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Sequencing the orthologs of human autosomal forensic short tandem repeats provides individual- and species-level identification in African great apes

Ettore Fedele, Jon H. Wetton, Mark A. Jobling

BMC Ecology and Evolution, Volume: 24, Start page: 134

Swansea University Author: Ettore Fedele

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DOI (Published version): 10.1186/s12862-024-02324-0

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Background: Great apes are a global conservation concern, with anthropogenic pressures threatening their survival. Genetic analysis can be used to assess the effects of reduced population sizes and the effectiveness of conservation measures. In humans, autosomal short tandem repeats (aSTRs) are wide...

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Published in: BMC Ecology and Evolution
ISSN: 2730-7182
Published: Springer Nature 2024
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In humans, autosomal short tandem repeats (aSTRs) are widely used in population genetics and for forensic individual identification and kinship testing. Traditionally, genotyping is length-based via capillary electrophoresis (CE), but there is an increasing move to direct analysis by massively parallel sequencing (MPS). An example is the ForenSeq DNA Signature Prep Kit, which amplifies multiple loci including 27 aSTRs, prior to sequencing via Illumina technology. Here we assess the applicability of this human-based kit in African great apes. We ask whether cross-species genotyping of the orthologs of these loci can provide both individual and (sub)species identification. Results: The ForenSeq kit was used to amplify and sequence aSTRs in 52 individuals (14 chimpanzees; 4 bonobos; 16 western lowland, 6 eastern lowland, and 12 mountain gorillas). The orthologs of 24/27 human aSTRs amplified across species, and a core set of thirteen loci could be genotyped in all individuals. Genotypes were individually and (sub)species identifying. Both allelic diversity and the power to discriminate (sub)species were greater when considering STR sequences rather than allele lengths. Comparing human and African great-ape STR sequences with an orangutan outgroup showed general conservation of repeat types and allele size ranges. Variation in repeat array structures and a weak relationship with the known phylogeny suggests stochastic origins of mutations giving rise to diverse imperfect repeat arrays. Interruptions within long repeat arrays in African great apes do not appear to reduce allelic diversity. Conclusions: Orthologs of most human aSTRs in the ForenSeq DNA Signature Prep Kit can be analysed in African great apes. Primer redesign would reduce observed variability in amplification across some loci. 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spelling v2 68143 2024-11-01 Sequencing the orthologs of human autosomal forensic short tandem repeats provides individual- and species-level identification in African great apes 17fe9074a0d38a405381f81a37ed3d76 Ettore Fedele Ettore Fedele true false 2024-11-01 BGPS Background: Great apes are a global conservation concern, with anthropogenic pressures threatening their survival. Genetic analysis can be used to assess the effects of reduced population sizes and the effectiveness of conservation measures. In humans, autosomal short tandem repeats (aSTRs) are widely used in population genetics and for forensic individual identification and kinship testing. Traditionally, genotyping is length-based via capillary electrophoresis (CE), but there is an increasing move to direct analysis by massively parallel sequencing (MPS). An example is the ForenSeq DNA Signature Prep Kit, which amplifies multiple loci including 27 aSTRs, prior to sequencing via Illumina technology. Here we assess the applicability of this human-based kit in African great apes. We ask whether cross-species genotyping of the orthologs of these loci can provide both individual and (sub)species identification. Results: The ForenSeq kit was used to amplify and sequence aSTRs in 52 individuals (14 chimpanzees; 4 bonobos; 16 western lowland, 6 eastern lowland, and 12 mountain gorillas). The orthologs of 24/27 human aSTRs amplified across species, and a core set of thirteen loci could be genotyped in all individuals. Genotypes were individually and (sub)species identifying. Both allelic diversity and the power to discriminate (sub)species were greater when considering STR sequences rather than allele lengths. Comparing human and African great-ape STR sequences with an orangutan outgroup showed general conservation of repeat types and allele size ranges. Variation in repeat array structures and a weak relationship with the known phylogeny suggests stochastic origins of mutations giving rise to diverse imperfect repeat arrays. Interruptions within long repeat arrays in African great apes do not appear to reduce allelic diversity. Conclusions: Orthologs of most human aSTRs in the ForenSeq DNA Signature Prep Kit can be analysed in African great apes. Primer redesign would reduce observed variability in amplification across some loci. MPS of the orthologs of human loci provides better resolution for both individual and (sub)species identification in great apes than standard CE-based approaches, and has the further advantage that there is no need to limit the number and size ranges of analysed loci. Journal Article BMC Ecology and Evolution 24 134 Springer Nature 2730-7182 Gorilla, Chimpanzee, Bonobo, Short-tandem repeat (STR), Individual identifcation, Single nucleotidepolymorphism (SNP), Massively parallel sequencing, Verogen ForenSeq™ DNA Signature Prep kit 31 10 2024 2024-10-31 10.1186/s12862-024-02324-0 COLLEGE NANME Biosciences Geography and Physics School COLLEGE CODE BGPS Swansea University Another institution paid the OA fee EF was supported by a PhD studentship from the Natural Environment Research Council CENTA doctoral training programme (grant no. NE/L002493/1). 2024-11-01T12:55:53.2235321 2024-11-01T12:35:00.0891246 Faculty of Science and Engineering School of Biosciences, Geography and Physics - Biosciences Ettore Fedele 1 Jon H. Wetton 2 Mark A. Jobling 3 68143__32819__24418863afa649eb8b678d9203611c7c.pdf 68143.VOR.pdf 2024-11-01T12:51:13.9168897 Output 2131186 application/pdf Version of Record true © The Author(s) 2024. Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0). true eng http://creativecommons.org/licenses/by/4.0/
title Sequencing the orthologs of human autosomal forensic short tandem repeats provides individual- and species-level identification in African great apes
spellingShingle Sequencing the orthologs of human autosomal forensic short tandem repeats provides individual- and species-level identification in African great apes
Ettore Fedele
title_short Sequencing the orthologs of human autosomal forensic short tandem repeats provides individual- and species-level identification in African great apes
title_full Sequencing the orthologs of human autosomal forensic short tandem repeats provides individual- and species-level identification in African great apes
title_fullStr Sequencing the orthologs of human autosomal forensic short tandem repeats provides individual- and species-level identification in African great apes
title_full_unstemmed Sequencing the orthologs of human autosomal forensic short tandem repeats provides individual- and species-level identification in African great apes
title_sort Sequencing the orthologs of human autosomal forensic short tandem repeats provides individual- and species-level identification in African great apes
author_id_str_mv 17fe9074a0d38a405381f81a37ed3d76
author_id_fullname_str_mv 17fe9074a0d38a405381f81a37ed3d76_***_Ettore Fedele
author Ettore Fedele
author2 Ettore Fedele
Jon H. Wetton
Mark A. Jobling
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container_title BMC Ecology and Evolution
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description Background: Great apes are a global conservation concern, with anthropogenic pressures threatening their survival. Genetic analysis can be used to assess the effects of reduced population sizes and the effectiveness of conservation measures. In humans, autosomal short tandem repeats (aSTRs) are widely used in population genetics and for forensic individual identification and kinship testing. Traditionally, genotyping is length-based via capillary electrophoresis (CE), but there is an increasing move to direct analysis by massively parallel sequencing (MPS). An example is the ForenSeq DNA Signature Prep Kit, which amplifies multiple loci including 27 aSTRs, prior to sequencing via Illumina technology. Here we assess the applicability of this human-based kit in African great apes. We ask whether cross-species genotyping of the orthologs of these loci can provide both individual and (sub)species identification. Results: The ForenSeq kit was used to amplify and sequence aSTRs in 52 individuals (14 chimpanzees; 4 bonobos; 16 western lowland, 6 eastern lowland, and 12 mountain gorillas). The orthologs of 24/27 human aSTRs amplified across species, and a core set of thirteen loci could be genotyped in all individuals. Genotypes were individually and (sub)species identifying. Both allelic diversity and the power to discriminate (sub)species were greater when considering STR sequences rather than allele lengths. Comparing human and African great-ape STR sequences with an orangutan outgroup showed general conservation of repeat types and allele size ranges. Variation in repeat array structures and a weak relationship with the known phylogeny suggests stochastic origins of mutations giving rise to diverse imperfect repeat arrays. Interruptions within long repeat arrays in African great apes do not appear to reduce allelic diversity. Conclusions: Orthologs of most human aSTRs in the ForenSeq DNA Signature Prep Kit can be analysed in African great apes. Primer redesign would reduce observed variability in amplification across some loci. MPS of the orthologs of human loci provides better resolution for both individual and (sub)species identification in great apes than standard CE-based approaches, and has the further advantage that there is no need to limit the number and size ranges of analysed loci.
published_date 2024-10-31T12:55:51Z
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