2b or not 2b? 2bRAD is an effective alternative to ddRAD for phylogenomics
Abstract Restriction‐site‐associated DNA sequencing (RADseq) has become an accessible way to obtain genome‐wide data in the form of single‐nucleotide polymorphisms (SNPs) for phylogenetic inference. Nonetheless, how differences in RADseq methods influence phylogenetic estimation is poorly understood...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2023-03-01
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| Series: | Ecology and Evolution |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/ece3.9842 |
| _version_ | 1797857503954862080 |
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| author | E. Anne Chambers Rebecca D. Tarvin Juan C. Santos Santiago R. Ron Mileidy Betancourth‐Cundar David M. Hillis Mikhail V. Matz David C. Cannatella |
| author_facet | E. Anne Chambers Rebecca D. Tarvin Juan C. Santos Santiago R. Ron Mileidy Betancourth‐Cundar David M. Hillis Mikhail V. Matz David C. Cannatella |
| author_sort | E. Anne Chambers |
| collection | DOAJ |
| description | Abstract Restriction‐site‐associated DNA sequencing (RADseq) has become an accessible way to obtain genome‐wide data in the form of single‐nucleotide polymorphisms (SNPs) for phylogenetic inference. Nonetheless, how differences in RADseq methods influence phylogenetic estimation is poorly understood because most comparisons have largely relied on conceptual predictions rather than empirical tests. We examine how differences in ddRAD and 2bRAD data influence phylogenetic estimation in two non‐model frog groups. We compare the impact of method choice on phylogenetic information, missing data, and allelic dropout, considering different sequencing depths. Given that researchers must balance input (funding, time) with output (amount and quality of data), we also provide comparisons of laboratory effort, computational time, monetary costs, and the repeatability of library preparation and sequencing. Both 2bRAD and ddRAD methods estimated well‐supported trees, even at low sequencing depths, and had comparable amounts of missing data, patterns of allelic dropout, and phylogenetic signal. Compared to ddRAD, 2bRAD produced more repeatable datasets, had simpler laboratory protocols, and had an overall faster bioinformatics assembly. However, many fewer parsimony‐informative sites per SNP were obtained from 2bRAD data when using native pipelines, highlighting a need for further investigation into the effects of each pipeline on resulting datasets. Our study underscores the importance of comparing RADseq methods, such as expected results and theoretical performance using empirical datasets, before undertaking costly experiments. |
| first_indexed | 2024-04-09T20:57:42Z |
| format | Article |
| id | doaj.art-abfff629a86f443881c709fa27262a94 |
| institution | Directory Open Access Journal |
| issn | 2045-7758 |
| language | English |
| last_indexed | 2024-04-09T20:57:42Z |
| publishDate | 2023-03-01 |
| publisher | Wiley |
| record_format | Article |
| series | Ecology and Evolution |
| spelling | doaj.art-abfff629a86f443881c709fa27262a942023-03-29T14:14:47ZengWileyEcology and Evolution2045-77582023-03-01133n/an/a10.1002/ece3.98422b or not 2b? 2bRAD is an effective alternative to ddRAD for phylogenomicsE. Anne Chambers0Rebecca D. Tarvin1Juan C. Santos2Santiago R. Ron3Mileidy Betancourth‐Cundar4David M. Hillis5Mikhail V. Matz6David C. Cannatella7Department of Integrative Biology and Biodiversity Center University of Texas at Austin Austin Texas USADepartment of Integrative Biology and Biodiversity Center University of Texas at Austin Austin Texas USADepartment of Biological Sciences St John's University New York New York USAMuseo de Zoología, Escuela de Ciencias Biológicas Pontificia Universidad Católica del Ecuador Quito EcuadorDepartamento de Ciencias Biológicas Universidad de los Andes Bogotá ColombiaDepartment of Integrative Biology and Biodiversity Center University of Texas at Austin Austin Texas USADepartment of Integrative Biology and Biodiversity Center University of Texas at Austin Austin Texas USADepartment of Integrative Biology and Biodiversity Center University of Texas at Austin Austin Texas USAAbstract Restriction‐site‐associated DNA sequencing (RADseq) has become an accessible way to obtain genome‐wide data in the form of single‐nucleotide polymorphisms (SNPs) for phylogenetic inference. Nonetheless, how differences in RADseq methods influence phylogenetic estimation is poorly understood because most comparisons have largely relied on conceptual predictions rather than empirical tests. We examine how differences in ddRAD and 2bRAD data influence phylogenetic estimation in two non‐model frog groups. We compare the impact of method choice on phylogenetic information, missing data, and allelic dropout, considering different sequencing depths. Given that researchers must balance input (funding, time) with output (amount and quality of data), we also provide comparisons of laboratory effort, computational time, monetary costs, and the repeatability of library preparation and sequencing. Both 2bRAD and ddRAD methods estimated well‐supported trees, even at low sequencing depths, and had comparable amounts of missing data, patterns of allelic dropout, and phylogenetic signal. Compared to ddRAD, 2bRAD produced more repeatable datasets, had simpler laboratory protocols, and had an overall faster bioinformatics assembly. However, many fewer parsimony‐informative sites per SNP were obtained from 2bRAD data when using native pipelines, highlighting a need for further investigation into the effects of each pipeline on resulting datasets. Our study underscores the importance of comparing RADseq methods, such as expected results and theoretical performance using empirical datasets, before undertaking costly experiments.https://doi.org/10.1002/ece3.9842Dendrobatidaemissing dataphylogenetic signalRanidaerestriction‐site‐associated DNA sequencing |
| spellingShingle | E. Anne Chambers Rebecca D. Tarvin Juan C. Santos Santiago R. Ron Mileidy Betancourth‐Cundar David M. Hillis Mikhail V. Matz David C. Cannatella 2b or not 2b? 2bRAD is an effective alternative to ddRAD for phylogenomics Ecology and Evolution Dendrobatidae missing data phylogenetic signal Ranidae restriction‐site‐associated DNA sequencing |
| title | 2b or not 2b? 2bRAD is an effective alternative to ddRAD for phylogenomics |
| title_full | 2b or not 2b? 2bRAD is an effective alternative to ddRAD for phylogenomics |
| title_fullStr | 2b or not 2b? 2bRAD is an effective alternative to ddRAD for phylogenomics |
| title_full_unstemmed | 2b or not 2b? 2bRAD is an effective alternative to ddRAD for phylogenomics |
| title_short | 2b or not 2b? 2bRAD is an effective alternative to ddRAD for phylogenomics |
| title_sort | 2b or not 2b 2brad is an effective alternative to ddrad for phylogenomics |
| topic | Dendrobatidae missing data phylogenetic signal Ranidae restriction‐site‐associated DNA sequencing |
| url | https://doi.org/10.1002/ece3.9842 |
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