and FI clusters and 0.48 between MC and FI clusters. Two mtDNA haplotypes were identified; R.u1 was found throughout EV and FI, and R.u2 was unique to MC. DNA isolated from scats provided reliable data and proved critical for sampling areas where hunting and culling of deer are not generally undertaken. Conclusions: Three genetically distinct sambar deer management units in south-eastern Australia are defined-MC, FI and EV. Sambar deer control strategies should be applied to each management unit independently. This may be difficult or infeasible for the EV management unit, which is large and geographically complex. Further research may help identify additional fine-scale genetic structure in EV, allowing smaller, more practicable management units to be identified. Implications: Genetic data can be used to identify management units for invasive species, which will be critical for the development of future management strategies and improving control operations. The approach outlined here could also be applied to improve the management of other introduced deer species in south-eastern Australia. © 2022 CSIRO Open Access.
- Authors: Davies, Christopher , Wright, Wendy , Wedrowicz, Faye , Pacioni, Carlo , Hogan, Fiona
- Date: 2022
- Type: Text , Journal article
- Relation: Wildlife Research Vol. 49, no. 2 (2022), p. 147-157
- Full Text:
- Reviewed:
- Description: Context: Invasive species are major drivers of biodiversity loss, requiring management to reduce their ecological impacts. Population genetics can be applied to delineate management units, providing information that can help plan and improve control strategies. Aim: The present study aims to use a genetic approach to test the existence of three previously proposed sambar deer populations in south-eastern Australia. In doing so, the study aims to delineate management units of sambar deer in south-eastern Australia. Methods: Sambar deer DNA was sourced opportunistically from tissue samples and targeted scat collection. Samples were collected from three areas in Victoria, south-eastern Australia: Mt Cole (MC), French Island (FI) and eastern Victoria (EV). Contemporary population structure was assessed using a suite of 11 polymorphic microsatellite markers. The number of maternal sambar deer lineages in south-eastern Australia was investigated through sequencing of the mitochondrial (mt)DNA control region. Key results: Three distinct genetic clusters were identified. Differentiation among inferred clusters was found to be high, with FST ranging from 0.24 between EV and FI clusters and 0.48 between MC and FI clusters. Two mtDNA haplotypes were identified; R.u1 was found throughout EV and FI, and R.u2 was unique to MC. DNA isolated from scats provided reliable data and proved critical for sampling areas where hunting and culling of deer are not generally undertaken. Conclusions: Three genetically distinct sambar deer management units in south-eastern Australia are defined-MC, FI and EV. Sambar deer control strategies should be applied to each management unit independently. This may be difficult or infeasible for the EV management unit, which is large and geographically complex. Further research may help identify additional fine-scale genetic structure in EV, allowing smaller, more practicable management units to be identified. Implications: Genetic data can be used to identify management units for invasive species, which will be critical for the development of future management strategies and improving control operations. The approach outlined here could also be applied to improve the management of other introduced deer species in south-eastern Australia. © 2022 CSIRO Open Access.
Validating the use of non-invasively sourced DNA for population genetic studies using pedigree data
- Wedrowicz, Faye, Mosse, Jennifer, Wright, Wendy, Hogan, Fiona
- Authors: Wedrowicz, Faye , Mosse, Jennifer , Wright, Wendy , Hogan, Fiona
- Date: 2017
- Type: Text , Journal article
- Relation: Web Ecology Vol. 17, no. 1 (2017), p. 9-18
- Full Text:
- Reviewed:
- Description: Non-invasive genetic sampling has provided valuable ecological data for many species - data which may have been unobtainable using invasive sampling methods. However, DNA obtained non-invasively may be prone to increased levels of amplification failure and genotyping error. Utilizing genotype data from 32 pedigreed koalas, this study aimed to validate the reliability of final consensus genotypes obtained using DNA isolated from koala scats. Pedigree analysis, duplicate genotyping, analysis of mismatched loci and tests for null alleles were used to look for evidence of errors. All genetically confirmed parent-offspring relationships were found to follow Mendelian rules of inheritance. Duplicate genotypes matched in all cases and there was no evidence of null alleles. Related individuals always had different 12-marker genotypes having a minimum of three unique loci (in one full sibling pair), a mode of seven unique loci and a maximum of 11 unique loci. This study demonstrates the capacity of DNA recovered from koala scats to provide reliable genotypes that can unequivocally discriminate individuals and infer parentage, provided data are missing from no more than two loci. Validating data obtained using non-invasive sampling is an important step, allowing potential problems to be identified at an early stage. © Author(s) 2017. CC Attribution 3.0 License.
- Description:
Non-invasive genetic sampling has provided valuable ecological data for many species - data which may have been unobtainable using invasive sampling methods. However, DNA obtained non-invasively may be prone to increased levels of amplification failure and genotyping error.
Utilizing genotype data from 32 pedigreed koalas, this study aimed to validate the reliability of final consensus genotypes obtained using DNA isolated from koala scats. Pedigree analysis, duplicate genotyping, analysis of mismatched loci and tests for null alleles were used to look for evidence of errors.
All genetically confirmed parent-offspring relationships were found to follow Mendelian rules of inheritance. Duplicate genotypes matched in all cases and there was no evidence of null alleles. Related individuals always had different 12-marker genotypes having a minimum of three unique loci (in one full sibling pair), a mode of seven unique loci and a maximum of 11 unique loci.
This study demonstrates the capacity of DNA recovered from koala scats to provide reliable genotypes that can unequivocally discriminate individuals and infer parentage, provided data are missing from no more than two loci. Validating data obtained using non-invasive sampling is an important step, allowing potential problems to be identified at an early stage. © Author(s) 2017. CC Attribution 3.0 License.
- Authors: Wedrowicz, Faye , Mosse, Jennifer , Wright, Wendy , Hogan, Fiona
- Date: 2017
- Type: Text , Journal article
- Relation: Web Ecology Vol. 17, no. 1 (2017), p. 9-18
- Full Text:
- Reviewed:
- Description: Non-invasive genetic sampling has provided valuable ecological data for many species - data which may have been unobtainable using invasive sampling methods. However, DNA obtained non-invasively may be prone to increased levels of amplification failure and genotyping error. Utilizing genotype data from 32 pedigreed koalas, this study aimed to validate the reliability of final consensus genotypes obtained using DNA isolated from koala scats. Pedigree analysis, duplicate genotyping, analysis of mismatched loci and tests for null alleles were used to look for evidence of errors. All genetically confirmed parent-offspring relationships were found to follow Mendelian rules of inheritance. Duplicate genotypes matched in all cases and there was no evidence of null alleles. Related individuals always had different 12-marker genotypes having a minimum of three unique loci (in one full sibling pair), a mode of seven unique loci and a maximum of 11 unique loci. This study demonstrates the capacity of DNA recovered from koala scats to provide reliable genotypes that can unequivocally discriminate individuals and infer parentage, provided data are missing from no more than two loci. Validating data obtained using non-invasive sampling is an important step, allowing potential problems to be identified at an early stage. © Author(s) 2017. CC Attribution 3.0 License.
- Description:
Non-invasive genetic sampling has provided valuable ecological data for many species - data which may have been unobtainable using invasive sampling methods. However, DNA obtained non-invasively may be prone to increased levels of amplification failure and genotyping error.
Utilizing genotype data from 32 pedigreed koalas, this study aimed to validate the reliability of final consensus genotypes obtained using DNA isolated from koala scats. Pedigree analysis, duplicate genotyping, analysis of mismatched loci and tests for null alleles were used to look for evidence of errors.
All genetically confirmed parent-offspring relationships were found to follow Mendelian rules of inheritance. Duplicate genotypes matched in all cases and there was no evidence of null alleles. Related individuals always had different 12-marker genotypes having a minimum of three unique loci (in one full sibling pair), a mode of seven unique loci and a maximum of 11 unique loci.
This study demonstrates the capacity of DNA recovered from koala scats to provide reliable genotypes that can unequivocally discriminate individuals and infer parentage, provided data are missing from no more than two loci. Validating data obtained using non-invasive sampling is an important step, allowing potential problems to be identified at an early stage. © Author(s) 2017. CC Attribution 3.0 License.
- «
- ‹
- 1
- ›
- »