Identifying sex and individual from faecal DNA of the Asian elephant using a single multiplex PCR for population monitoring

Abstract Information on the sex- and individual-specific space use by a species elucidates demography, resource selection and individual life history. However, traditional field surveys often lack information on sex and individual identity, thereby not maximizing the potential of the effort put in....
Ausführliche Beschreibung

Gespeichert in:

Autor*in:	De, Rahul [verfasserIn] Sharma, Reeta Nigam, Parag Williams, Amirtharaj Christy Habib, Bilal Goyal, Surendra Prakash

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2023

Schlagwörter:	Microsatellite Molecular sexing Genetic non-invasive sampling Molecular tracking

Anmerkung:	© The Author(s), under exclusive licence to Springer Nature B.V. 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Übergeordnetes Werk:	Enthalten in: Conservation genetics resources - Dordrecht : Springer Netherlands, 2009, 15(2023), 4 vom: 11. Sept., Seite 163-173
Übergeordnetes Werk:	volume:15 ; year:2023 ; number:4 ; day:11 ; month:09 ; pages:163-173

Links:	Volltext

DOI / URN:	10.1007/s12686-023-01316-4

Katalog-ID:	SPR053753194

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520			\|a Abstract Information on the sex- and individual-specific space use by a species elucidates demography, resource selection and individual life history. However, traditional field surveys often lack information on sex and individual identity, thereby not maximizing the potential of the effort put in. Recent advances in genetic non-invasive sampling provide cost-effective approaches to determine identity and sex from faecal DNA with high accuracy, which are advantageous for tracking individuals compared to field observations. Therefore, we describe the first single multiplex-based sex and individual identification protocol using faecal samples of the wild Asian elephant (Elephas maximus) collected from the vicinity of Rajaji Tiger Reserve, Uttarakhand, India. We co-amplified fluorescence-labelled microsatellites (n = 5) and a Y chromosome-linked sex marker in four replicates from faecal DNA extracts (n = 149). The mean per genotype allelic drop-out rate was 0.11 ± 0.02, while the false allele rate was 0.05 ± 0.01. The mean null allele frequency across the markers was 0.15 ± 0.02. We obtained 74.1% consensus genotypes across microsatellites and dropped samples with more than one-locus missing genotype from further analyses. The remaining dataset comprised 105 samples, 30.5% of which were females. We identified 51 unique individuals (25 males and 26 females) with a maximum of one-locus mismatch. With low genotyping error rates and adequate misidentification probabilities ($ P_{ID} $ = 4.2 × $ 10^{−4} $; $ P_{IDSib} $ = 3.0 × $ 10^{−2} $), the described panel provides a cost-effective method (US$ 18/sample) for molecular sexing and individual identification. Hence, the suggested multiplex panel would provide a thorough understanding of individual and sex-specific differences in habitat use across heterogeneous landscapes, facilitating effective conservation strategies.
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allfields	10.1007/s12686-023-01316-4 doi (DE-627)SPR053753194 (SPR)s12686-023-01316-4-e DE-627 ger DE-627 rakwb eng De, Rahul verfasserin (orcid)0000-0002-4518-9607 aut Identifying sex and individual from faecal DNA of the Asian elephant using a single multiplex PCR for population monitoring 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s), under exclusive licence to Springer Nature B.V. 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law. Abstract Information on the sex- and individual-specific space use by a species elucidates demography, resource selection and individual life history. However, traditional field surveys often lack information on sex and individual identity, thereby not maximizing the potential of the effort put in. Recent advances in genetic non-invasive sampling provide cost-effective approaches to determine identity and sex from faecal DNA with high accuracy, which are advantageous for tracking individuals compared to field observations. Therefore, we describe the first single multiplex-based sex and individual identification protocol using faecal samples of the wild Asian elephant (Elephas maximus) collected from the vicinity of Rajaji Tiger Reserve, Uttarakhand, India. We co-amplified fluorescence-labelled microsatellites (n = 5) and a Y chromosome-linked sex marker in four replicates from faecal DNA extracts (n = 149). The mean per genotype allelic drop-out rate was 0.11 ± 0.02, while the false allele rate was 0.05 ± 0.01. The mean null allele frequency across the markers was 0.15 ± 0.02. We obtained 74.1% consensus genotypes across microsatellites and dropped samples with more than one-locus missing genotype from further analyses. The remaining dataset comprised 105 samples, 30.5% of which were females. We identified 51 unique individuals (25 males and 26 females) with a maximum of one-locus mismatch. With low genotyping error rates and adequate misidentification probabilities ($ P_{ID} $ = 4.2 × $ 10^{−4} $; $ P_{IDSib} $ = 3.0 × $ 10^{−2} $), the described panel provides a cost-effective method (US$ 18/sample) for molecular sexing and individual identification. Hence, the suggested multiplex panel would provide a thorough understanding of individual and sex-specific differences in habitat use across heterogeneous landscapes, facilitating effective conservation strategies. Microsatellite (dpeaa)DE-He213 Molecular sexing (dpeaa)DE-He213 Genetic non-invasive sampling (dpeaa)DE-He213 Molecular tracking (dpeaa)DE-He213 Sharma, Reeta (orcid)0000-0001-9862-9218 aut Nigam, Parag (orcid)0000-0001-9472-6897 aut Williams, Amirtharaj Christy aut Habib, Bilal (orcid)0000-0003-0040-6214 aut Goyal, Surendra Prakash (orcid)0000-0002-2284-8796 aut Enthalten in Conservation genetics resources Dordrecht : Springer Netherlands, 2009 15(2023), 4 vom: 11. Sept., Seite 163-173 (DE-627)606030891 (DE-600)2508018-0 1877-7260 nnns volume:15 year:2023 number:4 day:11 month:09 pages:163-173 https://dx.doi.org/10.1007/s12686-023-01316-4 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4328 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 AR 15 2023 4 11 09 163-173
spelling	10.1007/s12686-023-01316-4 doi (DE-627)SPR053753194 (SPR)s12686-023-01316-4-e DE-627 ger DE-627 rakwb eng De, Rahul verfasserin (orcid)0000-0002-4518-9607 aut Identifying sex and individual from faecal DNA of the Asian elephant using a single multiplex PCR for population monitoring 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s), under exclusive licence to Springer Nature B.V. 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law. Abstract Information on the sex- and individual-specific space use by a species elucidates demography, resource selection and individual life history. However, traditional field surveys often lack information on sex and individual identity, thereby not maximizing the potential of the effort put in. Recent advances in genetic non-invasive sampling provide cost-effective approaches to determine identity and sex from faecal DNA with high accuracy, which are advantageous for tracking individuals compared to field observations. Therefore, we describe the first single multiplex-based sex and individual identification protocol using faecal samples of the wild Asian elephant (Elephas maximus) collected from the vicinity of Rajaji Tiger Reserve, Uttarakhand, India. We co-amplified fluorescence-labelled microsatellites (n = 5) and a Y chromosome-linked sex marker in four replicates from faecal DNA extracts (n = 149). The mean per genotype allelic drop-out rate was 0.11 ± 0.02, while the false allele rate was 0.05 ± 0.01. The mean null allele frequency across the markers was 0.15 ± 0.02. We obtained 74.1% consensus genotypes across microsatellites and dropped samples with more than one-locus missing genotype from further analyses. The remaining dataset comprised 105 samples, 30.5% of which were females. We identified 51 unique individuals (25 males and 26 females) with a maximum of one-locus mismatch. With low genotyping error rates and adequate misidentification probabilities ($ P_{ID} $ = 4.2 × $ 10^{−4} $; $ P_{IDSib} $ = 3.0 × $ 10^{−2} $), the described panel provides a cost-effective method (US$ 18/sample) for molecular sexing and individual identification. Hence, the suggested multiplex panel would provide a thorough understanding of individual and sex-specific differences in habitat use across heterogeneous landscapes, facilitating effective conservation strategies. Microsatellite (dpeaa)DE-He213 Molecular sexing (dpeaa)DE-He213 Genetic non-invasive sampling (dpeaa)DE-He213 Molecular tracking (dpeaa)DE-He213 Sharma, Reeta (orcid)0000-0001-9862-9218 aut Nigam, Parag (orcid)0000-0001-9472-6897 aut Williams, Amirtharaj Christy aut Habib, Bilal (orcid)0000-0003-0040-6214 aut Goyal, Surendra Prakash (orcid)0000-0002-2284-8796 aut Enthalten in Conservation genetics resources Dordrecht : Springer Netherlands, 2009 15(2023), 4 vom: 11. Sept., Seite 163-173 (DE-627)606030891 (DE-600)2508018-0 1877-7260 nnns volume:15 year:2023 number:4 day:11 month:09 pages:163-173 https://dx.doi.org/10.1007/s12686-023-01316-4 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4328 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 AR 15 2023 4 11 09 163-173
allfields_unstemmed	10.1007/s12686-023-01316-4 doi (DE-627)SPR053753194 (SPR)s12686-023-01316-4-e DE-627 ger DE-627 rakwb eng De, Rahul verfasserin (orcid)0000-0002-4518-9607 aut Identifying sex and individual from faecal DNA of the Asian elephant using a single multiplex PCR for population monitoring 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s), under exclusive licence to Springer Nature B.V. 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law. Abstract Information on the sex- and individual-specific space use by a species elucidates demography, resource selection and individual life history. However, traditional field surveys often lack information on sex and individual identity, thereby not maximizing the potential of the effort put in. Recent advances in genetic non-invasive sampling provide cost-effective approaches to determine identity and sex from faecal DNA with high accuracy, which are advantageous for tracking individuals compared to field observations. Therefore, we describe the first single multiplex-based sex and individual identification protocol using faecal samples of the wild Asian elephant (Elephas maximus) collected from the vicinity of Rajaji Tiger Reserve, Uttarakhand, India. We co-amplified fluorescence-labelled microsatellites (n = 5) and a Y chromosome-linked sex marker in four replicates from faecal DNA extracts (n = 149). The mean per genotype allelic drop-out rate was 0.11 ± 0.02, while the false allele rate was 0.05 ± 0.01. The mean null allele frequency across the markers was 0.15 ± 0.02. We obtained 74.1% consensus genotypes across microsatellites and dropped samples with more than one-locus missing genotype from further analyses. The remaining dataset comprised 105 samples, 30.5% of which were females. We identified 51 unique individuals (25 males and 26 females) with a maximum of one-locus mismatch. With low genotyping error rates and adequate misidentification probabilities ($ P_{ID} $ = 4.2 × $ 10^{−4} $; $ P_{IDSib} $ = 3.0 × $ 10^{−2} $), the described panel provides a cost-effective method (US$ 18/sample) for molecular sexing and individual identification. Hence, the suggested multiplex panel would provide a thorough understanding of individual and sex-specific differences in habitat use across heterogeneous landscapes, facilitating effective conservation strategies. Microsatellite (dpeaa)DE-He213 Molecular sexing (dpeaa)DE-He213 Genetic non-invasive sampling (dpeaa)DE-He213 Molecular tracking (dpeaa)DE-He213 Sharma, Reeta (orcid)0000-0001-9862-9218 aut Nigam, Parag (orcid)0000-0001-9472-6897 aut Williams, Amirtharaj Christy aut Habib, Bilal (orcid)0000-0003-0040-6214 aut Goyal, Surendra Prakash (orcid)0000-0002-2284-8796 aut Enthalten in Conservation genetics resources Dordrecht : Springer Netherlands, 2009 15(2023), 4 vom: 11. Sept., Seite 163-173 (DE-627)606030891 (DE-600)2508018-0 1877-7260 nnns volume:15 year:2023 number:4 day:11 month:09 pages:163-173 https://dx.doi.org/10.1007/s12686-023-01316-4 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4328 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 AR 15 2023 4 11 09 163-173
allfieldsGer	10.1007/s12686-023-01316-4 doi (DE-627)SPR053753194 (SPR)s12686-023-01316-4-e DE-627 ger DE-627 rakwb eng De, Rahul verfasserin (orcid)0000-0002-4518-9607 aut Identifying sex and individual from faecal DNA of the Asian elephant using a single multiplex PCR for population monitoring 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s), under exclusive licence to Springer Nature B.V. 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law. Abstract Information on the sex- and individual-specific space use by a species elucidates demography, resource selection and individual life history. However, traditional field surveys often lack information on sex and individual identity, thereby not maximizing the potential of the effort put in. Recent advances in genetic non-invasive sampling provide cost-effective approaches to determine identity and sex from faecal DNA with high accuracy, which are advantageous for tracking individuals compared to field observations. Therefore, we describe the first single multiplex-based sex and individual identification protocol using faecal samples of the wild Asian elephant (Elephas maximus) collected from the vicinity of Rajaji Tiger Reserve, Uttarakhand, India. We co-amplified fluorescence-labelled microsatellites (n = 5) and a Y chromosome-linked sex marker in four replicates from faecal DNA extracts (n = 149). The mean per genotype allelic drop-out rate was 0.11 ± 0.02, while the false allele rate was 0.05 ± 0.01. The mean null allele frequency across the markers was 0.15 ± 0.02. We obtained 74.1% consensus genotypes across microsatellites and dropped samples with more than one-locus missing genotype from further analyses. The remaining dataset comprised 105 samples, 30.5% of which were females. We identified 51 unique individuals (25 males and 26 females) with a maximum of one-locus mismatch. With low genotyping error rates and adequate misidentification probabilities ($ P_{ID} $ = 4.2 × $ 10^{−4} $; $ P_{IDSib} $ = 3.0 × $ 10^{−2} $), the described panel provides a cost-effective method (US$ 18/sample) for molecular sexing and individual identification. Hence, the suggested multiplex panel would provide a thorough understanding of individual and sex-specific differences in habitat use across heterogeneous landscapes, facilitating effective conservation strategies. Microsatellite (dpeaa)DE-He213 Molecular sexing (dpeaa)DE-He213 Genetic non-invasive sampling (dpeaa)DE-He213 Molecular tracking (dpeaa)DE-He213 Sharma, Reeta (orcid)0000-0001-9862-9218 aut Nigam, Parag (orcid)0000-0001-9472-6897 aut Williams, Amirtharaj Christy aut Habib, Bilal (orcid)0000-0003-0040-6214 aut Goyal, Surendra Prakash (orcid)0000-0002-2284-8796 aut Enthalten in Conservation genetics resources Dordrecht : Springer Netherlands, 2009 15(2023), 4 vom: 11. Sept., Seite 163-173 (DE-627)606030891 (DE-600)2508018-0 1877-7260 nnns volume:15 year:2023 number:4 day:11 month:09 pages:163-173 https://dx.doi.org/10.1007/s12686-023-01316-4 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4328 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 AR 15 2023 4 11 09 163-173
allfieldsSound	10.1007/s12686-023-01316-4 doi (DE-627)SPR053753194 (SPR)s12686-023-01316-4-e DE-627 ger DE-627 rakwb eng De, Rahul verfasserin (orcid)0000-0002-4518-9607 aut Identifying sex and individual from faecal DNA of the Asian elephant using a single multiplex PCR for population monitoring 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s), under exclusive licence to Springer Nature B.V. 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law. Abstract Information on the sex- and individual-specific space use by a species elucidates demography, resource selection and individual life history. However, traditional field surveys often lack information on sex and individual identity, thereby not maximizing the potential of the effort put in. Recent advances in genetic non-invasive sampling provide cost-effective approaches to determine identity and sex from faecal DNA with high accuracy, which are advantageous for tracking individuals compared to field observations. Therefore, we describe the first single multiplex-based sex and individual identification protocol using faecal samples of the wild Asian elephant (Elephas maximus) collected from the vicinity of Rajaji Tiger Reserve, Uttarakhand, India. We co-amplified fluorescence-labelled microsatellites (n = 5) and a Y chromosome-linked sex marker in four replicates from faecal DNA extracts (n = 149). The mean per genotype allelic drop-out rate was 0.11 ± 0.02, while the false allele rate was 0.05 ± 0.01. The mean null allele frequency across the markers was 0.15 ± 0.02. We obtained 74.1% consensus genotypes across microsatellites and dropped samples with more than one-locus missing genotype from further analyses. The remaining dataset comprised 105 samples, 30.5% of which were females. We identified 51 unique individuals (25 males and 26 females) with a maximum of one-locus mismatch. With low genotyping error rates and adequate misidentification probabilities ($ P_{ID} $ = 4.2 × $ 10^{−4} $; $ P_{IDSib} $ = 3.0 × $ 10^{−2} $), the described panel provides a cost-effective method (US$ 18/sample) for molecular sexing and individual identification. Hence, the suggested multiplex panel would provide a thorough understanding of individual and sex-specific differences in habitat use across heterogeneous landscapes, facilitating effective conservation strategies. Microsatellite (dpeaa)DE-He213 Molecular sexing (dpeaa)DE-He213 Genetic non-invasive sampling (dpeaa)DE-He213 Molecular tracking (dpeaa)DE-He213 Sharma, Reeta (orcid)0000-0001-9862-9218 aut Nigam, Parag (orcid)0000-0001-9472-6897 aut Williams, Amirtharaj Christy aut Habib, Bilal (orcid)0000-0003-0040-6214 aut Goyal, Surendra Prakash (orcid)0000-0002-2284-8796 aut Enthalten in Conservation genetics resources Dordrecht : Springer Netherlands, 2009 15(2023), 4 vom: 11. Sept., Seite 163-173 (DE-627)606030891 (DE-600)2508018-0 1877-7260 nnns volume:15 year:2023 number:4 day:11 month:09 pages:163-173 https://dx.doi.org/10.1007/s12686-023-01316-4 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4328 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 AR 15 2023 4 11 09 163-173
language	English
source	Enthalten in Conservation genetics resources 15(2023), 4 vom: 11. Sept., Seite 163-173 volume:15 year:2023 number:4 day:11 month:09 pages:163-173
sourceStr	Enthalten in Conservation genetics resources 15(2023), 4 vom: 11. Sept., Seite 163-173 volume:15 year:2023 number:4 day:11 month:09 pages:163-173
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Microsatellite Molecular sexing Genetic non-invasive sampling Molecular tracking
isfreeaccess_bool	false
container_title	Conservation genetics resources
authorswithroles_txt_mv	De, Rahul @@aut@@ Sharma, Reeta @@aut@@ Nigam, Parag @@aut@@ Williams, Amirtharaj Christy @@aut@@ Habib, Bilal @@aut@@ Goyal, Surendra Prakash @@aut@@
publishDateDaySort_date	2023-09-11T00:00:00Z
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author	De, Rahul
spellingShingle	De, Rahul misc Microsatellite misc Molecular sexing misc Genetic non-invasive sampling misc Molecular tracking Identifying sex and individual from faecal DNA of the Asian elephant using a single multiplex PCR for population monitoring
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topic_title	Identifying sex and individual from faecal DNA of the Asian elephant using a single multiplex PCR for population monitoring Microsatellite (dpeaa)DE-He213 Molecular sexing (dpeaa)DE-He213 Genetic non-invasive sampling (dpeaa)DE-He213 Molecular tracking (dpeaa)DE-He213
topic	misc Microsatellite misc Molecular sexing misc Genetic non-invasive sampling misc Molecular tracking
topic_unstemmed	misc Microsatellite misc Molecular sexing misc Genetic non-invasive sampling misc Molecular tracking
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title	Identifying sex and individual from faecal DNA of the Asian elephant using a single multiplex PCR for population monitoring
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title_full	Identifying sex and individual from faecal DNA of the Asian elephant using a single multiplex PCR for population monitoring
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author_browse	De, Rahul Sharma, Reeta Nigam, Parag Williams, Amirtharaj Christy Habib, Bilal Goyal, Surendra Prakash
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title_sort	identifying sex and individual from faecal dna of the asian elephant using a single multiplex pcr for population monitoring
title_auth	Identifying sex and individual from faecal DNA of the Asian elephant using a single multiplex PCR for population monitoring
abstract	Abstract Information on the sex- and individual-specific space use by a species elucidates demography, resource selection and individual life history. However, traditional field surveys often lack information on sex and individual identity, thereby not maximizing the potential of the effort put in. Recent advances in genetic non-invasive sampling provide cost-effective approaches to determine identity and sex from faecal DNA with high accuracy, which are advantageous for tracking individuals compared to field observations. Therefore, we describe the first single multiplex-based sex and individual identification protocol using faecal samples of the wild Asian elephant (Elephas maximus) collected from the vicinity of Rajaji Tiger Reserve, Uttarakhand, India. We co-amplified fluorescence-labelled microsatellites (n = 5) and a Y chromosome-linked sex marker in four replicates from faecal DNA extracts (n = 149). The mean per genotype allelic drop-out rate was 0.11 ± 0.02, while the false allele rate was 0.05 ± 0.01. The mean null allele frequency across the markers was 0.15 ± 0.02. We obtained 74.1% consensus genotypes across microsatellites and dropped samples with more than one-locus missing genotype from further analyses. The remaining dataset comprised 105 samples, 30.5% of which were females. We identified 51 unique individuals (25 males and 26 females) with a maximum of one-locus mismatch. With low genotyping error rates and adequate misidentification probabilities ($ P_{ID} $ = 4.2 × $ 10^{−4} $; $ P_{IDSib} $ = 3.0 × $ 10^{−2} $), the described panel provides a cost-effective method (US$ 18/sample) for molecular sexing and individual identification. Hence, the suggested multiplex panel would provide a thorough understanding of individual and sex-specific differences in habitat use across heterogeneous landscapes, facilitating effective conservation strategies. © The Author(s), under exclusive licence to Springer Nature B.V. 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
abstractGer	Abstract Information on the sex- and individual-specific space use by a species elucidates demography, resource selection and individual life history. However, traditional field surveys often lack information on sex and individual identity, thereby not maximizing the potential of the effort put in. Recent advances in genetic non-invasive sampling provide cost-effective approaches to determine identity and sex from faecal DNA with high accuracy, which are advantageous for tracking individuals compared to field observations. Therefore, we describe the first single multiplex-based sex and individual identification protocol using faecal samples of the wild Asian elephant (Elephas maximus) collected from the vicinity of Rajaji Tiger Reserve, Uttarakhand, India. We co-amplified fluorescence-labelled microsatellites (n = 5) and a Y chromosome-linked sex marker in four replicates from faecal DNA extracts (n = 149). The mean per genotype allelic drop-out rate was 0.11 ± 0.02, while the false allele rate was 0.05 ± 0.01. The mean null allele frequency across the markers was 0.15 ± 0.02. We obtained 74.1% consensus genotypes across microsatellites and dropped samples with more than one-locus missing genotype from further analyses. The remaining dataset comprised 105 samples, 30.5% of which were females. We identified 51 unique individuals (25 males and 26 females) with a maximum of one-locus mismatch. With low genotyping error rates and adequate misidentification probabilities ($ P_{ID} $ = 4.2 × $ 10^{−4} $; $ P_{IDSib} $ = 3.0 × $ 10^{−2} $), the described panel provides a cost-effective method (US$ 18/sample) for molecular sexing and individual identification. Hence, the suggested multiplex panel would provide a thorough understanding of individual and sex-specific differences in habitat use across heterogeneous landscapes, facilitating effective conservation strategies. © The Author(s), under exclusive licence to Springer Nature B.V. 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
abstract_unstemmed	Abstract Information on the sex- and individual-specific space use by a species elucidates demography, resource selection and individual life history. However, traditional field surveys often lack information on sex and individual identity, thereby not maximizing the potential of the effort put in. Recent advances in genetic non-invasive sampling provide cost-effective approaches to determine identity and sex from faecal DNA with high accuracy, which are advantageous for tracking individuals compared to field observations. Therefore, we describe the first single multiplex-based sex and individual identification protocol using faecal samples of the wild Asian elephant (Elephas maximus) collected from the vicinity of Rajaji Tiger Reserve, Uttarakhand, India. We co-amplified fluorescence-labelled microsatellites (n = 5) and a Y chromosome-linked sex marker in four replicates from faecal DNA extracts (n = 149). The mean per genotype allelic drop-out rate was 0.11 ± 0.02, while the false allele rate was 0.05 ± 0.01. The mean null allele frequency across the markers was 0.15 ± 0.02. We obtained 74.1% consensus genotypes across microsatellites and dropped samples with more than one-locus missing genotype from further analyses. The remaining dataset comprised 105 samples, 30.5% of which were females. We identified 51 unique individuals (25 males and 26 females) with a maximum of one-locus mismatch. With low genotyping error rates and adequate misidentification probabilities ($ P_{ID} $ = 4.2 × $ 10^{−4} $; $ P_{IDSib} $ = 3.0 × $ 10^{−2} $), the described panel provides a cost-effective method (US$ 18/sample) for molecular sexing and individual identification. Hence, the suggested multiplex panel would provide a thorough understanding of individual and sex-specific differences in habitat use across heterogeneous landscapes, facilitating effective conservation strategies. © The Author(s), under exclusive licence to Springer Nature B.V. 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
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container_issue	4
title_short	Identifying sex and individual from faecal DNA of the Asian elephant using a single multiplex PCR for population monitoring
url	https://dx.doi.org/10.1007/s12686-023-01316-4
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author2	Sharma, Reeta Nigam, Parag Williams, Amirtharaj Christy Habib, Bilal Goyal, Surendra Prakash
author2Str	Sharma, Reeta Nigam, Parag Williams, Amirtharaj Christy Habib, Bilal Goyal, Surendra Prakash
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doi_str	10.1007/s12686-023-01316-4
up_date	2024-07-03T21:47:00.701Z
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Identifying sex and individual from faecal DNA of the Asian elephant using a single multiplex PCR for population monitoring

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