Assessing the performance of historical skins and bones for museomics using wolf specimens as a case study
Advances in the field of museomics have promoted a high sampling demand for natural history collections (NHCs), eventually resulting in damage to invaluable resources to understand historical biodiversity. It is thus essential to achieve a consensus about which historical tissues present the best so...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2022-09-01
|
| Series: | Frontiers in Ecology and Evolution |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fevo.2022.970249/full |
| _version_ | 1798036854016049152 |
|---|---|
| author | Carolina Pacheco Carolina Pacheco Carolina Pacheco Diana Lobo Diana Lobo Diana Lobo Pedro Silva Pedro Silva Francisco Álvares Francisco Álvares Emilio J. García Diana Castro Diana Castro Jorge F. Layna José Vicente López-Bao Raquel Godinho Raquel Godinho Raquel Godinho Raquel Godinho |
| author_facet | Carolina Pacheco Carolina Pacheco Carolina Pacheco Diana Lobo Diana Lobo Diana Lobo Pedro Silva Pedro Silva Francisco Álvares Francisco Álvares Emilio J. García Diana Castro Diana Castro Jorge F. Layna José Vicente López-Bao Raquel Godinho Raquel Godinho Raquel Godinho Raquel Godinho |
| author_sort | Carolina Pacheco |
| collection | DOAJ |
| description | Advances in the field of museomics have promoted a high sampling demand for natural history collections (NHCs), eventually resulting in damage to invaluable resources to understand historical biodiversity. It is thus essential to achieve a consensus about which historical tissues present the best sources of DNA. In this study, we evaluated the performance of different historical tissues from Iberian wolf NHCs in genome-wide assessments. We targeted three tissues—bone (jaw and femur), maxilloturbinal bone, and skin—that have been favored by traditional taxidermy practices for mammalian carnivores. Specifically, we performed shotgun sequencing and target capture enrichment for 100,000 single nucleotide polymorphisms (SNPs) selected from the commercial Canine HD BeadChip across 103 specimens from 1912 to 2005. The performance of the different tissues was assessed using metrics based on endogenous DNA content, uniquely high-quality mapped reads after capture, and enrichment proportions. All samples succeeded as DNA sources, regardless of their collection year or sample type. Skin samples yielded significantly higher amounts of endogenous DNA compared to both bone types, which yielded equivalent amounts. There was no evidence for a direct effect of tissue type on capture efficiency; however, the number of genotyped SNPs was strictly associated with the starting amount of endogenous DNA. Evaluation of genotyping accuracy for distinct minimum read depths across tissue types showed a consistent overall low genotyping error rate (<7%), even at low (3x) coverage. We recommend the use of skins as reliable and minimally destructive sources of endogenous DNA for whole-genome and target enrichment approaches in mammalian carnivores. In addition, we provide a new 100,000 SNP capture array validated for historical DNA (hDNA) compatible to the Canine HD BeadChip for high-quality DNA. The increasing demand for NHCs as DNA sources should encourage the generation of genomic datasets comparable among studies. |
| first_indexed | 2024-04-11T21:18:41Z |
| format | Article |
| id | doaj.art-7db5533affba472d9434a149382851bf |
| institution | Directory Open Access Journal |
| issn | 2296-701X |
| language | English |
| last_indexed | 2024-04-11T21:18:41Z |
| publishDate | 2022-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Ecology and Evolution |
| spelling | doaj.art-7db5533affba472d9434a149382851bf2022-12-22T04:02:43ZengFrontiers Media S.A.Frontiers in Ecology and Evolution2296-701X2022-09-011010.3389/fevo.2022.970249970249Assessing the performance of historical skins and bones for museomics using wolf specimens as a case studyCarolina Pacheco0Carolina Pacheco1Carolina Pacheco2Diana Lobo3Diana Lobo4Diana Lobo5Pedro Silva6Pedro Silva7Francisco Álvares8Francisco Álvares9Emilio J. García10Diana Castro11Diana Castro12Jorge F. Layna13José Vicente López-Bao14Raquel Godinho15Raquel Godinho16Raquel Godinho17Raquel Godinho18CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, PortugalDepartamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, PortugalBIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, PortugalDepartamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, PortugalBIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, PortugalBIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, PortugalBIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, PortugalBiodiversity Research Institute (CSIC), Oviedo University, Mieres, SpainCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, PortugalBIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, PortugalConsultores en Iniciativas Ambientales, S.L., Madrid, SpainBiodiversity Research Institute (CSIC), Oviedo University, Mieres, SpainCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, PortugalDepartamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, PortugalBIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, PortugalDepartment of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, South AfricaAdvances in the field of museomics have promoted a high sampling demand for natural history collections (NHCs), eventually resulting in damage to invaluable resources to understand historical biodiversity. It is thus essential to achieve a consensus about which historical tissues present the best sources of DNA. In this study, we evaluated the performance of different historical tissues from Iberian wolf NHCs in genome-wide assessments. We targeted three tissues—bone (jaw and femur), maxilloturbinal bone, and skin—that have been favored by traditional taxidermy practices for mammalian carnivores. Specifically, we performed shotgun sequencing and target capture enrichment for 100,000 single nucleotide polymorphisms (SNPs) selected from the commercial Canine HD BeadChip across 103 specimens from 1912 to 2005. The performance of the different tissues was assessed using metrics based on endogenous DNA content, uniquely high-quality mapped reads after capture, and enrichment proportions. All samples succeeded as DNA sources, regardless of their collection year or sample type. Skin samples yielded significantly higher amounts of endogenous DNA compared to both bone types, which yielded equivalent amounts. There was no evidence for a direct effect of tissue type on capture efficiency; however, the number of genotyped SNPs was strictly associated with the starting amount of endogenous DNA. Evaluation of genotyping accuracy for distinct minimum read depths across tissue types showed a consistent overall low genotyping error rate (<7%), even at low (3x) coverage. We recommend the use of skins as reliable and minimally destructive sources of endogenous DNA for whole-genome and target enrichment approaches in mammalian carnivores. In addition, we provide a new 100,000 SNP capture array validated for historical DNA (hDNA) compatible to the Canine HD BeadChip for high-quality DNA. The increasing demand for NHCs as DNA sources should encourage the generation of genomic datasets comparable among studies.https://www.frontiersin.org/articles/10.3389/fevo.2022.970249/fullendogenous DNAhistorical DNAmuseomicsnatural history collectionsSNP genotyping errorstarget enrichment |
| spellingShingle | Carolina Pacheco Carolina Pacheco Carolina Pacheco Diana Lobo Diana Lobo Diana Lobo Pedro Silva Pedro Silva Francisco Álvares Francisco Álvares Emilio J. García Diana Castro Diana Castro Jorge F. Layna José Vicente López-Bao Raquel Godinho Raquel Godinho Raquel Godinho Raquel Godinho Assessing the performance of historical skins and bones for museomics using wolf specimens as a case study Frontiers in Ecology and Evolution endogenous DNA historical DNA museomics natural history collections SNP genotyping errors target enrichment |
| title | Assessing the performance of historical skins and bones for museomics using wolf specimens as a case study |
| title_full | Assessing the performance of historical skins and bones for museomics using wolf specimens as a case study |
| title_fullStr | Assessing the performance of historical skins and bones for museomics using wolf specimens as a case study |
| title_full_unstemmed | Assessing the performance of historical skins and bones for museomics using wolf specimens as a case study |
| title_short | Assessing the performance of historical skins and bones for museomics using wolf specimens as a case study |
| title_sort | assessing the performance of historical skins and bones for museomics using wolf specimens as a case study |
| topic | endogenous DNA historical DNA museomics natural history collections SNP genotyping errors target enrichment |
| url | https://www.frontiersin.org/articles/10.3389/fevo.2022.970249/full |
| work_keys_str_mv | AT carolinapacheco assessingtheperformanceofhistoricalskinsandbonesformuseomicsusingwolfspecimensasacasestudy AT carolinapacheco assessingtheperformanceofhistoricalskinsandbonesformuseomicsusingwolfspecimensasacasestudy AT carolinapacheco assessingtheperformanceofhistoricalskinsandbonesformuseomicsusingwolfspecimensasacasestudy AT dianalobo assessingtheperformanceofhistoricalskinsandbonesformuseomicsusingwolfspecimensasacasestudy AT dianalobo assessingtheperformanceofhistoricalskinsandbonesformuseomicsusingwolfspecimensasacasestudy AT dianalobo assessingtheperformanceofhistoricalskinsandbonesformuseomicsusingwolfspecimensasacasestudy AT pedrosilva assessingtheperformanceofhistoricalskinsandbonesformuseomicsusingwolfspecimensasacasestudy AT pedrosilva assessingtheperformanceofhistoricalskinsandbonesformuseomicsusingwolfspecimensasacasestudy AT franciscoalvares assessingtheperformanceofhistoricalskinsandbonesformuseomicsusingwolfspecimensasacasestudy AT franciscoalvares assessingtheperformanceofhistoricalskinsandbonesformuseomicsusingwolfspecimensasacasestudy AT emiliojgarcia assessingtheperformanceofhistoricalskinsandbonesformuseomicsusingwolfspecimensasacasestudy AT dianacastro assessingtheperformanceofhistoricalskinsandbonesformuseomicsusingwolfspecimensasacasestudy AT dianacastro assessingtheperformanceofhistoricalskinsandbonesformuseomicsusingwolfspecimensasacasestudy AT jorgeflayna assessingtheperformanceofhistoricalskinsandbonesformuseomicsusingwolfspecimensasacasestudy AT josevicentelopezbao assessingtheperformanceofhistoricalskinsandbonesformuseomicsusingwolfspecimensasacasestudy AT raquelgodinho assessingtheperformanceofhistoricalskinsandbonesformuseomicsusingwolfspecimensasacasestudy AT raquelgodinho assessingtheperformanceofhistoricalskinsandbonesformuseomicsusingwolfspecimensasacasestudy AT raquelgodinho assessingtheperformanceofhistoricalskinsandbonesformuseomicsusingwolfspecimensasacasestudy AT raquelgodinho assessingtheperformanceofhistoricalskinsandbonesformuseomicsusingwolfspecimensasacasestudy |