Testing Phylogenetic Placement Accuracy of DNA Barcode Sequences on a Fish Backbone Tree: Implications of Backbone Tree Completeness and Species Representation
ABSTRACT Advancements in DNA sequencing technology have facilitated the generation of a vast number of DNA sequences, posing opportunities and challenges for constructing large phylogenetic trees. DNA barcode sequences, particularly COI, represent extensive orthologous sequences suitable for phyloge...
Saved in:
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2025-01-01
|
| Series: | Ecology and Evolution |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/ece3.70817 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832583008143540224 |
|---|---|
| author | M. A. Thanuja M. Fernando Jinzhong Fu Sarah J. Adamowicz |
| author_facet | M. A. Thanuja M. Fernando Jinzhong Fu Sarah J. Adamowicz |
| author_sort | M. A. Thanuja M. Fernando |
| collection | DOAJ |
| description | ABSTRACT Advancements in DNA sequencing technology have facilitated the generation of a vast number of DNA sequences, posing opportunities and challenges for constructing large phylogenetic trees. DNA barcode sequences, particularly COI, represent extensive orthologous sequences suitable for phylogenetic analysis. Phylogenetic placement analysis offers a promising method to integrate COI data into tree‐building efforts, yet the impacts of backbone tree completeness and species composition remain under‐explored. Using a dataset comprising 27 genes and 4520 species of bony fishes, we assessed the accuracy of phylogenetic inference by “placing” COI sequences onto backbone trees. The backbone tree completeness was varied by subsampling 20%, 40%, 60%, 80%, and 99% of the total species separately, followed by placement of those missing species based on their COI sequences using software packages EPA‐ng and APPLES. We also compared the effects of biased, random, and stratified sampling strategies; the latter ensured the representation of all major lineages (Family) of bony fish. Our findings indicate that the placement accuracy is consistently high across all levels of backbone tree completeness, where 70%–78% missing species are correctly placed (by EPA‐ng) in the same locations as the reference tree derived from the complete data. High completeness produces slightly high placement accuracy, although in many cases the differences are nonsignificant. For example, at the 99% completeness level with stratified sampling, EPA‐ng placed 78% missing species correctly, and when only considering placement with high confidence (LWR > 0.9), the percentage is 87%. Additionally, stratified sampling outperforms random sampling in most cases, and biased sampling has the worst performance. The likelihood‐based EPA‐ng consistently provide higher accurate placements than the distance‐based APPLES. In conclusion, COI‐based placement analysis represents a potential route of using the available vast barcoding data for building large phylogenetic trees. |
| format | Article |
| id | doaj-art-31e7c611da194edfbb2682bb1e55ae40 |
| institution | Kabale University |
| issn | 2045-7758 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Ecology and Evolution |
| spelling | doaj-art-31e7c611da194edfbb2682bb1e55ae402025-01-29T05:08:41ZengWileyEcology and Evolution2045-77582025-01-01151n/an/a10.1002/ece3.70817Testing Phylogenetic Placement Accuracy of DNA Barcode Sequences on a Fish Backbone Tree: Implications of Backbone Tree Completeness and Species RepresentationM. A. Thanuja M. Fernando0Jinzhong Fu1Sarah J. Adamowicz2Department of Integrative Biology University of Guelph Guelph Ontario CanadaDepartment of Integrative Biology University of Guelph Guelph Ontario CanadaDepartment of Integrative Biology University of Guelph Guelph Ontario CanadaABSTRACT Advancements in DNA sequencing technology have facilitated the generation of a vast number of DNA sequences, posing opportunities and challenges for constructing large phylogenetic trees. DNA barcode sequences, particularly COI, represent extensive orthologous sequences suitable for phylogenetic analysis. Phylogenetic placement analysis offers a promising method to integrate COI data into tree‐building efforts, yet the impacts of backbone tree completeness and species composition remain under‐explored. Using a dataset comprising 27 genes and 4520 species of bony fishes, we assessed the accuracy of phylogenetic inference by “placing” COI sequences onto backbone trees. The backbone tree completeness was varied by subsampling 20%, 40%, 60%, 80%, and 99% of the total species separately, followed by placement of those missing species based on their COI sequences using software packages EPA‐ng and APPLES. We also compared the effects of biased, random, and stratified sampling strategies; the latter ensured the representation of all major lineages (Family) of bony fish. Our findings indicate that the placement accuracy is consistently high across all levels of backbone tree completeness, where 70%–78% missing species are correctly placed (by EPA‐ng) in the same locations as the reference tree derived from the complete data. High completeness produces slightly high placement accuracy, although in many cases the differences are nonsignificant. For example, at the 99% completeness level with stratified sampling, EPA‐ng placed 78% missing species correctly, and when only considering placement with high confidence (LWR > 0.9), the percentage is 87%. Additionally, stratified sampling outperforms random sampling in most cases, and biased sampling has the worst performance. The likelihood‐based EPA‐ng consistently provide higher accurate placements than the distance‐based APPLES. In conclusion, COI‐based placement analysis represents a potential route of using the available vast barcoding data for building large phylogenetic trees.https://doi.org/10.1002/ece3.70817analytical toolsDNA barcodesphylogenetic accuracyphylogenetic placement analysisstratified sampling method |
| spellingShingle | M. A. Thanuja M. Fernando Jinzhong Fu Sarah J. Adamowicz Testing Phylogenetic Placement Accuracy of DNA Barcode Sequences on a Fish Backbone Tree: Implications of Backbone Tree Completeness and Species Representation Ecology and Evolution analytical tools DNA barcodes phylogenetic accuracy phylogenetic placement analysis stratified sampling method |
| title | Testing Phylogenetic Placement Accuracy of DNA Barcode Sequences on a Fish Backbone Tree: Implications of Backbone Tree Completeness and Species Representation |
| title_full | Testing Phylogenetic Placement Accuracy of DNA Barcode Sequences on a Fish Backbone Tree: Implications of Backbone Tree Completeness and Species Representation |
| title_fullStr | Testing Phylogenetic Placement Accuracy of DNA Barcode Sequences on a Fish Backbone Tree: Implications of Backbone Tree Completeness and Species Representation |
| title_full_unstemmed | Testing Phylogenetic Placement Accuracy of DNA Barcode Sequences on a Fish Backbone Tree: Implications of Backbone Tree Completeness and Species Representation |
| title_short | Testing Phylogenetic Placement Accuracy of DNA Barcode Sequences on a Fish Backbone Tree: Implications of Backbone Tree Completeness and Species Representation |
| title_sort | testing phylogenetic placement accuracy of dna barcode sequences on a fish backbone tree implications of backbone tree completeness and species representation |
| topic | analytical tools DNA barcodes phylogenetic accuracy phylogenetic placement analysis stratified sampling method |
| url | https://doi.org/10.1002/ece3.70817 |
| work_keys_str_mv | AT mathanujamfernando testingphylogeneticplacementaccuracyofdnabarcodesequencesonafishbackbonetreeimplicationsofbackbonetreecompletenessandspeciesrepresentation AT jinzhongfu testingphylogeneticplacementaccuracyofdnabarcodesequencesonafishbackbonetreeimplicationsofbackbonetreecompletenessandspeciesrepresentation AT sarahjadamowicz testingphylogeneticplacementaccuracyofdnabarcodesequencesonafishbackbonetreeimplicationsofbackbonetreecompletenessandspeciesrepresentation |