CAnDI: A New Tool to Investigate Conflict in Homologous Gene Trees and Explain Convergent Trait Evolution.
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| Title: | CAnDI: A New Tool to Investigate Conflict in Homologous Gene Trees and Explain Convergent Trait Evolution. |
|---|---|
| Authors: | Robertson, Holly M1 (AUTHOR), Walker, Joseph F2 (AUTHOR), Moyroud, Edwige1 (AUTHOR) |
| Source: | Systematic Biology. Jul2026, Vol. 75 Issue 4, p796-813. 18p. |
| Subjects: | Convergent evolution, Carnivorous plants, Horizontal gene transfer, Molecular phylogeny, Introgression (Genetics), Gene families |
| Abstract: | Phenotypic convergence is found across the tree of life, and morphological similarities in distantly related species are often presumed to have evolved independently. However, clarifying the origins of traits has recently highlighted the complex nature of evolution, as apparent convergent features often share similar genetic foundations. Hence, the tree topology of genes that underlie such traits frequently conflicts with the overall history of species relationships. This conflict, which usually results from incomplete lineage sorting, introgression, or horizontal gene transfer, creates both a challenge for systematists and an exciting opportunity to investigate the rich, complex network of information that connects molecular trajectories with trait evolution. Here, we present a novel conflict identification program named CAnDI (Conflict And Duplication Identifier), which enables the analysis of conflict in homologous gene trees rather than inferred orthologs. We demonstrate that the analysis of conflicts in homologous trees using CAnDI yields more comparisons than in ortholog trees in six datasets from across the eukaryotic tree of life. Using the carnivorous trap of Caryophyllales, a charismatic group of flowering plants, as a case study we demonstrate that analyzing conflict on entire homolog trees can aid in inferring the contribution of standing genetic variation to trait evolution: by dissecting all gene relationships within homolog trees, we find genomic evidence that the molecular basis of the pleisiomorphic mucilaginous sticky trap was likely present in the ancestor of all carnivorous Caryophyllales. We also show that many genes whose evolutionary trajectories group species with similar trap devices code for proteins contributing to plant carnivory and identify a LATERAL ORGAN BOUNDARY DOMAIN transcription factor as a possible candidate for regulating sticky trap development. [ABSTRACT FROM AUTHOR] |
| Copyright of Systematic Biology is the property of Oxford University Press / USA and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Database: | Engineering Source |
| FullText | Text: Availability: 0 |
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| Header | DbId: egs DbLabel: Engineering Source An: 194674275 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: CAnDI: A New Tool to Investigate Conflict in Homologous Gene Trees and Explain Convergent Trait Evolution. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Robertson%2C+Holly+M%22">Robertson, Holly M</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Walker%2C+Joseph+F%22">Walker, Joseph F</searchLink><relatesTo>2</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Moyroud%2C+Edwige%22">Moyroud, Edwige</searchLink><relatesTo>1</relatesTo> (AUTHOR) – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Systematic+Biology%22">Systematic Biology</searchLink>. Jul2026, Vol. 75 Issue 4, p796-813. 18p. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Convergent+evolution%22">Convergent evolution</searchLink><br /><searchLink fieldCode="DE" term="%22Carnivorous+plants%22">Carnivorous plants</searchLink><br /><searchLink fieldCode="DE" term="%22Horizontal+gene+transfer%22">Horizontal gene transfer</searchLink><br /><searchLink fieldCode="DE" term="%22Molecular+phylogeny%22">Molecular phylogeny</searchLink><br /><searchLink fieldCode="DE" term="%22Introgression+%28Genetics%29%22">Introgression (Genetics)</searchLink><br /><searchLink fieldCode="DE" term="%22Gene+families%22">Gene families</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: Phenotypic convergence is found across the tree of life, and morphological similarities in distantly related species are often presumed to have evolved independently. However, clarifying the origins of traits has recently highlighted the complex nature of evolution, as apparent convergent features often share similar genetic foundations. Hence, the tree topology of genes that underlie such traits frequently conflicts with the overall history of species relationships. This conflict, which usually results from incomplete lineage sorting, introgression, or horizontal gene transfer, creates both a challenge for systematists and an exciting opportunity to investigate the rich, complex network of information that connects molecular trajectories with trait evolution. Here, we present a novel conflict identification program named CAnDI (Conflict And Duplication Identifier), which enables the analysis of conflict in homologous gene trees rather than inferred orthologs. We demonstrate that the analysis of conflicts in homologous trees using CAnDI yields more comparisons than in ortholog trees in six datasets from across the eukaryotic tree of life. Using the carnivorous trap of Caryophyllales, a charismatic group of flowering plants, as a case study we demonstrate that analyzing conflict on entire homolog trees can aid in inferring the contribution of standing genetic variation to trait evolution: by dissecting all gene relationships within homolog trees, we find genomic evidence that the molecular basis of the pleisiomorphic mucilaginous sticky trap was likely present in the ancestor of all carnivorous Caryophyllales. We also show that many genes whose evolutionary trajectories group species with similar trap devices code for proteins contributing to plant carnivory and identify a LATERAL ORGAN BOUNDARY DOMAIN transcription factor as a possible candidate for regulating sticky trap development. [ABSTRACT FROM AUTHOR] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Systematic Biology is the property of Oxford University Press / USA and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1093/sysbio/syaf028 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 18 StartPage: 796 Subjects: – SubjectFull: Convergent evolution Type: general – SubjectFull: Carnivorous plants Type: general – SubjectFull: Horizontal gene transfer Type: general – SubjectFull: Molecular phylogeny Type: general – SubjectFull: Introgression (Genetics) Type: general – SubjectFull: Gene families Type: general Titles: – TitleFull: CAnDI: A New Tool to Investigate Conflict in Homologous Gene Trees and Explain Convergent Trait Evolution. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Robertson, Holly M – PersonEntity: Name: NameFull: Walker, Joseph F – PersonEntity: Name: NameFull: Moyroud, Edwige IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 07 Text: Jul2026 Type: published Y: 2026 Identifiers: – Type: issn-print Value: 10635157 Numbering: – Type: volume Value: 75 – Type: issue Value: 4 Titles: – TitleFull: Systematic Biology Type: main |
| ResultId | 1 |
